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Tang J, Fan X, Milne RI, Yang H, Tao W, Zhang X, Guo M, Li J, Mao K. Across two phylogeographic breaks: Quaternary evolutionary history of a mountain aspen ( Populus rotundifolia) in the Hengduan Mountains. PLANT DIVERSITY 2024; 46:321-332. [PMID: 38798733 PMCID: PMC11119543 DOI: 10.1016/j.pld.2024.03.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Revised: 03/31/2024] [Accepted: 03/31/2024] [Indexed: 05/29/2024]
Abstract
Biogeographical barriers to gene flow are central to plant phylogeography. In East Asia, plant distribution is greatly influenced by two phylogeographic breaks, the Mekong-Salween Divide and Tanaka-Kaiyong Line, however, few studies have investigated how these barriers affect the genetic diversity of species that are distributed across both. Here we used 14 microsatellite loci and four chloroplast DNA fragments to examine genetic diversity and distribution patterns of 49 populations of Populus rotundifolia, a species that spans both the Mekong-Salween Divide and the Tanaka-Kaiyong Line in southwestern China. Demographic and migration hypotheses were tested using coalescent-based approaches. Limited historical gene flow was observed between the western and eastern groups of P. rotundifolia, but substantial flow occurred across both the Mekong-Salween Divide and Tanaka-Kaiyong Line, manifesting in clear admixture and high genetic diversity in the central group. Wind-borne pollen and seeds may have facilitated the dispersal of P. rotundifolia following prevalent northwest winds in the spring. We also found that the Hengduan Mountains, where multiple genetic barriers were detected, acted on the whole as a barrier between the western and eastern groups of P. rotundifolia. Ecological niche modeling suggested that P. rotundifolia has undergone range expansion since the last glacial maximum, and demographic reconstruction indicated an earlier population expansion around 600 Ka. The phylogeographic pattern of P. rotundifolia reflects the interplay of biological traits, wind patterns, barriers, niche differentiation, and Quaternary climate history. This study emphasizes the need for multiple lines of evidence in understanding the Quaternary evolution of plants in topographically complex areas.
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Affiliation(s)
- Jieshi Tang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610065, PR China
| | - Xiaoyan Fan
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610065, PR China
| | - Richard I. Milne
- Institute of Molecular Plant Sciences, University of Edinburgh, Edinburgh EH9 3JH, UK
| | - Heng Yang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610065, PR China
| | - Wenjing Tao
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610065, PR China
| | - Xinran Zhang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610065, PR China
| | - Mengyun Guo
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610065, PR China
| | - Jialiang Li
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610065, PR China
| | - Kangshan Mao
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610065, PR China
- School of Ecology and Environment, Tibet University, Lhasa 850000, PR China
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Iwata H, Ito T, Park JS, Kokubugata G, Kakezawa A, Kurosawa T, Nishimura A, Noda H, Takayama K. Intraspecific divergence in a coastal plant, Euphorbia jolkinii, at a major biogeographic boundary in East Asia. AMERICAN JOURNAL OF BOTANY 2024; 111:e16327. [PMID: 38725176 DOI: 10.1002/ajb2.16327] [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: 08/24/2023] [Revised: 03/11/2024] [Accepted: 03/12/2024] [Indexed: 05/29/2024]
Abstract
PREMISE Quaternary climatic fluctuations and long-distance seed dispersal across the sea are critical factors affecting the distribution of coastal plants, but the spatiotemporal nature of population expansion and distribution change of East Asian coastal plants during this period are rarely examined. To explore this process, we investigated the genome-wide phylogenetic patterns of Euphorbia jolkinii Boiss. (Euphorbiaceae), which grows widely on littoral areas of Japan, Korea, and Taiwan. METHODS We used plastome sequences and genome-wide single nucleotide polymorphisms in samples across the species range to reveal phylogeographic patterns and spatiotemporal distributional changes. We conducted ecological niche modeling for the present and the last glacial maximum (LGM). RESULTS Genetic differentiation was observed between the northern and southern populations of E. jolkinii, separated by the major biogeographic boundary, the Tokara Gap. These two groups of populations differentiated during the glacial period and subsequently intermingled in the intermorainic areas of the central Ryukyu Islands after the LGM. Ecological niche models suggested that the potential range of E. jolkinii was restricted to southern Kyushu; however, it was widespread in the southern Ryukyu Islands and Taiwan during the LGM. CONCLUSIONS This study provides evidence of genetic differentiation among coastal plant populations separated by the prominent biogeographical boundary. Although coastal plants are typically expected to maintain population connectivity through sea-drifted seed dispersal, our findings suggest that genetic differences may arise because of a combination of limited gene flow and changes in climate during the glacial period.
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Affiliation(s)
- Hiroyuki Iwata
- Department of Botany, Faculty of Science, Kyoto University, Kyoto, Japan
| | - Takuro Ito
- Botanical Gardens, Tohoku University, Sendai, Japan
| | - Jong-Soo Park
- Honam National Institute of Biological Resources, Mokpo-si, Jeollanam-do, South Korea
| | - Goro Kokubugata
- Department of Botany, National Museum of Nature and Science, Amakubo, Tsukuba, Japan
| | | | - Takahide Kurosawa
- Faculty of Symbiotic System Science, Fukushima University, Fukushima, Japan
| | - Akihiro Nishimura
- Department of Botany, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Hiroshi Noda
- Department of Botany, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Koji Takayama
- Department of Botany, Graduate School of Science, Kyoto University, Kyoto, Japan
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Harkness BAS, Ibarguchi G, Poland VF, Friesen VL. Historical fragmentation and stepping-stone gene flow led to population genetic differentiation in a coastal seabird. Ecol Evol 2024; 14:e11204. [PMID: 38633521 PMCID: PMC11021922 DOI: 10.1002/ece3.11204] [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: 02/25/2024] [Accepted: 03/18/2024] [Indexed: 04/19/2024] Open
Abstract
Understanding the forces that shape population genetic structure is fundamental both for understanding evolutionary trajectories and for conservation. Many factors can influence the geographic distribution of genetic variation, and the extent to which local populations differ can be especially difficult to predict in highly mobile organisms. For example, many species of seabirds are essentially panmictic, but some show strong structure. Pigeon Guillemots (Cepphus columba; Charadriiformes: Alcidae) breed in small colonies scattered along the North Pacific coastline and feed in shallow nearshore waters year-round. Given their distribution, gene flow is potentially lower and population genetic structure is stronger than in most other high-latitude Northern Hemisphere seabirds. We screened variation in the mitochondrial control region, four microsatellite loci, and two nuclear introns in 202 Pigeon Guillemots representing three of five subspecies. Mitochondrial sequences and nuclear loci both showed significant population differences, although structure was weaker for the nuclear loci. Genetic differentiation was correlated with geographic distance between sampling locations for both the mitochondrial and nuclear loci. Mitochondrial gene trees and demographic modeling both provided strong evidence for two refugial populations during the Pleistocene glaciations: one in the Aleutian Islands and one farther east and south. We conclude that historical fragmentation combined with a stepping-stone model of gene flow led to the relatively strong population differentiation in Pigeon Guillemots compared to other high-latitude Northern Hemisphere seabird species. Our study adds to growing evidence that Pleistocene glaciation events affected population genetic structure not only in terrestrial species but also in coastal marine animals.
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Affiliation(s)
- Bronwyn A. S. Harkness
- Department of BiologyQueen's UniversityKingstonOntarioCanada
- Present address:
Environment and Climate Change Canada, National Wildlife Research CentreOttawaOntarioCanada
| | - Gabriela Ibarguchi
- Department of BiologyQueen's UniversityKingstonOntarioCanada
- Present address:
Red Deer PolytechnicRed DeerAlbertaCanada
| | - Veronica F. Poland
- Department of BiologyQueen's UniversityKingstonOntarioCanada
- Present address:
KambahAustralian Capital TerritoryAustralia
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Zeng ZH, Zhong L, Sun HY, Wu ZK, Wang X, Wang H, Li DZ, Barrett SCH, Zhou W. Parallel evolution of morphological and genomic selfing syndromes accompany the breakdown of heterostyly. THE NEW PHYTOLOGIST 2024; 242:302-316. [PMID: 38214455 DOI: 10.1111/nph.19522] [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: 11/07/2023] [Accepted: 12/18/2023] [Indexed: 01/13/2024]
Abstract
Evolutionary transitions from outcrossing to selfing in flowering plants have convergent morphological and genomic signatures and can involve parallel evolution within related lineages. Adaptive evolution of morphological traits is often assumed to evolve faster than nonadaptive features of the genomic selfing syndrome. We investigated phenotypic and genomic changes associated with transitions from distyly to homostyly in the Primula oreodoxa complex. We determined whether the transition to selfing occurred more than once and investigated stages in the evolution of morphological and genomic selfing syndromes using 22 floral traits and both nuclear and plastid genomic data from 25 populations. Two independent transitions were detected representing an earlier and a more recently derived selfing lineage. The older lineage exhibited classic features of the morphological and genomic selfing syndrome. Although features of both selfing syndromes were less developed in the younger selfing lineage, they exhibited parallel development with the older selfing lineage. This finding contrasts with the prediction that some genomic changes should lag behind adaptive changes to morphological traits. Our findings highlight the value of comparative studies on the timing and extent of transitions from outcrossing to selfing between related lineages for investigating the tempo of morphological and molecular evolution.
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Affiliation(s)
- Zhi-Hua Zeng
- Germplasm Bank of Wild Species, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Li Zhong
- Germplasm Bank of Wild Species, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hua-Ying Sun
- School of Chinese Materia Medica, Yunnan University of Chinese Medicine, Kunming, Yunnan, 650500, China
| | - Zhi-Kun Wu
- Department of Pharmacy, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, 550002, China
| | - Xin Wang
- Germplasm Bank of Wild Species, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Hong Wang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Spencer C H Barrett
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - Wei Zhou
- Germplasm Bank of Wild Species, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
- Lijiang Forest Biodiversity National Observation and Research Station, Kunming Institute of Botany, Chinese Academy of Sciences, Lijiang, Yunnan, 674100, China
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Ascunce MS, Toloza AC, González-Oliver A, Reed DL. Nuclear genetic diversity of head lice sheds light on human dispersal around the world. PLoS One 2023; 18:e0293409. [PMID: 37939041 PMCID: PMC10631634 DOI: 10.1371/journal.pone.0293409] [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: 10/18/2022] [Accepted: 09/26/2023] [Indexed: 11/10/2023] Open
Abstract
The human louse, Pediculus humanus, is an obligate blood-sucking ectoparasite that has coevolved with humans for millennia. Given the intimate relationship between this parasite and the human host, the study of human lice has the potential to shed light on aspects of human evolution that are difficult to interpret using other biological evidence. In this study, we analyzed the genetic variation in 274 human lice from 25 geographic sites around the world by using nuclear microsatellite loci and female-inherited mitochondrial DNA sequences. Nuclear genetic diversity analysis revealed the presence of two distinct genetic clusters I and II, which are subdivided into subclusters: Ia-Ib and IIa-IIb, respectively. Among these samples, we observed the presence of the two most common louse mitochondrial haplogroups: A and B that were found in both nuclear Clusters I and II. Evidence of nuclear admixture was uncommon (12%) and was predominate in the New World potentially mirroring the history of colonization in the Americas. These findings were supported by novel DIYABC simulations that were built using both host and parasite data to define parameters and models suggesting that admixture between cI and cII was very recent. This pattern could also be the result of a reproductive barrier between these two nuclear genetic clusters. In addition to providing new evolutionary knowledge about this human parasite, our study could guide the development of new analyses in other host-parasite systems.
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Affiliation(s)
- Marina S. Ascunce
- Department of Plant Pathology, Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America
- USDA-ARS Center for Medical, Agricultural, and Veterinary Entomology, Gainesville, Florida, United States of America
| | - Ariel C. Toloza
- Centro de Investigaciones de Plagas e Insecticidas (CONICET-UNIDEF), Villa Martelli, Buenos Aires, Argentina
| | - Angélica González-Oliver
- Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - David L. Reed
- Florida Museum of Natural History, University of Florida, Gainesville, Florida, United States of America
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Ramirez JL, Machado CB, de Mello Affonso PRA, Galetti PM. Speciation in Coastal Basins Driven by Staggered Headwater Captures: Dispersal of a Species Complex, Leporinus bahiensis, as Revealed by Genome-wide SNP Data. Syst Biol 2023; 72:973-983. [PMID: 37260367 PMCID: PMC10627554 DOI: 10.1093/sysbio/syad034] [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: 03/03/2022] [Revised: 05/22/2023] [Accepted: 05/30/2023] [Indexed: 06/02/2023] Open
Abstract
Past sea level changes and geological instability along watershed boundaries have largely influenced fish distribution across coastal basins, either by dispersal via palaeodrainages now submerged or by headwater captures, respectively. Accordingly, the South American Atlantic coast encompasses several small and isolated drainages that share a similar species composition, representing a suitable model to infer historical processes. Leporinus bahiensis is a freshwater fish species widespread along adjacent coastal basins over narrow continental shelf with no evidence of palaeodrainage connections at low sea level periods. Therefore, this study aimed to reconstruct its evolutionary history to infer the role of headwater captures in the dispersal process. To accomplish this, we employed molecular-level phylogenetic and population structure analyses based on Sanger sequences (5 genes) and genome-wide SNP data. Phylogenetic trees based on Sanger data were inconclusive, but SNPs data did support the monophyletic status of L. bahiensis. Both COI and SNP data revealed structured populations according to each hydrographic basin. Species delimitation analyses revealed from 3 (COI) to 5 (multilocus approach) MOTUs, corresponding to the sampled basins. An intricate biogeographic scenario was inferred and supported by Approximate Bayesian Computation (ABC) analysis. Specifically, a staggered pattern was revealed and characterized by sequential headwater captures from basins adjacent to upland drainages into small coastal basins at different periods. These headwater captures resulted in dispersal throughout contiguous coastal basins, followed by deep genetic divergence among lineages. To decipher such recent divergences, as herein represented by L. bahiensis populations, we used genome-wide SNPs data. Indeed, the combined use of genome-wide SNPs data and ABC method allowed us to reconstruct the evolutionary history and speciation of L. bahiensis. This framework might be useful in disentangling the diversification process in other neotropical fishes subject to a reticulate geological history.
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Affiliation(s)
- Jorge L Ramirez
- Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Lima, Peru
- Museo de Historia Natural de la Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - Carolina B Machado
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brazil
| | | | - Pedro M Galetti
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brazil
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7
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Jackson AC, White OW, Carine M, Chapman MA. The role of geography, ecology, and hybridization in the evolutionary history of Canary Island Descurainia. AMERICAN JOURNAL OF BOTANY 2023; 110:e16162. [PMID: 36990083 DOI: 10.1002/ajb2.16162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 03/15/2023] [Accepted: 03/15/2023] [Indexed: 05/31/2023]
Abstract
PREMISE Oceanic islands offer the opportunity to understand evolutionary processes underlying rapid diversification. Along with geographic isolation and ecological shifts, a growing body of genomic evidence has suggested that hybridization can play an important role in island evolution. Here we use genotyping-by-sequencing (GBS) to understand the roles of hybridization, ecology, and geographic isolation in the radiation of Canary Island Descurainia (Brassicaceae). METHODS We carried out GBS for multiple individuals of all Canary Island species and two outgroups. Phylogenetic analyses of the GBS data were performed using both supermatrix and gene tree approaches and hybridization events were examined using D-statistics and Approximate Bayesian Computation. Climatic data were analyzed to examine the relationship between ecology and diversification. RESULTS Analysis of the supermatrix data set resulted in a fully resolved phylogeny. Species networks suggest a hybridization event has occurred for D. gilva, with these results being supported by Approximate Bayesian Computation analysis. Strong phylogenetic signals for temperature and precipitation indicate one major ecological shift within Canary Island Descurainia. CONCLUSIONS Inter-island dispersal played a significant role in the diversification of Descurainia, with evidence of only one major shift in climate preferences. Despite weak reproductive barriers and the occurrence of hybrids, hybridization appears to have played only a limited role in the diversification of the group with a single instance detected. The results highlight the need to use phylogenetic network approaches that can simultaneously accommodate incomplete lineage sorting and gene flow when studying groups prone to hybridization; patterns that might otherwise be obscured in species trees.
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Affiliation(s)
- Amy C Jackson
- Biological Sciences, University of Southampton, Southampton, SO17 1BJ, United Kingdom
- Algae, Fungi and Plants Division, Department of Life Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD, United Kingdom
| | - Oliver W White
- Biological Sciences, University of Southampton, Southampton, SO17 1BJ, United Kingdom
- Algae, Fungi and Plants Division, Department of Life Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD, United Kingdom
| | - Mark Carine
- Algae, Fungi and Plants Division, Department of Life Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD, United Kingdom
| | - Mark A Chapman
- Biological Sciences, University of Southampton, Southampton, SO17 1BJ, United Kingdom
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Kaya S, Kabasakal B, Erdoğan A. Geographic Genetic Structure of Alectoris chukar in Türkiye: Post-LGM-Induced Hybridization and Human-Mediated Contaminations. BIOLOGY 2023; 12:biology12030401. [PMID: 36979093 PMCID: PMC10045126 DOI: 10.3390/biology12030401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 02/19/2023] [Accepted: 03/01/2023] [Indexed: 03/06/2023]
Abstract
Türkiye is considered an important evolutionary area for Chukar partridge (Alectoris chukar), since it is both a potential ancestral area and a diversification center for the species. Using 2 mitochondrial (Cty-b and D-loop) and 13 polymorphic microsatellite markers, we investigated the geographic genetic structure of A. chukar populations to determine how past climatic fluctuations and human activities have shaped the gene pool of this species in Türkiye. Our results indicate, firstly, that only A. chukar of the genus Alectoris is present in Türkiye (Anatolia and Thrace), with no natural or artificial gene flow from congenerics. Secondly, the geographic genetic structure of the species in Türkiye has been shaped by topographic heterogeneity, Pleistocene climatic fluctuations, and artificial transport by humans. Third, there appears to be three genetic clusters: Thracian, Eastern, and Western. Fourth, the post-LGM demographic expansion of the Eastern and Western populations has formed a hybrid zone in Central Anatolia (~8 kyBP). Fifth, the rate of China clade-B contamination in Türkiye is about 8% in mtDNA and about 12% in nuDNA, with the Southeastern Anatolian population having the highest contamination. Sixth, the Thracian population was the most genetically distinct, with the lowest genetic diversity and highest level of inbreeding and no China clad-B contamination. These results can contribute to the conservation regarding A. chukar populations, especially the Thracian population.
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Affiliation(s)
- Sarp Kaya
- First and Emergency Aid Programme, Department of Medical Services and Techniques, Vocational School of Burdur Health Services, Burdur Mehmet Akif Ersoy University, Burdur 15030, Turkey
| | - Bekir Kabasakal
- Department of Biology, Akdeniz University, Antalya 07058, Turkey
- Anesthesia Programme, Department of Medical Services and Techniques, Vocational School of Health Services, Antalya Bilim University, Antalya 07190, Turkey
- Correspondence:
| | - Ali Erdoğan
- Department of Biology, Akdeniz University, Antalya 07058, Turkey
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Bilbija B, Spitzweg C, Papoušek I, Fritz U, Földvári G, Mullett M, Ihlow F, Sprong H, Civáňová Křížová K, Anisimov N, Belova OA, Bonnet SI, Bychkova E, Czułowska A, Duscher GG, Fonville M, Kahl O, Karbowiak G, Kholodilov IS, Kiewra D, Krčmar S, Kumisbek G, Livanova N, Majláth I, Manfredi MT, Mihalca AD, Miró G, Moutailler S, Nebogatkin IV, Tomanović S, Vatansever Z, Yakovich M, Zanzani S, Široký P. Dermacentor reticulatus - a tick on its way from glacial refugia to a panmictic Eurasian population. Int J Parasitol 2023; 53:91-101. [PMID: 36549441 DOI: 10.1016/j.ijpara.2022.11.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 10/26/2022] [Accepted: 11/04/2022] [Indexed: 12/23/2022]
Abstract
The ornate dog tick (Dermacentor reticulatus) shows a recently expanding geographic distribution. Knowledge on its intraspecific variability, population structure, rate of genetic diversity and divergence, including its evolution and geographic distribution, is crucial to understand its dispersal capacity. All such information would help to evaluate the potential risk of future spread of associated pathogens of medical and veterinary concern. A set of 865 D. reticulatus ticks was collected from 65 localities across 21 countries, from Portugal in the west to Kazakhstan and southern Russia in the east. Cluster analyses of 16 microsatellite loci were combined with nuclear (ITS2, 18S) and mitochondrial (12S, 16S, COI) sequence data to uncover the ticks' population structures and geographical patterns. Approximate Bayesian computation was applied to model evolutionary relationships among the found clusters. Low variability and a weak phylogenetic signal showing an east-west cline were detected both for mitochondrial and nuclear sequence markers. Microsatellite analyses revealed three genetic clusters, where the eastern and western cluster gradient was supplemented by a third, northern cluster. Alternative scenarios could explain such a tripartite population structure by independent formation of clusters in separate refugia, limited gene flow connected with isolation by distance causing a "bipolar pattern", and the northern cluster deriving from admixture between the eastern and western populations. The best supported demographic scenario of this tick species indicates that the northern cluster derived from admixture between the eastern and western populations 441 (median) to 224 (mode) generations ago, suggesting a possible link with the end of the Little Ice Age in Europe.
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Affiliation(s)
- Branka Bilbija
- Department of Biology and Wildlife Diseases, FVHE, University of Veterinary Sciences Brno, Palackého 1946/1, 61242 Brno, Czech Republic
| | - Cäcilia Spitzweg
- Museum of Zoology, Senckenberg Dresden, A. B. Meyer Building, 01109 Dresden, Germany
| | - Ivo Papoušek
- Department of Biology and Wildlife Diseases, FVHE, University of Veterinary Sciences Brno, Palackého 1946/1, 61242 Brno, Czech Republic
| | - Uwe Fritz
- Museum of Zoology, Senckenberg Dresden, A. B. Meyer Building, 01109 Dresden, Germany
| | - Gábor Földvári
- Institute of Evolution, Centre for Ecological Research, 1121 Budapest, Konkoly-Thege Miklós út 29-33, Hungary; Centre for Eco-Epidemiology, National Laboratory for Health Security, 1121 Budapest, Konkoly-Thege Miklós út 29-33, Hungary
| | - Martin Mullett
- Phytophthora Research Centre, Faculty of Forestry and Wood Technology, Department of Forest Protection and Wildlife Management, Mendel University in Brno, Zemědělská 3, 61300 Brno, Czech Republic
| | - Flora Ihlow
- Museum of Zoology, Senckenberg Dresden, A. B. Meyer Building, 01109 Dresden, Germany
| | - Hein Sprong
- National Institute of Public Health and Environment (RIVM), Centre for Infectious Disease Control (CIb), Laboratory for Zoonoses and Environmental Microbiology (Z&O), Mailbox 63, room V353, Antonie van Leeuwenhoeklaan 9, P.O. Box 1, 3720 BA Bilthoven, The Netherlands
| | - Kristína Civáňová Křížová
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Nikolay Anisimov
- Institute of Environmental and Agricultural Biology (X-BIO), University of Tyumen, Volodarskogo 6, 625003 Tyumen, Russia
| | - Oxana A Belova
- FSASI "Chumakov FSC R&D IBP RAS" (Institute of Poliomyelitis) prem. 8, k.17, pos. Institut Poliomyelita, Poselenie Moskovskiy, 108819 Moscow, Russia
| | - Sarah I Bonnet
- Functional Genetics of Infectious Diseases Unit, Institut Pasteur, CNRS UMR 2000, Université de Paris, 75015 Paris, France; Animal Health Department, INRAE, 37380 Nouzilly, France
| | - Elizabeth Bychkova
- Laboratory of Parasitology, State Scientific and Production Association "Scientific and Practical Center of the National Academy of Sciences of Belarus on Bioresources", 27, Akademicheskaya Str, 220072 Minsk, Belarus
| | - Aleksandra Czułowska
- Department of Microbial Ecology and Acaroentomology, Faculty of Biological Sciences, University of Wroclaw, Przybyszewskiego str. 63, 51-148 Wroclaw, Poland
| | - Georg G Duscher
- Department of Pathobiology, Institute of Parasitology, University of Veterinary Medicine Vienna, Vienna, Austria; AGES-Austrian Agency for Health and Food Safety, Spargelfeldstrasse 191, Vienna, 1220, Austria
| | - Manoj Fonville
- National Institute of Public Health and Environment (RIVM), Centre for Infectious Disease Control (CIb), Laboratory for Zoonoses and Environmental Microbiology (Z&O), Mailbox 63, room V353, Antonie van Leeuwenhoeklaan 9, P.O. Box 1, 3720 BA Bilthoven, The Netherlands
| | - Olaf Kahl
- Tick-radar GmbH, 10555 Berlin, Germany
| | - Grzegorz Karbowiak
- Witold Stefański Institute of Parasitology of Polish Academy of Sciences, Twarda street 51/55, 00-818 Warsaw, Poland
| | - Ivan S Kholodilov
- FSASI "Chumakov FSC R&D IBP RAS" (Institute of Poliomyelitis) prem. 8, k.17, pos. Institut Poliomyelita, Poselenie Moskovskiy, 108819 Moscow, Russia
| | - Dorota Kiewra
- Department of Microbial Ecology and Acaroentomology, Faculty of Biological Sciences, University of Wroclaw, Przybyszewskiego str. 63, 51-148 Wroclaw, Poland
| | - Stjepan Krčmar
- Department of Biology, Josip Juraj Strossmayer University of Osijek, Cara Hadrijana 8/A, HR-31000 Osijek, Croatia
| | - Gulzina Kumisbek
- Asfendiyarov Kazakh National Medical University, School of Pharmacy, Department of Engineering Disciplines, Tole Bi, 94, Almaty, Kazakhstan
| | - Natalya Livanova
- Institute of Systematics and Ecology of Animals, Frunze str. 11, Novosibirsk 630091, Russia
| | - Igor Majláth
- Pavol Jozef Safarik University in Kosice, Faculty of Science, Institute of Biology and Ecology, Department of Animal Physiology, Srobarova 2, 041 54 Kosice, Slovakia
| | - Maria Teresa Manfredi
- Department of Veterinary Medicine and Animal Sciences, Università degli Studi di Milano, via dell'Università 6, 26900 Lodi, Italy
| | - Andrei D Mihalca
- Department of Parasitology and Parasitic Diseases, Faculty of Veterinary Medicine, University of Agricultural Sciences and Veterinary Medicine Cluj-Napoca, Calea Manastur 3-5, Cluj-Napoca 400372, Romania
| | - Guadalupe Miró
- Animal Health Dept. Veterinary School, Universidad Complutense de Madrid, Spain
| | - Sara Moutailler
- Anses, INRAE, Ecole Nationale Vétérinaire d'Alfort, UMR BIPAR, Laboratoire de Santé Animale, Maisons-Alfort, F-94700, France
| | - Igor V Nebogatkin
- I.I. Schmalhausen Institute of Zoology of National Academy of Sciences of Ukraine, Bogdana Khmelnytskovo 15, 01030 Kyiv, Ukraine; Public Health Center of the Ministry of Health of Ukraine, Kyiv, Ukraine
| | - Snežana Tomanović
- University of Belgrade, Institute for Medical Research, National Institute of Republic of Serbia, Dr. Subotića 4, Belgrade, Serbia
| | - Zati Vatansever
- Kafkas University, Faculty of Veterinary Medicine, Dept. of Parasitology, Kars, Turkey
| | - Marya Yakovich
- Laboratory of Parasitology, State Scientific and Production Association "Scientific and Practical Center of the National Academy of Sciences of Belarus on Bioresources", 27, Akademicheskaya Str, 220072 Minsk, Belarus
| | - Sergio Zanzani
- Department of Veterinary Medicine and Animal Sciences, Università degli Studi di Milano, via dell'Università 6, 26900 Lodi, Italy
| | - Pavel Široký
- Department of Biology and Wildlife Diseases, FVHE, University of Veterinary Sciences Brno, Palackého 1946/1, 61242 Brno, Czech Republic; CEITEC-Central European Institute of Technology, University of Veterinary Sciences Brno, Palackého 1946/1, 612 42 Brno, Czech Republic.
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Lin XQ, Hou YM, Yang WZ, Shi SC, Zheng PY, Shih CK, Jiang JP, Xie F, Jiang JP, Xie F. A wide hybrid zone mediated by precipitation contributed to confused geographical structure of Scutiger boulengeri. Zool Res 2023; 44:3-19. [PMID: 36171715 PMCID: PMC9841186 DOI: 10.24272/j.issn.2095-8137.2022.108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Confused geographical structure of a population and mitonuclear discordance are shaped by a combination of rapid changes in population demographics and shifts in ecology. In this study, we generated a time-calibrated phylogeny of Scutiger boulengeri, an endemic Xizang alpine toad occurring in mountain streams on the Qinghai-Xizang (Tibet) Plateau (QTP). Based on three mitochondrial DNA (mtDNA) genes, eight clades were assigned to three deeply divergent lineages. Analysis of nuclear DNA (nuDNA) genes revealed three distinct clusters without geographic structure, indicating significantly high rates of gene flow. Coalescent theory framework analysis (approximate Bayesian computation model DIYABC and Migrate-N) suggested that divergence of the main intraspecific clusters was the result of hybridization after secondary contact in the Holocene around 0.59 million years ago (Ma). The ratio of mtDNA F ST (fixation index) to nuDNA F ST was 2.3, thus failing to show male-biased dispersal. Geographic cline analysis showed that a wide hybrid zone was initially established in southwestern China, without significant reproductive isolation but with strong introgression in S. boulengeri, suggesting high hybrid fitness. Furthermore, mtDNA genes exhibited isolation by distance (IBD) while nuDNA genes exhibited significant isolation by environment (IBE). Results suggested that mitonuclear discordance may have initially been caused by geographic isolation, followed by precipitation-mediated hybridization, producing a wide hybrid zone and geographic structure confusion of nuDNA genes in S. boulengeri. This study indicated that complicated historical processes may have led to specific genetic patterns, with a specific climate factor facilitating gene flow in the system.
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Affiliation(s)
- Xiu-Qin Lin
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization and Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan 610041, China,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yin-Meng Hou
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization and Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan 610041, China,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei-Zhao Yang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization and Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan 610041, China,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Sheng-Chao Shi
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization and Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan 610041, China,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Pu-Yang Zheng
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization and Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan 610041, China,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chung-Kun Shih
- College of Life Sciences, Capital Normal University, Beijing 100048, China,Department of Paleobiology, National Museum of Natural History, Smithsonian Institution, Washington DC 20013–7012, USA
| | - Jian-Ping Jiang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization and Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan 610041, China,University of Chinese Academy of Sciences, Beijing 100049, China,Mangkang Biodiversity and Ecological Station, Xizang Ecological Safety Monitor Network, Changdu, Xizang 854500, China
| | - Feng Xie
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization and Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan 610041, China,University of Chinese Academy of Sciences, Beijing 100049, China,Mangkang Biodiversity and Ecological Station, Xizang Ecological Safety Monitor Network, Changdu, Xizang 854500, China,E-mail:
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Huang L, Feng G, Li D, Shang W, Zhang L, Yan R, Jiang Y, Li S. Genetic variation of endangered Jankowski’s Bunting (Emberiza jankowskii): High connectivity and a moderate history of demographic decline. Front Ecol Evol 2023. [DOI: 10.3389/fevo.2022.996617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
IntroductionContinued discovery of “mismatch” patterns between population size and genetic diversity, involving wild species such as insects, amphibians, birds, mammals, and others, has raised issues about how population history, especially recent dynamics under human disturbance, affects currently standing genetic variation. Previous studies have revealed high genetic diversity in endangered Jankowski’s Bunting. However, it is unclear how the demographic history and recent habitat changes shape the genetic variation of Jankowski’s Bunting.MethodsTo explore the formation and maintenance of high genetic diversity in endangered Jankowski’s Bunting, we used a mitochondrial control region (partial mtDNA CR) and 15 nuclear microsatellite markers to explore the recent demographic history of Jankowski’s Bunting, and we compared the historical and contemporary gene flows between populations to reveal the impact of habitat change on population connectivity. Specifically, we aimed to test the following hypotheses: (1) Jankowski’s Bunting has a large historical Ne and a moderate demographic history; and (2) recent habitat change might have no significant impact on the species’ population connectivity.ResultsThe results suggested that large historical effective population size, as well as severe but slow population decline, may partially explain the high observable genetic diversity. Comparison of historical (over the past 4Ne generations) and contemporary (1–3 generations) gene flow indicated that the connectivity between five local populations was only marginally affected by landscape changes.DiscussionOur results suggest that high population connectivity and a moderate history of demographic decline are powerful explanations for the rich genetic variation in Jankowski’s Bunting. Although there is no evidence that the genetic health of Jankowski’s Bunting is threatened, the time-lag effects on the genetic response to recent environmental changes is a reminder to be cautious about the current genetic characteristics of this species. Where possible, factors influencing genetic variation should be integrated into a systematic framework for conducting robust population health assessments. Given the small contemporary population size, inbreeding, and ecological specialization, we recommend that habitat protection be maintained to maximize the genetic diversity and population connectivity of Jankowski’s Bunting.
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Feng S, Wan W, Li Y, Wang D, Ren G, Ma T, Ru D. Transcriptome-based analyses of adaptive divergence between two closely related spruce species on the Qinghai-Tibet plateau and adjacent regions. Mol Ecol 2023; 32:476-491. [PMID: 36320185 DOI: 10.1111/mec.16758] [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: 04/11/2022] [Revised: 10/07/2022] [Accepted: 10/17/2022] [Indexed: 11/17/2022]
Abstract
Speciation among populations connected by gene flow is driven by adaptation to different environments, but underlying gene-environment associations remain largely unknown. Here, 162 individuals from 32 populations were sampled to obtain 191,648 independent single nucleotide polymorphisms (SNPs) across the genomes of two closely related spruce species, Picea asperata and Picea crassifolia, which occur on the Qinghai-Tibet Plateau and in surrounding regions. Using the SNP data set, genotype-environment associations and demographic modelling were used to examine local adaptation and genetic divergence between these two species. While morphologically similar, the two Picea species were genetically differentiated in multiple analyses. These species diverged despite continuous gene flow, and their initial divergence was dated back to the late Quaternary. The effective population sizes of both species have expanded since their divergence, as confirmed by niche distribution simulations. A total of 6365 genes were associated with the tested environmental variables; of these, 41 were positively selected in P. asperata and were mainly associated with temperature, while 83 were positively selected in P. crassifolia and were primarily associated with precipitation. These results deepen our understanding of the adaptive divergence and demographic histories of these two spruce species and highlight the importance of genomic data in deciphering the environmental selection underlying Quaternary interspecific divergence.
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Affiliation(s)
- Shuo Feng
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China
| | - Wei Wan
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China
| | - Yang Li
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China
| | - DongLei Wang
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Guangpeng Ren
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Tao Ma
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Dafu Ru
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
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Zhang H, Tang Y, Li Q, Zhao S, Zhang Z, Chen Y, Shen Z, Chen C. Genetic and epigenetic variation separately contribute to range expansion and local metalliferous habitat adaptation during invasions of Chenopodium ambrosioides into China. ANNALS OF BOTANY 2022; 130:1041-1056. [PMID: 36413156 PMCID: PMC9851312 DOI: 10.1093/aob/mcac139] [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: 09/21/2022] [Accepted: 11/18/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND AND AIMS Invasive plants often colonize wide-ranging geographical areas with various local microenvironments. The specific roles of epigenetic and genetic variation during such expansion are still unclear. Chenopodium ambrosioides is a well-known invasive alien species in China that can thrive in metalliferous habitats. This study aims to comprehensively understand the effects of genetic and epigenetic variation on the successful invasion of C. ambrosioides. METHODS We sampled 367 individuals from 21 heavy metal-contaminated and uncontaminated sites with a wide geographical distribution in regions of China. We obtained environmental factors of these sampling sites, including 13 meteorological factors and the contents of four heavy metals in soils. Microsatellite markers were used to investigate the demographic history of C. ambrosioides populations in China. We also analysed the effect of epigenetic variation on metalliferous microhabitat adaptation using methylation-sensitive amplified polymorphism (MSAP) markers. A common garden experiment was conducted to compare heritable phenotypic variations among populations. KEY RESULTS Two distinct genetic clusters that diverged thousands of years ago were identified, suggesting that the eastern and south-western C. ambrosioides populations in China may have originated from independent introduction events without recombination. Genetic variation was shown to be a dominant determinant of phenotypic differentiation relative to epigenetic variation, and further affected the geographical distribution pattern of invasive C. ambrosioides. The global DNA unmethylation level was reduced in metalliferous habitats. Dozens of methylated loci were significantly associated with the heavy metal accumulation trait of C. ambrosioides and may contribute to coping with metalliferous microenvironments. CONCLUSIONS Our study of C. ambrosioides highlighted the dominant roles of genetic variation in large geographical range expansion and epigenetic variation in local metalliferous habitat adaptation.
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Affiliation(s)
- Hanchao Zhang
- College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, PR China
| | - Yongwei Tang
- College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, PR China
| | - Quanyuan Li
- College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, PR China
| | - Shangjun Zhao
- College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, PR China
| | - Zhou Zhang
- College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, PR China
| | - Yahua Chen
- College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, PR China
- Jiangsu Collaborative Innovation Centre for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, Jiangsu, PR China
| | - Zhenguo Shen
- College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, PR China
- Jiangsu Collaborative Innovation Centre for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, Jiangsu, PR China
| | - Chen Chen
- College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, PR China
- Jiangsu Collaborative Innovation Centre for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, Jiangsu, PR China
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Kitamura K, Namikawa K, Tsuda Y, Kobayashi M, Matsui T. Possible northern persistence of Siebold's beech, Fagus crenata, at its northernmost distribution limit on an island in Japan Sea: Okushiri Island, Hokkaido. FRONTIERS IN PLANT SCIENCE 2022; 13:990927. [PMID: 36589061 PMCID: PMC9797532 DOI: 10.3389/fpls.2022.990927] [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: 07/11/2022] [Accepted: 11/16/2022] [Indexed: 06/17/2023]
Abstract
Siebold's beech, Fagus crenata, is widely distributed across the Japanese Archipelago and islands in Japan Sea. Similar to the northern limit of the geographical distribution of F. crenata on the mainland of Hokkaido, the northern limit of the distribution of F. crenata on islands in the Japan Sea is observed on Okushiri Island (ca 42°N). To understand the genetic relationships of F. crenata on Okushiri Island, we examined chloroplast (cp) DNA haplotypes and 11 nuclear microsatellite (SSR) loci among 1,838 individuals from 44 populations from Okushiri Island, mainland Hokkaido, and the northern part of the Tohoku region on Honshu Island. We identified 2 cpDNA haplotypes, which represent not only populations on the Japan Sea coast but also those on the Pacific coast and this suggested the Okushiri Island populations might not be formed by single colonization. Genetic diversity of the Okushiri Island populations of nuclear SSR was not lower than the mainland and the STRUCTURE analysis revealed the Okushiri Island individuals were admixed between Hokkaido and Tohoku clusters. Approximate Bayesian computation inferred that divergence between Tohoku and Hokkaido, and admixture between two populations which generated Okushiri populations occurred before the last glacial maximum (LGM), that is, 7,890 (95% hyper probability density (HPD): 3,420 - 9,910) and 3,870 (95% HPD: 431- 8,540) generations ago, respectively. These inferences were well supported by a geological history which suggested an isolation of Okushiri Island from Hokkaido started prior to the Middle Pleistocene. We discuss the possible persistence of F. crenata during the last glacial maximum on northern islands in the Japan Sea such as Okushiri Island.
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Affiliation(s)
- Keiko Kitamura
- Hokkaido Research Centre, Forestry and Forest Products Research Institute, Sapporo, Japan
| | - Kanji Namikawa
- Biological Laboratory, Hokkaido University of Education, Sapporo, Japan
| | - Yoshiaki Tsuda
- Sugadaira Montane Research Center, University of Tsukuba, Ueda, Japan
| | - Makoto Kobayashi
- Department of Education and Culture, Echigo-Matsunoyama Museum of Natural Science, Tokamachi, Japan
| | - Tetsuya Matsui
- Center of Biodiversity and Climate Change, Forestry and Forest Products Research Institute, Tsukuba, Japan
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
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Maturana CS, Biersma EM, Díaz A, González-Wevar C, Contador T, Convey P, Jackson JA, Poulin E. Survivors and colonizers: Contrasting biogeographic histories reconciled in the Antarctic freshwater copepod Boeckella poppei. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.1012852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Two main hypotheses have been proposed to explain the contemporary distribution of Antarctic terrestrial biota. We assess whether the current distribution of maritime Antarctic populations of the freshwater copepod Boeckella poppei is the result of (1) a post-Last Glacial Maximum (LGM) colonization, or whether (2) the species survived in regional glacial refugia throughout the LGM and earlier glaciations. Using 438 specimens from 34 different sampling sites across Southern South America, South Georgia, South Orkney Islands, South Shetland Islands, and the Antarctic Peninsula, we analyzed mitochondrial and nuclear sequences to uncover patterns of genetic diversity and population structure. We also performed median-joining haplotype network, phylogenetic reconstruction, and divergence time analyses. Finally, we evaluated past demographic changes and historical scenarios using the Approximate Bayesian Computation (ABC) method. Our data support the existence of two clades with different and contrasting biogeographic histories. The first clade has been present in maritime Antarctica since at least the mid-Pleistocene, with the South Orkney Islands the most likely refugial area. The second clade has a broader distribution including southern South America, South Georgia, South Shetland Islands, and the Antarctic Peninsula. The ABC method identified long-distance dispersal (LDD) colonization event(s) from southern South America to South Georgia and the maritime Antarctic after the LGM deglaciation, supporting more recent colonization of Antarctic locations. The current Antarctic and sub-Antarctic distribution of B. poppei is likely derived from two independent biogeographic events. The combination of both (1) post-LGM colonization from southern South America and (2) longer-term persistence in in situ regional refugia throughout glacial periods challenges current understanding of the biogeographic history of Antarctic freshwater biota. Re-colonization of ice-impacted Antarctic areas would have occurred following a LDD and Establishment model, pointing to the existence of possible post-dispersal barriers, despite widely assumed high passive dispersal capacity in freshwater invertebrates.
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AKesson M, Singh P, Wrede F, Hellander A. Convolutional Neural Networks as Summary Statistics for Approximate Bayesian Computation. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2022; 19:3353-3365. [PMID: 34460381 PMCID: PMC9847490 DOI: 10.1109/tcbb.2021.3108695] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Approximate Bayesian Computation is widely used in systems biology for inferring parameters in stochastic gene regulatory network models. Its performance hinges critically on the ability to summarize high-dimensional system responses such as time series into a few informative, low-dimensional summary statistics. The quality of those statistics acutely impacts the accuracy of the inference task. Existing methods to select the best subset out of a pool of candidate statistics do not scale well with large pools of several tens to hundreds of candidate statistics. Since high quality statistics are imperative for good performance, this becomes a serious bottleneck when performing inference on complex and high-dimensional problems. This paper proposes a convolutional neural network architecture for automatically learning informative summary statistics of temporal responses. We show that the proposed network can effectively circumvent the statistics selection problem of the preprocessing step for ABC inference. The proposed approach is demonstrated on two benchmark problem and one challenging inference problem learning parameters in a high-dimensional stochastic genetic oscillator. We also study the impact of experimental design on network performance by comparing different data richness and data acquisition strategies.
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Aushev A, Pesonen H, Heinonen M, Corander J, Kaski S. Likelihood-free inference with deep Gaussian processes. Comput Stat Data Anal 2022. [DOI: 10.1016/j.csda.2022.107529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Kim H, Rodriguez-Saona C, Lee HS. Population Genetics of the Blueberry Gall Midge, Dasineura oxycoccana (Diptera: Cecidomyiidae), on Blueberry and Cranberry and Testing Invasion Scenarios. INSECTS 2022; 13:880. [PMID: 36292830 PMCID: PMC9604482 DOI: 10.3390/insects13100880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 09/16/2022] [Accepted: 09/25/2022] [Indexed: 06/16/2023]
Abstract
We compared the population genetic structure between populations of the blueberry gall midge-Dasineura oxycoccana (Johnson) (Diptera: Cecidomyiidae)-from blueberry and cranberry and determined the genetic relationships among geographical subgroups by genotyping 632 individuals from 31 different populations from their native USA regions (New Jersey, Michigan, and Georgia) and from invaded Korean regions using 12 microsatellite loci. Our population genetic analyses showed a clear separation between the two host-associated D. oxycoccana populations from blueberry and cranberry. Using data from only the blueberry-associated D. oxycoccana populations, we identified five genetically isolated subgroups. An analysis of the approximate Bayesian computation suggests that the invasive D. oxycoccana population from Korea appears to have been introduced from an unsampled source population rather than directly from its native range. Our findings will allow for an easier identification of the source of D. oxycoccana into newly invaded regions, as well as to determine their association with blueberry and cranberry, which based on our results can be considered as two distinct species.
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Affiliation(s)
- Hyojoong Kim
- Animal Systematics Laboratory, Department of Biological Science, Kunsan National University, Gunsan 54150, Korea
| | - Cesar Rodriguez-Saona
- Department of Entomology, P.E. Marucci Center, Rutgers University, Chatsworth, NJ 08019, USA
| | - Heung-Sik Lee
- Animal & Plant Quarantine Agency, Gimcheon 39660, Korea
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Zorrilla-Azcué S, González-Rodríguez A, Oyama K, González MA, Rodríguez-Correa H. Response to: A paleoecological context to assess the development of oak forest in Colombia: A comment on Zorrilla-Azcué, S., González-Rodríguez, A., Oyama, K., González, M.A. & Rodríguez-Correa, H., The DNA history of a lonely oak: Quercus humboldtii phylogeography in the Colombian Andes. Ecology and Evolution 2021, doi:10.1002/ece3.7529. Ecol Evol 2022; 12:e9271. [PMID: 36110879 PMCID: PMC9465396 DOI: 10.1002/ece3.9271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Revised: 07/04/2022] [Accepted: 07/15/2022] [Indexed: 11/29/2022] Open
Abstract
In this response, we address comments and clarify the rationale behind the choice of hypotheses aimed to describe the Quercus humboldtii phylogeography in the Colombian Andes. Finally, we explain our disagreement with the conclusions of a previous critique, since these are not necessarily adequate under the implemented population genetics approach.
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Affiliation(s)
- Sofía Zorrilla-Azcué
- Universidad Nacional Autónoma de México Morelia Mexico.,Posgrado en Ciencias Biológicas Universidad Nacional Autónoma de México, Unidad de Posgrado, Circuito de Posgrados, Ciudad Universitaria Ciudad de México Mexico
| | | | - Ken Oyama
- Universidad Nacional Autónoma de México Morelia Mexico
| | - Mailyn A González
- Laboratorio de Genética de la Conservación Instituto de Investigación de Recursos Biológicos Alexander von Humboldt Bogotá Colombia
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Molecular insights into the invasion dynamics of Carcinus crabs in South Africa. Biol Invasions 2022. [DOI: 10.1007/s10530-022-02865-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
AbstractKnowledge of the introduction history and spread dynamics of invasive species can provide important insights for management (Ens et al. in Environ Rev (in press), 2022), however such information is often unavailable for accidental introductions. Here we infer how the European shore crab, Carcinus maenas, and its congener, the Mediterranean shore crab, C. aestuarii, were introduced to and spread within South Africa. We do this using nuclear microsatellite data and Bayesian assignment tests and Approximate Bayesian Computation (ABC) modelling that included samples from the native and other invasive ranges of these two species. We also compared the genetic diversity and structure of one of the South African populations during and after intensive management, with that of another, unmanaged, population. South African populations had higher genetic diversity than invasive Carcinus populations from elsewhere in the world. Moreover, the ABC analyses suggest that South African populations originated from an admixture event between individuals of C. maenas from a population in the native range and an invasive population from Canada. We also identified instances of hybridisation between Carcinus maenas and C. aestuarii in South Africa. South African populations showed no genetic structure, suggesting either extensive migration between them or that populations arose from the same initial introduction. Management of Carcinus did not affect genetic diversity or structure, and we suspect that the management duration was insufficient to target a full generation of crabs. Together these results suggest multiple introductions and/or high propagule pressure to South Africa, crab (larval or adult) movement between existing populations, and some hybridisation. For eradication from South Africa to be achieved, management would need to concurrently target all known invasive populations and clearly establish that new introductions could be prevented.
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21
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Encinas‐Viso F, Morin L, Sathyamurthy R, Knerr N, Roux C, Broadhurst L. Population genomics reveal multiple introductions and admixture of
Sonchus oleraceus
in Australia. DIVERS DISTRIB 2022. [DOI: 10.1111/ddi.13597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Affiliation(s)
- Francisco Encinas‐Viso
- Centre for Australian National Biodiversity Research Commonwealth Scientific and Industrial Research Organisation (CSIRO) Canberra Australian Capital Territory Australia
| | - Louise Morin
- CSIRO Health and Biosecurity Canberra Australian Capital Territory Australia
| | | | - Nunzio Knerr
- Centre for Australian National Biodiversity Research Commonwealth Scientific and Industrial Research Organisation (CSIRO) Canberra Australian Capital Territory Australia
| | - Camille Roux
- UMR 8198 – Evo‐Eco‐Paleo CNRS – Univ Lille Lille France
| | - Linda Broadhurst
- Centre for Australian National Biodiversity Research Commonwealth Scientific and Industrial Research Organisation (CSIRO) Canberra Australian Capital Territory Australia
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22
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Wang G, Lai H, Bi S, Guo D, Zhao X, Chen X, Liu S, Liu X, Su Y, Yi H, Li G. ddRAD‐Seq
reveals evolutionary insights into population differentiation and the cryptic phylogeography of
Hyporhamphus intermedius
in Mainland China. Ecol Evol 2022; 12:e9053. [PMID: 35813915 PMCID: PMC9251877 DOI: 10.1002/ece3.9053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 05/28/2022] [Accepted: 06/08/2022] [Indexed: 11/12/2022] Open
Abstract
Species differentiation and local adaptation in heterogeneous environments have attracted much attention, although little is known about the mechanisms involved. Hyporhamphus intermedius is an anadromous, brackish‐water halfbeak that is widely distributed in coastal areas and hyperdiverse freshwater systems in China, making it an interesting model for research on phylogeography and local adaptation. Here, 156 individuals were sampled at eight sites from heterogeneous aquatic habitats to examine environmental and genetic contributions to phenotypic divergence. Using double‐digest restriction‐site‐associated DNA sequencing (ddRAD‐Seq) in the specimens from the different watersheds, 5498 single nucleotide polymorphisms (SNPs) were found among populations, with obvious population differentiation. We find that present‐day Mainland China populations are structured into distinct genetic clusters stretching from southern and northern ancestries, mirroring geography. Following a transplant event in Plateau Lakes, there were virtually no variations of genetic diversity occurred in two populations, despite the fact two main splits were unveiled in the demographic history. Additionally, dorsal, and anal fin traits varied widely between the southern group and the others, which highlighted previously unrecognized lineages. We then explore genotype–phenotype‐environment associations and predict candidate loci. Subgroup ranges appeared to correspond to geographic regions with heterogeneous hydrological factors, indicating that these features are likely important drivers of diversification. Accordingly, we conclude that genetic and phenotypic polymorphism and a moderate amount of genetic differentiation occurred, which might be ascribed to population subdivision, and the impact of abiotic factors.
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Affiliation(s)
- Gongpei Wang
- Guangdong Province Key Laboratory for Aquatic Economic Animals State Key Laboratory of Biocontrol School of Life Sciences Sun Yat‐Sen University Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) Guangzhou China
- State Key Laboratory of Ophthalmology Zhongshan Ophthalmic Center Sun Yat‐Sen University Guangzhou China
- Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish Guangzhou China
| | - Han Lai
- Guangdong Province Key Laboratory for Aquatic Economic Animals State Key Laboratory of Biocontrol School of Life Sciences Sun Yat‐Sen University Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) Guangzhou China
- Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish Guangzhou China
| | - Sheng Bi
- Guangdong Province Key Laboratory for Aquatic Economic Animals State Key Laboratory of Biocontrol School of Life Sciences Sun Yat‐Sen University Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) Guangzhou China
- Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish Guangzhou China
| | - Dingli Guo
- Guangdong Province Key Laboratory for Aquatic Economic Animals State Key Laboratory of Biocontrol School of Life Sciences Sun Yat‐Sen University Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) Guangzhou China
- Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish Guangzhou China
| | - Xiaopin Zhao
- Guangdong Province Key Laboratory for Aquatic Economic Animals State Key Laboratory of Biocontrol School of Life Sciences Sun Yat‐Sen University Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) Guangzhou China
- Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish Guangzhou China
| | - Xiaoli Chen
- Guangdong Province Key Laboratory for Aquatic Economic Animals State Key Laboratory of Biocontrol School of Life Sciences Sun Yat‐Sen University Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) Guangzhou China
- Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish Guangzhou China
| | - Shuang Liu
- Guangdong Province Key Laboratory for Aquatic Economic Animals State Key Laboratory of Biocontrol School of Life Sciences Sun Yat‐Sen University Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) Guangzhou China
- Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish Guangzhou China
| | - Xuange Liu
- Guangdong Province Key Laboratory for Aquatic Economic Animals State Key Laboratory of Biocontrol School of Life Sciences Sun Yat‐Sen University Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) Guangzhou China
- Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish Guangzhou China
| | - Yuqin Su
- Guangdong Province Key Laboratory for Aquatic Economic Animals State Key Laboratory of Biocontrol School of Life Sciences Sun Yat‐Sen University Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) Guangzhou China
- Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish Guangzhou China
| | - Huadong Yi
- Guangdong Province Key Laboratory for Aquatic Economic Animals State Key Laboratory of Biocontrol School of Life Sciences Sun Yat‐Sen University Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) Guangzhou China
- Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish Guangzhou China
| | - Guifeng Li
- Guangdong Province Key Laboratory for Aquatic Economic Animals State Key Laboratory of Biocontrol School of Life Sciences Sun Yat‐Sen University Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) Guangzhou China
- Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish Guangzhou China
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23
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Assessing the Genetic Identity of Tuscan Sweet Chestnut (Castanea sativa Mill.). FORESTS 2022. [DOI: 10.3390/f13070967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The sweet chestnut (Castanea sativa Mill.) is an important species of European trees, studied for both ecological and economic reasons. Its cultivation in the Italian peninsula can be linked to the Roman period and has been documented, especially in the Tuscan region, for centuries. We sampled 131 grafted trees from three separate areas to determine the genetic variability between populations and assess genetic identity for different varieties of trees, which is useful for future breeding programs and propagation efforts. Molecular analyses were performed using eight microsatellite loci. A total of 98 alleles was detected with an average of 12.3 alleles per locus. We found high levels of genetic diversity within the varieties of the same area, ranging between He = 0.682–0.745. Of the eight loci, seven were found to be at Hardy-Weinberg equilibrium. (FST values Differentiation between cultivation areas was significant between 0.052–0.147) with the two Southern Tuscan areas showing the closest relationship as also indicated by Bayesian inference of the population structure, which revealed the existence of three ancestral gene pools of origin. Demographic events were detected by a coalescent-based approximate Bayesian computation in two of the homogeneous clusters. This work is a step forward for the conservation of this iconic species, albeit at a regional level, as chestnut varieties have never received the full attention of breeders.
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24
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Tsumura Y. Genetic structure and local adaptation in natural forests of
Cryptomeria japonica
. Ecol Res 2022. [DOI: 10.1111/1440-1703.12320] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Yoshihiko Tsumura
- Faculty of Life and Environmental Sciences University of Tsukuba Tsukuba Ibaraki Japan
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25
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Konstantinidis I, Gkafas GA, Papathanasiou V, Orfanidis S, Küpper FC, Arnaud-Haond S, Exadactylos A. Biogeography pattern of the marine angiosperm Cymodocea nodosa in the eastern Mediterranean Sea related to the quaternary climatic changes. Ecol Evol 2022; 12:e8911. [PMID: 35646317 PMCID: PMC9131598 DOI: 10.1002/ece3.8911] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 04/19/2022] [Accepted: 04/21/2022] [Indexed: 11/07/2022] Open
Abstract
We investigated the population dynamics of a highly clonal marine angiosperm, Cymodocea nodosa, in the eastern Mediterranean Sea, to identify the historical dynamics, demography, and connectivity of the species in the area. Eighteen microsatellite loci were used in conjunction with coalescent methods to investigate the genetic structure and demographic history of C. nodosa meadows. Approximate Bayesian computation (ABC) modeling was used to examine the pattern of divergence over time in the context of environmental change over the course of the Quaternary period. ABC analysis revealed an initial split of the C. nodosa populations between the north-western, northern, and north-eastern Aegean Sea during the Pleistocene epoch, followed by a more recent divergence of the north-western population and the central-western part of the Aegean Sea. According to the results, the most parsimonious historical scenario is that of a pervasive genetic signature of the effects of the drop in sea level during the Pleistocene epoch. This scenario supports the isolation of the north-western, north, and north-eastern area, and the subsequent recolonization after post-glaciation sea level rise that may explain the north-western differentiation as well present-day detected dispersion of C. nodosa.
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Affiliation(s)
- Ioannis Konstantinidis
- Genomics Division Faculty of Biosciences and Aquaculture Nord University Bodø Norway.,Department of Ichthyology and Aquatic Environment School of Agricultural Sciences University of Thessaly Volos Greece
| | - Georgios A Gkafas
- Department of Ichthyology and Aquatic Environment School of Agricultural Sciences University of Thessaly Volos Greece
| | | | | | - Frithjof C Küpper
- School of Biological Sciences University of Aberdeen Aberdeen UK.,Department of Chemistry Marine Biodiscovery Centre University of Aberdeen Aberdeen UK
| | - Sophie Arnaud-Haond
- Ifremer UMR MARBEC (Marine Biodiversity, Exploitation and Conservation) Sète Cedex France
| | - Athanasios Exadactylos
- Department of Ichthyology and Aquatic Environment School of Agricultural Sciences University of Thessaly Volos Greece
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26
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Darwell CT, Wanchana S, Ruanjaichon V, Siangliw M, Thunnom B, Aesomnuk W, Toojinda T. riceExplorer: Uncovering the Hidden Potential of a National Genomic Resource Against a Global Database. FRONTIERS IN PLANT SCIENCE 2022; 13:781153. [PMID: 35574109 PMCID: PMC9100803 DOI: 10.3389/fpls.2022.781153] [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: 09/22/2021] [Accepted: 04/06/2022] [Indexed: 06/15/2023]
Abstract
Agricultural crop breeding programs, particularly at the national level, typically consist of a core panel of elite breeding cultivars alongside a number of local landrace varieties (or other endemic cultivars) that provide additional sources of phenotypic and genomic variation or contribute as experimental materials (e.g., in GWAS studies). Three issues commonly arise. First, focusing primarily on core development accessions may mean that the potential contributions of landraces or other secondary accessions may be overlooked. Second, elite cultivars may accumulate deleterious alleles away from nontarget loci due to the strong effects of artificial selection. Finally, a tendency to focus solely on SNP-based methods may cause incomplete or erroneous identification of functional variants. In practice, integration of local breeding programs with findings from global database projects may be challenging. First, local GWAS experiments may only indicate useful functional variants according to the diversity of the experimental panel, while other potentially useful loci-identifiable at a global level-may remain undiscovered. Second, large-scale experiments such as GWAS may prove prohibitively costly or logistically challenging for some agencies. Here, we present a fully automated bioinformatics pipeline (riceExplorer) that can easily integrate local breeding program sequence data with international database resources, without relying on any phenotypic experimental procedure. It identifies associated functional haplotypes that may prove more robust in determining the genotypic determinants of desirable crop phenotypes. In brief, riceExplorer evaluates a global crop database (IRRI 3000 Rice Genomes) to identify haplotypes that are associated with extreme phenotypic variation at the global level and recorded in the database. It then examines which potentially useful variants are present in the local crop panel, before distinguishing between those that are already incorporated into the elite breeding accessions and those only found among secondary varieties (e.g., landraces). Results highlight the effectiveness of our pipeline, identifying potentially useful functional haplotypes across the genome that are absent from elite cultivars and found among landraces and other secondary varieties in our breeding program. riceExplorer can automatically conduct a full genome analysis and produces annotated graphical output of chromosomal maps, potential global diversity sources, and summary tables.
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27
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Lyman RA, Edwards CE. Revisiting the comparative phylogeography of unglaciated eastern North America: 15 years of patterns and progress. Ecol Evol 2022; 12:e8827. [PMID: 35475178 PMCID: PMC9019306 DOI: 10.1002/ece3.8827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 03/17/2022] [Accepted: 03/18/2022] [Indexed: 11/28/2022] Open
Abstract
In a landmark comparative phylogeographic study, “Comparative phylogeography of unglaciated eastern North America,” Soltis et al. (Molecular Ecology, 2006, 15, 4261) identified geographic discontinuities in genetic variation shared across taxa occupying unglaciated eastern North America and proposed several common biogeographical discontinuities related to past climate fluctuations and geographic barriers. Since 2006, researchers have published many phylogeographical studies and achieved many advances in genotyping and analytical techniques; however, it is unknown how this work has changed our understanding of the factors shaping the phylogeography of eastern North American taxa. We analyzed 184 phylogeographical studies of eastern North American taxa published between 2007 and 2019 to evaluate: (1) the taxonomic focus of studies and whether a previously detected taxonomic bias towards studies focused on vertebrates has changed over time, (2) the extent to which studies have adopted genotyping technologies that improve the resolution of genetic groups (i.e., NGS DNA sequencing) and analytical approaches that facilitate hypothesis‐testing (i.e., divergence time estimation and niche modeling), and (3) whether new studies support the hypothesized biogeographic discontinuities proposed by Soltis et al. (Molecular Ecology, 2006, 15, 4261) or instead support new, previously undetected discontinuities. We observed little change in taxonomic focus over time, with studies still biased toward vertebrates. Although many technological and analytical advances became available during the period, uptake was slow and they were employed in only a small proportion of studies. We found variable support for previously identified discontinuities and identified one new recurrent discontinuity. However, the limited resolution and taxonomic breadth of many studies hindered our ability to clarify the most important climatological or geographical factors affecting taxa in the region. Broadening the taxonomic focus to include more non‐vertebrate taxa, employing technologies that improve genetic resolution, and using analytical approaches that improve hypothesis testing are necessary to strengthen our inference of the forces shaping the phylogeography of eastern North America.
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Affiliation(s)
- Rachel Ann Lyman
- Ecology, Evolution, and Population Biology Program Washington University in St. Louis St. Louis Missouri USA
- Center for Conservation and Sustainable Development Missouri Botanical Garden St. Louis Missouri USA
| | - Christine E. Edwards
- Center for Conservation and Sustainable Development Missouri Botanical Garden St. Louis Missouri USA
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28
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Conservation genetics of Firmiana major, a threatened tree species with potential for afforestation of hot, arid climates. Glob Ecol Conserv 2022. [DOI: 10.1016/j.gecco.2022.e02136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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29
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Rosetti N, Krohling D, Remis MI. Evolutionary history and colonization patterns of the wing dimorphic grasshopper Dichroplus vittatus in two Argentinean biomes. Sci Rep 2022; 12:2920. [PMID: 35190570 PMCID: PMC8861051 DOI: 10.1038/s41598-022-05162-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 12/30/2021] [Indexed: 12/03/2022] Open
Abstract
Quaternary climate oscillations and modification of the environment by humans have played an important role in shaping species distribution and genetic structure of modern species. Here, population genetic parameters were inferred from the analysis of 168 individuals belonging to 11 populations of the South American grasshopper, Dichroplus vittatus, distributed in two Argentinean Biomes (Grassland and Savanna), by sequencing a 543 bp of the mitochondrial COI gene. Overall, we detected considerable haplotype diversity and low nucleotide diversity. AMOVA analyses showed a significant degree of differentiation among Biomes and between populations. Two major mitochondrial lineages can be distinguished. The haplogroup containing the most common haplotype split 17,000 years BP while the haplogroup including the second most common haplotype has a divergence date of about 11,700 years. Approximate Bayesian Computation (ABC) analyses showed that the palaeodemographic scenario that best fitted our data is consistent with a hypothesis of divergence from an ancestral population and subsequent admixture with Grassland-Savanna (South–North) direction. Our results suggest that populations located in both Biomes would derive from a single ancestral population that colonized the region after the Last Glacial Maximum and Grassland would have a more ancestral origin than Savanna. Further, our results emphasize the importance of human-mediated dispersal in the reconfiguration of genetic diversity of species with potential pest capacity.
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30
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Origin, Persistence, and Vulnerability to Climate Changes of Podocarpus Populations in Central African Mountains. FORESTS 2022. [DOI: 10.3390/f13020208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Background and objectives—Podocarpus latifolius (synonym of P. milanjianus) is a key tree representative of Afromontane forests where it is highly threatened by climate and land-use changes. While large populations occur in East Africa, only a few isolated and usually small populations remain in western Central Africa (Cameroon to Angola). Studying the evolutionary history of such relictual populations can thus be relevant to understand their resilience under changing environments. Materials and Methods—we developed nine polymorphic nuclear microsatellites (nSSRs) to estimate genetic variability, (historical) gene flow, and demographic changes among natural populations from Central to East Africa. Results—despite the extended distribution range of P. latifolius, a strong isolation-by-distance pattern emerges at the intra-population scale, indicating low seed and pollen dispersal capacities. Central African populations display a lower genetic diversity (He = 0.34 to 0.61) and are more differentiated from each other (FST = 0.28) than are East African populations (He = 0.65 to 0.71; FST = 0.10), suggesting high genetic drift in the Central African populations. Spatial genetic structure reveals past connections between East and West Africa but also a gene flow barrier across the equator in western Central Africa. Demographic modelling anchors the history of current lineages in the Pleistocene and supports a strong demographic decline in most western populations during the last glacial period. By contrast, no signature of demographic change was detected in East African populations. Conclusions—in Cameroon, our results exclude a recent (re)colonization from one source population of all mountain ranges, but rather indicate long-term persistence of populations in each mountain with fluctuating sizes. A higher impact of genetic drift and further loss of diversity can be expected by survival through climatically unfavorable periods in such small refugial populations. Tracking the Quaternary legacy of podocarp populations is thus essential for their conservation since there is a temporal gap between environment crises and an ecological/genetic answer at the population level.
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31
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Baumdicker F, Bisschop G, Goldstein D, Gower G, Ragsdale AP, Tsambos G, Zhu S, Eldon B, Ellerman EC, Galloway JG, Gladstein AL, Gorjanc G, Guo B, Jeffery B, Kretzschmar WW, Lohse K, Matschiner M, Nelson D, Pope NS, Quinto-Cortés CD, Rodrigues MF, Saunack K, Sellinger T, Thornton K, van Kemenade H, Wohns AW, Wong Y, Gravel S, Kern AD, Koskela J, Ralph PL, Kelleher J. Efficient ancestry and mutation simulation with msprime 1.0. Genetics 2021; 220:6460344. [PMID: 34897427 PMCID: PMC9176297 DOI: 10.1093/genetics/iyab229] [Citation(s) in RCA: 84] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 12/03/2021] [Indexed: 11/13/2022] Open
Abstract
Stochastic simulation is a key tool in population genetics, since the models involved are often analytically intractable and simulation is usually the only way of obtaining ground-truth data to evaluate inferences. Because of this, a large number of specialized simulation programs have been developed, each filling a particular niche, but with largely overlapping functionality and a substantial duplication of effort. Here, we introduce msprime version 1.0, which efficiently implements ancestry and mutation simulations based on the succinct tree sequence data structure and the tskit library. We summarize msprime’s many features, and show that its performance is excellent, often many times faster and more memory efficient than specialized alternatives. These high-performance features have been thoroughly tested and validated, and built using a collaborative, open source development model, which reduces duplication of effort and promotes software quality via community engagement.
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Affiliation(s)
- Franz Baumdicker
- Cluster of Excellence "Controlling Microbes to Fight Infections", Mathematical and Computational Population Genetics, University of Tübingen, 72076 Tübingen, Germany
| | - Gertjan Bisschop
- Institute of Evolutionary Biology,The University of Edinburgh, EH9 3FL, UK
| | - Daniel Goldstein
- Khoury College of Computer Sciences, Northeastern University, MA 02115, USA.,No affiliation
| | - Graham Gower
- Lundbeck GeoGenetics Centre, Globe Institute, University of Copenhagen, 1350 Copenhagen K, Denmark
| | - Aaron P Ragsdale
- Department of Integrative Biology, University of Wisconsin-Madison, WI 53706, USA
| | - Georgia Tsambos
- Melbourne Integrative Genomics, School of Mathematics and Statistics, University of Melbourne, Victoria, 3010, Australia
| | - Sha Zhu
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, OX3 7LF, UK
| | - Bjarki Eldon
- Leibniz Institute for Evolution and Biodiversity Science,Museum für Naturkunde Berlin, 10115, Germany
| | | | - Jared G Galloway
- Institute of Ecology and Evolution, Department of Biology, University of Oregon, OR 97403-5289, USA.,Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98102, USA
| | - Ariella L Gladstein
- Department of Genetics, University of North Carolina at Chapel Hill, NC 27599-7264, USA.,Embark Veterinary, Inc., Boston, MA 02111, USA
| | - Gregor Gorjanc
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, EH25 9RG, UK
| | - Bing Guo
- Institute for Genome Sciences,University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Ben Jeffery
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, OX3 7LF, UK
| | - Warren W Kretzschmar
- Center for Hematology and Regenerative Medicine, Karolinska Institute, 141 83 Huddinge, Sweden
| | - Konrad Lohse
- Institute of Evolutionary Biology,The University of Edinburgh, EH9 3FL, UK
| | | | - Dominic Nelson
- Department of Human Genetics, McGill University, Montréal, QC H3A 0C7, Canada
| | - Nathaniel S Pope
- Department of Entomology, Pennsylvania State University, PA 16802, USA
| | - Consuelo D Quinto-Cortés
- National Laboratory of Genomics for Biodiversity (LANGEBIO), Unit of Advanced Genomics, CINVESTAV, Irapuato, Mexico
| | - Murillo F Rodrigues
- Institute of Ecology and Evolution, Department of Biology, University of Oregon, OR 97403-5289, USA
| | - Kumar Saunack
- IIT Bombay, Powai, Mumbai 400 076, Maharashtra, India
| | - Thibaut Sellinger
- Professorship for Population Genetics, Department of Life Science Systems, Technical University of Munich, 85354 Freising, Germany
| | - Kevin Thornton
- Ecology and Evolutionary Biology, University of California, Irvine, CA 92697, USA
| | | | - Anthony W Wohns
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, OX3 7LF, UK.,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Yan Wong
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, OX3 7LF, UK
| | - Simon Gravel
- Department of Human Genetics, McGill University, Montréal, QC H3A 0C7, Canada
| | - Andrew D Kern
- Institute of Ecology and Evolution, Department of Biology, University of Oregon, OR 97403-5289, USA
| | - Jere Koskela
- Department of Statistics, University of Warwick, CV4 7AL, UK
| | - Peter L Ralph
- Institute of Ecology and Evolution, Department of Biology, University of Oregon, OR 97403-5289, USA.,Department of Mathematics, University of Oregon, OR 97403-5289 USA
| | - Jerome Kelleher
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, OX3 7LF, UK
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32
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Bi J, Shen W, Zhu W. Random Forest Adjustment for Approximate Bayesian Computation. J Comput Graph Stat 2021. [DOI: 10.1080/10618600.2021.1981341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Jiefeng Bi
- Wang Yanan Institute for Studies in Economics (WISE), Xiamen University, Xiamen, China
| | - Weining Shen
- Department of Statistics, University of California, Irvine, CA
| | - Weixuan Zhu
- Wang Yanan Institute for Studies in Economics (WISE), Department of Statistics and Data Science, School of Economics, Xiamen University, Xiamen, China
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33
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Zhao Z, Oosthuizen J, Heideman N. How many species does the
Psammobates tentorius
(tent tortoise) species complex (Reptilia, Testudinidae) comprise? A taxonomic solution potentially applicable to species complexes. J ZOOL SYST EVOL RES 2021. [DOI: 10.1111/jzs.12525] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Zhongning Zhao
- Department of Zoology and Entomology University of the Free State Bloemfontein South Africa
| | - Jaco Oosthuizen
- School of Pathology University of the Free Bloemfontein South Africa
| | - Neil Heideman
- Department of Zoology and Entomology University of the Free State Bloemfontein South Africa
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34
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Kidner J, Theodorou P, Engler JO, Taubert M, Husemann M. A brief history and popularity of methods and tools used to estimate micro-evolutionary forces. Ecol Evol 2021; 11:13723-13743. [PMID: 34707813 PMCID: PMC8525119 DOI: 10.1002/ece3.8076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 07/12/2021] [Accepted: 08/12/2021] [Indexed: 11/30/2022] Open
Abstract
Population genetics is a field of research that predates the current generations of sequencing technology. Those approaches, that were established before massively parallel sequencing methods, have been adapted to these new marker systems (in some cases involving the development of new methods) that allow genome-wide estimates of the four major micro-evolutionary forces-mutation, gene flow, genetic drift, and selection. Nevertheless, classic population genetic markers are still commonly used and a plethora of analysis methods and programs is available for these and high-throughput sequencing (HTS) data. These methods employ various and diverse theoretical and statistical frameworks, to varying degrees of success, to estimate similar evolutionary parameters making it difficult to get a concise overview across the available approaches. Presently, reviews on this topic generally focus on a particular class of methods to estimate one or two evolutionary parameters. Here, we provide a brief history of methods and a comprehensive list of available programs for estimating micro-evolutionary forces. We furthermore analyzed their usage within the research community based on popularity (citation bias) and discuss the implications of this bias for the software community. We found that a few programs received the majority of citations, with program success being independent of both the parameters estimated and the computing platform. The only deviation from a model of exponential growth in the number of citations was found for the presence of a graphical user interface (GUI). Interestingly, no relationship was found for the impact factor of the journals, when the tools were published, suggesting accessibility might be more important than visibility.
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Affiliation(s)
- Jonathan Kidner
- General Zoology Institute for Biology Martin Luther University Halle-Wittenberg Halle (Saale) Germany
| | - Panagiotis Theodorou
- General Zoology Institute for Biology Martin Luther University Halle-Wittenberg Halle (Saale) Germany
| | - Jan O Engler
- Terrestrial Ecology Unit Department of Biology Ghent University Ghent Belgium
| | - Martin Taubert
- Aquatic Geomicrobiology Institute for Biodiversity Friedrich Schiller University Jena Jena Germany
| | - Martin Husemann
- General Zoology Institute for Biology Martin Luther University Halle-Wittenberg Halle (Saale) Germany
- Centrum für Naturkunde University of Hamburg Hamburg Germany
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35
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Rico Y, León-Tapia MÁ, Zurita-Solís M, Rodríguez-Gómez F, Vásquez-Morales SG. Influence of Pleistocene climatic oscillations on the phylogeography and demographic history of endemic vulnerable trees (section Magnolia) of the Tropical Montane Cloud Forest in Mexico. PeerJ 2021; 9:e12181. [PMID: 34692249 PMCID: PMC8485838 DOI: 10.7717/peerj.12181] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 08/29/2021] [Indexed: 11/20/2022] Open
Abstract
The Tropical Montane Cloud Forest (TMCF) is a highly dynamic ecosystem that has undergone frequent spatial changes in response to the interglacial-glacial cycles of the Pleistocene. These climatic fluctuations between cold and warm cycles have led to species range shifts and contractions-expansions, resulting in complex patterns of genetic structure and lineage divergence in forest tree species. In this study, we sequenced four regions of the chloroplast DNA (trnT-trnL, trnK5-matk, rpl32-trnL, trnS-trnG) for 20 populations and 96 individuals to evaluate the phylogeography, historical demography, and paleodistributions of vulnerable endemic TMCF trees in Mexico: Magnolia pedrazae (north-region), M. schiedeana (central-region), and M. schiedeana population Oaxaca (south-region). Our data recovered 49 haplotypes that showed a significant phylogeographic structure in three regions: north, central, and south. Bayesian Phylogeographic and Ecological Clustering (BPEC) analysis also supported the divergence in three lineages and highlighted the role of environmental factors (temperature and precipitation) in genetic differentiation. Our historical demography analyses revealed demographic expansions predating the Last Interglacial (LIG, ~125,000 years ago), while Approximate Bayesian Computation (ABC) simulations equally supported two contrasting demographic scenarios. The BPEC and haplotype network analyses suggested that ancestral haplotypes were geographically found in central Veracruz. Our paleodistributions modeling showed evidence of range shifts and expansions-contractions from the LIG to the present, which suggested the complex evolutionary dynamics associated to the climatic oscillations of the Pleistocene. Habitat management of remnant forest fragments where large and genetically diverse populations occur in the three TMCF regions analyzed would be key for the conservation of these magnolia populations.
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Affiliation(s)
- Yessica Rico
- Red de Diversidad Biológica del Occidente Mexicano, Instituto de Ecología A.C., Pátzcuaro, Michoacán, México
- CONACYT, Ciudad de México, México
| | - M. Ángel León-Tapia
- Laboratorio de Sistemática Filogenética, Red de Biología Evolutiva, Instituto de Ecología A.C., Xalapa, Veracruz, Mexico
| | - Marisol Zurita-Solís
- Red de Diversidad Biológica del Occidente Mexicano, Instituto de Ecología A.C., Pátzcuaro, Michoacán, México
| | - Flor Rodríguez-Gómez
- Departamento de Ciencias Computacionales, División de Electrónica y Computación, Centro Universitario de Ciencias Exactas e Ingenierías, Universidad de Guadalajara, Guadalajara, Jalisco, Mexico
| | - Suria Gisela Vásquez-Morales
- Departamento de Biología, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Guanajuato, México
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Kim H, Kim S, Kim S, Lee Y, Lee HS, Lee SJ, Choi DS, Jeon J, Lee JH. Population Genetics for Inferring Introduction Sources of the Oriental Fruit Fly, Bactrocera dorsalis: A Test for Quarantine Use in Korea. INSECTS 2021; 12:851. [PMID: 34680620 PMCID: PMC8541597 DOI: 10.3390/insects12100851] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 09/16/2021] [Accepted: 09/17/2021] [Indexed: 11/16/2022]
Abstract
To infer the introduction sources of the oriental fruit fly, Bactrocera dorsalis, we used a mitochondrial marker to reconstruct the haplotype network and 15 microsatellite loci to reveal genetic structure and relationships between the geographically or temporally different collections from Asia. We performed Approximate Bayesian computations to infer a global origin and a source of the quarantine collections found in Korea. As a result, the 40 populations were divided into three groups, of which genetic similarity is not related to the geographic vicinity. Korean samples had a similar genetic structure to Taiwan and Thailand ones. Our results suggest that the place of origin of the B. dorsalis specimens found in Korea's border quarantine is likely to be Taiwan or Thailand. As the global origin of B. dorsalis, we estimated that Taiwan and Thailand were most likely the global origins of Southeast Asian populations by testing hypothetical scenarios by the approximate Bayesian computation analyses. Our results will allow easier identification of the source region of the forthcoming invasion of quarantined B. dorsalis specimens.
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Affiliation(s)
- Hyojoong Kim
- Animal Systematics Laboratory, Department of Biology, Kunsan National University, Gunsan 54150, Jeonbuk, Korea; (S.K.); (S.K.)
| | - Sohee Kim
- Animal Systematics Laboratory, Department of Biology, Kunsan National University, Gunsan 54150, Jeonbuk, Korea; (S.K.); (S.K.)
- Animal & Plant Quarantine Agency, Gimcheon 39660, Gyeongbuk, Korea; (S.-J.L.); (D.-S.C.); (J.J.); (J.-H.L.)
| | - Sangjin Kim
- Animal Systematics Laboratory, Department of Biology, Kunsan National University, Gunsan 54150, Jeonbuk, Korea; (S.K.); (S.K.)
| | - Yerim Lee
- Animal Systematics Laboratory, Department of Biology, Kunsan National University, Gunsan 54150, Jeonbuk, Korea; (S.K.); (S.K.)
| | - Heung-Sik Lee
- Animal & Plant Quarantine Agency, Gimcheon 39660, Gyeongbuk, Korea; (S.-J.L.); (D.-S.C.); (J.J.); (J.-H.L.)
| | - Seong-Jin Lee
- Animal & Plant Quarantine Agency, Gimcheon 39660, Gyeongbuk, Korea; (S.-J.L.); (D.-S.C.); (J.J.); (J.-H.L.)
| | - Deuk-Soo Choi
- Animal & Plant Quarantine Agency, Gimcheon 39660, Gyeongbuk, Korea; (S.-J.L.); (D.-S.C.); (J.J.); (J.-H.L.)
| | - Jaeyong Jeon
- Animal & Plant Quarantine Agency, Gimcheon 39660, Gyeongbuk, Korea; (S.-J.L.); (D.-S.C.); (J.J.); (J.-H.L.)
| | - Jong-Ho Lee
- Animal & Plant Quarantine Agency, Gimcheon 39660, Gyeongbuk, Korea; (S.-J.L.); (D.-S.C.); (J.J.); (J.-H.L.)
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37
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Rotger A, Igual JM, Genovart M, Rodríguez V, Ramon C, Pérez-Mellado V, Bibiloni G, Rita J, Tavecchia G. Contrasting Adult Body-Size in Sister Populations of the Balearic Lizard, Podarcis lilfordi (Günther 1874) Suggests Anthropogenic Selective Pressures. HERPETOLOGICAL MONOGRAPHS 2021. [DOI: 10.1655/herpmonographs-d-19-00005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Andreu Rotger
- Animal Demography and Ecology Unit, IMEDEA, CSIC-UIB, Miquel Marquès 21, 07190 Esporles, Spain
| | - José Manuel Igual
- Animal Demography and Ecology Unit, IMEDEA, CSIC-UIB, Miquel Marquès 21, 07190 Esporles, Spain
| | | | - Virginia Rodríguez
- Human Genetic Group, University of the Balearic Islands, ctra. Valldemossa, km 7.5, 07122 Palma de Mallorca, Spain
| | - Cori Ramon
- Departamento de Biologia, Universitat de les Illes Balears, ctra. Valldemossa km 7,5, 07122 Palma de Mallorca, Spain
| | | | - Gabriel Bibiloni
- Departamento de Biologia, Universitat de les Illes Balears, ctra. Valldemossa km 7,5, 07122 Palma de Mallorca, Spain
| | - Juan Rita
- Departamento de Biologia, Universitat de les Illes Balears, ctra. Valldemossa km 7,5, 07122 Palma de Mallorca, Spain
| | - Giacomo Tavecchia
- Animal Demography and Ecology Unit, IMEDEA, CSIC-UIB, Miquel Marquès 21, 07190 Esporles, Spain
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38
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Scotti‐Saintagne C, Boivin T, Suez M, Musch B, Scotti I, Fady B. Signature of mid-Pleistocene lineages in the European silver fir ( Abies alba Mill.) at its geographic distribution margin. Ecol Evol 2021; 11:10984-10999. [PMID: 34429896 PMCID: PMC8366861 DOI: 10.1002/ece3.7886] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 06/11/2021] [Accepted: 06/22/2021] [Indexed: 11/25/2022] Open
Abstract
In a conservation and sustainable management perspective, we identify the ecological, climatic, and demographic factors responsible for the genetic diversity patterns of the European silver fir (Abies alba Mill.) at its southwestern range margin (Pyrenees Mountains, France, Europe). We sampled 45 populations throughout the French Pyrenees and eight neighboring reference populations in the Massif Central, Alps, and Corsica. We genotyped 1,620 individuals at three chloroplast and ten nuclear microsatellite loci. We analyzed within- and among-population genetic diversity using phylogeographic reconstructions, tests of isolation-by-distance, Bayesian population structure inference, modeling of demographic scenarios, and regression analyses of genetic variables with current and past environmental variables. Genetic diversity decreased from east to west suggesting isolation-by-distance from the Alps to the Pyrenees and from the Eastern to the Western Pyrenees. We identified two Pyrenean lineages that diverged from a third Alpine-Corsica-Massif Central lineage 0.8 to 1.1 M years ago and subsequently formed a secondary contact zone in the Central Pyrenees. Population sizes underwent contrasted changes, with a contraction in the west and an expansion in the east. Glacial climate affected the genetic composition of the populations, with the western genetic cluster only observed in locations corresponding to the coldest past climate and highest elevations. The eastern cluster was observed over a larger range of temperatures and elevations. All demographic events shaping the current spatial structure of genetic diversity took place during the Mid-Pleistocene Transition, long before the onset of the Holocene. The Western Pyrenees lineage may require additional conservation efforts, whereas the eastern lineage is well protected in in situ gene conservation units. Due to past climate oscillations and the likely emergence of independent refugia, east-west oriented mountain ranges may be important reservoir of genetic diversity in a context of past and ongoing climate change in Europe.
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Affiliation(s)
| | - Thomas Boivin
- INRAEEcologie des Forêts Méditerranéennes (URFM)AvignonFrance
| | - Marie Suez
- INRAEEcologie des Forêts Méditerranéennes (URFM)AvignonFrance
| | | | - Ivan Scotti
- INRAEEcologie des Forêts Méditerranéennes (URFM)AvignonFrance
| | - Bruno Fady
- INRAEEcologie des Forêts Méditerranéennes (URFM)AvignonFrance
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Zheng Y, Zhang S, Lu Q, Zhang S, Wang L, Hong M, Nguyen T, Zhao J, Yao M. Population genetic patterns of a mangrove‐associated frog reveal its colonization history and habitat connectivity. DIVERS DISTRIB 2021. [DOI: 10.1111/ddi.13304] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Affiliation(s)
- Yitao Zheng
- School of Life Sciences Peking University Beijing China
- Institute of Ecology College of Urban and Environmental Sciences Peking University Beijing China
| | - Shan Zhang
- School of Life Sciences Peking University Beijing China
- Institute of Ecology College of Urban and Environmental Sciences Peking University Beijing China
| | - Qi Lu
- School of Life Sciences Peking University Beijing China
- Institute of Ecology College of Urban and Environmental Sciences Peking University Beijing China
| | - Siyu Zhang
- School of Life Sciences Peking University Beijing China
- Institute of Ecology College of Urban and Environmental Sciences Peking University Beijing China
| | - Lijun Wang
- College of Life Sciences Hainan Normal University Haikou China
| | - Meiling Hong
- College of Life Sciences Hainan Normal University Haikou China
| | - Truong Nguyen
- Institute of Ecology and Biological Resources Academy of Science and Technology Hanoi Vietnam
- Vietnam Academy of Science and Technology Graduate University of Science and Technology Hanoi Vietnam
| | - Jindong Zhao
- School of Life Sciences Peking University Beijing China
- Institute of Ecology College of Urban and Environmental Sciences Peking University Beijing China
| | - Meng Yao
- School of Life Sciences Peking University Beijing China
- Institute of Ecology College of Urban and Environmental Sciences Peking University Beijing China
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40
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Recent population expansion in wild gaur (Bos gaurus gaurus) as revealed by microsatellite markers. Mamm Biol 2021. [DOI: 10.1007/s42991-021-00145-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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41
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Andersen JC, Havill NP, Caccone A, Elkinton JS. Four times out of Europe: Serial invasions of the winter moth, Operophtera brumata, to North America. Mol Ecol 2021; 30:3439-3452. [PMID: 34033202 DOI: 10.1111/mec.15983] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 05/07/2021] [Accepted: 05/10/2021] [Indexed: 11/30/2022]
Abstract
Reconstructing the geographic origins of non-native species is important for studying the factors that influence invasion success, however; these analyses can be constrained by the amount of diversity present in the native and invaded regions, and by changes in the genetic background of the invading population following bottlenecks and/or hybridization events. Here we explore the geographical origins of the invasive winter moth (Operopthera brumata L.) that has caused widespread defoliation to forests, orchards, and crops in Nova Scotia, British Columbia, Oregon, and the northeastern United States. It is not known whether these represent independent introductions to North America, or a "stepping stone" spread among regions. Using a combination of Bayesian assignment and approximate Bayesian computation methods, we analysed a population genetic data set of 24 microsatellite loci. We estimate that winter moth was introduced to North America on at least four occasions, with the Nova Scotian and British Columbian populations probably being introduced from France and Sweden, respectively; the Oregonian population probably being introduced from either the British Isles or northern Fennoscandia; and the population in the northeastern United States probably being introduced from somewhere in Central Europe. We discuss the impact of genetic bottlenecks on analyses meant to determine region of origin.
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Affiliation(s)
- Jeremy C Andersen
- Department of Environmental Conservation, University of Massachusetts, Amherst, MA, USA
| | - Nathan P Havill
- Northern Research Station, USDA Forest Service, Hamden, CT, USA
| | - Adalgisa Caccone
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT, USA
| | - Joseph S Elkinton
- Department of Environmental Conservation, University of Massachusetts, Amherst, MA, USA
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42
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Kim H, Kim S, Lee Y, Lee HS, Lee SJ, Lee JH. Tracing the Origin of Korean Invasive Populations of the Spotted Lanternfly, Lycorma delicatula (Hemiptera: Fulgoridae). INSECTS 2021; 12:539. [PMID: 34200556 PMCID: PMC8227202 DOI: 10.3390/insects12060539] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 06/08/2021] [Accepted: 06/08/2021] [Indexed: 11/28/2022]
Abstract
Lycorma delicatula (White) suddenly arrived in Korea where it rapidly spread out in the central region of Korea and caused serious damage to grape vineyards. To trace the source region of its invasiveness, population genetic structures were compared between the native region, China, and the introduced regions, Korea and Japan. We examined 762 individuals from 38 different population collections using 15 microsatellite loci. Both principal coordinate and structure analyses displayed that the Chinese populations were separated into three subgroups which were located significantly far apart from each other. Among them, the Shanghai population was located closest to most Korean populations. Based on the genetic relationships and structures, it was revealed that the multiple introductions into Korea occurred at least three times. In addition, the Shanghai population was strongly estimated to be a source of initial invasive populations of Korea. In addition, analysis of the approximate Bayesian computation suggested simultaneous spread from two distant locations early in the invasion by artificial transportation of the host plants bearing egg masses. Our population genetics study can provide a precedent case with regards to identifying spreads by anthropogenic outcomes in other invasive regions.
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Affiliation(s)
- Hyojoong Kim
- Animal Systematics Laboratory, Department of Biology, Kunsan National University, Gunsan 54150, Korea;
| | - Sohee Kim
- Animal Systematics Laboratory, Department of Biology, Kunsan National University, Gunsan 54150, Korea;
- Animal & Plant Quarantine Agency, Gimcheon 39660, Korea; (H.-S.L.); (S.-J.L.); (J.-H.L.)
| | - Yerim Lee
- Animal Systematics Laboratory, Department of Biology, Kunsan National University, Gunsan 54150, Korea;
| | - Heung-Sik Lee
- Animal & Plant Quarantine Agency, Gimcheon 39660, Korea; (H.-S.L.); (S.-J.L.); (J.-H.L.)
| | - Seong-Jin Lee
- Animal & Plant Quarantine Agency, Gimcheon 39660, Korea; (H.-S.L.); (S.-J.L.); (J.-H.L.)
| | - Jong-Ho Lee
- Animal & Plant Quarantine Agency, Gimcheon 39660, Korea; (H.-S.L.); (S.-J.L.); (J.-H.L.)
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Yu L, Zhao S, Meng F, Shi Y, Xu C. Dispersal and mating patterns determine the fate of naturally dispersed populations: evidence from Bombina orientalis. BMC Ecol Evol 2021; 21:111. [PMID: 34098874 PMCID: PMC8182911 DOI: 10.1186/s12862-021-01844-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 06/02/2021] [Indexed: 12/05/2022] Open
Abstract
Background In contrast to the explosive increase of a population following biological invasion, natural dispersal, i.e., when a population disperses from its original range into a new range, is a passive process that is affected by resources, the environment, and other factors. Natural dispersal is also negatively impacted by genetic drift and the founder effect. Although the fates of naturally dispersed populations are unknown, they can adapt evolutionarily over time to the new environment. Can naturally dispersed populations evolve beneficial adaptive strategies to offset these negative effects to maintain their population in a stable state? Results The current study addressed this question by focusing on the toad Bombina orientalis, the population of which underwent natural dispersal following the Last Glacial Maximum in Northeast Asia. Population genetic approaches were used to determine the genetic structure, dispersal pattern, and mating system of the population of B. orientalis in northeast China (Northern population). The results showed that this northern population of B. orientalis is a typical naturally dispersed population, in which the stable genetic structure and high level of genetic diversity of the population have been maintained through the long-distance biased dispersal behavior of males and the pattern of promiscuity within the population. Conclusions Our findings suggest that naturally dispersed populations can evolve effective adaptive strategies to maintain a stable population. Different species may have different strategies. The relevance of these maintenance mechanisms for naturally dispersed populations provide a new perspective for further understanding the processes of speciation and evolution. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-021-01844-3.
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Affiliation(s)
- Liqun Yu
- College of Life Science, Northeast Agricultural University, No. 600 Changjiang Road Xiangfang District, Harbin, 150030, China
| | - Shuai Zhao
- College of Life Science, Northeast Agricultural University, No. 600 Changjiang Road Xiangfang District, Harbin, 150030, China
| | - Fanbing Meng
- College of Life Science, Northeast Agricultural University, No. 600 Changjiang Road Xiangfang District, Harbin, 150030, China
| | - Yanshuang Shi
- College of Life Science, Northeast Agricultural University, No. 600 Changjiang Road Xiangfang District, Harbin, 150030, China
| | - Chunzhu Xu
- College of Life Science, Northeast Agricultural University, No. 600 Changjiang Road Xiangfang District, Harbin, 150030, China.
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Sherpa S, Després L. The evolutionary dynamics of biological invasions: A multi-approach perspective. Evol Appl 2021; 14:1463-1484. [PMID: 34178098 PMCID: PMC8210789 DOI: 10.1111/eva.13215] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 02/22/2021] [Accepted: 03/02/2021] [Indexed: 01/02/2023] Open
Abstract
Biological invasions, the establishment and spread of non-native species in new regions, can have extensive economic and environmental consequences. Increased global connectivity accelerates introduction rates, while climate and land-cover changes may decrease the barriers to invasive populations spread. A detailed knowledge of the invasion history, including assessing source populations, routes of spread, number of independent introductions, and the effects of genetic bottlenecks and admixture on the establishment success, adaptive potential, and further spread, is crucial from an applied perspective to mitigate socioeconomic impacts of invasive species, as well as for addressing fundamental questions on the evolutionary dynamics of the invasion process. Recent advances in genomics together with the development of geographic information systems provide unprecedented large genetic and environmental datasets at global and local scales to link population genomics, landscape ecology, and species distribution modeling into a common framework to study the invasion process. Although the factors underlying population invasiveness have been extensively reviewed, analytical methods currently available to optimally combine molecular and environmental data for inferring invasive population demographic parameters and predicting further spreading are still under development. In this review, we focus on the few recent insect invasion studies that combine different datasets and approaches to show how integrating genetic, observational, ecological, and environmental data pave the way to a more integrative biological invasion science. We provide guidelines to study the evolutionary dynamics of invasions at each step of the invasion process, and conclude on the benefits of including all types of information and up-to-date analytical tools from different research areas into a single framework.
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Affiliation(s)
- Stéphanie Sherpa
- CNRSLECAUniversité Grenoble AlpesUniversité Savoie Mont BlancGrenobleFrance
| | - Laurence Després
- CNRSLECAUniversité Grenoble AlpesUniversité Savoie Mont BlancGrenobleFrance
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Zorrilla‐Azcué S, González‐Rodríguez A, Oyama K, González MA, Rodríguez‐Correa H. The DNA history of a lonely oak: Quercus humboldtii phylogeography in the Colombian Andes. Ecol Evol 2021; 11:6814-6828. [PMID: 34141258 PMCID: PMC8207385 DOI: 10.1002/ece3.7529] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Revised: 02/22/2021] [Accepted: 03/15/2021] [Indexed: 11/06/2022] Open
Abstract
The climatic and geological changes that occurred during the Quaternary, particularly the fluctuations during the glacial and interglacial periods of the Pleistocene, shaped the population demography and geographic distribution of many species. These processes have been studied in several groups of organisms in the Northern Hemisphere, but their influence on the evolution of Neotropical montane species and ecosystems remains unclear. This study contributes to the understanding of the effect of climatic fluctuations during the late Pleistocene on the evolution of Andean mountain forests. First, we describe the nuclear and plastidic DNA patterns of genetic diversity, structure, historical demography, and landscape connectivity of Quercus humboldtii, which is a typical species in northern Andean montane forests. Then, these patterns were compared with the palynological and evolutionary hypotheses postulated for montane forests of the Colombian Andes under climatic fluctuation scenarios during the Quaternary. Our results indicated that populations of Q. humboldtii have high genetic diversity and a lack of genetic structure and that they have experienced a historical increase in connectivity from the last glacial maximum (LGM) to the present. Furthermore, our results showed a dramatic reduction in the effective population size followed by an expansion before the LGM, which is consistent with the results found by palynological studies, suggesting a change in dominance in Andean forests that may be related to ecological factors rather than climate change.
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Affiliation(s)
- Sofía Zorrilla‐Azcué
- Escuela Nacional de Estudios Superiores (ENES) Unidad MoreliaUniversidad Nacional Autónoma de México (UNAM)MoreliaMexico
- Posgrado en Ciencias BiológicasUniversidad Nacional Autónoma de México (UNAM)CoyoacánMexico
| | - Antonio González‐Rodríguez
- Instituto de Investigaciones en Ecosistemas y SustentabilidadUniversidad Nacional Autónoma de México (UNAM)MoreliaMexico
| | - Ken Oyama
- Escuela Nacional de Estudios Superiores (ENES) Unidad MoreliaUniversidad Nacional Autónoma de México (UNAM)MoreliaMexico
| | - Mailyn A. González
- Laboratorio de Genética de la ConservaciónInstituto de Investigación de Recursos Biológicos Alexander von HumboldtBogotáColombia
| | - Hernando Rodríguez‐Correa
- Escuela Nacional de Estudios Superiores (ENES) Unidad MoreliaUniversidad Nacional Autónoma de México (UNAM)MoreliaMexico
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Bourgeois YXC, Warren BH. An overview of current population genomics methods for the analysis of whole-genome resequencing data in eukaryotes. Mol Ecol 2021; 30:6036-6071. [PMID: 34009688 DOI: 10.1111/mec.15989] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 04/26/2021] [Accepted: 05/11/2021] [Indexed: 01/01/2023]
Abstract
Characterizing the population history of a species and identifying loci underlying local adaptation is crucial in functional ecology, evolutionary biology, conservation and agronomy. The constant improvement of high-throughput sequencing techniques has facilitated the production of whole genome data in a wide range of species. Population genomics now provides tools to better integrate selection into a historical framework, and take into account selection when reconstructing demographic history. However, this improvement has come with a profusion of analytical tools that can confuse and discourage users. Such confusion limits the amount of information effectively retrieved from complex genomic data sets, and impairs the diffusion of the most recent analytical tools into fields such as conservation biology. It may also lead to redundancy among methods. To address these isssues, we propose an overview of more than 100 state-of-the-art methods that can deal with whole genome data. We summarize the strategies they use to infer demographic history and selection, and discuss some of their limitations. A website listing these methods is available at www.methodspopgen.com.
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Affiliation(s)
| | - Ben H Warren
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, UA, CP 51, Paris, France
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Late Pleistocene Expansion of Small Murid Rodents across the Palearctic in Relation to the Past Environmental Changes. Genes (Basel) 2021; 12:genes12050642. [PMID: 33925980 PMCID: PMC8145813 DOI: 10.3390/genes12050642] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 04/19/2021] [Accepted: 04/20/2021] [Indexed: 11/16/2022] Open
Abstract
We investigated the evolutionary history of the striped field mouse to identify factors that initiated its past demographic changes and to shed light on the causes of its current genetic structure and trans-Eurasian distribution. We sequenced mitochondrial cyt b from 184 individuals, obtained from 35 sites in central Europe and eastern Mongolia. We compared genetic analyses with previously published historical distribution models and data on environmental and climatic changes. The past demographic changes displayed similar population trends in the case of recently expanded clades C1 and C3, with the glacial (MIS 3–4) expansion and postglacial bottleneck preceding the recent expansion initiated in the late Holocene and were related to environmental changes during the upper Pleistocene and Holocene. The past demographic trends of the eastern Asian clade C3 were correlated with changes in sea level and the formation of new land bridges formed by the exposed sea shelf during the glaciations. These data were supported by reconstructed historical distribution models. The results of our genetic analyses, supported by the reconstruction of the historical spatial distributions of the distinct clades, confirm that over time the local populations mixed as a consequence of environmental and climatic changes resulting from cyclical glaciation and the interglacial period during the Pleistocene.
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Rankin AM, Anderson FE, Clutts SA, Espíndola A, Carstens BC, Lucid M, Sullivan J. Comparative phylogeography of two Northern Rocky Mountain endemics: the widespread Anguispira kochi occidentalis and the narrow-range Anguispira nimapuna (Gastropoda: Discidae). Biol J Linn Soc Lond 2021; 133:817-834. [PMID: 34220190 DOI: 10.1093/biolinnean/blab030] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 02/08/2021] [Accepted: 02/12/2021] [Indexed: 11/14/2022]
Abstract
The Northern Rocky Mountain ecosystem supports rich biological diversity with many endemic and rare species. Extant endemics display two biogeographic patterns: widespread species with fragmented populations, and narrow-range endemics. These distributions are shown by the congeneric snails Anguispira kochi occidentalis and Anguispira nimapuna. These two taxa are disjunct from the remaining species of the genus, which achieves its greatest diversity in eastern North America. Given the disjunct nature of A. k. occidentalis and A. nimapuna, we here present a mtDNA phylogeny of the genus that includes both eastern and western species to assess the phylogenetic position of A. k. occidentalis and A. nimapuna. We then reconstruct the demographic history of A. k. occidentalis and A. nimapuna by analysing current patterns of genetic variation and interpreting the results considering the historical biogeography of the region. Both A. k. occidentalis and A. nimapuna represent unique taxa that are genetically and geographically distinct from their congeners. The current distribution and genetic structure of A. k. occidentalis has been shaped by both historical isolation in refugia and more recent northward shifts, whereas A. nimapuna is represented by two populations with shallow divergence in an area of long-term habitat stability.
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Affiliation(s)
- Andrew M Rankin
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA.,Institute for Bioinformatics and Evolutionary Studies (IBEST), Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA
| | - Frank E Anderson
- School of Biological Sciences, Southern Illinois University, Carbondale, IL 62901, USA
| | - Stephanie A Clutts
- School of Biological Sciences, Southern Illinois University, Carbondale, IL 62901, USA
| | - Anahí Espíndola
- Department of Entomology, University of Maryland, College Park, 4291 Fieldhouse Drive, 3138 Plant Sciences Building, College Park, MD 20742-4454, USA
| | - Bryan C Carstens
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, OH 43210, USA
| | | | - Jack Sullivan
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA.,Institute for Bioinformatics and Evolutionary Studies (IBEST), Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA
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The palaeoendemic conifer Pherosphaera hookeriana (Podocarpaceae) exhibits high genetic diversity despite Quaternary range contraction and post glacial bottlenecking. CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01338-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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50
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Castillo-Chora VDJ, Sánchez-González LA, Mastretta-Yanes A, Prieto-Torres DA, Navarro-Sigüenza AG. Insights into the importance of areas of climatic stability in the evolution and maintenance of avian diversity in the Mesoamerican dry forests. Biol J Linn Soc Lond 2021. [DOI: 10.1093/biolinnean/blaa202] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
We analysed the phylogeographic structure of five resident bird lineages distributed in the seasonally dry tropical forests (SDTF) of Mesoamerica to test whether they show patterns of synchronous and geographically coincident genetic divergence during the Quaternary. We generated phylogenetic trees, estimated divergence times and analysed the genetic structure of populations (based on sequences of mitochondrial genes), as well as estimating historical distributions (range extension and areas of long-term climate stability) during the Late Pleistocene. We tested and selected the phylogeographic divergence scenarios that best explain the current divergence patterns of taxa using the Approximate Bayesian Computation (ABC) approach. For most species, phylogenetic trees and haplotype networks showed a clear genetic structure associated with geographical distribution. Overall, the divergence times ranged from 0.29–2.0 Mya, suggesting that diversification of populations occurred at different times during the Pleistocene. The palaeodistribution models predicted at least two areas of climatic stability within the current SDTF that probably allowed glacial-interglacial persistence of isolated bird populations along the Mexican Pacific, thus promoting their genetic divergence. The results provide information relevant to the identification of diversification hotspots for the Mesoamerican SDTF avifauna.
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Affiliation(s)
- Vicente De J Castillo-Chora
- Museo de Zoología, Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, A.P., Mexico City, México
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México
| | - Luis A Sánchez-González
- Museo de Zoología, Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, A.P., Mexico City, México
| | - Alicia Mastretta-Yanes
- CONACYT—CONABIO, Comisión Nacional para el Conocimiento y Uso de la Biodiversidad, Liga Periférico-Insurgentes Sur No. 4903, Parques del Pedregal, Tlalpan, Mexico City, México
| | - David A Prieto-Torres
- Museo de Zoología, Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, A.P., Mexico City, México
| | - Adolfo G Navarro-Sigüenza
- Museo de Zoología, Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, A.P., Mexico City, México
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