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Song M, Dodson J, Lu F, Yan H. Central China as LGM plant refugia: Insights from biome reconstruction for palaeoclimate information. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 942:173783. [PMID: 38851335 DOI: 10.1016/j.scitotenv.2024.173783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Revised: 05/24/2024] [Accepted: 06/03/2024] [Indexed: 06/10/2024]
Abstract
The demonstration of survival of forest stands in relatively stable refugia during cold glacial stages has offered an increased understanding of the response of vegetation to climate change, but also provides insight into considerations for the conversation of biodiversity hotspots. However, refugia studies in China remain in question due to the lack of plant macrofossils, especially those of endemic and relict species. Palynology, while more broad brush, provides a method for exploring whether refugia occur, and can provide some details of palaeovegetation composition and temporal dynamics. Here, three pollen records derived from subalpine wetlands in central China, spanning the Last Glacial Maximum (LGM), have been coupled with biome and mean annual precipitation (MAP) reconstructions to identify the presence of trees that endured cold climate. The results indicated that some forest, including temperate deciduous broadleaf forest and cool mixed forest, survived the LGM at the three locations, and was thus at odds with the hypothesis that forests were replaced by herbs and grasses in central China at that time. Refugia favored by protection from cold air drainage and the availability of adequate water can explain the survival of the trees during otherwise harsh episodes. Our findings are consistent with other records from central China that argue for tree dominated refugia during the LGM.
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Affiliation(s)
- Menglin Song
- State Key Laboratory of Loess and Quaternary Geology, Institute of Earth Environment, Chinese Academy of Sciences, Xi'an 710061, China; University of Chinese Academy of Sciences, Beijing 100049, China; School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - John Dodson
- State Key Laboratory of Loess and Quaternary Geology, Institute of Earth Environment, Chinese Academy of Sciences, Xi'an 710061, China; School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Fengyan Lu
- State Key Laboratory of Loess and Quaternary Geology, Institute of Earth Environment, Chinese Academy of Sciences, Xi'an 710061, China
| | - Hong Yan
- State Key Laboratory of Loess and Quaternary Geology, Institute of Earth Environment, Chinese Academy of Sciences, Xi'an 710061, China
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2
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Pathak AK, Simonian H, Ibrahim IAA, Hrechdakian P, Behar DM, Ayub Q, Arsanov P, Metspalu E, Yepiskoposyan L, Rootsi S, Endicott P, Villems R, Sahakyan H. Human Y chromosome haplogroup L1-M22 traces Neolithic expansion in West Asia and supports the Elamite and Dravidian connection. iScience 2024; 27:110016. [PMID: 38883810 PMCID: PMC11177204 DOI: 10.1016/j.isci.2024.110016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 04/06/2024] [Accepted: 05/14/2024] [Indexed: 06/18/2024] Open
Abstract
West and South Asian populations profoundly influenced Eurasian genetic and cultural diversity. We investigate the genetic history of the Y chromosome haplogroup L1-M22, which, while prevalent in these regions, lacks in-depth study. Robust Bayesian analyses of 165 high-coverage Y chromosomes favor a West Asian origin for L1-M22 ∼20.6 thousand years ago (kya). Moreover, this haplogroup parallels the genome-wide genetic ancestry of hunter-gatherers from the Iranian Plateau and the Caucasus. We characterized two L1-M22 harboring population groups during the Early Holocene. One expanded with the West Asian Neolithic transition. The other moved to South Asia ∼8-6 kya but showed no expansion. This group likely participated in the spread of Dravidian languages. These South Asian L1-M22 lineages expanded ∼4-3 kya, coinciding with the Steppe ancestry introduction. Our findings advance the current understanding of Eurasian historical dynamics, emphasizing L1-M22's West Asian origin, associated population movements, and possible linguistic impacts.
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Affiliation(s)
- Ajai Kumar Pathak
- Estonian Biocentre, Institute of Genomics, University of Tartu, 51010 Tartu, Estonia
- Department of Human Genetics, KU Leuven, 3000 Leuven, Belgium
| | - Hovann Simonian
- Armenian DNA Project at Family Tree DNA, Houston, TX 77008, USA
| | - Ibrahim Abdel Aziz Ibrahim
- Department of Pharmacology and Toxicology, Faculty of Medicine, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | | | - Doron M Behar
- Estonian Biocentre, Institute of Genomics, University of Tartu, 51010 Tartu, Estonia
| | - Qasim Ayub
- Monash University Malaysia Genomics Platform, School of Science, Monash University, Bandar Sunway, Selangor Darul Ehsan 47500, Malaysia
| | - Pakhrudin Arsanov
- Chechen-Noahcho DNA Project at Family Tree DNA, Kostanay 110008, Kazakhstan
| | - Ene Metspalu
- Estonian Biocentre, Institute of Genomics, University of Tartu, 51010 Tartu, Estonia
| | - Levon Yepiskoposyan
- Laboratory of Evolutionary Genomics, Institute of Molecular Biology of National Academy of Sciences of the Republic of Armenia, Yerevan 0014, Armenia
| | - Siiri Rootsi
- Estonian Biocentre, Institute of Genomics, University of Tartu, 51010 Tartu, Estonia
| | - Phillip Endicott
- Estonian Biocentre, Institute of Genomics, University of Tartu, 51010 Tartu, Estonia
- Department of Archaeology and Anthropology, Bournemouth University, Fern Barrow, Poole, Dorset BH12 5BB, UK
- Department of Linguistics, University of Hawai'i at Mānoa, Honolulu, Hawai'i 96822, USA
- DFG Center for Advanced Studies, University of Tübingen, 72074 Tübingen, Germany
| | - Richard Villems
- Estonian Biocentre, Institute of Genomics, University of Tartu, 51010 Tartu, Estonia
| | - Hovhannes Sahakyan
- Estonian Biocentre, Institute of Genomics, University of Tartu, 51010 Tartu, Estonia
- Laboratory of Evolutionary Genomics, Institute of Molecular Biology of National Academy of Sciences of the Republic of Armenia, Yerevan 0014, Armenia
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3
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Chen Z, Chen L, Tan J, Mao Y, Hao M, Li Y, Wang Y, Li J, Wang J, Jin L, Zheng HX. Natural selection shaped the protective effect of the mtDNA lineage against obesity in Han Chinese populations. J Genet Genomics 2024:S1673-8527(24)00129-2. [PMID: 38880354 DOI: 10.1016/j.jgg.2024.06.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 06/06/2024] [Accepted: 06/06/2024] [Indexed: 06/18/2024]
Abstract
Mitochondria play a key role in lipid metabolism, and mitochondrial DNA (mtDNA) mutations are thus considered to affect obesity susceptibility by altering oxidative phosphorylation and mitochondrial function. In this study, we investigated mtDNA variants that may affect obesity risk in 2,877 Han Chinese individuals from three independent populations. The association analysis of 16 basal mtDNA haplogroups with body mass index (BMI), waist circumference (WC) and waist-to-hip ratio (WHR) revealed that only haplogroup M7 was significantly negatively correlated with all three adiposity-related anthropometric traits in the overall cohort (P=0.003 for BMI, P=1×10-5 for WC, P=0.005 for WHR), which was verified by the analysis of a single population, i.e., the Zhengzhou population. Furthermore, subhaplogroup analysis suggested that M7b1a1 was the most likely haplogroup associated with a decreased obesity risk, and the variation T12811C (causing Y159H in ND5) harbored in M7b1a1 may be the most likely candidate for altering mitochondrial function. Specifically, we found that proportionally more nonsynonymous mutations accumulated in M7b1a1 carriers, indicating that M7b1a1 was either under positive selection or subject to a relaxation of selective constraints. We also found that nuclear variants, especially in DACT2 and PIEZO1, may functionally interact with M7b1a1.
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Affiliation(s)
- Ziwei Chen
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Center for Evolutionary Biology, Fudan University, Shanghai, China
| | - Lu Chen
- Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, China
| | - Jingze Tan
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Center for Evolutionary Biology, Fudan University, Shanghai, China
| | - Yizhen Mao
- Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, China
| | - Meng Hao
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Center for Evolutionary Biology, Fudan University, Shanghai, China
| | - Yi Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Center for Evolutionary Biology, Fudan University, Shanghai, China
| | - Yi Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Center for Evolutionary Biology, Fudan University, Shanghai, China; Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai, China
| | - Jinxi Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Center for Evolutionary Biology, Fudan University, Shanghai, China
| | - Jiucun Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Center for Evolutionary Biology, Fudan University, Shanghai, China; Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai, China; Research Unit of Dissecting Population Genetics and Developing New Technologies for Treatment and Prevention of Skin Phenotypes and Dermatological Diseases (2019RU058), Chinese Academy of Medical Sciences, Shanghai, China.
| | - Li Jin
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Center for Evolutionary Biology, Fudan University, Shanghai, China; Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai, China; Research Unit of Dissecting Population Genetics and Developing New Technologies for Treatment and Prevention of Skin Phenotypes and Dermatological Diseases (2019RU058), Chinese Academy of Medical Sciences, Shanghai, China.
| | - Hong-Xiang Zheng
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Center for Evolutionary Biology, Fudan University, Shanghai, China; Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai, China.
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Sun X, Pan Q, Hubley B, Ye Z, Zhang P, Xie Q. Geomorphic impacts within Red River Fault and island shifting as witnessed by the phylogeography of the largest water strider. Mol Phylogenet Evol 2024; 195:108062. [PMID: 38485104 DOI: 10.1016/j.ympev.2024.108062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 02/16/2024] [Accepted: 03/11/2024] [Indexed: 03/18/2024]
Abstract
Palaeogeological events and climate oscillations profoundly impact the demographics and distributions of small-range species, increasing the extinction risk. The largest water strider worldwide, Gigantometra gigas (Hemiptera: Gerridae), exhibits restricted distributions in Vietnam and southern China. Herein, we generated three genomic datasets (mitogenomes, 146 nuclear protein-coding genes and single nucleotide polymorphisms) with ecological niche modelling (ENM) to explicitly test whether the present-day distribution of G. gigas actually resulted from geographical and climatic effects. We found that the origin of this largest water strider reached the divergence time of the genus within Gerridae, providing a greater opportunity to explore its response to geographic movements. The right-lateral motion of the Red River Fault facilitated the divergence of two phylogeographic lineages, resulting in the "north-south component" genetic pattern in G. gigas. The Hainan and southeast Vietnam populations of the southern linage were completely separated by the Beibu Gulf but exhibited similar genetic compositions, confirming that Hainan had a continental origin and that Hainan Island joined with the Indo-China Peninsula to promote gene exchange among populations. Additionally, we noticed the low genetic diversity but long demographic history of the northern lineage, which displayed population dynamics opposite to those of other organisms. Integrating the demographic changes and ENM findings revealed that suitable habitat contraction and rapid demographic decline during the Last Glacial Maximum (LGM) triggered the low genetic diversity of the northern lineage. Overall, the demographic history of the largest water strider was mainly shaped by geographical features, and first provided evidence from the phylogeographic perspective of aquatic insects to support the hypothesis of Hainan Island shifting.
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Affiliation(s)
- Xiaoya Sun
- Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity & Tianjin Key Laboratory of Animal and Plant Resistance, Tianjin Normal University, Tianjin, China.
| | - Qiqi Pan
- School of Life Sciences, State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Brad Hubley
- Natural History - Entomology Royal Ontario Museum, 100 Queen's Park, Toronto, Canada
| | - Zhen Ye
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China.
| | - Peng Zhang
- School of Life Sciences, State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou, Guangdong, China.
| | - Qiang Xie
- School of Life Sciences, State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou, Guangdong, China
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5
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Bozlak E, Pokharel K, Weldenegodguad M, Paasivaara A, Stammler F, Røed KH, Kantanen J, Wallner B. Inferences about the population history of Rangifer tarandus from Y chromosome and mtDNA phylogenies. Ecol Evol 2024; 14:e11573. [PMID: 38863721 PMCID: PMC11164974 DOI: 10.1002/ece3.11573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 05/27/2024] [Accepted: 05/30/2024] [Indexed: 06/13/2024] Open
Abstract
Reindeer, called caribou in North America, has a circumpolar distribution and all extant populations belong to the same species (Rangifer tarandus). It has survived the Holocene thanks to its immense adaptability and successful coexistence with humans in different forms of hunting and herding cultures. Here, we examine the paternal and maternal history of Rangifer based on robust Y-chromosomal and mitochondrial DNA (mtDNA) trees representing Eurasian tundra reindeer, Finnish forest reindeer, Svalbard reindeer, Alaska tundra caribou, and woodland caribou. We first assembled Y-chromosomal contigs, representing 1.3 Mb of single-copy Y regions. Based on 545 Y-chromosomal and 458 mtDNA SNPs defined in 55 males, maximum parsimony trees were created. We observed two well separated clades in both phylogenies: the "EuroBeringian clade" formed by animals from Arctic Islands, Eurasia, and a few from North America and the "North American clade" formed only by caribou from North America. The time calibrated Y tree revealed an expansion and dispersal of lineages across continents after the Last Glacial Maximum. We show for the first time unique paternal lineages in Svalbard reindeer and Finnish forest reindeer and reveal a circumscribed Y haplogroup in Fennoscandian tundra reindeer. The Y chromosome in domesticated reindeer is markedly diverse indicating that several male lineages have undergone domestication and less intensive selection on males. This study places R. tarandus onto the list of species with resolved Y and mtDNA phylogenies and builds the basis for studies of the distribution and origin of paternal and maternal lineages in the future.
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Affiliation(s)
- Elif Bozlak
- Department of Biomedical Sciences, Institute of Animal Breeding and GeneticsUniversity of Veterinary Medicine ViennaViennaAustria
- Vienna Graduate School of Population GeneticsUniversity of Veterinary Medicine ViennaViennaAustria
| | | | | | | | | | - Knut H. Røed
- Department of Preclinical Sciences and PathologyNorwegian University of Life SciencesÅsNorway
| | | | - Barbara Wallner
- Department of Biomedical Sciences, Institute of Animal Breeding and GeneticsUniversity of Veterinary Medicine ViennaViennaAustria
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6
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Wang Y, Gou Y, Yuan R, Zou Q, Zhang X, Zheng T, Fei K, Shi R, Zhang M, Li Y, Gong Z, Luo C, Xiong Y, Shan D, Wei C, Shen L, Tang G, Li M, Zhu L, Li X, Jiang Y. A chromosome-level genome of Chenghua pig provides new insights into the domestication and local adaptation of pigs. Int J Biol Macromol 2024; 270:131796. [PMID: 38677688 DOI: 10.1016/j.ijbiomac.2024.131796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 03/24/2024] [Accepted: 04/04/2024] [Indexed: 04/29/2024]
Abstract
As a country with abundant genetic resources of pigs, the domestication history of pigs in China and the adaptive evolution of Chinese pig breeds at different latitudes have rarely been elucidated at the genome-wide level. To fill this gap, we first assembled a high-quality chromosome-level genome of the Chenghua pig and used it as a benchmark to analyse the genomes of 272 samples from three genera of three continents. The divergence of the three species belonging to three genera, Phacochoerus africanus, Potamochoerus porcus, and Sus scrofa, was assessed. The introgression of pig breeds redefined that the migration routes were basically from southern China to central and southwestern China, then spread to eastern China, arrived in northern China, and finally reached Europe. The domestication of pigs in China occurred ∼12,000 years ago, earlier than the available Chinese archaeological domestication evidence. In addition, FBN1 and NR6A1 were identified in our study as candidate genes related to extreme skin thickness differences in Eurasian pig breeds and adaptive evolution at different latitudes in Chinese pig breeds, respectively. Our study provides a new resource for the pig genomic pool and refines our understanding of pig genetic diversity, domestication, migration, and adaptive evolution at different latitudes.
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Affiliation(s)
- Yifei Wang
- Department of Zoology, College of Life Science, Sichuan Agricultural University, Ya'an, Sichuan 625014, China
| | - Yuwei Gou
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Rong Yuan
- Chengdu Livestock and Poultry Genetic Resources Protection Center, Chengdu, Sichuan 610081, China
| | - Qin Zou
- Department of Zoology, College of Life Science, Sichuan Agricultural University, Ya'an, Sichuan 625014, China
| | - Xukun Zhang
- Academy for Engineering and Technology, Fudan University, Shanghai 200433, China
| | - Ting Zheng
- Department of Zoology, College of Life Science, Sichuan Agricultural University, Ya'an, Sichuan 625014, China
| | - Kaixin Fei
- Department of Zoology, College of Life Science, Sichuan Agricultural University, Ya'an, Sichuan 625014, China
| | - Rui Shi
- Department of Zoology, College of Life Science, Sichuan Agricultural University, Ya'an, Sichuan 625014, China
| | - Mei Zhang
- Department of Zoology, College of Life Science, Sichuan Agricultural University, Ya'an, Sichuan 625014, China
| | - Yujing Li
- Department of Zoology, College of Life Science, Sichuan Agricultural University, Ya'an, Sichuan 625014, China
| | - Zhengyin Gong
- Department of Zoology, College of Life Science, Sichuan Agricultural University, Ya'an, Sichuan 625014, China
| | - Chenggang Luo
- Chengdu Livestock and Poultry Genetic Resources Protection Center, Chengdu, Sichuan 610081, China
| | - Ying Xiong
- Department of Zoology, College of Life Science, Sichuan Agricultural University, Ya'an, Sichuan 625014, China
| | - Dai Shan
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Chenyang Wei
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Linyuan Shen
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Guoqing Tang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Mingzhou Li
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Li Zhu
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Xuewei Li
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Yanzhi Jiang
- Department of Zoology, College of Life Science, Sichuan Agricultural University, Ya'an, Sichuan 625014, China.
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Hošek J, Pokorný P, Storch D, Kvaček J, Havig J, Novák J, Hájková P, Jamrichová E, Brengman L, Radoměřský T, Křížek M, Magna T, Rapprich V, Laufek F, Hamilton T, Pack A, Di Rocco T, Horáček I. Hot spring oases in the periglacial desert as the Last Glacial Maximum refugia for temperate trees in Central Europe. SCIENCE ADVANCES 2024; 10:eado6611. [PMID: 38820152 PMCID: PMC11141633 DOI: 10.1126/sciadv.ado6611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Accepted: 04/30/2024] [Indexed: 06/02/2024]
Abstract
Northern glacial refugia are a hotly debated concept. The idea that many temperate organisms survived the Last Glacial Maximum (LGM; ~26.5 to 19 thousand years) in several sites across central and northern Europe stems from phylogeographic analyses, yet direct fossil evidence has thus far been missing. Here, we present the first unequivocal proof that thermophilous trees such as oak (Quercus), linden (Tilia), and common ash (Fraxinus excelsior) survived the LGM in Central Europe. The persistence of the refugium was promoted by a steady influx of hydrothermal waters that locally maintained a humid and warm microclimate. We reconstructed the geological and palaeohydrological factors responsible for the emergence of hot springs during the LGM and argue that refugia of this type, allowing the long-term survival and rapid post-LGM dispersal of temperate elements, were not exceptional in the European periglacial zone.
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Affiliation(s)
- Jan Hošek
- Czech Geological Survey, Klárov 3, Prague 1, Czech Republic
- Center for Theoretical Study, Charles University and the Czech Academy of Sciences, Jilská 1, Prague 1, Czech Republic
| | - Petr Pokorný
- Center for Theoretical Study, Charles University and the Czech Academy of Sciences, Jilská 1, Prague 1, Czech Republic
| | - David Storch
- Center for Theoretical Study, Charles University and the Czech Academy of Sciences, Jilská 1, Prague 1, Czech Republic
- Department of Ecology, Faculty of Science, Charles University, Viničná 7, Prague 2, Czech Republic
| | - Jiří Kvaček
- Department of Palaeontology, National Museum Prague, Václavské nám. 68, Prague, Czech Republic
| | - Jeff Havig
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN 55108, USA
- Department of Earth and Environmental Sciences, University of Minnesota, Minneapolis, MN 55455, USA
| | - Jan Novák
- Department of Botany, Faculty of Science, Charles University, Benátská 2, Prague 2, Czech Republic
| | - Petra Hájková
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, Brno, Czech Republic
- Department of Paleoecology, Institute of Botany, The Czech Academy of Sciences, Lidická 25/27, Brno, Czech Republic
| | - Eva Jamrichová
- Department of Paleoecology, Institute of Botany, The Czech Academy of Sciences, Lidická 25/27, Brno, Czech Republic
| | - Latisha Brengman
- Earth and Environmental Sciences Department, University of Minnesota Duluth, Duluth, MN 55812, USA
| | - Tomáš Radoměřský
- Czech Geological Survey, Klárov 3, Prague 1, Czech Republic
- Institute of Geology and Palaeontology, Faculty of Science, Charles University, Albertov 6, 128 43 Prague 2, Czech Republic
| | - Marek Křížek
- Department of Physical Geography and Geoecology, Faculty of Science, Charles University, Albertov 6, Prague 2, Czech Republic
| | - Tomáš Magna
- Czech Geological Survey, Klárov 3, Prague 1, Czech Republic
| | | | | | - Trinity Hamilton
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN 55108, USA
| | - Andreas Pack
- Universität Göttingen, Geowissenschaftliches Zentrum, Goldschmidtstraße 1, Göttingen, Germany
| | - Tommaso Di Rocco
- Universität Göttingen, Geowissenschaftliches Zentrum, Goldschmidtstraße 1, Göttingen, Germany
| | - Ivan Horáček
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, Prague 2, Czech Republic
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Wang Y, Zeng B, Deng M, Zhao T, Liao Y, Ren R, Wang H, Yuan Y. Whole-genome resequencing reveals genetic diversity and adaptive evolution in Chinese honeybee ( Apis cerana cerana) in Guizhou, China. Front Genet 2024; 15:1352455. [PMID: 38826805 PMCID: PMC11140131 DOI: 10.3389/fgene.2024.1352455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 04/29/2024] [Indexed: 06/04/2024] Open
Abstract
Introduction: Guizhou Province, characterized by complex and diverse geographic and climatic environments, has rich genetic resources for the Chinese honeybee (Apis cerana cerana) and is one of the main bee-producing areas in China. However, research on the genetic diversity of Chinese honeybee in the Guizhou region is very limited, despite implications for conservation of biodiversity. Methods: In this study, we analyzed the genetic diversity, differentiation, and selection signals based on 116 Chinese honeybees from 12 regions in Guizhou Province using whole-genome sequencing. Results: We identified 1,400,430 high-quality SNPs across all samples. A population structure analysis revealed two independent genetic subgroups of Chinese honeybees in Guizhou, a Yunnan-Guizhou Plateau population in western Guizhou and a hilly-mountainous population in eastern Guizhou. The average nucleotide diversity (Pi) ranged from 0.00138 to 0.00161 and average expected heterozygosity (He) ranged from 0.2592 to 0.2604. The average genetic differentiation index (F ST) for Chinese honeybees in pairwise comparisons of 12 regions ranged from 0.0094 to 0.0293. There was clear genetic differentiation between the western plateau and the eastern hilly mountainous areas of Guizhou; however, F ST values between the eastern and western populations ranged from 0.0170 to 0.0293, indicating a low degree of differentiation. A genome-wide scan revealed a number of genes under selection in the Yunnan-Guizhou Plateau environment. These genes were related to growth and development, reproduction, and cold resistance, and several candidate genes involved in environmental adaptation were identified, including CTR, MAPK, MAST, HSF, and MKKK. Discussion: The results of the present study provide important theoretical bases for the conservation, evaluation, development, and utilization of genetic resources for Chinese honeybees in the Guizhou region and for further investigations of environmental adaptation and underlying mechanisms in the species.
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Affiliation(s)
- Yinchen Wang
- Guizhou Institute of Animal Husbandry and Veterinary Science, Guiyang, China
| | - Bing Zeng
- College of Animal Science and Technology, Southwest University, Chongqing, China
| | - Mengqing Deng
- Guizhou Institute of Animal Husbandry and Veterinary Science, Guiyang, China
| | - Tian Zhao
- Guizhou Institute of Animal Husbandry and Veterinary Science, Guiyang, China
| | - Yan Liao
- Guizhou Institute of Animal Husbandry and Veterinary Science, Guiyang, China
| | - Rongqing Ren
- Guizhou Institute of Animal Husbandry and Veterinary Science, Guiyang, China
| | - Hua Wang
- Guizhou Institute of Animal Husbandry and Veterinary Science, Guiyang, China
| | - Yang Yuan
- Guizhou Institute of Animal Husbandry and Veterinary Science, Guiyang, China
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9
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Jirapatrasilp P, Cuny G, Kocsis L, Sutcharit C, Ngamnisai N, Charoentitirat T, Kumpitak S, Suraprasit K. Mid-Holocene marine faunas from the Bangkok Clay deposits in Nakhon Nayok, the Central Plain of Thailand. Zookeys 2024; 1202:1-110. [PMID: 38800563 PMCID: PMC11112167 DOI: 10.3897/zookeys.1202.119389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 03/24/2024] [Indexed: 05/29/2024] Open
Abstract
Based on several field investigations, many molluscan shells and chondrichthyan teeth, together with other invertebrate and actinopterygian remains were found from the marine Bangkok Clay deposits in Ongkharak, Nakhon Nayok, at a depth of ~ 5-7 m below the topsoil surface. Animal macrofossils recovered from these Holocene marine deposits were identified and their chronological context was investigated in order to reconstruct the paleoenvironments of the area at that time. The majority of marine fossils recovered from the site consist of molluscs, with a total of 63 species identified. Other invertebrate species include a stony coral, a mud lobster, barnacles, and a sea urchin. The vertebrates are represented by fish remains, including carcharhinid shark teeth from at least nine species, stingray and trichiurid teeth, and one sciaenid otolith. The molluscan fauna indicates that the paleoenvironments of the area corresponded to intertidal to sublittoral zones, where some areas were mangrove forests and intertidal mudflats. The fish fauna is dominated by the river shark Glyphis, indicating freshwater influences and possibly occasional brackish conditions. The carbon-14 analysis of mollusc and charcoal remains shows that deposition of the marine sediment sequence began during the mid-Holocene, spanning approximately from 8,800 to 5,300 cal yr BP. This study provides in-depth insights into the diversity of fishes, marine molluscs, and other invertebrates from the Bangkok Clay deposits, supporting the existence of a marine transgression onto the Lower Central Plain of Thailand during the mid-Holocene.
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Affiliation(s)
- Parin Jirapatrasilp
- Animal Systematics Research Unit, Department of Biology, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
- Leibniz-Institut zur Analyse des Biodiversitätswandels - Standort Hamburg, Martin-Luther-King-Platz 3, Hamburg 20146, Germany
| | - Gilles Cuny
- Université Claude Bernard Lyon 1, LEHNA UMR 5023, CNRS, ENTPE, F-69622, Villeurbanne, France
| | - László Kocsis
- Institute of Earth Surface Dynamics, University of Lausanne, Rue de la Mouline, 1015 Lausanne, Switzerland
| | - Chirasak Sutcharit
- Animal Systematics Research Unit, Department of Biology, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Nom Ngamnisai
- Department of Geography, Faculty of Social Sciences, Srinakharinwirot University, Bangkok 10110, Thailand
| | - Thasinee Charoentitirat
- Animal Systematics Research Unit, Department of Biology, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Satapat Kumpitak
- Animal Systematics Research Unit, Department of Biology, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Kantapon Suraprasit
- Animal Systematics Research Unit, Department of Biology, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
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10
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Rota F, Carnicero P, Casazza G, Nascimbene J, Schönswetter P, Wellstein C. Survival in nunatak and peripheral glacial refugia of three alpine plant species is partly predicted by altitudinal segregation. Mol Ecol 2024; 33:e17343. [PMID: 38596873 DOI: 10.1111/mec.17343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 03/12/2024] [Indexed: 04/11/2024]
Abstract
Mountain biota survived the Quaternary cold stages most probably in peripheral refugia and/or ice-free peaks within ice-sheets (nunataks). While survival in peripheral refugia has been broadly demonstrated, evidence for nunatak refugia is still scarce. We generated RADseq data from three mountain plant species occurring at different elevations in the southeastern European Alps to investigate the role of different glacial refugia during the Last Glacial Maximum (LGM). We tested the following hypotheses. (i) The deep Piave Valley forms the deepest genetic split in the species distributed across it, delimiting two peripheral refugia. (ii) The montane to alpine species Campanula morettiana and Primula tyrolensis survived the LGM in peripheral refugia, while high-alpine to subnival Saxifraga facchinii likely survived in several nunatak refugia. (iii) The lower elevation species suffered a strong population decline during the LGM. By contrast, the higher elevation species shows long-term stability of population sizes due to survival on permanently ice-free peaks and small population sizes at present. We found peripheral refugia on both sides of the Piave Valley, which acted as a major genetic barrier. Demographic modelling confirmed nunatak survival not only for S. facchinii but also for montane to alpine C. morettiana. Altitudinal segregation influenced the species' demographic fluctuations, with the lower elevation species showing a significant population increase at the end of the LGM, and the higher elevation species either showing decrease towards the present or stable population sizes with a short bottleneck. Our results highlight the role of nunatak survival and species ecology in the demographic history of mountain species.
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Affiliation(s)
- Francesco Rota
- Faculty of Agricultural, Environmental and Food Sciences, Free University of Bozen-Bolzano, Bolzano, Italy
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| | - Pau Carnicero
- Department of Botany, University of Innsbruck, Innsbruck, Austria
| | - Gabriele Casazza
- Department of Earth, Environmental and Life Sciences (DISTAV), University of Genoa, Genova, Italy
| | - Juri Nascimbene
- BIOME Group, Department of Biological, Geological and Environmental Sciences, Alma Mater Studiorum - University of Bologna, Bologna, Italy
| | | | - Camilla Wellstein
- Faculty of Agricultural, Environmental and Food Sciences, Free University of Bozen-Bolzano, Bolzano, Italy
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11
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Tian L, Xu R, Chen D, Ananjeva NB, Brown RM, Min MS, Cai B, Mijidsuren B, Zhang B, Guo X. Range-Wide Phylogeography and Ecological Niche Modeling Provide Insights into the Evolutionary History of the Mongolian Racerunner ( Eremias argus) in Northeast Asia. Animals (Basel) 2024; 14:1124. [PMID: 38612363 PMCID: PMC11011046 DOI: 10.3390/ani14071124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 04/03/2024] [Accepted: 04/04/2024] [Indexed: 04/14/2024] Open
Abstract
The Mongolian racerunner, Eremias argus, is a small lizard endemic to Northeast Asia that can serve as an excellent model for investigating how geography and past climate change have jointly influenced the evolution of biodiversity in this region. To elucidate the processes underlying its diversification and demography, we reconstructed the range-wide phylogeographic pattern and evolutionary trajectory, using phylogenetic, population genetic, landscape genetic, Bayesian phylogeographic reconstruction and ecological niche modeling approaches. Phylogenetic analyses of the mtDNA cyt b gene revealed eight lineages that were unbounded by geographic region. The genetic structure of E. argus was mainly determined by geographic distance. Divergence dating indicated that E. argus and E. brenchleyi diverged during the Mid-Pliocene Warm Period. E. argus was estimated to have coalesced at~0.4351 Ma (Marine Isotope Stage 19). Bayesian phylogeographic diffusion analysis revealed out-of-Inner Mongolia and rapid colonization events from the end of the Last Interglacial to the Last Glacial Maximum, which is consistent with the expanded suitable range of the Last Glacial Maximum. Pre-Last Glacial Maximum growth of population is presented for most lineages of E. argus. The Glacial Maximum contraction model and the previous multiple glacial refugia hypotheses are rejected. This may be due to an increase in the amount of climatically favorable habitats in Northeast Asia. Furthermore, E. argus barbouri most likely represents an invalid taxon. The present study is the first to report a range-wide phylogeography of reptiles over such a large region in Northeast Asia. Our results make a significant contribution towards understanding the biogeography of the entire Northeast Asia.
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Affiliation(s)
- Lili Tian
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610223, China; (L.T.); (R.X.); (B.C.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Rui Xu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610223, China; (L.T.); (R.X.); (B.C.)
| | - Dali Chen
- Department of Pathogenic Biology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu 610041, China;
| | - Natalia B. Ananjeva
- Zoological Institute, Russian Academy of Sciences, St. Petersburg 199034, Russia;
| | - Rafe M. Brown
- Biodiversity Institute, Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045, USA;
| | - Mi-Sook Min
- Conservation Genome Resource Bank for Korean Wildlife, Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 151-742, Republic of Korea;
| | - Bo Cai
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610223, China; (L.T.); (R.X.); (B.C.)
| | - Byambasuren Mijidsuren
- Plant Protection Research Institute, Mongolian University of Life Sciences, Ulaanbaatar 210153, Mongolia;
| | - Bin Zhang
- College of Life Sciences and Technology, Inner Mongolia Normal University, Hohhot 010022, China;
| | - Xianguang Guo
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610223, China; (L.T.); (R.X.); (B.C.)
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12
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Antoine PO, Wieringa LN, Adnet S, Aguilera O, Bodin SC, Cairns S, Conejeros-Vargas CA, Cornée JJ, Ežerinskis Ž, Fietzke J, Gribenski NO, Grouard S, Hendy A, Hoorn C, Joannes-Boyau R, Langer MR, Luque J, Marivaux L, Moissette P, Nooren K, Quillévéré F, Šapolaitė J, Sciumbata M, Valla PG, Witteveen NH, Casanova A, Clavier S, Bidgrain P, Gallay M, Rhoné M, Heuret A. A Late Pleistocene coastal ecosystem in French Guiana was hyperdiverse relative to today. Proc Natl Acad Sci U S A 2024; 121:e2311597121. [PMID: 38527199 PMCID: PMC10998618 DOI: 10.1073/pnas.2311597121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Accepted: 02/15/2024] [Indexed: 03/27/2024] Open
Abstract
Warmer temperatures and higher sea level than today characterized the Last Interglacial interval [Pleistocene, 128 to 116 thousand years ago (ka)]. This period is a remarkable deep-time analog for temperature and sea-level conditions as projected for 2100 AD, yet there has been no evidence of fossil assemblages in the equatorial Atlantic. Here, we report foraminifer, metazoan (mollusks, bony fish, bryozoans, decapods, and sharks among others), and plant communities of coastal tropical marine and mangrove affinities, dating precisely from a ca. 130 to 115 ka time interval near the Equator, at Kourou, in French Guiana. These communities include ca. 230 recent species, some being endangered today and/or first recorded as fossils. The hyperdiverse Kourou mollusk assemblage suggests stronger affinities between Guianese and Caribbean coastal waters by the Last Interglacial than today, questioning the structuring role of the Amazon Plume on tropical Western Atlantic communities at the time. Grassland-dominated pollen, phytoliths, and charcoals from younger deposits in the same sections attest to a marine retreat and dryer conditions during the onset of the last glacial (ca. 110 to 50 ka), with a savanna-dominated landscape and episodes of fire. Charcoals from the last millennia suggest human presence in a mosaic of modern-like continental habitats. Our results provide key information about the ecology and biogeography of pristine Pleistocene tropical coastal ecosystems, especially relevant regarding the-widely anthropogenic-ongoing global warming.
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Affiliation(s)
- Pierre-Olivier Antoine
- Equipe de Paléontologie, Institut des Sciences de l’Évolution de Montpellier, Univ Montpellier, CNRS, Institut de Recherche pour le Développement, Montpellier34095, France
| | - Linde N. Wieringa
- Equipe de Paléontologie, Institut des Sciences de l’Évolution de Montpellier, Univ Montpellier, CNRS, Institut de Recherche pour le Développement, Montpellier34095, France
| | - Sylvain Adnet
- Equipe de Paléontologie, Institut des Sciences de l’Évolution de Montpellier, Univ Montpellier, CNRS, Institut de Recherche pour le Développement, Montpellier34095, France
| | - Orangel Aguilera
- Paleoecology and Global Changes Laboratory, Marine Biology Department, Fluminense Federal University, Niterói 24210-201, Rio de Janeiro, Brazil
| | - Stéphanie C. Bodin
- Department of Paleoanthropology, Senckenberg Research Institute, Frankfurt am Main60325, Germany
| | - Stephen Cairns
- Department of Invertebrate Zoology, Smithsonian Institution, National Museum of Natural History, Washington D.C.20013-7012
| | - Carlos A. Conejeros-Vargas
- Departamento de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Coyoacán, Ciudad de México04510, México
| | - Jean-Jacques Cornée
- Equipe Dynamique de la Lithosphère, Géosciences Montpellier, Univ Montpellier, CNRS, Montpellier34095, France
| | - Žilvinas Ežerinskis
- Mass Spectrometry Laboratory, Center for Physical Sciences and Technology, Vilnius10257, Lithuania
| | - Jan Fietzke
- Geomar, Helmholtz Centre for Ocean Research Kiel, Kiel24148, Germany
| | - Natacha O. Gribenski
- Institute of Geological Sciences, Oeschger Centre for Climate Change Research, University of Bern, Bern3012, Switzerland
| | - Sandrine Grouard
- Archéozoologie et Archéobotanique—Sociétés, Pratiques et Environnements, CNRS, Muséum National d’Histoire Naturelle, Paris75005, France
| | - Austin Hendy
- Invertebrate Paleontology Department, Natural History Museum of Los Angeles County, Los Angeles, CA90007
| | - Carina Hoorn
- Ecosystem & Landscape Dynamics Department, Institute for Biodiversity and Ecosystem Dynamics, Universiteit van Amsterdam, Amsterdam1098 XH, The Netherlands
| | - Renaud Joannes-Boyau
- Geoarchaeology and Archaeometry Research Group, Southern Cross GeoScience, Southern Cross University, East Lismore, NSW2480, Australia
- Centre for Anthropological Research, University of Johannesburg, Johannesburg2092, South Africa
| | - Martin R. Langer
- Arbeitsgruppe Mikropaläontologie, Institut für Geowissenschaften, Paläontologie, Universität Bonn, Bonn53115, Germany
| | - Javier Luque
- Department of Zoology, Museum of Zoology, University of Cambridge, CambridgeCB2 3EJ, United Kingdom
| | - Laurent Marivaux
- Equipe de Paléontologie, Institut des Sciences de l’Évolution de Montpellier, Univ Montpellier, CNRS, Institut de Recherche pour le Développement, Montpellier34095, France
| | - Pierre Moissette
- Department of Historical Geology-Paleontology, National and Kapodistrian University of Athens, Panepistimiopolis, Zografou, Athens15784, Greece
| | - Kees Nooren
- Ecosystem & Landscape Dynamics Department, Institute for Biodiversity and Ecosystem Dynamics, Universiteit van Amsterdam, Amsterdam1098 XH, The Netherlands
| | - Frédéric Quillévéré
- Laboratoire de Géologie de Lyon - Terre, Planètes, Environnement, Université Claude Bernard Lyon 1, Ecole Normale Supérieure de Lyon, CNRS, VilleurbanneF-69622, France
| | - Justina Šapolaitė
- Mass Spectrometry Laboratory, Center for Physical Sciences and Technology, Vilnius10257, Lithuania
| | - Matteo Sciumbata
- Ecosystem & Landscape Dynamics Department, Institute for Biodiversity and Ecosystem Dynamics, Universiteit van Amsterdam, Amsterdam1098 XH, The Netherlands
- Section Systems Ecology, Amsterdam Institute for Life and Environment, Vrije Universiteit, Amsterdam1081 BT, The Netherlands
| | - Pierre G. Valla
- Equipe Tectonique, Reliefs et Bassins, Institut des Sciences de la Terre, Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, Université Gustave Eiffel, Grenoble38058, France
| | - Nina H. Witteveen
- Ecosystem & Landscape Dynamics Department, Institute for Biodiversity and Ecosystem Dynamics, Universiteit van Amsterdam, Amsterdam1098 XH, The Netherlands
| | - Alexandre Casanova
- Département Formation et Recherche Sciences et Technologie, Université de Guyane, Cayenne97300, Guyane
| | | | - Philibert Bidgrain
- Département Formation et Recherche Sciences et Technologie, Université de Guyane, Cayenne97300, Guyane
| | | | | | - Arnauld Heuret
- Equipe Dynamique de la Lithosphère, Géosciences Montpellier, Univ Montpellier, CNRS, Montpellier34095, France
- Département Formation et Recherche Sciences et Technologie, Université de Guyane, Cayenne97300, Guyane
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13
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Weber MD, Richards TM, Sutton TT, Carter JE, Eytan RI. Deep-pelagic fishes: Demographic instability in a stable environment. Ecol Evol 2024; 14:e11267. [PMID: 38638366 PMCID: PMC11024635 DOI: 10.1002/ece3.11267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 03/10/2024] [Accepted: 04/01/2024] [Indexed: 04/20/2024] Open
Abstract
Demographic histories are frequently a product of the environment, as populations expand or contract in response to major environmental changes, often driven by changes in climate. Meso- and bathy-pelagic fishes inhabit some of the most temporally and spatially stable habitats on the planet. The stability of the deep-pelagic could make deep-pelagic fishes resistant to the demographic instability commonly reported in fish species inhabiting other marine habitats, however the demographic histories of deep-pelagic fishes are unknown. We reconstructed the historical demography of 11 species of deep-pelagic fishes using mitochondrial and nuclear DNA sequence data. We uncovered widespread evidence of population expansions in our study species, a counterintuitive result based on the nature of deep-pelagic ecosystems. Frequency-based methods detected potential demographic changes in nine species of fishes, while extended Bayesian skyline plots identified population expansions in four species. These results suggest that despite the relatively stable nature of the deep-pelagic environment, the fishes that reside here have likely been impacted by past changes in climate. Further investigation is necessary to better understand how deep-pelagic fishes, by far Earth's most abundant vertebrates, will respond to future climatic changes.
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Affiliation(s)
- Max D. Weber
- Texas A&M University at GalvestonGalvestonTexasUSA
| | | | | | | | - Ron I. Eytan
- Texas A&M University at GalvestonGalvestonTexasUSA
- Department of Biological SciencesLouisiana State UniversityBaton RougeLouisianaUSA
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14
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Hagemann JR, Lamy F, Arz HW, Lembke-Jene L, Auderset A, Harada N, Ho SL, Iwasaki S, Kaiser J, Lange CB, Murayama M, Nagashima K, Nowaczyk N, Martínez-García A, Tiedemann R. A marine record of Patagonian ice sheet changes over the past 140,000 years. Proc Natl Acad Sci U S A 2024; 121:e2302983121. [PMID: 38437529 PMCID: PMC10962970 DOI: 10.1073/pnas.2302983121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 01/03/2024] [Indexed: 03/06/2024] Open
Abstract
Terrestrial glacial records from the Patagonian Andes and New Zealand Alps document quasi-synchronous Southern Hemisphere-wide glacier advances during the late Quaternary. However, these records are inherently incomplete. Here, we provide a continuous marine record of western-central Patagonian ice sheet (PIS) extent over a complete glacial-interglacial cycle back into the penultimate glacial (~140 ka). Sediment core MR16-09 PC03, located at 46°S and ~150 km offshore Chile, received high terrestrial sediment and meltwater input when the central PIS extended westward. We use biomarkers, foraminiferal oxygen isotopes, and major elemental data to reconstruct terrestrial sediment and freshwater input related to PIS variations. Our sediment record documents three intervals of general PIS marginal fluctuations, during Marine Isotope Stage (MIS) 6 (140 to 135 ka), MIS 4 (~70 to 60 ka), and late MIS 3 to MIS 2 (~40 to 18 ka). These higher terrigenous input intervals occurred during sea-level low stands, when the western PIS covered most of the Chilean fjords, which today retain glaciofluvial sediments. During these intervals, high-amplitude phases of enhanced sediment supply occur at millennial timescales, reflecting increased ice discharge most likely due to a growing PIS. We assign the late MIS 3 to MIS 2 phases and, by inference, older advances to Antarctic cold stages. We conclude that the increased sediment/meltwater release during Southern Hemisphere millennial-scale cold phases was likely related to higher precipitation caused by enhanced westerly winds at the northwestern margin of the PIS. Our records complement terrestrial archives and provide evidence for PIS climate sensitivity.
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Affiliation(s)
- Julia R. Hagemann
- Division of Geoscience, Marine Geology Section, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven27570, Germany
- Department of Climate Geochemistry, Organic Isotope Geochemistry Group, Max Planck Institute for Chemistry, Mainz55128, Germany
| | - Frank Lamy
- Division of Geoscience, Marine Geology Section, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven27570, Germany
- Center for Marine Environmental Sciences, University of Bremen, Bremen28359, Germany
| | - Helge W. Arz
- Department of Marine Geology, Paleoceanography and Sedimentology Group, Leibniz Institute for Baltic Sea Research Warnemünde, Rostock18119, Germany
| | - Lester Lembke-Jene
- Division of Geoscience, Marine Geology Section, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven27570, Germany
| | - Alexandra Auderset
- Department of Climate Geochemistry, Organic Isotope Geochemistry Group, Max Planck Institute for Chemistry, Mainz55128, Germany
- School of Ocean and Earth Science, University of Southampton, SouthamptonSO17 1BJ, United Kingdom
| | - Naomi Harada
- Atmosphere and Ocean Research Institute, Center for International and Local Research Cooperation, The University of Tokyo, Kashiwa277-8564, Japan
- Research Institute for Global Change, Earth Surface System Research Center, Japan Agency for Marine-Earth Science and Technology, Yokosuka237-0061, Japan
| | - Sze Ling Ho
- Institute of Oceanography, National Taiwan University, Taipei10617, Taiwan
| | - Shinya Iwasaki
- Graduate School of Environmental Science, Hokkaido University, Sapporo060-0810, Japan
| | - Jérôme Kaiser
- Department of Marine Geology, Paleoceanography and Sedimentology Group, Leibniz Institute for Baltic Sea Research Warnemünde, Rostock18119, Germany
| | - Carina B. Lange
- Departamento de Oceanografía & Centro de Investigación Oceanográfica en el Pacífico Suroriental (Coastal), Universidad de Concepción, Concepción4030000, Chile
- Centro de Investigación Dinámica de Ecosistemas Marinos de Altas Latitudes, Universidad Austral de Chile,Valdivia5110566, Chile
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA92037, United States
| | - Masafumi Murayama
- Faculty of Agriculture and Marine Science, Kochi University, Nankoku, Kochi783-8502, Japan
- Center for Advanced Marine Core Research, Kochi University, Nankoku, Kochi783-8502, Japan
| | - Kana Nagashima
- Research Institute for Global Change, Earth Surface System Research Center, Japan Agency for Marine-Earth Science and Technology, Yokosuka237-0061, Japan
| | - Norbert Nowaczyk
- Department of Geosystems, Section of Climate Dynamics and Landscape Evolution, Helmholtz Centre Potsdam German Research Centre for Geosciences, Potsdam14473, Germany
| | - Alfredo Martínez-García
- Department of Climate Geochemistry, Organic Isotope Geochemistry Group, Max Planck Institute for Chemistry, Mainz55128, Germany
| | - Ralf Tiedemann
- Division of Geoscience, Marine Geology Section, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven27570, Germany
- Center for Marine Environmental Sciences, University of Bremen, Bremen28359, Germany
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15
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Pavić M, Briški M, Pola M, Borović S. Hydrogeochemical and environmental isotope study of Topusko thermal waters, Croatia. ENVIRONMENTAL GEOCHEMISTRY AND HEALTH 2024; 46:133. [PMID: 38483667 DOI: 10.1007/s10653-024-01904-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 02/06/2024] [Indexed: 03/19/2024]
Abstract
Thermal waters in Topusko (Croatia), with temperatures of up to 65 °C, have been used for heating, health, and recreational tourism for the past fifty years. Hydrogeochemical monitoring can provide insights into deeper geological processes and indicate system changes from baseline levels. It helps to identify potential anthropogenic impacts, as well as natural changes. Hydrogeochemical, geothermometrical, and environmental isotope studies of thermal waters in Topusko were conducted to improve the existing conceptual model of the Topusko hydrothermal system (THS), providing a baseline for continuous monitoring of the thermal resource. 2-year thermal springs and precipitation monitoring took place from March 2021 until March 2023. Major anions and cations, stable and radioactive isotopes (i.e. 18O, 2H, SO42-, 3H and 14C) and geothermometers were used to assess the origin of thermal waters in Topusko and their interaction with thermal aquifer. The results indicate the meteoric origin of thermal water, which was recharged in colder climatic conditions around the late Pleistocene-Early Holocene. Thermal water was last in contact with the atmosphere before approximately 9.5 kyr. Ca-HCO3 hydrochemical facies suggests carbonate dissolution as the dominant process driving the solute content. Geothermometrical results indicate an equilibrium temperature in the reservoir of 90 °C.
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Affiliation(s)
- Mirja Pavić
- Croatian Geological Survey, Sachsova 2, 10000, Zagreb, Croatia
| | - Maja Briški
- Croatian Geological Survey, Sachsova 2, 10000, Zagreb, Croatia
| | - Marco Pola
- Croatian Geological Survey, Sachsova 2, 10000, Zagreb, Croatia
| | - Staša Borović
- Croatian Geological Survey, Sachsova 2, 10000, Zagreb, Croatia.
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16
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Belcik JT, Ashley MV. Riverscape genetics of the orangethroat darter complex. JOURNAL OF FISH BIOLOGY 2024; 104:837-850. [PMID: 37971888 DOI: 10.1111/jfb.15619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 09/16/2023] [Accepted: 11/15/2023] [Indexed: 11/19/2023]
Abstract
Freshwater darters belonging to the orangethroat darter species complex, or Ceasia, are widely distributed in the Central and Southern United States, with ranges that span both glaciated and unglaciated regions. Up to 15 species have been recognized in the complex, with one, Etheostoma spectabile, having a widespread northern distribution and another, Etheostoma pulchellum, having a sizeable southern distribution. The other species in the complex have much more restricted distributions in unglaciated regions of the Central Highlands. We sampled 384 darters from 52 sites covering much of the range of Ceasia and evaluated patterns of genetic diversity, genetic structure, and pre- and post-glacial patterns of range contraction and expansion. We anticipated finding much stronger signals of genetic differentiation and diversification in unglaciated regions, given the higher species diversity and levels of endemism reported there. Surprisingly, microsatellite genotyping revealed two well-differentiated genetic clusters of E. spectabile in samples from glaciated regions, one confined to the Illinois River basin and another found in the Wabash drainage and Great Lakes tributaries. This suggests that there was expansion from two isolated glacial refugia, with little subsequent post-glacial gene flow. Fish collected from throughout the unglaciated region were less genetically differentiated. Fish assigned to Etheostoma burri and Etheostoma uniporum based on collection sites and morphological characters were not genetically differentiated from E. spectabile samples from the region. Hybridization and introgression occurring in the Central Highlands may confound genetic delineation of species in this region of high endemism and diversity.
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Affiliation(s)
- John T Belcik
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, Illinois, USA
- U.S. Army Corps of Engineers Chicago District, Chicago, Illinois, USA
| | - Mary V Ashley
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, Illinois, USA
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17
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Karabanina E, Lansink GMJ, Ponnikas S, Kvist L. A renewed glance at the Palearctic golden eagle: Genetic variation in space and time. Ecol Evol 2024; 14:e11109. [PMID: 38469039 PMCID: PMC10925523 DOI: 10.1002/ece3.11109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 02/16/2024] [Accepted: 02/21/2024] [Indexed: 03/13/2024] Open
Abstract
Anthropogenic pressures on nature have been causing population declines for centuries. Intensified persecution of apex predators, like the golden eagle, resulted in population bottlenecks during the 19th and 20th centuries. To study population genetics and demographic history of the golden eagle throughout its distribution, we collected museum samples from previously underrepresented regions, such as Russia and Central Asia. We used 12 microsatellite loci and a fragment of the mitochondrial DNA control region to re-evaluate phylogeography of Eurasian golden eagles and study the impacts of the population bottleneck. Our results revealed a north-south genetic gradient, expressed by the difference between Mediterranean and Holarctic lineages, as well as genetically distinct Northern Europe and Central Asia and Caucasus regions. Furthermore, Northern Europe exhibited the lowest, whereas Central Asia and Caucasus had the highest genetic diversity. Although golden eagles maintained relatively high genetic diversity, we detected genetic signatures of the recent bottleneck, including reduced genetic diversity and a decline in the effective female population size around the year 1975. Our study improves the knowledge of the genetic composition of Eurasian golden eagles and highlights the importance of understanding their historical population dynamics in the face of ongoing and future conservation efforts.
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Affiliation(s)
| | | | - Suvi Ponnikas
- Ecology and Genetics Research UnitUniversity of OuluOuluFinland
| | - Laura Kvist
- Ecology and Genetics Research UnitUniversity of OuluOuluFinland
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18
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Kessler C, Shafer ABA. Genomic Analyses Capture the Human-Induced Demographic Collapse and Recovery in a Wide-Ranging Cervid. Mol Biol Evol 2024; 41:msae038. [PMID: 38378172 PMCID: PMC10917209 DOI: 10.1093/molbev/msae038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 02/08/2024] [Accepted: 02/14/2024] [Indexed: 02/22/2024] Open
Abstract
The glacial cycles of the Quaternary heavily impacted species through successions of population contractions and expansions. Similarly, populations have been intensely shaped by human pressures such as unregulated hunting and land use changes. White-tailed and mule deer survived in different refugia through the Last Glacial Maximum, and their populations were severely reduced after the European colonization. Here, we analyzed 73 resequenced deer genomes from across their North American range to understand the consequences of climatic and anthropogenic pressures on deer demographic and adaptive history. We found strong signals of climate-induced vicariance and demographic decline; notably, multiple sequentially Markovian coalescent recovers a severe decline in mainland white-tailed deer effective population size (Ne) at the end of the Last Glacial Maximum. We found robust evidence for colonial overharvest in the form of a recent and dramatic drop in Ne in all analyzed populations. Historical census size and restocking data show a clear parallel to historical Ne estimates, and temporal Ne/Nc ratio shows patterns of conservation concern for mule deer. Signatures of selection highlight genes related to temperature, including a cold receptor previously highlighted in woolly mammoth. We also detected immune genes that we surmise reflect the changing land use patterns in North America. Our study provides a detailed picture of anthropogenic and climatic-induced decline in deer diversity and clues to understanding the conservation concerns of mule deer and the successful demographic recovery of white-tailed deer.
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Affiliation(s)
- Camille Kessler
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, Ontario, Canada
| | - Aaron B A Shafer
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, Ontario, Canada
- Department of Forensic Science, Trent University, Peterborough, Ontario, Canada
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19
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Steffen ML. New age constraints for human entry into the Americas on the north Pacific coast. Sci Rep 2024; 14:4291. [PMID: 38383701 PMCID: PMC10881565 DOI: 10.1038/s41598-024-54592-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Accepted: 02/14/2024] [Indexed: 02/23/2024] Open
Abstract
The timing of the initial peopling of the Americas is unresolved. Because the archaeological record necessitates discussion of human entry from Beringia into southern North America during the last glaciation, addressing this problem routinely involves evaluating environmental parameters then targeting areas suitable for human settlement. Vertebrate remains indicate landscape quality and are a key dataset for assessing coastal migration theories and the viability of coastal routes. Here, radiocarbon dates on vertebrate specimens and archaeological sites are calibrated to document species occurrences and the ages of human settlements across the western expansion and decay of the Cordilleran Ice Sheet (CIS) during the Late Wisconsin Fraser Glaciation in four subregions of the north Pacific coast of North America. The results show archaeological sites occur after glacial maxima and are generally consistent with the age of other securely dated earliest sites in southern North America. They also highlight gaps in the vertebrate chronologies around CIS maxima in each of the subregions that point to species redistributions and extirpations and signal times of low potential for human settlement and subsistence in a key portion of the proposed coastal migration route. This study, therefore, defines new age constraints for human coastal migration theories in the peopling of the Americas debate.
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20
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Le MH, Morgan B, Lu MY, Moctezuma V, Burgos O, Huang JP. The genomes of Hercules beetles reveal putative adaptive loci and distinct demographic histories in pristine North American forests. Mol Ecol Resour 2024; 24:e13908. [PMID: 38063363 DOI: 10.1111/1755-0998.13908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Revised: 01/14/2023] [Accepted: 11/20/2023] [Indexed: 01/12/2024]
Abstract
Beetles, despite their remarkable biodiversity and a long history of research, remain lacking in reference genomes annotated with structural variations in loci of adaptive significance. We sequenced and assembled high-quality chromosome-level genomes of four Hercules beetles which exhibit divergence in male horn size and shape and body colouration. The four Hercules beetle genomes were assembled to 11 pseudo-chromosomes, where the three genomes assembled using Nanopore data (Dynastes grantii, D. hyllus and D. tityus) were mapped to the genome assembled using PacBio + Hi-C data (D. maya). We demonstrated a striking similarity in genome structure among the four species. This conservative genome structure may be attributed to our use of the D. maya assembly as the reference; however, it is worth noting that such a conservative genome structure is a recurring phenomenon among scarab beetles. We further identified homologues of nine and three candidate-gene families that may be associated with the evolution of horn structure and body colouration respectively. Structural variations in Scr and Ebony2 were detected and discussed for their putative impacts on generating morphological diversity in beetles. We also reconstructed the demographic histories of the four Hercules beetles using heterozygosity information from the diploid genomes. We found that the demographic histories of the beetles closely recapitulated historical changes in suitable forest habitats driven by climate shifts.
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Affiliation(s)
- My-Hanh Le
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Brett Morgan
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
- Smithsonian Environmental Research Center, Edgewater, Maryland, USA
| | - Mei-Yeh Lu
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Victor Moctezuma
- Centro Tlaxcala de Biología de la Conducta, Universidad Autónoma de Tlaxcala, Tlaxcala de Xicohténcatl, Tlaxcala, Mexico
| | - Oscar Burgos
- Centro de Investigaciones Biológicas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
| | - Jen-Pan Huang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
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21
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Liu M, Song Y, Zhang S, Yu L, Yuan Z, Yang H, Zhang M, Zhou Z, Seim I, Liu S, Fan G, Yang H. A chromosome-level genome of electric catfish ( Malapterurus electricus) provided new insights into order Siluriformes evolution. MARINE LIFE SCIENCE & TECHNOLOGY 2024; 6:1-14. [PMID: 38433969 PMCID: PMC10901758 DOI: 10.1007/s42995-023-00197-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 09/22/2023] [Indexed: 03/05/2024]
Abstract
The electric catfish (Malapterurus electricus), belonging to the family Malapteruridae, order Siluriformes (Actinopterygii: Ostariophysi), is one of the six branches that has independently evolved electrical organs. We assembled a 796.75 Mb M. electricus genome and anchored 88.72% sequences into 28 chromosomes. Gene family analysis revealed 295 expanded gene families that were enriched on functions related to glutamate receptors. Convergent evolutionary analyses of electric organs among different lineage of electric fishes further revealed that the coding gene of rho guanine nucleotide exchange factor 4-like (arhgef4), which is associated with G-protein coupled receptor (GPCR) signaling pathway, underwent adaptive parallel evolution. Gene identification suggests visual degradation in catfishes, and an important role for taste in environmental adaptation. Our findings fill in the genomic data for a branch of electric fish and provide a relevant genetic basis for the adaptive evolution of Siluriformes. Supplementary Information The online version contains supplementary material available at 10.1007/s42995-023-00197-8.
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Affiliation(s)
- Meiru Liu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049 China
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555 China
- BGI-Shenzhen, Shenzhen, 518083 China
| | - Yue Song
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555 China
- BGI-Shenzhen, Shenzhen, 518083 China
| | - Suyu Zhang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049 China
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555 China
- BGI-Shenzhen, Shenzhen, 518083 China
| | - Lili Yu
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555 China
| | - Zengbao Yuan
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049 China
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555 China
- BGI-Shenzhen, Shenzhen, 518083 China
| | - Hengjia Yang
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555 China
| | - Mengqi Zhang
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555 China
| | - Zhuocheng Zhou
- Professional Committee of Native Aquatic Organisms and Water Ecosystem of China Fisheries Association, Beijing, 100125 China
| | - Inge Seim
- Integrative Biology Laboratory, College of Life Sciences, Nanjing Normal University, Nanjing, 210023 China
| | - Shanshan Liu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Guangyi Fan
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555 China
- BGI-Shenzhen, Shenzhen, 518083 China
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083 China
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen, 518083 China
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083 China
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22
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Ro S, Park J, Yoo H, Han C, Lee A, Lee Y, Kim M, Han Y, Svensson A, Shin J, Ro CU, Hong S. Millennial-scale variability of Greenland dust provenance during the last glacial maximum as determined by single particle analysis. Sci Rep 2024; 14:2040. [PMID: 38263283 PMCID: PMC10805741 DOI: 10.1038/s41598-024-52546-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 01/19/2024] [Indexed: 01/25/2024] Open
Abstract
Greenland ice core records exhibited 100-fold higher dust concentrations during the Last Glacial Maximum (LGM) than during the Holocene, and dust input temporal variability corresponded to different climate states in the LGM. While East Asian deserts, the Sahara, and European loess have been suggested as the potential source areas (PSAs) for Greenland LGM dust, millennial-scale variability in their relative contributions within the LGM remains poorly constrained. Here, we present the morphological, mineralogical, and geochemical characteristics of insoluble microparticles to constrain the provenance of dust in Greenland NEEM ice core samples covering cold Greenland Stadials (GS)-2.1a to GS-3 (~ 14.7 to 27.1 kyr ago) in the LGM. The analysis was conducted on individual particles in microdroplet samples by scanning electron microscopy with energy dispersive X-ray spectroscopy and Raman microspectroscopy. We found that the kaolinite-to-chlorite (K/C) ratios and chemical index of alteration (CIA) values were substantially higher (K/C: 1.4 ± 0.7, CIA: 74.7 ± 2.9) during GS-2.1a to 2.1c than during GS-3 (K/C: 0.5 ± 0.1, CIA: 65.8 ± 2.8). Our records revealed a significant increase in Saharan dust contributions from GS-2.1a to GS-2.1c and that the Gobi Desert and/or European loess were potential source(s) during GS-3. This conclusion is further supported by distinctly different carbon contents in particles corresponding to GS-2.1 and GS-3. These results are consistent with previous estimates of proportional dust source contributions obtained using a mixing model based on Pb and Sr isotopic compositions in NEEM LGM ice and indicate millennial-scale changes in Greenland dust provenance that are probably linked to large-scale atmospheric circulation variabilities during the LGM.
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Affiliation(s)
- Seokhyun Ro
- Department of Ocean Sciences, Inha University, 100 Inha-ro, Michuhol-gu, Incheon, 22212, Republic of Korea
- Division of Glacial Environment Research, Korea Polar Research Institute, 26 Songdomirae-ro, Yeonsu-gu, Incheon, 21990, Republic of Korea
| | - Jonghyeon Park
- Department of Chemistry, Inha University, 100 Inha-ro, Michuhol-gu, Incheon, 22212, Republic of Korea
- Marine Environment Research Department, Ara Consulting and Technology, 30 Songdomirae-ro, Yeonsu-gu, Incheon, 21990, Republic of Korea
| | - Hanjin Yoo
- Department of Chemistry, Inha University, 100 Inha-ro, Michuhol-gu, Incheon, 22212, Republic of Korea
- Particle Pollution Research and Management Center, Inha University, 36 Gaetbeol-ro, Yeonsu-gu, Incheon, 21999, Republic of Korea
| | - Changhee Han
- Department of Water Environmental Safety Management, Korea Water Resources Corporation, 200 Sintanjin-ro, Daedeok-gu, Daejeon, 34350, Republic of Korea
| | - Ahhyung Lee
- Department of Ocean Sciences, Inha University, 100 Inha-ro, Michuhol-gu, Incheon, 22212, Republic of Korea
- Unit of Frontier Exploration, Korea Polar Research Institute, 26 Songdomirae-ro, Yeonsu-gu, Incheon, 21990, Republic of Korea
| | - Yoojin Lee
- Department of Chemistry, Inha University, 100 Inha-ro, Michuhol-gu, Incheon, 22212, Republic of Korea
| | - Minjeong Kim
- Division of Glacial Environment Research, Korea Polar Research Institute, 26 Songdomirae-ro, Yeonsu-gu, Incheon, 21990, Republic of Korea
- Department of Chemistry, Inha University, 100 Inha-ro, Michuhol-gu, Incheon, 22212, Republic of Korea
| | - Yeongcheol Han
- Division of Glacial Environment Research, Korea Polar Research Institute, 26 Songdomirae-ro, Yeonsu-gu, Incheon, 21990, Republic of Korea
| | - Anders Svensson
- Centre for Ice and Climate, Niels Bohr Institute, University of Copenhagen, Julian 10 Maries Vej 30, 2100, Copenhagen, Denmark
| | - Jinhwa Shin
- Division of Glacial Environment Research, Korea Polar Research Institute, 26 Songdomirae-ro, Yeonsu-gu, Incheon, 21990, Republic of Korea
| | - Chul-Un Ro
- Department of Chemistry, Inha University, 100 Inha-ro, Michuhol-gu, Incheon, 22212, Republic of Korea.
- Particle Pollution Research and Management Center, Inha University, 36 Gaetbeol-ro, Yeonsu-gu, Incheon, 21999, Republic of Korea.
| | - Sungmin Hong
- Department of Ocean Sciences, Inha University, 100 Inha-ro, Michuhol-gu, Incheon, 22212, Republic of Korea.
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23
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Zunino L, Cubry P, Sarah G, Mournet P, El Bakkali A, Aqbouch L, Sidibé-Bocs S, Costes E, Khadari B. Genomic evidence of genuine wild versus admixed olive populations evolving in the same natural environments in western Mediterranean Basin. PLoS One 2024; 19:e0295043. [PMID: 38232071 DOI: 10.1371/journal.pone.0295043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 11/14/2023] [Indexed: 01/19/2024] Open
Abstract
Crop-to-wild gene flow is a mechanism process widely documented, both in plants and animals. This can have positive or negative impacts on the evolution of admixed populations in natural environments, yet the phenomenon is still misunderstood in long-lived woody species, contrary to short-lived crops. Wild olive Olea europaea L. occurs in the same eco-geographical range as domesticated olive, i.e. the Mediterranean Basin (MB). Moreover, it is an allogamous and anemophilous species whose seeds are disseminated by birds, i.e. factors that drive gene flow between crops and their wild relatives. Here we investigated the genetic structure of western MB wild olive populations in natural environments assuming a homogenous gene pool with limited impact of cultivated alleles, as previously suggested. We used a target sequencing method based on annotated genes from the Farga reference genome to analyze 27 western MB olive tree populations sampled in natural environments in France, Spain and Morocco. We also target sequenced cultivated olive tree accessions from the Worldwide Olive Germplasm Bank of Marrakech and Porquerolles and from an eastern MB wild olive tree population. We combined PCA, sNMF, pairwise FST and TreeMix and clearly identified genuine wild olive trees throughout their natural distribution range along a north-south gradient including, for the first time, in southern France. However, contrary to our assumption, we highlighted more admixed than genuine wild olive trees. Our results raise questions regarding the admixed population evolution pattern in this environment, which might be facilitated by crop-to-wild gene flow.
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Affiliation(s)
- Lison Zunino
- AGAP Institut, University of Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
- DIADE, University of Montpellier, CIRAD, IRD, Montpellier, France
| | - Philippe Cubry
- DIADE, University of Montpellier, CIRAD, IRD, Montpellier, France
| | - Gautier Sarah
- AGAP Institut, University of Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Pierre Mournet
- AGAP Institut, University of Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
- CIRAD, UMR AGAP Institut, Montpellier, France
| | - Ahmed El Bakkali
- INRA, UR Amélioration des Plantes et Conservation des Ressources Phytogénétiques, Meknes, Morocco
| | - Laila Aqbouch
- AGAP Institut, University of Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Stéphanie Sidibé-Bocs
- AGAP Institut, University of Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
- CIRAD, UMR AGAP Institut, Montpellier, France
| | - Evelyne Costes
- AGAP Institut, University of Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Bouchaib Khadari
- AGAP Institut, University of Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
- Conservatoire Botanique National Méditerranéen (CBNMed), UMR AGAP Institut, Montpellier, France
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24
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Buchwald SZ, Herzschuh U, Nürnberg D, Harms L, Stoof-Leichsenring KR. Plankton community changes during the last 124 000 years in the subarctic Bering Sea derived from sedimentary ancient DNA. THE ISME JOURNAL 2024; 18:wrad006. [PMID: 38365253 PMCID: PMC10811732 DOI: 10.1093/ismejo/wrad006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 11/01/2023] [Accepted: 11/09/2023] [Indexed: 02/18/2024]
Abstract
Current global warming results in rising sea-water temperatures, and the loss of sea ice in Arctic and subarctic oceans impacts the community composition of primary producers with cascading effects on the food web and potentially on carbon export rates. This study analyzes metagenomic shotgun and diatom rbcL amplicon sequencing data from sedimentary ancient DNA of the subarctic western Bering Sea that records phyto- and zooplankton community changes over the last glacial-interglacial cycles, including the last interglacial period (Eemian). Our data show that interglacial and glacial plankton communities differ, with distinct Eemian and Holocene plankton communities. The generally warm Holocene period is dominated by picosized cyanobacteria and bacteria-feeding heterotrophic protists, while the Eemian period is dominated by eukaryotic picosized chlorophytes and Triparmaceae. By contrast, the glacial period is characterized by microsized phototrophic protists, including sea ice-associated diatoms in the family Bacillariaceae and co-occurring diatom-feeding crustaceous zooplankton. Our deep-time record of plankton community changes reveals a long-term decrease in phytoplankton cell size coeval with increasing temperatures, resembling community changes in the currently warming Bering Sea. The phytoplankton community in the warmer-than-present Eemian period is distinct from modern communities and limits the use of the Eemian as an analog for future climate scenarios. However, under enhanced future warming, the expected shift toward the dominance of small-sized phytoplankton and heterotrophic protists might result in an increased productivity, whereas the community's potential of carbon export will be decreased, thereby weakening the subarctic Bering Sea's function as an effective carbon sink.
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Affiliation(s)
- Stella Z Buchwald
- Polar Terrestrial Environmental Systems, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Potsdam D-14473, Germany
- Department of Earth System Sciences, Universität Hamburg, Hamburg D-20146, Germany
| | - Ulrike Herzschuh
- Polar Terrestrial Environmental Systems, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Potsdam D-14473, Germany
- Institute of Biochemistry and Biology, University of Potsdam, Potsdam D-14476, Germany
- Institute of Environmental Sciences and Geography, University of Potsdam, Potsdam D-14476, Germany
| | - Dirk Nürnberg
- Ocean Circulation and Climate Dynamics, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel D-24148, Germany
| | - Lars Harms
- Data Science Support, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven D-27568, Germany
| | - Kathleen R Stoof-Leichsenring
- Polar Terrestrial Environmental Systems, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Potsdam D-14473, Germany
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25
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Glückler R, Gloy J, Dietze E, Herzschuh U, Kruse S. Simulating long-term wildfire impacts on boreal forest structure in Central Yakutia, Siberia, since the Last Glacial Maximum. FIRE ECOLOGY 2024; 20:1. [PMID: 38186675 PMCID: PMC10766680 DOI: 10.1186/s42408-023-00238-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 11/30/2023] [Indexed: 01/09/2024]
Abstract
Background Wildfires are recognized as an important ecological component of larch-dominated boreal forests in eastern Siberia. However, long-term fire-vegetation dynamics in this unique environment are poorly understood. Recent paleoecological research suggests that intensifying fire regimes may induce millennial-scale shifts in forest structure and composition. This may, in turn, result in positive feedback on intensifying wildfires and permafrost degradation, apart from threatening human livelihoods. Most common fire-vegetation models do not explicitly include detailed individual-based tree population dynamics, but a focus on patterns of forest structure emerging from interactions among individual trees may provide a beneficial perspective on the impacts of changing fire regimes in eastern Siberia. To simulate these impacts on forest structure at millennial timescales, we apply the individual-based, spatially explicit vegetation model LAVESI-FIRE, expanded with a new fire module. Satellite-based fire observations along with fieldwork data were used to inform the implementation of wildfire occurrence and adjust model parameters. Results Simulations of annual forest development and wildfire activity at a study site in the Republic of Sakha (Yakutia) since the Last Glacial Maximum (c. 20,000 years BP) highlight the variable impacts of fire regimes on forest structure throughout time. Modeled annual fire probability and subsequent burned area in the Holocene compare well with a local reconstruction of charcoal influx in lake sediments. Wildfires can be followed by different forest regeneration pathways, depending on fire frequency and intensity and the pre-fire forest conditions. We find that medium-intensity wildfires at fire return intervals of 50 years or more benefit the dominance of fire-resisting Dahurian larch (Larix gmelinii (Rupr.) Rupr.), while stand-replacing fires tend to enable the establishment of evergreen conifers. Apart from post-fire mortality, wildfires modulate forest development mainly through competition effects and a reduction of the model's litter layer. Conclusion With its fine-scale population dynamics, LAVESI-FIRE can serve as a highly localized, spatially explicit tool to understand the long-term impacts of boreal wildfires on forest structure and to better constrain interpretations of paleoecological reconstructions of fire activity. Supplementary Information The online version contains supplementary material available at 10.1186/s42408-023-00238-8.
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Affiliation(s)
- Ramesh Glückler
- Polar Terrestrial Environmental Systems, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Telegrafenberg A45, Potsdam, 14473 Germany
- Institute of Environmental Science and Geography, University of Potsdam, Karl-Liebknecht-Strasse 24-25, Potsdam, 14476 Germany
- Faculty of Environmental Earth Science, Hokkaido University, N10W5, Sapporo, 060-0810 Japan
| | - Josias Gloy
- Polar Terrestrial Environmental Systems, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Telegrafenberg A45, Potsdam, 14473 Germany
| | - Elisabeth Dietze
- Institute of Geography, Georg-August-University Göttingen, Goldschmidtstrasse 5, Göttingen, 37077 Germany
| | - Ulrike Herzschuh
- Polar Terrestrial Environmental Systems, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Telegrafenberg A45, Potsdam, 14473 Germany
- Institute of Environmental Science and Geography, University of Potsdam, Karl-Liebknecht-Strasse 24-25, Potsdam, 14476 Germany
- Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Strasse 24-25, Potsdam, 14476 Germany
| | - Stefan Kruse
- Polar Terrestrial Environmental Systems, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Telegrafenberg A45, Potsdam, 14473 Germany
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26
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Cai L, Liu D, Yang F, Zhang R, Yun Q, Dao Z, Ma Y, Sun W. The chromosome-scale genome of Magnolia sinica (Magnoliaceae) provides insights into the conservation of plant species with extremely small populations (PSESP). Gigascience 2024; 13:giad110. [PMID: 38206588 PMCID: PMC10999834 DOI: 10.1093/gigascience/giad110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 07/28/2023] [Accepted: 12/04/2023] [Indexed: 01/12/2024] Open
Abstract
Magnolia sinica (Magnoliaceae) is a highly threatened tree endemic to southeast Yunnan, China. In this study, we generated for the first time a high-quality chromosome-scale genome sequence from M. sinica, by combining Illumina and ONT data with Hi-C scaffolding methods. The final assembled genome size of M. sinica was 1.84 Gb, with a contig N50 of ca. 45 Mb and scaffold N50 of 92 Mb. Identified repeats constituted approximately 57% of the genome, and 43,473 protein-coding genes were predicted. Phylogenetic analysis shows that the magnolias form a sister clade with the eudicots and the order Ceratophyllales, while the monocots are sister to the other core angiosperms. In our study, a total of 21 individuals from the 5 remnant populations of M. sinica, as well as 22 specimens belonging to 8 related Magnoliaceae species, were resequenced. The results showed that M. sinica had higher genetic diversity (θw = 0.01126 and θπ = 0.01158) than other related species in the Magnoliaceae. However, population structure analysis suggested that the genetic differentiation among the 5 M. sinica populations was very low. Analyses of the demographic history of the species using different models consistently revealed that 2 bottleneck events occurred. The contemporary effective population size of M. sinica was estimated to be 10.9. The different patterns of genetic loads (inbreeding and numbers of deleterious mutations) suggested constructive strategies for the conservation of these 5 different populations of M. sinica. Overall, this high-quality genome will be a valuable genomic resource for conservation of M. sinica.
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Affiliation(s)
- Lei Cai
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations/Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Detuan Liu
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations/Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Fengmao Yang
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations/Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Rengang Zhang
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations/Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Quanzheng Yun
- Department of Bioinformatics, Ori (Shandong) Gene Science and Technology Co., Ltd., Weifang, 261000, Shandong, China
| | - Zhiling Dao
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations/Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Yongpeng Ma
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations/Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Weibang Sun
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations/Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
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Li H, Zhang H, Li H, Duan L, Zhang X, Gao Y, Hall IR, Hemming SR, LeVay LJ. Sedimentary DNA reveals the link between microbial community dynamics and climate during the late last glaciation in the offshore region of the Zambezi River, Southwest Indian Ocean. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 906:167787. [PMID: 37844644 DOI: 10.1016/j.scitotenv.2023.167787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 10/04/2023] [Accepted: 10/10/2023] [Indexed: 10/18/2023]
Abstract
Reconstructing the relationship between microbial communities and past abrupt climate change is of great importance for understanding current biodiversity patterns and predicting changes under future climate scenarios. However, little is currently known about how microbial communities respond to changes in key environmental stages due to a lack of research in this area. Here, we examine the variability in the communities of bacteria, archaea, and fungi from sediments deposited offshore region of the Zambezi River between 21.7 and 9.6 thousand years ago (ka) (covering the last glacial maximum, or LGM, and the early Holocene) using DNA metabarcoding approach via high-throughput sequencing. The results showed that (1) microbial assemblages differed across three key time intervals, with the last deglaciation having the most homogeneous prokaryotic assemblages, while for fungal communities in the LGM, and the early Holocene and LGM differing the most; (2) the warm early Holocene showed the highest diversity, whereas the lowest diversity was found in the LGM; and (3) the selected indicator species better reflected the climatic characteristics of different environmental stages. These results highlight the power of ancient sedimentary DNA to refine our understanding of microbial dynamics in marine sedimentary systems near large rivers, thus providing a basis for better modeling ecological processes in further research.
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Affiliation(s)
- Haoyu Li
- Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Science, Yunnan University, 650500 Kunming, China
| | - Hucai Zhang
- Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Science, Yunnan University, 650500 Kunming, China.
| | - Huayong Li
- School of Resource Environment and Tourism, Anyang Normal University, Anyang 455000, China
| | - Lizeng Duan
- Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Science, Yunnan University, 650500 Kunming, China
| | - Xiaonan Zhang
- Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Science, Yunnan University, 650500 Kunming, China
| | - Youhong Gao
- Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Science, Yunnan University, 650500 Kunming, China
| | - Ian R Hall
- Department of Earth Sciences, Cardiff University, Main College, Park Place, PO Box 914, Cardiff, Wales CF10 3AT, United Kingdom
| | - Sidney R Hemming
- Lamont-Doherty Earth Observatory, Columbia University, 61 Route 9W, Palisades, NY, 10964, USA
| | - Leah J LeVay
- International Ocean Discovery Program, Texas A&M University, College Station, TX 77845, USA
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28
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Raman G, Choi KS, Park S. Population Structure and Genetic Diversity Analyses Provide New Insight into the Endemic Species Aster spathulifolius Maxim. and Its Evolutionary History. PLANTS (BASEL, SWITZERLAND) 2023; 13:88. [PMID: 38202396 PMCID: PMC10780962 DOI: 10.3390/plants13010088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 12/23/2023] [Accepted: 12/25/2023] [Indexed: 01/12/2024]
Abstract
Aster spathulifolius, an ecologically significant plant species native to the coastal regions of Korea and Japan, remains understudied in terms of its genetic structure and evolutionary history. In this study, we employed four chloroplast markers and the nuclear ITS region from 15 populations of A. spathulifolius from both Korea and Japan, including their islands, to unravel the spatial genetic structure, differentiation, gene flow, phylogenetic, and biogeographical relationships. Analysis based on multiple methods identified a low level of genetic diversity, genetic differentiation and gene flow among A. spathulifolius populations. Network analysis and principal coordinates analysis showed that 15 populations could be divided into two groups: mainland and island. Furthermore, UPGMA, neighbor-net, maximum-likelihood and Bayesian inference-based phylogenetic tree confirmed that these populations formed two distinct clades. Therefore, the island populations might be treated as A. spathulifolius populations rather than A. oharai populations. Divergence time analysis estimated the divergence of A. spathulifolius lineages approximately 23.09 million years ago, while ancestral area reconstruction analysis suggested Korea as the potential origin, conflicting with alternative scenarios. These findings contribute to a comprehensive understanding of the evolutionary history, genetic structure, and adaptive strategies of A. spathulifolius in coastal environments. Our study challenges previous assumptions and underscores the necessity for further population studies to elucidate the intricate dynamics of this distinctive plant species.
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Affiliation(s)
- Gurusamy Raman
- Department of Life Sciences, Yeungnam University, Gyeongsan 38541, Gyeongsanbuk-do, Republic of Korea;
| | - Kyoung Su Choi
- Plant Research Team, Animal and Plant Research Department, Nakdonggang National Institute of Biological Resources, Sangju 37242, Republic of Korea;
| | - SeonJoo Park
- Department of Life Sciences, Yeungnam University, Gyeongsan 38541, Gyeongsanbuk-do, Republic of Korea;
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29
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Pilowsky JA, Brown SC, Llamas B, van Loenen AL, Kowalczyk R, Hofman-Kamińska E, Manaseryan NH, Rusu V, Križnar M, Rahbek C, Fordham DA. Millennial processes of population decline, range contraction and near extinction of the European bison. Proc Biol Sci 2023; 290:20231095. [PMID: 38087919 PMCID: PMC10716654 DOI: 10.1098/rspb.2023.1095] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 11/19/2023] [Indexed: 12/18/2023] Open
Abstract
European bison (Bison bonasus) were widespread throughout Europe during the late Pleistocene. However, the contributions of environmental change and humans to their near extinction have never been resolved. Using process-explicit models, fossils and ancient DNA, we disentangle the combinations of threatening processes that drove population declines and regional extinctions of European bison through space and across time. We show that the population size of European bison declined abruptly at the termination of the Pleistocene in response to rapid environmental change, hunting by humans and their interaction. Human activities prevented populations of European bison from rebounding in the Holocene, despite improved environmental conditions. Hunting caused range loss in the north and east of its distribution, while land use change was responsible for losses in the west and south. Advances in hunting technologies from 1500 CE were needed to simulate low abundances observed in 1870 CE. While our findings show that humans were an important driver of the extinction of the European bison in the wild, vast areas of its range vanished during the Pleistocene-Holocene transition because of post-glacial environmental change. These areas of its former range have been climatically unsuitable for millennia and should not be considered in reintroduction efforts.
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Affiliation(s)
- July A. Pilowsky
- The Environment Institute and School of Biological Sciences, University of Adelaide, South Australia 5005, Australia
- Center for Macroecology, Evolution and Climate, Globe Institute, University of Copenhagen, Copenhagen Ø 2100, Denmark
| | - Stuart C. Brown
- The Environment Institute and School of Biological Sciences, University of Adelaide, South Australia 5005, Australia
- Section for Evolutionary Genomics, Globe Institute, University of Copenhagen, Copenhagen K 1350, Denmark
| | - Bastien Llamas
- The Environment Institute and School of Biological Sciences, University of Adelaide, South Australia 5005, Australia
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, South Australia 5005, Australia
- ARC Centre of Excellence for Australian Biodiversity and Heritage, University of Adelaide, South Australia 5005, Australia
- Indigenous Genomics Research Group, Telethon Kids Institute, Adelaide, South Australia 5001, Australia
- National Centre for Indigenous Genomics, Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Ayla L. van Loenen
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, South Australia 5005, Australia
| | - Rafał Kowalczyk
- Mammal Research Institute, Polish Academy of Sciences, 17-230 Białowieża, Poland
| | | | - Ninna H. Manaseryan
- The Scientific Centre of Zoology and Hydroecology of National Academy of Sciences of Armenia, Institute of Zoology, 0014 Yerevan, Republic of Armenia
| | - Viorelia Rusu
- Institute of Zoology, Academy of Sciences of Moldova, Chisinau MD-2028, Republic of Moldova
| | - Matija Križnar
- Slovenian Museum of Natural History, Department of Geology, SI-1001 Ljubljana, Slovenia
| | - Carsten Rahbek
- Center for Macroecology, Evolution and Climate, Globe Institute, University of Copenhagen, Copenhagen Ø 2100, Denmark
- Center for Mountain Biodiversity, Globe Institute, University of Copenhagen, Copenhagen Ø 2100, Denmark
- Danish Institute for Advanced Study, University of Southern Denmark, Odense M 5230, Denmark
- Institute of Ecology, Peking University, Beijing, People's Republic of China
| | - Damien A. Fordham
- The Environment Institute and School of Biological Sciences, University of Adelaide, South Australia 5005, Australia
- Center for Macroecology, Evolution and Climate, Globe Institute, University of Copenhagen, Copenhagen Ø 2100, Denmark
- Center for Mountain Biodiversity, Globe Institute, University of Copenhagen, Copenhagen Ø 2100, Denmark
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30
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Tumulty JP, Miller SE, Van Belleghem SM, Weller HI, Jernigan CM, Vincent S, Staudenraus RJ, Legan AW, Polnaszek TJ, Uy FMK, Walton A, Sheehan MJ. Evidence for a selective link between cooperation and individual recognition. Curr Biol 2023; 33:5478-5487.e5. [PMID: 38065097 PMCID: PMC11074921 DOI: 10.1016/j.cub.2023.11.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 09/05/2023] [Accepted: 11/15/2023] [Indexed: 12/21/2023]
Abstract
The ability to recognize others is a frequent assumption of models of the evolution of cooperation. At the same time, cooperative behavior has been proposed as a selective agent favoring the evolution of individual recognition abilities. Although theory predicts that recognition and cooperation may co-evolve, data linking recognition abilities and cooperative behavior with evidence of selection are elusive. Here, we provide evidence of a selective link between individual recognition and cooperation in the paper wasp Polistes fuscatus through a combination of clinal, common garden, and population genomics analyses. We identified latitudinal clines in both rates of cooperative nesting and color pattern diversity, consistent with a selective link between recognition and cooperation. In behavioral experiments, we replicated previous results demonstrating individual recognition in cooperative and phenotypically diverse P. fuscatus from New York. In contrast, wasps from a less cooperative and phenotypically uniform Louisiana population showed no evidence of individual recognition. In a common garden experiment, groups of wasps from northern populations formed more stable and individually biased associations, indicating that recognition facilitates group stability. The strength of recent positive selection on cognition-associated loci likely to mediate individual recognition is substantially greater in northern compared with southern P. fuscatus populations. Collectively, these data suggest that individual recognition and cooperative nesting behavior have co-evolved in P. fuscatus because recognition helps stabilize social groups. This work provides evidence of a specific cognitive phenotype under selection because of social interactions, supporting the idea that social behavior can be a key driver of cognitive evolution.
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Affiliation(s)
- James P Tumulty
- Laboratory for Animal Social Evolution and Recognition, Department of Neurobiology and Behavior, Cornell University, Ithaca, NY 14853, USA.
| | - Sara E Miller
- Laboratory for Animal Social Evolution and Recognition, Department of Neurobiology and Behavior, Cornell University, Ithaca, NY 14853, USA; Department of Biology, University of Missouri-St. Louis, St. Louis, MO 63121, USA
| | - Steven M Van Belleghem
- Ecology, Evolution and Conservation Biology, Biology Department, KU Leuven, 3000 Leuven, Belgium
| | - Hannah I Weller
- Department of Ecology and Evolutionary Biology, Brown University, Providence, RI 02912, USA
| | - Christopher M Jernigan
- Laboratory for Animal Social Evolution and Recognition, Department of Neurobiology and Behavior, Cornell University, Ithaca, NY 14853, USA
| | - Sierra Vincent
- Laboratory for Animal Social Evolution and Recognition, Department of Neurobiology and Behavior, Cornell University, Ithaca, NY 14853, USA
| | - Regan J Staudenraus
- Laboratory for Animal Social Evolution and Recognition, Department of Neurobiology and Behavior, Cornell University, Ithaca, NY 14853, USA
| | - Andrew W Legan
- Laboratory for Animal Social Evolution and Recognition, Department of Neurobiology and Behavior, Cornell University, Ithaca, NY 14853, USA
| | | | - Floria M K Uy
- Laboratory for Animal Social Evolution and Recognition, Department of Neurobiology and Behavior, Cornell University, Ithaca, NY 14853, USA; Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Alexander Walton
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Michael J Sheehan
- Laboratory for Animal Social Evolution and Recognition, Department of Neurobiology and Behavior, Cornell University, Ithaca, NY 14853, USA.
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31
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Panitsina VA, Bodrov SY, Boulygina ES, Slobodova NV, Kosintsev PA, Abramson NI. In Search of the Elusive North: Evolutionary History of the Arctic Fox ( Vulpes lagopus) in the Palearctic from the Late Pleistocene to the Recent Inferred from Mitogenomic Data. BIOLOGY 2023; 12:1517. [PMID: 38132343 PMCID: PMC10740874 DOI: 10.3390/biology12121517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 12/07/2023] [Accepted: 12/09/2023] [Indexed: 12/23/2023]
Abstract
Despite the high level of interest, the population history of arctic foxes during the Late Pleistocene and Holocene remains poorly understood. Here we aimed to fill gaps in the demographic and colonization history of the arctic fox by analyzing new ancient DNA data from fossil specimens aged from 50 to 1 thousand years from the Northern and Polar Urals, historic DNA from museum specimens from the Novaya Zemlya Archipelago and the Taymyr Peninsula and supplementing these data by previously published sequences of recent and extinct arctic foxes from other regions. This dataset was used for reconstruction of a time-calibrated phylogeny and a temporal haplotype network covering four time intervals: Late Pleistocene (ranging from 30 to 13 thousand years bp), Holocene (ranging from 4 to 1 thousand years bp), historical (approximately 150 years), and modern. Our results revealed that Late Pleistocene specimens showed no genetic similarity to either modern or historical specimens, thus supporting the earlier hypothesis on local extinction rather than habitat tracking.
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Affiliation(s)
- Valentina A. Panitsina
- Zoological Institute, Russian Academy of Sciences, 199034 Saint-Petersburg, Russia; (V.A.P.); (S.Y.B.)
| | - Semyon Yu. Bodrov
- Zoological Institute, Russian Academy of Sciences, 199034 Saint-Petersburg, Russia; (V.A.P.); (S.Y.B.)
| | | | | | - Pavel A. Kosintsev
- Institute of Plant and Animal Ecology, Ural Branch, Russian Academy of Sciences, 620144 Yekaterinburg, Russia
| | - Natalia I. Abramson
- Zoological Institute, Russian Academy of Sciences, 199034 Saint-Petersburg, Russia; (V.A.P.); (S.Y.B.)
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32
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Zhao Y, Su C, He B, Nie R, Wang Y, Ma J, Song J, Yang Q, Hao J. Dispersal from the Qinghai-Tibet plateau by a high-altitude butterfly is associated with rapid expansion and reorganization of its genome. Nat Commun 2023; 14:8190. [PMID: 38081828 PMCID: PMC10713551 DOI: 10.1038/s41467-023-44023-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 11/28/2023] [Indexed: 12/18/2023] Open
Abstract
Parnassius glacialis is a typical "Out of the QTP" alpine butterfly that originated on the Qinghai-Tibet Plateau (QTP) and dispersed into relatively low-altitude mountainous. Here we assemble a chromosome-level genome of P. glacialis and resequence 9 populations in order to explore the genome evolution and local adaptation of this species. These results indicated that the rapid accumulation and slow unequal recombination of transposable elements (TEs) contributed to the formation of its large genome. Several ribosomal gene families showed extensive expansion and selective evolution through transposon-mediated processed pseudogenes. Additionally, massive structural variations (SVs) of TEs affected the genetic differentiation of low-altitude populations. These low-altitude populations might have experienced a genetic bottleneck in the past and harbor genes with selective signatures which may be responsible for the potential adaptation to low-altitude environments. These results provide a foundation for understanding genome evolution and local adaptation for "Out of the QTP" of P. glacialis.
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Affiliation(s)
- Youjie Zhao
- College of Life Sciences, Anhui Normal University, Wuhu, 241000, China
- College of Big Data and Intelligent Engineering, Southwest Forestry University, Kunming, 650224, Yunnan, China
| | - Chengyong Su
- College of Life Sciences, Anhui Normal University, Wuhu, 241000, China
| | - Bo He
- College of Life Sciences, Anhui Normal University, Wuhu, 241000, China
| | - Ruie Nie
- College of Life Sciences, Anhui Normal University, Wuhu, 241000, China
| | - Yunliang Wang
- College of Life Sciences, Anhui Normal University, Wuhu, 241000, China
| | - Junye Ma
- State Key Laboratory of Palaeobiology and Stratigraphy, Center for Excellence in Life and Palaeoenvironment, Nanjing Institute of Geology and Paleontology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Jingyu Song
- College of Animal Science, Shandong Agricultural University, Taian, 271000, China
| | - Qun Yang
- State Key Laboratory of Palaeobiology and Stratigraphy, Center for Excellence in Life and Palaeoenvironment, Nanjing Institute of Geology and Paleontology, Chinese Academy of Sciences, Nanjing, 210008, China.
- Nanjing College, University of Chinese Academy of Sciences, Nanjing, 211135, China.
| | - Jiasheng Hao
- College of Life Sciences, Anhui Normal University, Wuhu, 241000, China.
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De León LF, Arias CF, Sharpe DMT, Bravo V, González R, Krahe R, Aguilar C. Unraveling the complex phylogeographic history of freshwater fishes in Lower Central America: A study of the electric fish Brachyhypopomus occidentalis. Mol Phylogenet Evol 2023; 189:107941. [PMID: 37804958 DOI: 10.1016/j.ympev.2023.107941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 10/03/2023] [Accepted: 10/04/2023] [Indexed: 10/09/2023]
Abstract
Lower Central America (LCA) has a complex biogeographic history shaped by the rise of the Isthmus of Panama and the global climatic oscillations of the Pleistocene. These events have been crucial in structuring biodiversity in LCA, but their consequences for the distribution and partitions of genetic diversity across the region remain to be elucidated. We combined complete mitochondrial genomes and nuclear ultraconserved elements (UCEs) to study the phylogeographic history and population genetic structure of the electric fish Brachyhypopomus occidentalis in LCA. Our results are consistent with the known phylogeographic history of B. occidentalis in LCA, but we update this history in several important ways that help illuminate the phylogeographic history of freshwater fishes in the region. We provide: i) support for three waves of colonization, two of which occurred prior to the final closure of the Panama Isthmus; ii) a more precise understanding of each colonization event, with evidence for a larger footprint of the first event, as well as genetic exchange across the continental divide in subsequent events; and iii) evidence for high levels of previously unrecognized population genetic structure across LCA. This updated model of colonization and diversification of B. occidentalis consists of three waves of dispersal and colonization, which triggered the evolution of geographic breaks in both nuclear and mitochondrial genomes across LCA. These processes are tightly linked to the dynamic uplift of the Isthmus, recent volcanic activity in the region, and the sea-level oscillations of the Pleistocene. These results improve previous phylogeographic inferences regarding the distribution and diversification of freshwater fishes in LCA, and generate testable hypotheses to guide future research exploring the factors shaping biodiversity in the region.
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Affiliation(s)
- Luis F De León
- Department of Biology, University of Massachusetts Boston, Boston, MA, USA; Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), P. O. Box 0843-01103, Panamá, Panama; Smithsonian Tropical Research Institute, P.O. Box 0843-03092, Balboa Ancón, Panamá, Panama.
| | - Carlos F Arias
- Smithsonian Tropical Research Institute, P.O. Box 0843-03092, Balboa Ancón, Panamá, Panama; Data Science Lab, Office of the Chief Information Officer, Smithsonian Institution, Washington DC, USA
| | - Diana M T Sharpe
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Víctor Bravo
- Department of Biology, University of Massachusetts Boston, Boston, MA, USA
| | - Rigoberto González
- Smithsonian Tropical Research Institute, P.O. Box 0843-03092, Balboa Ancón, Panamá, Panama
| | - Rüdiger Krahe
- Institute of Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Celestino Aguilar
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), P. O. Box 0843-01103, Panamá, Panama; Smithsonian Tropical Research Institute, P.O. Box 0843-03092, Balboa Ancón, Panamá, Panama
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Ong HG, Kim Y, Lee J, Kim B, Kang D, Jung E, Shin J, Kim Y. Approximate Bayesian computation and ecological niche models elucidate the demographic history and current fragmented population distribution of a Korean endemic shrub. Ecol Evol 2023; 13:e10792. [PMID: 38077507 PMCID: PMC10700048 DOI: 10.1002/ece3.10792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 09/15/2023] [Accepted: 11/20/2023] [Indexed: 12/26/2023] Open
Abstract
Climatic fluctuations and geological events since the LGM are believed to have significantly impacted the population size, distribution, and mobility of many species that we observe today. In this paper, we determined the processes driving the phylogeographic structure of the Korean endemic white forsythia by combining the use of genome-wide SNPs and predicting paleoclimatic habitats during the LGM (21 kya), Early Holocene (10 kya), Mid-Holocene (6 kya), and Late Holocene (3 kya). Using a maximum of 1897 SNPs retrieved from 124 samples across nine wild populations, five environmental predictors, and the species' natural occurrence records, we aimed to infer the species' demographic history and reconstruct its possible paleodistributions with the use of approximate Bayesian computation and ecological niche models, respectively. Under this integrated framework, we found strong evidence for patterns of range shift and expansion, and population divergence events from the onset of the Holocene, resulting in the formation of its five distinct genetic units. The most highly supported model inferred that after the split of an ancestral population into the southern group and a larger central metapopulation lineage, the latter gave rise to the eastern and northern clusters, before finally dividing into two sub-central groups. While the use of molecular data allowed us to identify and refine the (phylo)genetic relationships of the species' lineages and populations, the use of ecological data helped us infer a past LGM refugium and the directions of post-glacial range dynamics. The time frames of these demographic events were shown to be congruent with climatic and geological events that affected the central Korean Peninsula during these periods. These findings gave us a better understanding of the consequences of past spatiotemporal factors that may have resulted in the current fragmented population distribution of this endangered plant.
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Affiliation(s)
| | - Yong‐In Kim
- On Biological Resource Research Institute (OBRRI)ChuncheonSouth Korea
| | - Jung‐Hoon Lee
- On Biological Resource Research Institute (OBRRI)ChuncheonSouth Korea
| | - Bo‐Yun Kim
- National Institute of Biological Resources (NIBR)IncheonSouth Korea
| | - Dae‐Hyun Kang
- Korea National Park Research InstituteWonjuSouth Korea
| | - Eui‐Kwon Jung
- Department of Life ScienceHallym UniversityChuncheonSouth Korea
| | - Jae‐Seo Shin
- Department of Life ScienceHallym UniversityChuncheonSouth Korea
| | - Young‐Dong Kim
- Multidisciplinary Genome InstituteHallym UniversityChuncheonSouth Korea
- Department of Life ScienceHallym UniversityChuncheonSouth Korea
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Molnár ÁP, Demeter L, Biró M, Chytrý M, Bartha S, Gantuya B, Molnár Z. Is there a massive glacial-Holocene flora continuity in Central Europe? Biol Rev Camb Philos Soc 2023; 98:2307-2319. [PMID: 37646107 DOI: 10.1111/brv.13007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 07/26/2023] [Accepted: 07/28/2023] [Indexed: 09/01/2023]
Abstract
The prevailing paradigm about the Quaternary ecological and evolutionary history of Central European ecosystems is that they were repeatedly impoverished by regional extinctions of most species during the glacial periods, followed by massive recolonizations from southern and eastern refugia during interglacial periods. Recent literature partially contradicts this view and provides evidence to re-evaluate this Postglacial Recolonization Hypothesis and develop an alternative one. We examined the long-term history of the flora of the Carpathian (Pannonian) Basin by synthesising recent advances in ecological, phylogeographical, palaeoecological and palaeoclimatological research, and analysing the cold tolerance of the native flora of a test area (Hungary, the central part of the Carpathian Basin). We found that (1) many species have likely occurred there continuously since before the Last Glacial Maximum (LGM); (2) most of the present-day native flora (1404 species, about 80%) can occur in climates as cold as or colder than the LGM (mean annual temperature ≤+3.5°C); and (3) grasslands and forests can be species-rich under an LGM-like cold climate. These arguments support an alternative hypothesis, which we call the Flora Continuity Hypothesis. It states that long-term continuity of much of the flora in the Carpathian Basin is more plausible than regional extinctions during the LGM followed by massive postglacial recolonizations. The long-term continuity of the region's flora may have fundamental implications not only for understanding local biogeography and ecology (e.g. the temporal scale of processes), but also for conservation strategies focusing on protecting ancient species-rich ecosystems and local gene pools.
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Affiliation(s)
- Ábel Péter Molnár
- Hungarian University of Agriculture and Life Sciences, Institute for Wildlife Management and Nature Conservation, Páter Károly u. 1., Gödöllő, 2100, Hungary
- Doctoral School of Biological Sciences, Hungarian University of Agriculture and Life Sciences, Páter Károly u. 1., Gödöllő, 2100, Hungary
| | - László Demeter
- Centre for Ecological Research, Institute of Ecology and Botany, Alkotmány u. 2-4., Vácrátót, 2163, Hungary
| | - Marianna Biró
- Centre for Ecological Research, Institute of Ecology and Botany, Alkotmány u. 2-4., Vácrátót, 2163, Hungary
| | - Milan Chytrý
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, Brno, 611 37, Czech Republic
| | - Sándor Bartha
- Centre for Ecological Research, Institute of Ecology and Botany, Alkotmány u. 2-4., Vácrátót, 2163, Hungary
| | - Batdelger Gantuya
- Botanic Garden and Research Institute, Mongolian Academy of Sciences, 13th Street, Peace Avenue 54a, Bayanzurkh district, Ulaanbaatar, 13330, Mongolia
- Doctoral School of Biology, Eötvös Lorand University, Budapest, Pázmány P. stny. 1/C., Budapest, 1117, Hungary
| | - Zsolt Molnár
- Centre for Ecological Research, Institute of Ecology and Botany, Alkotmány u. 2-4., Vácrátót, 2163, Hungary
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Jaisamut K, Pitiwararom R, Sukawutthiya P, Sathirapatya T, Noh H, Worrapitirungsi W, Vongpaisarnsin K. Unraveling the mitochondrial phylogenetic landscape of Thailand reveals complex admixture and demographic dynamics. Sci Rep 2023; 13:20396. [PMID: 37990137 PMCID: PMC10663463 DOI: 10.1038/s41598-023-47762-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 11/17/2023] [Indexed: 11/23/2023] Open
Abstract
The evolutionary dynamics of mitochondrial DNA within the Thai population were comprehensively explored with a specific focus on the influence of South Asian admixture. A total of 166 samples were collected through randomized sampling, ensuring a diverse representation. Our findings unveil substantial genetic and haplogroup diversity within the Thai population. We have identified 164 haplotypes categorized into 97 haplogroups, with a notable inclusion of 20 novel haplogroups. The distribution of haplogroups exhibited variations across different populations and countries. The central Thai population displayed a high diversity of haplogroups from both the M and N clades. Maternal lineage affinities were discerned between several Mainland Southeast Asia (MSEA) and South Asian populations, implying ancestral genetic connections and a substantial influence of South Asian women in establishing these relationships. f4-statistics indicates the presence of a Tibeto-Burman genetic component within the Mon population from Thailand. New findings demonstrate two phases of population expansion occurring 22,000-26,000 and 2500-3800 years ago, coinciding with the Last Glacial Maximum, and Neolithic demographic transition, respectively. This research significantly enhances our understanding of the maternal genetic history of Thailand and MSEA, emphasizing the influence of South Asian admixture. Moreover, it underscores the critical role of prior information, such as mutation rates, within the Bayesian framework for accurate estimation of coalescence times and inferring demographic history.
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Affiliation(s)
- Kitipong Jaisamut
- Forensic Genetics Research Unit, Department of Forensic Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Department of Forensic Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Rachtipan Pitiwararom
- Forensic Genetics Research Unit, Department of Forensic Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Department of Forensic Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Poonyapat Sukawutthiya
- Forensic Genetics Research Unit, Department of Forensic Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Department of Forensic Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Tikumphorn Sathirapatya
- Forensic Genetics Research Unit, Department of Forensic Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Department of Forensic Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Hasnee Noh
- Forensic Genetics Research Unit, Department of Forensic Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Department of Forensic Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Wikanda Worrapitirungsi
- Forensic Genetics Research Unit, Department of Forensic Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Department of Forensic Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Kornkiat Vongpaisarnsin
- Forensic Genetics Research Unit, Department of Forensic Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.
- Department of Forensic Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.
- Forensic Serology and DNA, King Chulalongkorn Memorial Hospital and Thai Red Cross Society, Bangkok, Thailand.
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37
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Tayyeh AM, Sequeira JJ, Kumar L, Babu I, van Driem G, Mustak MS. The maternal ancestry of the Kavaratti islanders and the last glacial maximum aftermath. Mol Genet Genomics 2023; 298:1467-1477. [PMID: 37823939 DOI: 10.1007/s00438-023-02072-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 09/23/2023] [Indexed: 10/13/2023]
Abstract
The prehistoric human settlement of the Lakshadweep islands remains a mystery for various reasons. Uncertainty about the existence of indigenous tribes in these islands and the lack of folklore records present major obstacles to the reconstruction of Lakshadweep ancestry. However, with extant population data, we seek to understand the maternal ancestry of the Kavaratti islanders. Mitochondrial control region variation analysis of 80 individuals from this island shows maternal links with the populations in the northwestern region of the South Asian mainland. The founder clade R30b2, observed in the Kavaratti islanders, is so far present only in the Scheduled Castes from the Punjab region, Jat Sikhs and Nairs. All other mainland populations carry basal R30 or R30a subclades. The presence of a specific Uralic U4 lineage in our samples, in addition to the Indo-European affinity observed in the phylogeny tree, substantiates a northwestern maternal ancestry of the Kavaratti islanders and implies an ancestral admixture with early humans in the Near East at the time of the last glacial maximum (LGM). Based on our Bayesian analysis, we furthermore propose that a group bearing mostly R30b2 during the LGM recovery, moved eastward and southward, where they received Indian-specific M haplogroups. Hence, the maternal ancestry of the Kavaratti islanders is evidently a consequence of the demographic changes in the northwestern region of the Indian subcontinent caused by the Last Glacial Maximum. The haplogroup distribution pattern and nucleotide sequence data produced in this study will enrich the forensic database of the Lakshadweep islands.
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Affiliation(s)
- Alnoman Mundher Tayyeh
- Department of Applied Zoology, Mangalore University, Mangalagangothri, 574199, India
- Department of Biosciences, Biotechnology Unit, Mangalore University, Mangalagangothri, 574199, India
| | | | - Lomous Kumar
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana, 500007, India
| | - Idrees Babu
- Department of Science and Technology, Lakshadweep Administration, Kavaratti, 682555, India
| | - George van Driem
- Institut für Sprachwissenschaft, Universität Bern, Länggassstrasse 49, 3012, Bern, Switzerland
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Godbout PM, Brouard E, Roy M. 1-km resolution rebound surfaces and paleotopography of glaciated North America since the Last Glacial Maximum. Sci Data 2023; 10:735. [PMID: 37872190 PMCID: PMC10593785 DOI: 10.1038/s41597-023-02566-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 09/13/2023] [Indexed: 10/25/2023] Open
Abstract
We present a series of 1-km spatial resolution rebound (isobase) surfaces based on publicly distributed predictions obtained from the glacio-isostatic adjustment models known as ICE-5G (VM2 L90), ICE-6G_C (VM5a) and ICE-7G_NA (VM7). Our objective is to provide readily accessible tools for a broad range of geological and paleoenvironmental studies, and to facilitate direct comparison between models' predictions and field-based observations. Rebound surfaces were interpolated at the scale of North American ice sheets (35.5°-89.5°N; 45°-165°W) and for each time increment of the models (1,000-500 yrs, between 26,000-21,000 yrs BP and present-day). The assessment of the interpolations indicates that the rebound surfaces have an overall vertical accuracy of ∼0.4 m compared to original ICE-xG outputs. These rebound surfaces were combined with the GEBCO 2021 present-day elevation grid to reconstruct the paleotopography for each time increment of the models and are all presented as raster files that can be easily integrated into geographical information systems. The resulting datasets therefore provide a unique support for geological, paleoenvironmental and archeological studies.
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Affiliation(s)
- Pierre-Marc Godbout
- Geological Survey of Canada, Natural Resources Canada, 601 Booth Street, Ottawa, ON, K1A 0E8, Canada.
| | - Etienne Brouard
- Geological Survey of Canada, Natural Resources Canada, 601 Booth Street, Ottawa, ON, K1A 0E8, Canada
| | - Martin Roy
- Department of Earth and Atmospheric Sciences & GEOTOP Research Center, University of Quebec at Montreal, C.P. 8888, Succ. Centre-ville, Montreal, QC, H3C 3P8, Canada
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Zinevich L, Prommer M, Laczkó L, Rozhkova D, Sorokin A, Karyakin I, Bagyura J, Cserkész T, Sramkó G. Phylogenomic insights into the polyphyletic nature of Altai falcons within eastern sakers (Falco cherrug) and the origins of gyrfalcons (Falco rusticolus). Sci Rep 2023; 13:17800. [PMID: 37853004 PMCID: PMC10584951 DOI: 10.1038/s41598-023-44534-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 10/10/2023] [Indexed: 10/20/2023] Open
Abstract
The Altai falcon from Central Asia always attracted the attention of humans. Long considered a totemic bird in its native area, modern falconers still much appreciated this large-bodied and mighty bird of prey due to its rarity and unique look. The peculiar body characteristics halfway between the saker falcon (Falco cherrug) and the gyrfalcon (F. rusticolus) triggered debates about its contentious taxonomy. The weak phylogenetic signal associated with traditional genetic methods could not resolve this uncertainty. Here, we address the controversial evolutionary origin of Altai falcons by means of a genome-wide approach, Restriction-site Associated DNA sequencing, using sympatric eastern sakers falcons, allopatric western saker falcons and gyrfalcons as outgroup. This approach provided an unprecedented insight into the phylogenetic relationships of the studied populations by delivering 17,095 unlinked SNPs shedding light on the polyphyletic nature of Altai falcons within eastern sakers. Thus we concluded that the former must correspond to a low taxonomic rank, probably an ecotype or form of the latter. Also, we found that eastern sakers are paraphyletic without gyrfalcons, thus, these latter birds are best regarded as the direct sister lineage of the eastern sakers. This evolutionary relationship, corroborated also by re-analyzing the dataset with the inclusion of outgroup samples (F. biarmicus and F. peregrinus), put eastern sakers into a new light as the potential ancestral genetic source of high latitude and altitude adaptation in descendent populations. Finally, conservation genomic values hint at the stable genetic background of the studied saker populations.
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Affiliation(s)
- Liudmila Zinevich
- Koltzov Institute of Developmental Biology Russian Academy of Sciences, Moscow, Russian Federation
- All-Russian Research Institute for Environmental Protection, Moscow, Russian Federation
| | | | - Levente Laczkó
- HUN-REN-UD Conservation Biology Research Group, Egyetem tér 1, Debrecen, 4032, Hungary
- Evolutionary Genomics Research Group, Department of Botany, University of Debrecen, Egyetem tér 1, Debrecen, 4032, Hungary
| | - Daria Rozhkova
- Koltzov Institute of Developmental Biology Russian Academy of Sciences, Moscow, Russian Federation
- All-Russian Research Institute for Environmental Protection, Moscow, Russian Federation
| | - Alexander Sorokin
- All-Russian Research Institute for Environmental Protection, Moscow, Russian Federation
| | | | - János Bagyura
- MME - BirdLife Hungary, Költő utca 21, Budapest, 1121, Hungary
| | - Tamás Cserkész
- Hungarian Natural History Museum, Baross utca 13, Budapest, 1088, Hungary
| | - Gábor Sramkó
- HUN-REN-UD Conservation Biology Research Group, Egyetem tér 1, Debrecen, 4032, Hungary.
- Evolutionary Genomics Research Group, Department of Botany, University of Debrecen, Egyetem tér 1, Debrecen, 4032, Hungary.
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40
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Sadatzki H, Opdyke B, Menviel L, Leventer A, Hope JM, Brocks JJ, Fallon S, Post AL, O’Brien PE, Grant K, Armand L. Early sea ice decline off East Antarctica at the last glacial-interglacial climate transition. SCIENCE ADVANCES 2023; 9:eadh9513. [PMID: 37824627 PMCID: PMC10569715 DOI: 10.1126/sciadv.adh9513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 09/07/2023] [Indexed: 10/14/2023]
Abstract
Antarctic climate warming and atmospheric CO2 rise during the last deglaciation may be attributed in part to sea ice reduction in the Southern Ocean. Yet, glacial-interglacial Antarctic sea ice dynamics and underlying mechanisms are poorly constrained, as robust sea ice proxy evidence is sparse. Here, we present a molecular biomarker-based sea ice record that resolves the spring/summer sea ice variability off East Antarctica during the past 40 thousand years (ka). Our results indicate that substantial sea ice reduction culminated rapidly and contemporaneously with upwelling of carbon-enriched waters in the Southern Ocean at the onset of the last deglaciation but began at least ~2 ka earlier probably driven by an increasing local integrated summer insolation. Our findings suggest that sea ice reduction and associated feedbacks facilitated stratification breakup and outgassing of CO2 in the Southern Ocean and warming in Antarctica but may also have played a leading role in initializing these deglacial processes in the Southern Hemisphere.
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Affiliation(s)
- Henrik Sadatzki
- Marine Geology Section, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, 27568 Bremerhaven, Germany
| | - Bradley Opdyke
- Research School of Earth Sciences, Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Laurie Menviel
- Climate Change Research Centre, University of New South Wales, Sydney, New South Wales 2052, Australia
- The Australian Centre for Excellence in Antarctic Science, University of Tasmania, Hobart, Tasmania 7001, Australia
| | - Amy Leventer
- Department of Geology, Colgate University, Hamilton, NY 13346, USA
| | - Janet M. Hope
- Research School of Earth Sciences, Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Jochen J. Brocks
- Research School of Earth Sciences, Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Stewart Fallon
- Research School of Earth Sciences, Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Alexandra L. Post
- Geoscience Australia, GPO Box 378, Canberra, Australian Capital Territory 2601, Australia
| | - Philip E. O’Brien
- Research School of Earth Sciences, Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Katharine Grant
- Research School of Earth Sciences, Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Leanne Armand
- Research School of Earth Sciences, Australian National University, Canberra, Australian Capital Territory 2601, Australia
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41
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Kersten O, Star B, Krabberød AK, Atmore LM, Tørresen OK, Anker-Nilssen T, Descamps S, Strøm H, Johansson US, Sweet PR, Jakobsen KS, Boessenkool S. Hybridization of Atlantic puffins in the Arctic coincides with 20th-century climate change. SCIENCE ADVANCES 2023; 9:eadh1407. [PMID: 37801495 PMCID: PMC10558128 DOI: 10.1126/sciadv.adh1407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 09/06/2023] [Indexed: 10/08/2023]
Abstract
The Arctic is experiencing the fastest rates of global warming, leading to shifts in the distribution of its biota and increasing the potential for hybridization. However, genomic evidence of recent hybridization events in the Arctic remains unexpectedly rare. Here, we use whole-genome sequencing of contemporary and 122-year-old historical specimens to investigate the origin of an Arctic hybrid population of Atlantic puffins (Fratercula arctica) on Bjørnøya, Norway. We show that the hybridization between the High Arctic, large-bodied subspecies F. a. naumanni and the temperate, smaller-sized subspecies F. a. arctica began as recently as six generations ago due to an unexpected southward range expansion of F. a. naumanni. Moreover, we find a significant temporal loss of genetic diversity across Arctic and temperate puffin populations. Our observations provide compelling genomic evidence of the impacts of recent distributional shifts and loss of diversity in Arctic communities during the 20th century.
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Affiliation(s)
- Oliver Kersten
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Bastiaan Star
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Anders K. Krabberød
- Section for Genetics and Evolutionary Biology (Evogene), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Lane M. Atmore
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Ole K. Tørresen
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | | | | | - Hallvard Strøm
- Norwegian Polar Institute, Fram Centre, Langnes, Tromsø, Norway
| | | | - Paul R. Sweet
- American Museum of Natural History, New York, NY, USA
| | - Kjetill S. Jakobsen
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Sanne Boessenkool
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
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42
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Pigati JS, Springer KB, Honke JS, Wahl D, Champagne MR, Zimmerman SRH, Gray HJ, Santucci VL, Odess D, Bustos D, Bennett MR. Independent age estimates resolve the controversy of ancient human footprints at White Sands. Science 2023; 382:73-75. [PMID: 37797035 DOI: 10.1126/science.adh5007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 08/10/2023] [Indexed: 10/07/2023]
Abstract
Human footprints at White Sands National Park, New Mexico, USA, reportedly date to between ~23,000 and 21,000 years ago according to radiocarbon dating of seeds from the aquatic plant Ruppia cirrhosa. These ages remain controversial because of potential old carbon reservoir effects that could compromise their accuracy. We present new calibrated 14C ages of terrestrial pollen collected from the same stratigraphic horizons as those of the Ruppia seeds, along with optically stimulated luminescence ages of sediments from within the human footprint-bearing sequence, to evaluate the veracity of the seed ages. The results show that the chronologic framework originally established for the White Sands footprints is robust and reaffirm that humans were present in North America during the Last Glacial Maximum.
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Affiliation(s)
- Jeffrey S Pigati
- US Geological Survey, Denver Federal Center, Denver, CO 80225, USA
| | | | - Jeffrey S Honke
- US Geological Survey, Denver Federal Center, Denver, CO 80225, USA
| | - David Wahl
- US Geological Survey, Menlo Park, CA 94025, USA
- Department of Geography, University of California, Berkeley, Berkeley, CA 94720, USA
| | | | - Susan R H Zimmerman
- Center for Accelerator Mass Spectrometry, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - Harrison J Gray
- US Geological Survey, Denver Federal Center, Denver, CO 80225, USA
| | - Vincent L Santucci
- National Park Service, Geologic Resources Division, Washington, DC 20240, USA
| | - Daniel Odess
- National Park Service, Cultural Resources Directorate, Washington, DC 20240, USA
| | - David Bustos
- National Park Service, White Sands National Park, Holloman Air Force Base, NM 88330, USA
| | - Matthew R Bennett
- Department of Life and Environmental Sciences, Bournemouth University, Poole BH12 5BB, UK
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43
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Ge X, Lu Y, Chen S, Gao Y, Ma L, Liu L, Liu J, Ma X, Kang L, Xu S. Genetic Origins and Adaptive Evolution of the Deng People on the Tibetan Plateau. Mol Biol Evol 2023; 40:msad205. [PMID: 37713634 PMCID: PMC10584363 DOI: 10.1093/molbev/msad205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 07/01/2023] [Accepted: 08/30/2023] [Indexed: 09/17/2023] Open
Abstract
The Tibetan Plateau is populated by diverse ethnic groups, but most of them are underrepresented in genomics studies compared with the Tibetans (TIB). Here, to gain further insight into the genetic diversity and evolutionary history of the people living in the Tibetan Plateau, we sequenced 54 whole genomes of the Deng people with high coverage (30-60×) and analyzed the data together with that of TIB and Sherpas, as well as 968 ancient Asian genomes and available archaic and modern human data. We identified 17.74 million novel single-nucleotide variants from the newly sequenced genomes, although the Deng people showed reduced genomic diversity and a relatively small effective population size. Compared with the other Tibetan highlander groups which are highly admixed, the Deng people are dominated by a sole ancestry that could be traced to some ancient northern East Asian populations. The divergence between Deng and Tibetan people (∼4,700-7,200 years) was more recent than that between highlanders and the Han Chinese (Deng-HAN, ∼9,000-14,000 years; TIB-HAN, 7,200-10,000 years). Adaptive genetic variants (AGVs) identified in the Deng are only partially shared with those previously reported in the TIB like HLA-DQB1, whereas others like KLHL12 were not reported in TIB. In contrast, the top candidate genes harboring AGVs as previously identified in TIB, like EPAS1 and EGLN1, do not show strong positive selection signals in Deng. Interestingly, Deng also showed a different archaic introgression scenario from that observed in the TIB. Our results suggest that convergent adaptation might be prevalent on the Tibetan Plateau.
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Affiliation(s)
- Xueling Ge
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yan Lu
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Shuanghui Chen
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Yang Gao
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Lifeng Ma
- Key Laboratory of High-Altitude Environment and Genes Related to Disease of Tibet Ministry of Education, Xizang Minzu University, Xianyang, Shaanxi, China
- Research Center for Tibetan Social Governance, Key Research Institute of Humanities and Social Sciences in Xizang Minzu University, State Ethnic Affairs Commission, Xizang Minzu University, Xianyang, Shaanxi, China
| | - Lijun Liu
- Key Laboratory of High-Altitude Environment and Genes Related to Disease of Tibet Ministry of Education, Xizang Minzu University, Xianyang, Shaanxi, China
- Research Center for Tibetan Social Governance, Key Research Institute of Humanities and Social Sciences in Xizang Minzu University, State Ethnic Affairs Commission, Xizang Minzu University, Xianyang, Shaanxi, China
| | - Jiaojiao Liu
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Xixian Ma
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Longli Kang
- Key Laboratory of High-Altitude Environment and Genes Related to Disease of Tibet Ministry of Education, Xizang Minzu University, Xianyang, Shaanxi, China
- Research Center for Tibetan Social Governance, Key Research Institute of Humanities and Social Sciences in Xizang Minzu University, State Ethnic Affairs Commission, Xizang Minzu University, Xianyang, Shaanxi, China
| | - Shuhua Xu
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- Department of Liver Surgery and Transplantation Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China
- Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai, China
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44
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Aragoncillo-del Río J, Alcolea-González JJ, Luque L, Castillo-Jiménez S, Jiménez-Gisbert G, López-Sáez JA, Maíllo-Fernández JM, Ruiz-Alonso M, Triguero I, Yravedra J, Alcaraz-Castaño M. Human occupations of upland and cold environments in inland Spain during the Last Glacial Maximum and Heinrich Stadial 1: The new Magdalenian sequence of Charco Verde II. PLoS One 2023; 18:e0291516. [PMID: 37792682 PMCID: PMC10550185 DOI: 10.1371/journal.pone.0291516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 08/30/2023] [Indexed: 10/06/2023] Open
Abstract
The settlement of cold and arid environments by Pleistocene hunter-gatherers has been a heated topic in Paleolithic Archaeology and the Quaternary Sciences for years. In the Iberian Peninsula, a key area for studying human adaptations to such environments is composed by the large interior and upland regions of the northern and southern plateaus (Mesetas) and bordering areas. As, traditionally, these regions have been relatively under-investigated compared to the ecologically more favored coastal areas of the peninsula, our knowledge of the human settlement of the whole Iberian hinterland remains scarce for the Last Glacial. In this paper we present the discovery and first geoarcheological, paleoenvironmental and chronometric evidence obtained at Charco Verde II, a new site close to the southwestern foothills of the Iberian system range (Guadalajara province, Spain), bearing a sequence of Magdalenian human occupations starting at least at 20.8-21.4 ka cal BP during the Last Glacial Maximum, and covering Greenland Stadial 2 until ∼15.1-16.6 ka cal BP, including Heinrich stadial 1. As this site is located in an upland region which today faces one of the harshest climates in Iberia, such occupation sequence, occurred during some of the coldest and most arid phases of the Last Glacial, has relevant implications for our understanding of human-environment-climate interactions and population dynamics in Iberia and Western Europe. These findings support the hypothesis that the Iberian hinterland was not avoided by Upper Paleolithic hunter-gatherers due to ecological constraints, but it hosted a complex and relatively dense settlement at least in some areas, even during cold periods. This suggest, one more time, that the historical scarcity of Upper Paleolithic sites in inland Iberia is, to a significant extent, an artifact of research bias.
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Affiliation(s)
- Javier Aragoncillo-del Río
- Molina-Alto Tajo UNESCO Global Geopark, Molina de Aragón, Guadalajara, Spain
- Escuela Internacional de Doctorado de la UNED (EIDUNED), Madrid, Spain
| | | | - Luis Luque
- Area of Prehistory (Department of History and Philosophy), University of Alcalá, Alcalá de Henares, Spain
| | - Samuel Castillo-Jiménez
- Area of Prehistory (Department of History and Philosophy), University of Alcalá, Alcalá de Henares, Spain
| | - Guillermo Jiménez-Gisbert
- Area of Prehistory (Department of History and Philosophy), University of Alcalá, Alcalá de Henares, Spain
| | | | - José-Manuel Maíllo-Fernández
- Institute of Evolution in Africa (IDEA), University of Alcalá, Madrid, Spain
- Department of Prehistory and Archaeology, Universidad Nacional de Educación a Distancia (UNED), Madrid, Spain
| | - Mónica Ruiz-Alonso
- Environmental Archeology Research Group, Institute of History, CCHS CSIC, Madrid, Spain
| | - Ignacio Triguero
- Area of Prehistory (Department of History and Philosophy), University of Alcalá, Alcalá de Henares, Spain
| | - José Yravedra
- Department of Prehistory, Ancient History and Archaeology, Complutense University, Madrid, Spain
| | - Manuel Alcaraz-Castaño
- Area of Prehistory (Department of History and Philosophy), University of Alcalá, Alcalá de Henares, Spain
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Yang F, Ge J, Guo Y, Olmstead R, Sun W. Deciphering complex reticulate evolution of Asian Buddleja (Scrophulariaceae): insights into the taxonomy and speciation of polyploid taxa in the Sino-Himalayan region. ANNALS OF BOTANY 2023; 132:15-28. [PMID: 36722368 PMCID: PMC10550280 DOI: 10.1093/aob/mcad022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 01/31/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND AND AIMS Species of the genus Buddleja in Asia are mainly distributed in the Sino-Himalayan region and form a challenging taxonomic group, with extensive hybridization and polyploidization. A phylogenetic approach to unravelling the history of reticulation in this lineage will deepen our understanding of the speciation in biodiversity hotspots. METHODS For this study, we obtained 80 accessions representing all the species in the Asian Buddleja clade, and the ploidy level of each taxon was determined by flow cytometry analyses. Whole plastid genomes, nuclear ribosomal DNA, single nucleotide polymorphisms and a large number of low-copy nuclear genes assembled from genome skimming data were used to investigate the reticulate evolutionary history of Asian Buddleja. Complex cytonuclear conflicts were detected through a comparison of plastid and species trees. Gene tree incongruence was also analysed to detect any reticulate events in the history of this lineage. KEY RESULTS Six hybridization events were detected, which are able to explain the cytonuclear conflict in Asian Buddleja. Furthermore, PhyloNet analysis combining species ploidy data indicated several allopolyploid speciation events. A strongly supported species tree inferred from a large number of low-copy nuclear genes not only corrected some earlier misinterpretations, but also indicated that there are many Asian Buddleja species that have been lumped mistakenly. Divergent time estimation shows two periods of rapid diversification (8-10 and 0-3 Mya) in the Asian Buddleja clade, which might coincide with the final uplift of the Hengduan Mountains and Quaternary climate fluctuations, respectively. CONCLUSIONS This study presents a well-supported phylogenetic backbone for the Asian Buddleja species, elucidates their complex and reticulate evolutionary history and suggests that tectonic activity, climate fluctuations, polyploidization and hybridization together promoted the diversification of this lineage.
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Affiliation(s)
- Fengmao Yang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences (CAS), Kunming 650201, Yunnan, China
| | - Jia Ge
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences (CAS), Kunming 650201, Yunnan, China
| | - Yongjie Guo
- Germplasm Bank of Wild Species of China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Richard Olmstead
- Department of Biology and Burke Museum, University of Washington, Seattle, WA 98195, USA
| | - Weibang Sun
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences (CAS), Kunming 650201, Yunnan, China
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46
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Ruiz-Puerta EJ, Keighley X, Desjardins SPA, Gotfredsen AB, Pan SE, Star B, Boessenkool S, Barrett JH, McCarthy ML, Andersen LW, Born EW, Howse LR, Szpak P, Pálsson S, Malmquist HJ, Rufolo S, Jordan PD, Olsen MT. Holocene deglaciation drove rapid genetic diversification of Atlantic walrus. Proc Biol Sci 2023; 290:20231349. [PMID: 37752842 PMCID: PMC10523089 DOI: 10.1098/rspb.2023.1349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Accepted: 08/27/2023] [Indexed: 09/28/2023] Open
Abstract
Rapid global warming is severely impacting Arctic ecosystems and is predicted to transform the abundance, distribution and genetic diversity of Arctic species, though these linkages are poorly understood. We address this gap in knowledge using palaeogenomics to examine how earlier periods of global warming influenced the genetic diversity of Atlantic walrus (Odobenus rosmarus rosmarus), a species closely associated with sea ice and shallow-water habitats. We analysed 82 ancient and historical Atlantic walrus mitochondrial genomes (mitogenomes), including now-extinct populations in Iceland and the Canadian Maritimes, to reconstruct the Atlantic walrus' response to Arctic deglaciation. Our results demonstrate that the phylogeography and genetic diversity of Atlantic walrus populations was initially shaped by the last glacial maximum (LGM), surviving in distinct glacial refugia, and subsequently expanding rapidly in multiple migration waves during the late Pleistocene and early Holocene. The timing of diversification and establishment of distinct populations corresponds closely with the chronology of the glacial retreat, pointing to a strong link between walrus phylogeography and sea ice. Our results indicate that accelerated ice loss in the modern Arctic may trigger further dispersal events, likely increasing the connectivity of northern stocks while isolating more southerly stocks putatively caught in small pockets of suitable habitat.
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Affiliation(s)
- Emily J. Ruiz-Puerta
- Section for Molecular Ecology and Evolution, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5-7, 1353 Copenhagen Kobenhavn, Denmark
- Arctic Centre & Groningen Institute of Archaeology, Faculty of Arts, University of Groningen, PO Box 716, 9700 AS Groningen, The Netherlands
| | - Xénia Keighley
- Section for Molecular Ecology and Evolution, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5-7, 1353 Copenhagen Kobenhavn, Denmark
- The Bureau of Meteorology, The Treasury Building, Parkes Place West, Parkes, Australian Capital Territory 2600, Australia
| | - Sean P. A. Desjardins
- Arctic Centre & Groningen Institute of Archaeology, Faculty of Arts, University of Groningen, PO Box 716, 9700 AS Groningen, The Netherlands
- Palaeobiology Section, Canadian Museum of Nature, PO Box 3443, Station D, Ottawa, Ontario, Canada K1P 6P4
| | - Anne Birgitte Gotfredsen
- Section for GeoGenetics, Globe Institute, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen Kobenhavn, Denmark
| | - Shyong En Pan
- Palaeobiology Section, Canadian Museum of Nature, PO Box 3443, Station D, Ottawa, Ontario, Canada K1P 6P4
| | - Bastiaan Star
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Blindernveien 31, 0371 Oslo, Norway
| | - Sanne Boessenkool
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Blindernveien 31, 0371 Oslo, Norway
| | - James H. Barrett
- Department of Archaeology and Cultural History, NTNU University Museum, 7491 Trondheim, Norway
- McDonald Institute for Archaeological Research, Department of Archaeology, University of Cambridge, Downing Street, Cambridge CB2 3ER, UK
| | - Morgan L. McCarthy
- Section for Molecular Ecology and Evolution, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5-7, 1353 Copenhagen Kobenhavn, Denmark
| | - Liselotte W. Andersen
- Department of Ecoscience, Aarhus University, CF Møllers Allé 4-8, build. 1110, 8000 Aarhus C, Denmark
| | - Erik W. Born
- Greenland Institute of Natural Resources, PO Box 570, 3900 Nuuk, Greenland
| | - Lesley R. Howse
- Archaeology Centre, University of Toronto, 19 Ursula Franklin Street, Toronto, Ontario Canada M5S 2S2
| | - Paul Szpak
- Department of Anthropology, Trent University, 1600 West Bank Drive, Peterborough, Ontario, Canada K9L 0G2
| | - Snæbjörn Pálsson
- Faculty of Life and Environmental Sciences, University of Iceland, Askja, Sturlugata 7, 101 Reykjavik, Iceland
| | - Hilmar J. Malmquist
- Icelandic Museum of Natural History, Suðurlandsbraut 24, 108 Reykjavík, Iceland
| | - Scott Rufolo
- Palaeobiology Section, Canadian Museum of Nature, PO Box 3443, Station D, Ottawa, Ontario, Canada K1P 6P4
| | - Peter D. Jordan
- Department of Archaeology and Ancient History, Lund University, Helgonavägen 3, 223 62 Lund, Sweden
- Global Station for Indigenous Studies and Cultural Diversity (GSI), GI-CoRE, HokkaidoUniversity, Japan
| | - Morten Tange Olsen
- Section for Molecular Ecology and Evolution, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5-7, 1353 Copenhagen Kobenhavn, Denmark
- Natural History Museum of Denmark, University of Copenhagen, Denmark
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Nigenda-Morales SF, Lin M, Nuñez-Valencia PG, Kyriazis CC, Beichman AC, Robinson JA, Ragsdale AP, Urbán R J, Archer FI, Viloria-Gómora L, Pérez-Álvarez MJ, Poulin E, Lohmueller KE, Moreno-Estrada A, Wayne RK. The genomic footprint of whaling and isolation in fin whale populations. Nat Commun 2023; 14:5465. [PMID: 37699896 PMCID: PMC10497599 DOI: 10.1038/s41467-023-40052-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 07/10/2023] [Indexed: 09/14/2023] Open
Abstract
Twentieth century industrial whaling pushed several species to the brink of extinction, with fin whales being the most impacted. However, a small, resident population in the Gulf of California was not targeted by whaling. Here, we analyzed 50 whole-genomes from the Eastern North Pacific (ENP) and Gulf of California (GOC) fin whale populations to investigate their demographic history and the genomic effects of natural and human-induced bottlenecks. We show that the two populations diverged ~16,000 years ago, after which the ENP population expanded and then suffered a 99% reduction in effective size during the whaling period. In contrast, the GOC population remained small and isolated, receiving less than one migrant per generation. However, this low level of migration has been crucial for maintaining its viability. Our study exposes the severity of whaling, emphasizes the importance of migration, and demonstrates the use of genome-based analyses and simulations to inform conservation strategies.
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Affiliation(s)
- Sergio F Nigenda-Morales
- Advanced Genomics Unit, National Laboratory of Genomics for Biodiversity (Langebio), Center for Research and Advanced Studies (Cinvestav), Irapuato, Guanajuato, 36824, Mexico.
- Department of Biological Sciences, California State University San Marcos, San Marcos, CA, 92096, USA.
| | - Meixi Lin
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA.
| | - Paulina G Nuñez-Valencia
- Advanced Genomics Unit, National Laboratory of Genomics for Biodiversity (Langebio), Center for Research and Advanced Studies (Cinvestav), Irapuato, Guanajuato, 36824, Mexico
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Morelos, México
| | - Christopher C Kyriazis
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Annabel C Beichman
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA
| | - Jacqueline A Robinson
- Institute for Human Genetics, University of California, San Francisco (UCSF), San Francisco, CA, 94143, USA
| | - Aaron P Ragsdale
- Advanced Genomics Unit, National Laboratory of Genomics for Biodiversity (Langebio), Center for Research and Advanced Studies (Cinvestav), Irapuato, Guanajuato, 36824, Mexico
- Department of Integrative Biology, University of Wisconsin, Madison, WI, 53706, USA
| | - Jorge Urbán R
- Departamento de Ciencias Marinas y Costeras, Universidad Autónoma de Baja California Sur (UABCS), La Paz, Baja California Sur, Mexico
| | - Frederick I Archer
- Marine Mammal and Turtle Division, Southwest Fisheries Science Center, La Jolla, CA, 92037, USA
| | - Lorena Viloria-Gómora
- Departamento de Ciencias Marinas y Costeras, Universidad Autónoma de Baja California Sur (UABCS), La Paz, Baja California Sur, Mexico
| | - María José Pérez-Álvarez
- Escuela de Medicina Veterinaria, Facultad de Medicina y Ciencias de la Salud, Universidad Mayor, Santiago, Chile
- Millennium Institute Biodiversity of Antarctic and Subantarctic Ecosystems (BASE), Universidad de Chile, Santiago, Chile
| | - Elie Poulin
- Millennium Institute Biodiversity of Antarctic and Subantarctic Ecosystems (BASE), Universidad de Chile, Santiago, Chile
| | - Kirk E Lohmueller
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
- Interdepartmental Program in Bioinformatics, University of California, Los Angeles, CA, 90095, USA.
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA.
| | - Andrés Moreno-Estrada
- Advanced Genomics Unit, National Laboratory of Genomics for Biodiversity (Langebio), Center for Research and Advanced Studies (Cinvestav), Irapuato, Guanajuato, 36824, Mexico.
| | - Robert K Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
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Boyle JH, Strickler S, Twyford AD, Ricono A, Powell A, Zhang J, Xu H, Smith R, Dalgleish HJ, Jander G, Agrawal AA, Puzey JR. Temporal matches between monarch butterfly and milkweed population changes over the past 25,000 years. Curr Biol 2023; 33:3702-3710.e5. [PMID: 37607548 DOI: 10.1016/j.cub.2023.07.057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 04/13/2023] [Accepted: 07/26/2023] [Indexed: 08/24/2023]
Abstract
In intimate ecological interactions, the interdependency of species may result in correlated demographic histories. For species of conservation concern, understanding the long-term dynamics of such interactions may shed light on the drivers of population decline. Here, we address the demographic history of the monarch butterfly, Danaus plexippus, and its dominant host plant, the common milkweed Asclepias syriaca (A. syriaca), using broad-scale sampling and genomic inference. Because genetic resources for milkweed have lagged behind those for monarchs, we first release a chromosome-level genome assembly and annotation for common milkweed. Next, we show that despite its enormous geographic range across eastern North America, A. syriaca is best characterized as a single, roughly panmictic population. Using approximate Bayesian computation with random forests (ABC-RF), a machine learning method for reconstructing demographic histories, we show that both monarchs and milkweed experienced population expansion during the most recent recession of North American glaciers 10,000-20,000 years ago. Our data also identify concurrent population expansions in both species during the large-scale clearing of eastern forests (∼200 years ago). Finally, we find no evidence that either species experienced a reduction in effective population size over the past 75 years. Thus, the well-documented decline of monarch abundance over the past 40 years is not visible in our genomic dataset, reflecting a possible mismatch of the overwintering census population to effective population size in this species.
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Affiliation(s)
- John H Boyle
- Biology Department, College of William & Mary, 540 Landrum Dr., Williamsburg, VA 23185, USA; Biology Department, University of Mary, 7500 University Dr., Bismarck, ND 58504, USA
| | - Susan Strickler
- Boyce Thompson Institute, 533 Tower Rd., Ithaca, NY 14853, USA; Chicago Botanic Garden, Plant Science and Conservation, 1000 Lake Cook Rd., Glencoe, IL 60022, USA; Northwestern University, Plant Biology and Conservation Program, 2145 Sheridan Rd., Evanston, IL 60208, USA
| | - Alex D Twyford
- Institute of Ecology and Evolution, University of Edinburgh, Charlotte Auerbach Rd., Edinburgh EH9 3FL, UK; Royal Botanic Garden Edinburgh, Edinburgh EH3 5NZ, UK
| | - Angela Ricono
- Biology Department, College of William & Mary, 540 Landrum Dr., Williamsburg, VA 23185, USA
| | - Adrian Powell
- Boyce Thompson Institute, 533 Tower Rd., Ithaca, NY 14853, USA
| | - Jing Zhang
- Boyce Thompson Institute, 533 Tower Rd., Ithaca, NY 14853, USA
| | - Hongxing Xu
- Boyce Thompson Institute, 533 Tower Rd., Ithaca, NY 14853, USA; College of Life Sciences, Shaanxi Normal University, South Chang'an Rd., Xi'an 710062, China
| | - Ronald Smith
- Data Science Program, College of William & Mary, 540 Landrum Dr., Williamsburg, VA 23185, USA
| | - Harmony J Dalgleish
- Biology Department, College of William & Mary, 540 Landrum Dr., Williamsburg, VA 23185, USA
| | - Georg Jander
- Boyce Thompson Institute, 533 Tower Rd., Ithaca, NY 14853, USA
| | - Anurag A Agrawal
- Department of Ecology and Evolutionary Biology, Cornell University, Corson Hall, Ithaca, NY 14853, USA
| | - Joshua R Puzey
- Biology Department, College of William & Mary, 540 Landrum Dr., Williamsburg, VA 23185, USA.
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49
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Liu F, Zhao J, Sun H, Xiong C, Sun X, Wang X, Wang Z, Jarret R, Wang J, Tang B, Xu H, Hu B, Suo H, Yang B, Ou L, Li X, Zhou S, Yang S, Liu Z, Yuan F, Pei Z, Ma Y, Dai X, Wu S, Fei Z, Zou X. Genomes of cultivated and wild Capsicum species provide insights into pepper domestication and population differentiation. Nat Commun 2023; 14:5487. [PMID: 37679363 PMCID: PMC10484947 DOI: 10.1038/s41467-023-41251-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 08/28/2023] [Indexed: 09/09/2023] Open
Abstract
Pepper (Capsicum spp.) is one of the earliest cultivated crops and includes five domesticated species, C. annuum var. annuum, C. chinense, C. frutescens, C. baccatum var. pendulum and C. pubescens. Here, we report a pepper graph pan-genome and a genome variation map of 500 accessions from the five domesticated Capsicum species and close wild relatives. We identify highly differentiated genomic regions among the domesticated peppers that underlie their natural variations in flowering time, characteristic flavors, and unique resistances to biotic and abiotic stresses. Domestication sweeps detected in C. annuum var. annuum and C. baccatum var. pendulum are mostly different, and the common domestication traits, including fruit size, shape and pungency, are achieved mainly through the selection of distinct genomic regions between these two cultivated species. Introgressions from C. baccatum into C. chinense and C. frutescens are detected, including those providing genetic sources for various biotic and abiotic stress tolerances.
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Affiliation(s)
- Feng Liu
- Engineering Research Center for Germplasm Innovation and New Varieties Breeding of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha, China
| | - Jiantao Zhao
- Engineering Research Center for Germplasm Innovation and New Varieties Breeding of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha, China
- Boyce Thompson Institute, Ithaca, NY, USA
| | - Honghe Sun
- Boyce Thompson Institute, Ithaca, NY, USA
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | - Cheng Xiong
- Engineering Research Center for Germplasm Innovation and New Varieties Breeding of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha, China
| | - Xuepeng Sun
- Boyce Thompson Institute, Ithaca, NY, USA
- College of Horticulture Science, Zhejiang A&F University, Hangzhou, China
| | - Xin Wang
- Boyce Thompson Institute, Ithaca, NY, USA
- Department of Vegetable Crops, College of Horticulture and Forestry, Huazhong Agricultural University, Wuhan, China
| | - Zhongyi Wang
- Engineering Research Center for Germplasm Innovation and New Varieties Breeding of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha, China
| | - Robert Jarret
- U.S. Department of Agriculture-Agricultural Research Service, Plant Genetic Resources Conservation Unit, Griffin, GA, USA
| | - Jin Wang
- Engineering Research Center for Germplasm Innovation and New Varieties Breeding of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha, China
| | - Bingqian Tang
- Engineering Research Center for Germplasm Innovation and New Varieties Breeding of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha, China
| | - Hao Xu
- Engineering Research Center for Germplasm Innovation and New Varieties Breeding of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha, China
| | - Bowen Hu
- Engineering Research Center for Germplasm Innovation and New Varieties Breeding of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha, China
| | - Huan Suo
- Engineering Research Center for Germplasm Innovation and New Varieties Breeding of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha, China
| | - Bozhi Yang
- Engineering Research Center for Germplasm Innovation and New Varieties Breeding of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha, China
| | - Lijun Ou
- Engineering Research Center for Germplasm Innovation and New Varieties Breeding of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha, China
| | - Xuefeng Li
- Institute of Vegetable Research, Hunan Academy of Agricultural Science, Changsha, China
| | - Shudong Zhou
- Institute of Vegetable Research, Hunan Academy of Agricultural Science, Changsha, China
| | - Sha Yang
- Institute of Vegetable Research, Hunan Academy of Agricultural Science, Changsha, China
| | - Zhoubing Liu
- Engineering Research Center for Germplasm Innovation and New Varieties Breeding of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha, China
| | - Fang Yuan
- Engineering Research Center for Germplasm Innovation and New Varieties Breeding of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha, China
| | - Zhenming Pei
- Engineering Research Center for Germplasm Innovation and New Varieties Breeding of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha, China
| | - Yanqing Ma
- Engineering Research Center for Germplasm Innovation and New Varieties Breeding of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha, China
| | - Xiongze Dai
- Engineering Research Center for Germplasm Innovation and New Varieties Breeding of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha, China
| | - Shan Wu
- Boyce Thompson Institute, Ithaca, NY, USA.
| | - Zhangjun Fei
- Boyce Thompson Institute, Ithaca, NY, USA.
- U.S. Department of Agriculture-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY, USA.
| | - Xuexiao Zou
- Engineering Research Center for Germplasm Innovation and New Varieties Breeding of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha, China.
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Liu DT, Chen JY, Sun WB. Distributional responses to climate change of two maple species in southern China. Ecol Evol 2023; 13:e10490. [PMID: 37664510 PMCID: PMC10468973 DOI: 10.1002/ece3.10490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 08/05/2023] [Accepted: 08/22/2023] [Indexed: 09/05/2023] Open
Abstract
Climate change is a major factor affecting biodiversity and species distribution, particularly of montane species. Species may respond to climate change by shifting their range to higher elevations. The southeastern Qinghai-Tibetan Plateau (QTP) and the Hengduan Mountains are considered as global biodiversity hotspots. However, information on the response of maple species to climate change in these regions was limited. Therefore, we selected two maple species that occur there and assessed changes in their habitat suitability under past, present and future climate scenarios in Biomod2. The results showed that temperature seasonality (bio4) was the most critical factor influencing their potential distributions. The distribution of potentially suitable habitat for Acer caesium and Acer stachyophyllum was predicted to be larger during the LGM compared to the present. Under the current climate scenario, the largest areas of potentially suitable habitat for these species were mainly located in southeastern Tibet, the Hengduan Mountains in northwestern Yunnan and western Sichuan, the Qinling-Daba Mountains in southern Gansu and the Wumeng-Daliang Mountains in northeastern Yunnan, western Guizhou and southeastern Sichuan. Under future climate change scenarios, the predicted loss of suitable habitat areas for these two species ranged from 13.78% to 45.71% and the increase ranged from 18.88% to 57.98%, with an overall increasing trend. The suitable habitat areas were predicted to shift towards the eastern parts of the QTP under both the pessimistic and optimistic future climate change scenarios in the 2050s and the 2070s, which became evident as global warming intensified, particularly in the eastern QTP and the Hengduan Mountains. Our results highlight the possibility that the diverse topography along altitudinal gradients in the QTP and the Hengduan Mountains may potentially mitigate the range contraction of mountain plants in response to climate warming. These findings provide a basis for planning conservation areas, planting and species conservation in the mountainous areas of southern China under the anticipated global warming.
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Affiliation(s)
- De Tuan Liu
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small PopulationsKey Laboratory for Plant Diversity and Biogeography of East AsiaKunming Institute of Botany, Chinese Academy of SciencesKunmingChina
- University of the Chinese Academy of SciencesBeijingChina
- School of Life SciencesYunnan UniversityKunmingChina
| | - Jian Ying Chen
- Forest Seed and Seedling General Station of Yunnan ProvinceKunmingChina
| | - Wei Bang Sun
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small PopulationsKey Laboratory for Plant Diversity and Biogeography of East AsiaKunming Institute of Botany, Chinese Academy of SciencesKunmingChina
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