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Fordham DA, Brown SC, Canteri E, Austin JJ, Lomolino MV, Haythorne S, Armstrong E, Bocherens H, Manica A, Rey-Iglesia A, Rahbek C, Nogués-Bravo D, Lorenzen ED. 52,000 years of woolly rhinoceros population dynamics reveal extinction mechanisms. Proc Natl Acad Sci U S A 2024; 121:e2316419121. [PMID: 38830089 DOI: 10.1073/pnas.2316419121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Accepted: 04/29/2024] [Indexed: 06/05/2024] Open
Abstract
The extinction of the woolly rhinoceros (Coelodonta antiquitatis) at the onset of the Holocene remains an enigma, with conflicting evidence regarding its cause and spatiotemporal dynamics. This partly reflects challenges in determining demographic responses of late Quaternary megafauna to climatic and anthropogenic causal drivers with available genetic and paleontological techniques. Here, we show that elucidating mechanisms of ancient extinctions can benefit from a detailed understanding of fine-scale metapopulation dynamics, operating over many millennia. Using an abundant fossil record, ancient DNA, and high-resolution simulation models, we untangle the ecological mechanisms and causal drivers that are likely to have been integral in the decline and later extinction of the woolly rhinoceros. Our 52,000-y reconstruction of distribution-wide metapopulation dynamics supports a pathway to extinction that began long before the Holocene, when the combination of cooling temperatures and low but sustained hunting by humans trapped woolly rhinoceroses in suboptimal habitats along the southern edge of their range. Modeling indicates that this ecological trap intensified after the end of the last ice age, preventing colonization of newly formed suitable habitats, weakening stabilizing metapopulation processes, triggering the extinction of the woolly rhinoceros in the early Holocene. Our findings suggest that fragmentation and resultant metapopulation dynamics should be explicitly considered in explanations of late Quaternary megafauna extinctions, sending a clarion call to the fragility of the remaining large-bodied grazers restricted to disjunct fragments of poor-quality habitat due to anthropogenic environmental change.
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Affiliation(s)
- Damien A Fordham
- The Environment Institute, School of Biological Sciences, University of Adelaide, Adelaide SA, 5005, Australia
- Center for Macroecology, Evolution, and Climate, Globe Institute, University of Copenhagen, Copenhagen Ø 2100, Denmark
- Center for Global Mountain Biodiversity, Globe Institute, University of Copenhagen, Copenhagen Ø 2100, Denmark
| | - Stuart C Brown
- The Environment Institute, School of Biological Sciences, University of Adelaide, Adelaide SA, 5005, Australia
- Globe Institute, University of Copenhagen, Copenhagen K 1350, Denmark
| | - Elisabetta Canteri
- The Environment Institute, School of Biological Sciences, University of Adelaide, Adelaide SA, 5005, Australia
- Center for Macroecology, Evolution, and Climate, Globe Institute, University of Copenhagen, Copenhagen Ø 2100, Denmark
| | - Jeremy J Austin
- The Environment Institute, School of Biological Sciences, University of Adelaide, Adelaide SA, 5005, Australia
| | - Mark V Lomolino
- Department of Environmental and Forest Biology, College of Environmental Science, Syracuse, NY 13210
| | - Sean Haythorne
- The Environment Institute, School of Biological Sciences, University of Adelaide, Adelaide SA, 5005, Australia
- Centre of Excellence for Biosecurity Risk Analysis, School of Biosciences, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Edward Armstrong
- Department of Geosciences and Geography, University of Helsinki, Helsinki, FI-00014, Finland
| | - Hervé Bocherens
- Senckenberg Centre for Human Evolution and Palaeoenvironment, Tübingen 72074, Germany
- Department of Geosciences, Biogeology, University of Tübingen, Tübingen 72074, Germany
| | - Andrea Manica
- Department of Zoology, University of Cambridge, CB23EJ Cambridge, United Kingdom
| | - Alba Rey-Iglesia
- Globe Institute, University of Copenhagen, Copenhagen K 1350, Denmark
| | - Carsten Rahbek
- Center for Macroecology, Evolution, and Climate, Globe Institute, University of Copenhagen, Copenhagen Ø 2100, Denmark
- Center for Global Mountain Biodiversity, Globe Institute, University of Copenhagen, Copenhagen Ø 2100, Denmark
- Institute of Ecology, Peking University, Beijing 100871, China
- Danish Institute for Advanced Study, University of Southern Denmark, Odense M 5230, Denmark
| | - David Nogués-Bravo
- Center for Macroecology, Evolution, and Climate, Globe Institute, University of Copenhagen, Copenhagen Ø 2100, Denmark
| | - Eline D Lorenzen
- Globe Institute, University of Copenhagen, Copenhagen K 1350, Denmark
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2
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Séguigne M, Leroy C, Carrias JF, Corbara B, Lafont Rapnouil T, Céréghino R. Interactive effects of drought and deforestation on multitrophic communities and aquatic ecosystem functions in the Neotropics-a test using tank bromeliads. PeerJ 2024; 12:e17346. [PMID: 38737739 PMCID: PMC11088369 DOI: 10.7717/peerj.17346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 04/15/2024] [Indexed: 05/14/2024] Open
Abstract
Background Together with the intensification of dry seasons in Neotropical regions, increasing deforestation is expected to exacerbate species extinctions, something that could lead to dramatic shifts in multitrophic communities and ecosystem functions. Recent studies suggest that the effects of habitat loss are greater where precipitation has decreased. Yet, experimental studies of the pure and interactive effects of drought and deforestation at ecosystem level remain scarce. Methods Here, we used rainshelters and transplantation from rainforest to open areas of natural microcosms (the aquatic ecosystem and microbial-faunal food web found within the rainwater-filled leaves of tank bromeliads) to emulate drought and deforestation in a full factorial experimental design. We analysed the pure and interactive effects of our treatments on functional community structure (including microorganisms, detritivore and predatory invertebrates), and on leaf litter decomposition in tank bromeliad ecosystems. Results Drought or deforestation alone had a moderate impact on biomass at the various trophic level, but did not eliminate species. However, their interaction synergistically reduced the biomass of all invertebrate functional groups and bacteria. Predators were the most impacted trophic group as they were totally eliminated, while detritivore biomass was reduced by about 95%. Fungal biomass was either unaffected or boosted by our treatments. Decomposition was essentially driven by microbial activity, and did not change across treatments involving deforestation and/or drought. Conclusions Our results suggest that highly resistant microorganisms such as fungi (plus a few detritivores) maintain key ecosystem functions in the face of drought and habitat change. We conclude that habitat destruction compounds the problems of climate change, that the impacts of the two phenomena on food webs are mutually reinforcing, and that the stability of ecosystem functions depends on the resistance of a core group of organisms. Assuming that taking global action is more challenging than taking local-regional actions, policy-makers should be encouraged to implement environmental action plans that will halt habitat destruction, to dampen any detrimental interactive effect with the impacts of global climate change.
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Affiliation(s)
- Marie Séguigne
- Centre de Recherche sur la Biodiversité et l’Environnement (CRBE), Université de Toulouse, CNRS, IRD, Toulouse INP, Université Toulouse 3—Paul Sabatier (UT3), Toulouse, France
| | - Céline Leroy
- AMAP, Université de Montpellier, CIRAD, CNRS, INRAE, IRD, Montpellier, France
- EcoFoG, AgroParisTech, CIRAD, CNRS, INRAE, Université des Antilles, Université de Guyane, Campus agronomique, Kourou, France
| | - Jean-François Carrias
- Laboratoire Microorganismes: Génome et Environnement (LMGE), Université Clermont Auvergne, CNRS, F-63000, Clermont-Ferrand, France
| | - Bruno Corbara
- Laboratoire Microorganismes: Génome et Environnement (LMGE), Université Clermont Auvergne, CNRS, F-63000, Clermont-Ferrand, France
| | - Tristan Lafont Rapnouil
- Centre de Recherche sur la Biodiversité et l’Environnement (CRBE), Université de Toulouse, CNRS, IRD, Toulouse INP, Université Toulouse 3—Paul Sabatier (UT3), Toulouse, France
- AMAP, Université de Montpellier, CIRAD, CNRS, INRAE, IRD, Montpellier, France
- EcoFoG, AgroParisTech, CIRAD, CNRS, INRAE, Université des Antilles, Université de Guyane, Campus agronomique, Kourou, France
| | - Régis Céréghino
- Centre de Recherche sur la Biodiversité et l’Environnement (CRBE), Université de Toulouse, CNRS, IRD, Toulouse INP, Université Toulouse 3—Paul Sabatier (UT3), Toulouse, France
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3
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Kellner FL, Le Moullec M, Ellegaard MR, Rosvold J, Peeters B, Burnett HA, Pedersen ÅØ, Brealey JC, Dussex N, Bieker VC, Hansen BB, Martin MD. A palaeogenomic investigation of overharvest implications in an endemic wild reindeer subspecies. Mol Ecol 2024; 33:e17274. [PMID: 38279681 DOI: 10.1111/mec.17274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 12/11/2023] [Accepted: 01/09/2024] [Indexed: 01/28/2024]
Abstract
Overharvest can severely reduce the abundance and distribution of a species and thereby impact its genetic diversity and threaten its future viability. Overharvest remains an ongoing issue for Arctic mammals, which due to climate change now also confront one of the fastest changing environments on Earth. The high-arctic Svalbard reindeer (Rangifer tarandus platyrhynchus), endemic to Svalbard, experienced a harvest-induced demographic bottleneck that occurred during the 17-20th centuries. Here, we investigate changes in genetic diversity, population structure, and gene-specific differentiation during and after this overharvesting event. Using whole-genome shotgun sequencing, we generated the first ancient and historical nuclear (n = 11) and mitochondrial (n = 18) genomes from Svalbard reindeer (up to 4000 BP) and integrated these data with a large collection of modern genome sequences (n = 90) to infer temporal changes. We show that hunting resulted in major genetic changes and restructuring in reindeer populations. Near-extirpation followed by pronounced genetic drift has altered the allele frequencies of important genes contributing to diverse biological functions. Median heterozygosity was reduced by 26%, while the mitochondrial genetic diversity was reduced only to a limited extent, likely due to already low pre-harvest diversity and a complex post-harvest recolonization process. Such genomic erosion and genetic isolation of populations due to past anthropogenic disturbance will likely play a major role in metapopulation dynamics (i.e., extirpation, recolonization) under further climate change. Our results from a high-arctic case study therefore emphasize the need to understand the long-term interplay of past, current, and future stressors in wildlife conservation.
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Affiliation(s)
- Fabian L Kellner
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
- Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Mathilde Le Moullec
- Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
- Department of Mammals and Birds, Greenland Institute of Natural Resources (GINR), Nuuk, Greenland
| | - Martin R Ellegaard
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Jørgen Rosvold
- Department of Terrestrial Biodiversity, Norwegian Institute for Nature Research (NINA), Trondheim, Norway
| | - Bart Peeters
- Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Hamish A Burnett
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
- Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | | | - Jaelle C Brealey
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Nicolas Dussex
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Vanessa C Bieker
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Brage B Hansen
- Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
- Department of Terrestrial Ecology, Norwegian Institute for Nature Research (NINA), Trondheim, Norway
| | - Michael D Martin
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
- Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
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4
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Kessler C, Shafer ABA. Genomic Analyses Capture the Human-Induced Demographic Collapse and Recovery in a Wide-Ranging Cervid. Mol Biol Evol 2024; 41:msae038. [PMID: 38378172 PMCID: PMC10917209 DOI: 10.1093/molbev/msae038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 02/08/2024] [Accepted: 02/14/2024] [Indexed: 02/22/2024] Open
Abstract
The glacial cycles of the Quaternary heavily impacted species through successions of population contractions and expansions. Similarly, populations have been intensely shaped by human pressures such as unregulated hunting and land use changes. White-tailed and mule deer survived in different refugia through the Last Glacial Maximum, and their populations were severely reduced after the European colonization. Here, we analyzed 73 resequenced deer genomes from across their North American range to understand the consequences of climatic and anthropogenic pressures on deer demographic and adaptive history. We found strong signals of climate-induced vicariance and demographic decline; notably, multiple sequentially Markovian coalescent recovers a severe decline in mainland white-tailed deer effective population size (Ne) at the end of the Last Glacial Maximum. We found robust evidence for colonial overharvest in the form of a recent and dramatic drop in Ne in all analyzed populations. Historical census size and restocking data show a clear parallel to historical Ne estimates, and temporal Ne/Nc ratio shows patterns of conservation concern for mule deer. Signatures of selection highlight genes related to temperature, including a cold receptor previously highlighted in woolly mammoth. We also detected immune genes that we surmise reflect the changing land use patterns in North America. Our study provides a detailed picture of anthropogenic and climatic-induced decline in deer diversity and clues to understanding the conservation concerns of mule deer and the successful demographic recovery of white-tailed deer.
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Affiliation(s)
- Camille Kessler
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, Ontario, Canada
| | - Aaron B A Shafer
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, Ontario, Canada
- Department of Forensic Science, Trent University, Peterborough, Ontario, Canada
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5
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Pečnerová P, Lord E, Garcia-Erill G, Hanghøj K, Rasmussen MS, Meisner J, Liu X, van der Valk T, Santander CG, Quinn L, Lin L, Liu S, Carøe C, Dalerum F, Götherström A, Måsviken J, Vartanyan S, Raundrup K, Al-Chaer A, Rasmussen L, Hvilsom C, Heide-Jørgensen MP, Sinding MHS, Aastrup P, Van Coeverden de Groot PJ, Schmidt NM, Albrechtsen A, Dalén L, Heller R, Moltke I, Siegismund HR. Population genomics of the muskox' resilience in the near absence of genetic variation. Mol Ecol 2024; 33:e17205. [PMID: 37971141 DOI: 10.1111/mec.17205] [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: 06/23/2023] [Revised: 10/07/2023] [Accepted: 11/01/2023] [Indexed: 11/19/2023]
Abstract
Genomic studies of species threatened by extinction are providing crucial information about evolutionary mechanisms and genetic consequences of population declines and bottlenecks. However, to understand how species avoid the extinction vortex, insights can be drawn by studying species that thrive despite past declines. Here, we studied the population genomics of the muskox (Ovibos moschatus), an Ice Age relict that was at the brink of extinction for thousands of years at the end of the Pleistocene yet appears to be thriving today. We analysed 108 whole genomes, including present-day individuals representing the current native range of both muskox subspecies, the white-faced and the barren-ground muskox (O. moschatus wardi and O. moschatus moschatus) and a ~21,000-year-old ancient individual from Siberia. We found that the muskox' demographic history was profoundly shaped by past climate changes and post-glacial re-colonizations. In particular, the white-faced muskox has the lowest genome-wide heterozygosity recorded in an ungulate. Yet, there is no evidence of inbreeding depression in native muskox populations. We hypothesize that this can be explained by the effect of long-term gradual population declines that allowed for purging of strongly deleterious mutations. This study provides insights into how species with a history of population bottlenecks, small population sizes and low genetic diversity survive against all odds.
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Affiliation(s)
- Patrícia Pečnerová
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
- Copenhagen Zoo, Frederiksberg, Denmark
| | - Edana Lord
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
- Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Genís Garcia-Erill
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Kristian Hanghøj
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Malthe Sebro Rasmussen
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Jonas Meisner
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Xiaodong Liu
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Tom van der Valk
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Cindy G Santander
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Liam Quinn
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Immunology, Zealand University Hospital, Køge, Denmark
| | - Long Lin
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Shanlin Liu
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, China
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Christian Carøe
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Fredrik Dalerum
- Department of Zoology, Stockholm University, Stockholm, Sweden
- Biodiversity Research Institute (CSIC-UO-PA), Mieres, Spain
- Department of Zoology and Entomology, Mammal Research Institute, University of Pretoria, Hatfield, South Africa
| | - Anders Götherström
- Centre for Palaeogenetics, Stockholm, Sweden
- Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Johannes Måsviken
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
- Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Sergey Vartanyan
- North-East Interdisciplinary Scientific Research Institute N.A.N.A. Shilo, Russian Academy of Sciences, Magadan, Russia
| | | | - Amal Al-Chaer
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Linett Rasmussen
- Copenhagen Zoo, Frederiksberg, Denmark
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Mads Peter Heide-Jørgensen
- Greenland Institute of Natural Resources, Nuuk, Greenland
- Greenland Institute of Natural Resources, Copenhagen, Denmark
| | - Mikkel-Holger S Sinding
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
- Greenland Institute of Natural Resources, Nuuk, Greenland
| | - Peter Aastrup
- Department of Ecoscience, Aarhus University, Roskilde, Denmark
- Arctic Research Centre, Aarhus University, Aarhus, Denmark
| | | | - Niels Martin Schmidt
- Department of Ecoscience, Aarhus University, Roskilde, Denmark
- Arctic Research Centre, Aarhus University, Aarhus, Denmark
| | - Anders Albrechtsen
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Love Dalén
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
- Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Rasmus Heller
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Ida Moltke
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Hans Redlef Siegismund
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
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Yuan J, Sun G, Xiao B, Hu J, Wang L, Taogetongqimuge, Bao L, Hou Y, Song S, Jiang S, Wu Y, Pan D, Liu Y, Westbury MV, Lai X, Sheng G. Ancient mitogenomes reveal a high maternal genetic diversity of Pleistocene woolly rhinoceros in Northern China. BMC Ecol Evol 2023; 23:56. [PMID: 37752413 PMCID: PMC10521388 DOI: 10.1186/s12862-023-02168-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Accepted: 09/18/2023] [Indexed: 09/28/2023] Open
Abstract
BACKGROUND Woolly rhinoceros (Coelodonta antiquitatis) is a typical indicator of cold-stage climate that was widely distributed in Northern Hemisphere during the Middle-Late Pleistocene. Although a plethora of fossils have been excavated from Northern China, their phylogenetic status, intraspecific diversity and phylogeographical structure are still vague. RESULTS In the present study, we generated four mitogenomes from Late Pleistocene woolly rhinoceros in Northern China and compared them with published data. Bayesian and network analyses indicate that the analyzed individuals contain at least four maternal haplogroups, and Chinese samples fall in three of them. One of our samples belongs to a previously unidentified early diverging clade (haplogroup D), which separated from other woolly rhinoceros around 0.57 Ma (95% CI: 0.76-0.41 Ma). The timing of this clade's origin coincides with the first occurrence of woolly rhinoceros, which are thought to have evolved in Europe. Our other three samples cluster in haplogroup C, previously only identified from one specimen from Wrangel Island (ND030) and initially considered to be an isolated clade. Herein, our findings suggest that ND030 is likely descended from a northward dispersal of the individuals carrying haplogroup C from Northern China. Additionally, Chinese woolly rhinoceros specimens exhibit higher nucleotide diversity than those from Siberia. CONCLUSION Our findings highlight Northern China as a possible refugium and a key evolution center of the Pleistocene woolly rhinoceros.
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Affiliation(s)
- Junxia Yuan
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430078, China.
- Bioarchaeology Laboratory, Jilin University, Changchun, 130012, China.
- Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan, 430078, China.
| | - Guojiang Sun
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430078, China
- Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan, 430078, China
| | - Bo Xiao
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430078, China
- School of Earth Science, China University of Geosciences, Wuhan, 430074, China
| | - Jiaming Hu
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430078, China
- School of Earth Science, China University of Geosciences, Wuhan, 430074, China
| | - Linying Wang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430078, China
- Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan, 430078, China
- College of Earth and Environmental Science, Lanzhou University, Lanzhou, 730099, China
| | | | - Lei Bao
- Ordos Institute of Cultural Relics and Archaeology, Ordos, 017010, China
| | - Yamei Hou
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, 100044, China
| | - Shiwen Song
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430078, China
- School of Environmental Studies, China University of Geosciences, Wuhan, 430078, China
| | - Shan Jiang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430078, China
- Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan, 430078, China
| | - Yong Wu
- The Third Geological and Mineral Exploration Institute of Gansu Bureau of Geology and Mineral Resources, Lanzhou, 730050, China
| | - Dong Pan
- Palaeontological Fossil Conservation Center, Qinggang County, Suihua, 151600, China
| | - Yang Liu
- School of Sociology & Anthropology, Sun Yat-sen University, Guangzhou, 510275, China
| | | | - Xulong Lai
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430078, China
- School of Earth Science, China University of Geosciences, Wuhan, 430074, China
| | - Guilian Sheng
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430078, China.
- School of Environmental Studies, China University of Geosciences, Wuhan, 430078, China.
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7
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Rasmussen CMØ, Vandenbroucke TRA, Nogues-Bravo D, Finnegan S. Was the Late Ordovician mass extinction truly exceptional? Trends Ecol Evol 2023; 38:812-821. [PMID: 37183151 DOI: 10.1016/j.tree.2023.04.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 04/14/2023] [Accepted: 04/17/2023] [Indexed: 05/16/2023]
Abstract
The Late Ordovician mass extinction event is the oldest of the five great extinction events in the fossil record. It has long been regarded as an outlier among mass extinctions, primarily due to its association with a cooling climate. However, recent temporally better resolved fossil biodiversity estimates complicate this view, providing growing evidence for a prolonged but punctuated biodiversity decline modulated by changes in atmospheric composition, ocean chemistry, and viable habitat area. This evolving view invokes extinction drivers similar to those that occurred during other major extinctions; some are even factors in the current human-induced biodiversity crisis. Even this very ancient and, at first glance, exceptional event conveys important lessons about the intensifying 'sixth mass extinction'.
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Affiliation(s)
| | | | - David Nogues-Bravo
- Center for Macroecology, Evolution and Climate, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Seth Finnegan
- University of California Museum of Paleontology and Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720, USA
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8
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Peng X, Cheng J, Li H, Feijó A, Xia L, Ge D, Wen Z, Yang Q. Whole-genome sequencing reveals adaptations of hairy-footed jerboas (Dipus, Dipodidae) to diverse desert environments. BMC Biol 2023; 21:182. [PMID: 37649052 PMCID: PMC10469962 DOI: 10.1186/s12915-023-01680-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 08/10/2023] [Indexed: 09/01/2023] Open
Abstract
BACKGROUND Environmental conditions vary among deserts across the world, spanning from hyper-arid to high-elevation deserts. However, prior genomic studies on desert adaptation have focused on desert and non-desert comparisons overlooking the complexity of conditions within deserts. Focusing on the adaptation mechanisms to diverse desert environments will advance our understanding of how species adapt to extreme desert environments. The hairy-footed jerboas are well adapted to diverse desert environments, inhabiting high-altitude arid regions, hyper-arid deserts, and semi-deserts, but the genetic basis of their adaptation to different deserts remains unknown. RESULTS Here, we sequenced the whole genome of 83 hairy-footed jerboas from distinct desert zones in China to assess how they responded under contrasting conditions. Population genomics analyses reveal the existence of three species in hairy-footed jerboas distributed in China: Dipus deasyi, Dipus sagitta, and Dipus sowerbyi. Analyses of selection between high-altitude desert (elevation ≥ 3000m) and low-altitude desert (< 500m) populations identified two strongly selected genes, ATR and HIF1AN, associated with intense UV radiation and hypoxia in high-altitude environments. A number of candidate genes involved in energy and water homeostasis were detected in the comparative genomic analyses of hyper-arid desert (average annual precipitation < 70mm) and arid desert (< 200mm) populations versus semi-desert (> 360mm) populations. Hyper-arid desert animals also exhibited stronger adaptive selection in energy homeostasis, suggesting water and resource scarcity may be the main drivers of desert adaptation in hairy-footed jerboas. CONCLUSIONS Our study challenges the view of deserts as homogeneous environments and shows that distinct genomic adaptations can be found among desert animals depending on their habitats.
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Affiliation(s)
- Xingwen Peng
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District, Beijing, 100101, China
- University of Chinese Academy of Sciences, Shijingshan District, Beijing, 100049, China
| | - Jilong Cheng
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District, Beijing, 100101, China
| | - Hong Li
- Novogene Bioinformatics Institute, Haidian District, Beijing, 100083, China
| | - Anderson Feijó
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District, Beijing, 100101, China
- Negaunee Integrative Research Center, Field Museum of Natural History, Chicago, IL, 60605, USA
| | - Lin Xia
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District, Beijing, 100101, China
| | - Deyan Ge
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District, Beijing, 100101, China
| | - Zhixin Wen
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District, Beijing, 100101, China
| | - Qisen Yang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District, Beijing, 100101, China.
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9
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Doan K, Schnitzler A, Preston F, Griggo C, Lang G, Belhaoues F, Blaise E, Crégut-Bonnoure E, Frère S, Foucras S, Gardeisen A, Laurent A, Müller W, Picavet R, Puissant S, Yvinec JH, Pilot M. Evolutionary history of the extinct wolf population from France in the context of global phylogeographic changes throughout the Holocene. Mol Ecol 2023; 32:4627-4647. [PMID: 37337956 DOI: 10.1111/mec.17054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 05/20/2023] [Accepted: 06/05/2023] [Indexed: 06/21/2023]
Abstract
Phylogeographic patterns in large mammals result from natural environmental factors and anthropogenic effects, which in some cases include domestication. The grey wolf was once widely distributed across the Holarctic, but experienced phylogeographic shifts and demographic declines during the Holocene. In the 19th-20th centuries, the species became extirpated from large parts of Europe due to direct extermination and habitat loss. We reconstructed the evolutionary history of the extinct Western European wolves based on the mitogenomic composition of 78 samples from France (Neolithic-20th century) in the context of other populations of wolves and dogs worldwide. We found a close genetic similarity of French wolves from ancient, medieval and recent populations, which suggests the long-term continuity of maternal lineages. MtDNA haplotypes of the French wolves showed large diversity and fell into two main haplogroups of modern Holarctic wolves. Our worldwide phylogeographic analysis indicated that haplogroup W1, which includes wolves from Eurasia and North America, originated in Northern Siberia. Haplogroup W2, which includes only European wolves, originated in Europe ~35 kya and its frequency was reduced during the Holocene due to an expansion of haplogroup W1 from the east. Moreover, we found that dog haplogroup D, currently restricted to Europe and the Middle East, was nested within the wolf haplogroup W2. This suggests European origin of haplogroup D, probably as a result of an ancient introgression from European wolves. Our results highlight the dynamic evolutionary history of European wolves during the Holocene, with a partial lineage replacement and introgressive hybridization with local dog populations.
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Affiliation(s)
- Karolina Doan
- Museum and Institute of Zoology, Polish Academy of Sciences, Warsaw, Poland
| | - Annik Schnitzler
- UMR 7194 HNHP CNRS/MNHN/UPVD, Equipe NOMADE, Muséum national d'histoire naturelle, Paris, France
| | | | - Christophe Griggo
- Université Grenoble Alpes, Laboratoire EDYTEM, URM 5204 Bâtiment "Pôle Montagne", 5 bd de la mer Caspienne, France
| | - Gérard Lang
- Espace Chasse et Nature Chemin de Strasbourg, France
| | - Fabien Belhaoues
- ASM - Archéologie des Sociétés Méditerranéennes, UMR 5140, Université Paul-Valéry, CNRS, MCC, Montpellier, France
- Labex ARCHIMEDE programme IA-ANR-11-LABX-0032-01, Montpellier, France
| | - Emilie Blaise
- ASM - Archéologie des Sociétés Méditerranéennes, UMR 5140, Université Paul-Valéry, CNRS, MCC, Montpellier, France
- Labex ARCHIMEDE programme IA-ANR-11-LABX-0032-01, Montpellier, France
| | - Evelyne Crégut-Bonnoure
- Muséum Requien, Avignon; Laboratoire TRACES-UMR 5608, Université Toulouse-Jean Jaurès, Toulouse, France
| | - Stéphane Frère
- Inrap, UMR 7209 AASPE, Muséum National d'Histoire Naturelle, La Courneuve, France
| | | | - Armelle Gardeisen
- ASM - Archéologie des Sociétés Méditerranéennes, UMR 5140, Université Paul-Valéry, CNRS, MCC, Montpellier, France
- Labex ARCHIMEDE programme IA-ANR-11-LABX-0032-01, Montpellier, France
| | | | - Werner Müller
- Laboratoire d'archéozoologie, Université de Neuchâtel, Avenue de Bellevaux 51, Neuchâtel, Switzerland
| | | | - Stéphane Puissant
- Muséum d'Histoire naturelle - Jardin de l'Arquebuse CS 73310 F-21033 Dijon Cedex, France
| | - Jean-Hervé Yvinec
- INRAP, UMR 7209 AASPE, Laboratoire d'archéozoologie de Compiègne, CRAVO, Compiègne, France
| | - Małgorzata Pilot
- Museum and Institute of Zoology, Polish Academy of Sciences, Warsaw, Poland
- School of Life Sciences, University of Lincoln, Lincoln, UK
- Faculty of Biology, University of Gdańsk, Gdańsk, Poland
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10
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Ovchinnikov IV, McCann B. Mitogenomes revealed the history of bison colonization of Northern Plains after the Last Glacial Maximum. Sci Rep 2023; 13:11417. [PMID: 37452114 PMCID: PMC10349043 DOI: 10.1038/s41598-023-37599-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 06/23/2023] [Indexed: 07/18/2023] Open
Abstract
American bison demonstrated differential patterns of extinction, survival, and expansion since the terminal Pleistocene. We determined population dynamics of the Northern Great Plains bison using 40 mitochondrial genomes from radiocarbon dated remains with the age ranging from 12,226 to 167 calibrated years before present. Population dynamics correlated with environmental and anthropogenic factors and was characterized by three primary periods: terminal Pleistocene population growth starting 14,000 years ago, mid Holocene demographic stability between 6700 and 2700 years ago, and late Holocene population decline in the last 2700 years. Most diversification of mtDNA haplotypes occurred in the early Holocene when bison colonized new territories opened by retreating ice sheets. Holocene mtDNA lineages were not found in modern bison and lacked association with archaeological sites and morphological forms.
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Affiliation(s)
- Igor V Ovchinnikov
- Department of Biology, University of North Dakota, Grand Forks, ND, USA.
| | - Blake McCann
- Theodore Roosevelt National Park, Medora, ND, USA
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11
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Jones EL, Carvalho M. Ecospaces of the Middle to Upper Paleolithic transition: The archaeofaunal record of the Iberian Peninsula. J Hum Evol 2023; 177:103331. [PMID: 36871458 DOI: 10.1016/j.jhevol.2023.103331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 01/26/2023] [Accepted: 01/27/2023] [Indexed: 03/06/2023]
Abstract
The rich archaeofaunal record of Iberia provides a means of exploring potential differences between Neanderthal and anatomically modern human interactions with the environment. In this article, we present an analysis of Iberian archaeofaunas dating between 60 and 30 ka to explore if, how, and why the faunal ecospaces of Neanderthals and anatomically modern humans differed. We test for impacts of chronology (as a proxy for Neanderthal and anatomically modern human exploitation) and environmental regionalization (using bioclimatic regions) on archaeofaunal composition, using a combination of cluster (unweighted pair-group method using arithmetic averages) and nonmetric multidimensional scaling. Our chronological analysis finds no significant compositional difference between Neanderthal and anatomically modern mammalian faunal assemblages; however, bioclimatic regionalization is stronger in anatomically modern human-affiliated assemblages than in Neanderthal ones, a finding that may indicate a difference in site occupation duration or foraging mobility between Neanderthals and anatomically modern humans.
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Affiliation(s)
- Emily Lena Jones
- Department of Anthropology, University of New Mexico, Postal Address, Albuquerque, NM, USA; Latin American and Iberian Institute, University of New Mexico, Albuquerque, NM, USA.
| | - Milena Carvalho
- Department of Anthropology, University of New Mexico, Postal Address, Albuquerque, NM, USA; Interdisciplinary Center for Archaeology and Evolution of Human Behaviour, FCHS - Universidade Do Algarve, Campus de Gambelas, Faro, Portugal
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12
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Climate-driven habitat shifts of high-ranked prey species structure Late Upper Paleolithic hunting. Sci Rep 2023; 13:4238. [PMID: 36918697 PMCID: PMC10015039 DOI: 10.1038/s41598-023-31085-x] [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: 01/19/2023] [Accepted: 03/06/2023] [Indexed: 03/16/2023] Open
Abstract
Changing climates in the past affected both human and faunal population distributions, thereby structuring human diets, demography, and cultural evolution. Yet, separating the effects of climate-driven and human-induced changes in prey species abundances remains challenging, particularly during the Late Upper Paleolithic, a period marked by rapid climate change and marked ecosystem transformation. To disentangle the effects of climate and hunter-gatherer populations on animal prey species during the period, we synthesize disparate paleoclimate records, zooarchaeological data, and archaeological data using ecological methods and theory to test to what extent climate and anthropogenic impacts drove broad changes in human subsistence observed in the Late Upper Paleolithic zooarchaeological records. We find that the observed changes in faunal assemblages during the European Late Upper Paleolithic are consistent with climate-driven animal habitat shifts impacting the natural abundances of high-ranked prey species on the landscape rather than human-induced resource depression. The study has important implications for understanding how past climate change impacted and structured the diet and demography of human populations and can serve as a baseline for considerations of resilience and adaptation in the present.
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13
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Cao L, Dai Z, Tan H, Zheng H, Wang Y, Chen J, Kuang H, Chong RA, Han M, Hu F, Sun W, Sun C, Zhang Z. Population Structure, Demographic History, and Adaptation of Giant Honeybees in China Revealed by Population Genomic Data. Genome Biol Evol 2023; 15:7044694. [PMID: 36799935 PMCID: PMC9991589 DOI: 10.1093/gbe/evad025] [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: 06/26/2022] [Revised: 02/05/2023] [Accepted: 02/11/2023] [Indexed: 02/18/2023] Open
Abstract
There have been many population-based genomic studies on human-managed honeybees (Apis mellifera and Apis cerana), but there has been a notable lack of analysis with regard to wild honeybees, particularly in relation to their evolutionary history. Nevertheless, giant honeybees have been found to occupy distinct habitats and display remarkable characteristics, which are attracting an increased amount of attention. In this study, we de novo sequenced and then assembled the draft genome sequence of the Himalayan giant honeybee, Apis laboriosa. Phylogenetic analysis based on genomic information indicated that A. laboriosa and its tropical sister species Apis dorsata diverged ∼2.61 Ma, which supports the speciation hypothesis that links A. laboriosa to geological changes throughout history. Furthermore, we re-sequenced A. laboriosa and A. dorsata samples from five and six regions, respectively, across their population ranges in China. These analyses highlighted major genetic differences for Tibetan A. laboriosa as well as the Hainan Island A. dorsata. The demographic history of most giant honeybee populations has mirrored glacial cycles. More importantly, contrary to what has occurred among human-managed honeybees, the demographic history of these two wild honeybee species indicates a rapid decline in effective population size in the recent past, reflecting their differences in evolutionary histories. Several genes were found to be subject to selection, which may help giant honeybees to adapt to specific local conditions. In summary, our study sheds light on the evolutionary and adaptational characteristics of two wild giant honeybee species, which was useful for giant honeybee conservation.
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Affiliation(s)
- Lianfei Cao
- Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Zhijun Dai
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Hongwei Tan
- School of Life Sciences, Chongqing University, Chongqing, China.,Chongqing General Station of Animal Husbandry Technology Extension, Chongqing, China
| | - Huoqing Zheng
- College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Yun Wang
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Jie Chen
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Haiou Kuang
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Rebecca A Chong
- School of Life Sciences, University of Hawai'i at Mānoa, Honolulu, Hawai'i, USA
| | - Minjin Han
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
| | - Fuliang Hu
- College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Wei Sun
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Cheng Sun
- College of Life Sciences, Capital Normal University, Beijing, China
| | - Ze Zhang
- School of Life Sciences, Chongqing University, Chongqing, China
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14
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Baca M, Popović D, Agadzhanyan AK, Baca K, Conard NJ, Fewlass H, Filek T, Golubiński M, Horáček I, Knul MV, Krajcarz M, Krokhaleva M, Lebreton L, Lemanik A, Maul LC, Nagel D, Noiret P, Primault J, Rekovets L, Rhodes SE, Royer A, Serdyuk NV, Soressi M, Stewart JR, Strukova T, Talamo S, Wilczyński J, Nadachowski A. Ancient DNA of narrow-headed vole reveal common features of the Late Pleistocene population dynamics in cold-adapted small mammals. Proc Biol Sci 2023; 290:20222238. [PMID: 36787794 PMCID: PMC9928523 DOI: 10.1098/rspb.2022.2238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023] Open
Abstract
The narrow-headed vole, collared lemming and common vole were the most abundant small mammal species across the Eurasian Late Pleistocene steppe-tundra environment. Previous ancient DNA studies of the collared lemming and common vole have revealed dynamic population histories shaped by climatic fluctuations. To investigate the extent to which species with similar adaptations share common evolutionary histories, we generated a dataset comprised the mitochondrial genomes of 139 ancient and 6 modern narrow-headed voles from several sites across Europe and northwestern Asia covering approximately the last 100 thousand years (kyr). We inferred Bayesian time-aware phylogenies using 11 radiocarbon-dated samples to calibrate the molecular clock. Divergence of the main mtDNA lineages across the three species occurred during marine isotope stages (MIS) 7 and MIS 5, suggesting a common response of species adapted to open habitat during interglacials. We identified several time-structured mtDNA lineages in European narrow-headed vole, suggesting lineage turnover. The timing of some of these turnovers was synchronous across the three species, allowing us to identify the main drivers of the Late Pleistocene dynamics of steppe- and cold-adapted species.
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Affiliation(s)
- Mateusz Baca
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Danijela Popović
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | | | - Katarzyna Baca
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Nicholas J Conard
- Department of Early Prehistory and Quaternary Ecology and.,Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, Tübingen, Germany
| | - Helen Fewlass
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Thomas Filek
- Department of Palaeontology, University of Vienna, Vienna, Austria
| | | | - Ivan Horáček
- Department of Zoology, Charles University, Prague, Czechia
| | - Monika V Knul
- Department of Archaeology, Anthropology and Geography, University of Winchester, Winchester, UK
| | - Magdalena Krajcarz
- Institute of Archaeology, Nicolaus Copernicus University in Toruń, Toruń, Poland
| | - Maria Krokhaleva
- Institute of Plant and Animal Ecology, Ural Branch, Russian Academy of Sciences, Yekaterinburg, Russia
| | - Loïc Lebreton
- Department of Human and Environment, (HNHP) UMR 7194MNHN-CNRS-UPVD, National Museum of Natural History, Paris, France.,Catalan Institute of Human Paleoecology and Social Evolution (IPHES-CERCA), Tarragona, Spain.,Department of History and Art History, Rovira i Virgili University, Tarragona, Spain
| | - Anna Lemanik
- Institute of Systematics and Evolution of Animals, Polish Academy of Sciences, Cracow, Poland
| | - Lutz C Maul
- Senckenberg Research Station of Quaternary Palaeontology, Weimar, Germany
| | - Doris Nagel
- Department of Palaeontology, University of Vienna, Vienna, Austria
| | - Pierre Noiret
- Research Group Prehistory, University of Liège, Liège, Belgium
| | - Jérome Primault
- DRAC/SRA Poitou-Charentes, Ministry of Culture and Communications, Poitiers, France
| | - Leonid Rekovets
- Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | - Sara E Rhodes
- Interdisciplinary Center for Archaeology and Evolution of Human Behavior, University of Algavre, Faro, Portugal
| | - Aurélien Royer
- Biogéosciences, UMR 6282 CNRS, University of Burgundy, Dijon, France
| | - Natalia V Serdyuk
- Borissiak Paleontological Institute, Russian Academy of Sciences, Moscow, Russia
| | - Marie Soressi
- Faculty of Archaeology, Leiden University, Leiden, The Netherlands
| | - John R Stewart
- Faculty of Science and Technology, Bournemouth University, Poole, UK
| | - Tatiana Strukova
- Institute of Plant and Animal Ecology, Ural Branch, Russian Academy of Sciences, Yekaterinburg, Russia
| | - Sahra Talamo
- Department of Chemistry G. Ciamician, Alma Mater Studiorum, University of Bologna, Bologna, Italy
| | - Jarosław Wilczyński
- Institute of Systematics and Evolution of Animals, Polish Academy of Sciences, Cracow, Poland
| | - Adam Nadachowski
- Institute of Systematics and Evolution of Animals, Polish Academy of Sciences, Cracow, Poland
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15
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The Exceptional Presence of Megaloceros giganteus in North-Eastern Iberia and Its Palaeoecological Implications: The Case of Teixoneres Cave (Moià, Barcelona, Spain). DIVERSITY 2023. [DOI: 10.3390/d15020299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
In this article we announce the discovery of the first remains of Megaloceros giganteus found in Catalonia (north-eastern Iberia) from the Late Pleistocene: a fragment of maxillary. Dated between 35,000 and 37,000 cal BP, it is also among the youngest occurrence of this taxon in the Iberian Peninsula, while its last known occurrence is dated to the Neolithic period. Through a comparison with the giant deer of the northern Pyrenees, we analyzed the herbivore guilds in which this taxon was associated to understand the context in which it was able to enter the Iberian Peninsula. By comparing its diet with those of specimens from Northern Europe, we detail the ecological adaptations of this taxon in this new environment. We suggest that Megaloceros accompanied the migrations of cold-adapted species by taking advantage of the opening of corridors on both sides of the Pyrenees during the coldest periods of the Late Pleistocene. The diet of the Iberian individuals, which is oriented towards abrasive plants, suggests an adaptation to a different ecological niche than that found in Northern European individuals. The northern Iberian Peninsula may have been an extreme in the geographical expansion of M. giganteus. More specimens will be needed in the future to establish the variability of the southern Megaloceros populations.
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16
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Kefford BJ, Nichols SJ, Duncan RP. The cumulative impacts of anthropogenic stressors vary markedly along environmental gradients. GLOBAL CHANGE BIOLOGY 2023; 29:590-602. [PMID: 36114730 PMCID: PMC10087255 DOI: 10.1111/gcb.16435] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 07/21/2022] [Accepted: 08/25/2022] [Indexed: 06/15/2023]
Abstract
Understanding the cumulative effects of multiple stressors on biodiversity is key to managing their impacts. Stressor interactions are often studied using an additive/antagonistic/synergistic typology, aimed at identifying situations where individual stressor effects are reduced or amplified when they act in combination. Here, we analysed variation in the family richness of stream macroinvertebrates in the groups Ephemeroptera, Plecoptera and Trichoptera (EPT) at 4658 sites spanning a 32° latitudinal range in eastern Australia in relation to two largely human-induced stressors, salinity and turbidity, and two environmental gradients, temperature and slope. The cumulative and interactive effect of salinity and turbidity on EPT family richness varied across the landscape and by habitat (edge or riffle) such that we observed additive, antagonistic and synergistic outcomes depending on the environmental context. Our findings highlight the importance of understanding the consistency of multiple stressor impacts, which will involve higher-order interactions between multiple stressors and environmental factors.
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Affiliation(s)
- Ben J. Kefford
- Centre for Applied Water ScienceInstitute for Applied Ecology, University of CanberraCanberraAustralian Capital TerritoryAustralia
| | - Susan J. Nichols
- Centre for Applied Water ScienceInstitute for Applied Ecology, University of CanberraCanberraAustralian Capital TerritoryAustralia
| | - Richard P. Duncan
- Centre for Conservation Ecology and GenomicsInstitute for Applied Ecology, University of CanberraCanberraAustralian Capital TerritoryAustralia
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17
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Berlioz E, Capdepon E, Discamps E. A long-term perspective on Neanderthal environment and subsistence: Insights from the dental microwear texture analysis of hunted ungulates at Combe-Grenal (Dordogne, France). PLoS One 2023; 18:e0278395. [PMID: 36652426 PMCID: PMC9847971 DOI: 10.1371/journal.pone.0278395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 11/15/2022] [Indexed: 01/19/2023] Open
Abstract
Large bovids and cervids constituted major components of the European Middle Palaeolithic faunas and hence a key resource for Neanderthal populations. In paleoenvironmental reconstructions, red deer (Cervus elaphus) occurrence is classically considered as a tree-cover indicator while Bovinae (Bison priscus and Bos primigenius) and reindeer (Rangifer tarandus) occurrences are typically associated with open landscapes. However, insights into the ecology of extant ungulate populations show a more complex reality. Exploring the diet of past ungulates allows to better comprehend the hunting strategies of Palaeolithic populations and to reconstruct the modifications through time of past landscapes. By reflecting what animals have eaten during the last days or weeks of their life, dental microwear textures of herbivores link a population and its environment. Here we analyzed, via Dental Microwear Texture Analysis (DMTA), the diet of 50 Bos/Bison, 202 R. tarandus and 116 C. elaphus preyed upon by the Neanderthals that occupied Combe-Grenal rock-shelter, one of the most important Mousterian archaeo-sequences in southwestern France considering its long stratigraphy, abundance of faunal remains and the variations perceptible in Palaeolithic material culture. Grazers and mixed-feeders are the most represented dietary categories among Combe-Grenal's guild of herbivores, highlighting the availability, along the sequence, of open landscapes. The absence of clear changes in the use of plant resources by hunted ungulates through time, even though palaeoenvironmental changes were well-documented by previous studies along the sequence, is interpreted as resulting from the hunting of non-randomly selected prey by Neanderthals, preferentially in open environments. Thus, these results provide further insight into the hunting strategies of Neanderthals and modify our perception of potential links between subsistence and material culture. Combe-Grenal hunters "stayed in the open" through millennia, and were not forced to switch to hunting tactics and material technology adapted to close encounters in forested environments.
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Affiliation(s)
- Emilie Berlioz
- UMR5608 TRACES, Team SMP3C, Toulouse, France
- Grupo I+D+i EVOADAPTA, Universidad de Cantabria, Santander, Spain
- * E-mail:
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18
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Salis AT, Bray SCE, Lee MSY, Heiniger H, Barnett R, Burns JA, Doronichev V, Fedje D, Golovanova L, Harington CR, Hockett B, Kosintsev P, Lai X, Mackie Q, Vasiliev S, Weinstock J, Yamaguchi N, Meachen JA, Cooper A, Mitchell KJ. Lions and brown bears colonized North America in multiple synchronous waves of dispersal across the Bering Land Bridge. Mol Ecol 2022; 31:6407-6421. [PMID: 34748674 DOI: 10.1111/mec.16267] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 10/15/2021] [Accepted: 10/25/2021] [Indexed: 01/13/2023]
Abstract
The Bering Land Bridge connecting North America and Eurasia was periodically exposed and inundated by oscillating sea levels during the Pleistocene glacial cycles. This land connection allowed the intermittent dispersal of animals, including humans, between Western Beringia (far northeast Asia) and Eastern Beringia (northwest North America), changing the faunal community composition of both continents. The Pleistocene glacial cycles also had profound impacts on temperature, precipitation and vegetation, impacting faunal community structure and demography. While these palaeoenvironmental impacts have been studied in many large herbivores from Beringia (e.g., bison, mammoths, horses), the Pleistocene population dynamics of the diverse guild of carnivorans present in the region are less well understood, due to their lower abundances. In this study, we analyse mitochondrial genome data from ancient brown bears (Ursus arctos; n = 103) and lions (Panthera spp.; n = 39), two megafaunal carnivorans that dispersed into North America during the Pleistocene. Our results reveal striking synchronicity in the population dynamics of Beringian lions and brown bears, with multiple waves of dispersal across the Bering Land Bridge coinciding with glacial periods of low sea levels, as well as synchronous local extinctions in Eastern Beringia during Marine Isotope Stage 3. The evolutionary histories of these two taxa underline the crucial biogeographical role of the Bering Land Bridge in the distribution, turnover and maintenance of megafaunal populations in North America.
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Affiliation(s)
- Alexander T Salis
- Australian Centre for Ancient DNA (ACAD), School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia.,Division of Vertebrate Zoology, American Museum of Natural History, New York, New York, USA
| | - Sarah C E Bray
- Australian Centre for Ancient DNA (ACAD), School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia.,Registry of Senior Australians (ROSA), South Australian Health and Medical Research Institute (SAHMRI), Adelaide, South Australia, Australia
| | - Michael S Y Lee
- College of Science and Engineering, Flinders University, Bedford Park, South Australia, Australia.,South Australian Museum, Adelaide, South Australia, Australia
| | - Holly Heiniger
- Australian Centre for Ancient DNA (ACAD), School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Ross Barnett
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - James A Burns
- Curator Emeritus, Royal Alberta Museum, Edmonton, Alberta, Canada
| | | | - Daryl Fedje
- Department of Anthropology, University of Victoria, Victoria, B.C, Canada
| | | | - C Richard Harington
- Curator Emeritus and Research Associate, Research Division (Paleobiology), Canadian Museum of Nature, Ottawa, Canada
| | - Bryan Hockett
- US Department of Interior, Bureau of Land Management, Nevada State Office, Reno, Nevada, USA
| | - Pavel Kosintsev
- Institute of Plant and Animal Ecology, Ural Branch of the Russian Academy of Sciences, Yekaterinburg, Russia.,Department of History, Ural Federal University, Yekaterinburg, Russia
| | - Xulong Lai
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, Hubei, China
| | - Quentin Mackie
- Department of Anthropology, University of Victoria, Victoria, B.C, Canada
| | - Sergei Vasiliev
- Institute of Archaeology and Ethnography, Russian Academy of Sciences, Russia
| | - Jacobo Weinstock
- Faculty of Humanities (Archaeology), University of Southampton, UK
| | - Nobuyuki Yamaguchi
- Institute of Tropical Biodiversity and Sustainable Development, University Malaysia Terengganu, Kuala Nerus, Malaysia
| | - Julie A Meachen
- Anatomy Department, Des Moines University, Des Moines, Iowa, USA
| | - Alan Cooper
- South Australian Museum, Adelaide, South Australia, Australia
| | - Kieren J Mitchell
- Australian Centre for Ancient DNA (ACAD), School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia.,Department of Zoology, Otago Palaeogenetics Laboratory, University of Otago, Dunedin, New Zealand
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19
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Lord E, Marangoni A, Baca M, Popović D, Goropashnaya AV, Stewart JR, Knul MV, Noiret P, Germonpré M, Jimenez EL, Abramson NI, Vartanyan S, Prost S, Smirnov NG, Kuzmina EA, Olsen RA, Fedorov VB, Dalén L. Population dynamics and demographic history of Eurasian collared lemmings. BMC Ecol Evol 2022; 22:126. [PMID: 36329382 PMCID: PMC9632076 DOI: 10.1186/s12862-022-02081-y] [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: 08/23/2021] [Accepted: 10/19/2022] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND Ancient DNA studies suggest that Late Pleistocene climatic changes had a significant effect on population dynamics in Arctic species. The Eurasian collared lemming (Dicrostonyx torquatus) is a keystone species in the Arctic ecosystem. Earlier studies have indicated that past climatic fluctuations were important drivers of past population dynamics in this species. RESULTS Here, we analysed 59 ancient and 54 modern mitogenomes from across Eurasia, along with one modern nuclear genome. Our results suggest population growth and genetic diversification during the early Late Pleistocene, implying that collared lemmings may have experienced a genetic bottleneck during the warm Eemian interglacial. Furthermore, we find multiple temporally structured mitogenome clades during the Late Pleistocene, consistent with earlier results suggesting a dynamic late glacial population history. Finally, we identify a population in northeastern Siberia that maintained genetic diversity and a constant population size at the end of the Pleistocene, suggesting suitable conditions for collared lemmings in this region during the increasing temperatures associated with the onset of the Holocene. CONCLUSIONS This study highlights an influence of past warming, in particular the Eemian interglacial, on the evolutionary history of the collared lemming, along with spatiotemporal population structuring throughout the Late Pleistocene.
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Affiliation(s)
- Edana Lord
- Centre for Palaeogenetics, Svante Arrhenius Väg 20C, 10691, Stockholm, Sweden. .,Department of Zoology, Stockholm University, 10691, Stockholm, Sweden. .,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Box 50007, 10405, Stockholm, Sweden.
| | - Aurelio Marangoni
- Centre for Palaeogenetics, Svante Arrhenius Väg 20C, 10691, Stockholm, Sweden.,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Box 50007, 10405, Stockholm, Sweden
| | - Mateusz Baca
- Centre of New Technologies, University of Warsaw, S. Banacha 2C, 02-097, Warsaw, Poland
| | - Danijela Popović
- Centre of New Technologies, University of Warsaw, S. Banacha 2C, 02-097, Warsaw, Poland
| | - Anna V Goropashnaya
- Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, AK, 99775-7000, USA
| | - John R Stewart
- Faculty of Science and Technology, Bournemouth University, Talbot Campus, Fern Barrow, Poole, BH12 5BB, Dorset, UK
| | - Monika V Knul
- Department of Archaeology, Anthropology and Geography, University of Winchester, Winchester, SO22 4NR, UK
| | - Pierre Noiret
- Service de Préhistoire, Université de Liège, Place du 20 Août 7, 4000, Liège, Belgium
| | - Mietje Germonpré
- OD Earth and History of Life, Royal Belgian Institute of Natural Sciences, Vautierstraat 29, Brussels, Belgium
| | - Elodie-Laure Jimenez
- OD Earth and History of Life, Royal Belgian Institute of Natural Sciences, Vautierstraat 29, Brussels, Belgium.,School of Geosciences, University of Aberdeen, Aberdeen, Scotland
| | - Natalia I Abramson
- Department of Molecular Systematics, Zoological Institute RAS, St Petersburg, Russia
| | - Sergey Vartanyan
- Far East Branch, N.A. Shilo North-East Interdisciplinary Scientific Research Institute Russian Academy of Sciences (NEISRI FEB RAS), 685000, Magadan, Russia
| | - Stefan Prost
- Central Research Laboratories, Natural History Museum Vienna, 1010, Vienna, Austria.,Department of Cognitive Biology, University of Vienna, 1090, Vienna, Austria.,Konrad Lorenz Institute of Ethology, 1160, Vienna, Austria.,South African National Biodiversity Institute, National Zoological Garden, Pretoria, South Africa
| | - Nickolay G Smirnov
- Institute of Plant and Animal Ecology UB RAS, Russian Academy of Sciences, 202 8 Marta Street, 620144, Ekaterinburg, Russia
| | - Elena A Kuzmina
- Institute of Plant and Animal Ecology UB RAS, Russian Academy of Sciences, 202 8 Marta Street, 620144, Ekaterinburg, Russia
| | - Remi-André Olsen
- Science for Life Laboratory (SciLifeLab), Dept of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Vadim B Fedorov
- Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, AK, 99775-7000, USA
| | - Love Dalén
- Centre for Palaeogenetics, Svante Arrhenius Väg 20C, 10691, Stockholm, Sweden. .,Department of Zoology, Stockholm University, 10691, Stockholm, Sweden. .,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Box 50007, 10405, Stockholm, Sweden.
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20
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Canteri E, Brown SC, Schmidt NM, Heller R, Nogués‐Bravo D, Fordham DA. Spatiotemporal influences of climate and humans on muskox range dynamics over multiple millennia. GLOBAL CHANGE BIOLOGY 2022; 28:6602-6617. [PMID: 36031712 PMCID: PMC9804684 DOI: 10.1111/gcb.16375] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 07/28/2022] [Indexed: 06/15/2023]
Abstract
Processes leading to range contractions and population declines of Arctic megafauna during the late Pleistocene and early Holocene are uncertain, with intense debate on the roles of human hunting, climatic change, and their synergy. Obstacles to a resolution have included an overreliance on correlative rather than process-explicit approaches for inferring drivers of distributional and demographic change. Here, we disentangle the ecological mechanisms and threats that were integral in the decline and extinction of the muskox (Ovibos moschatus) in Eurasia and in its expansion in North America using process-explicit macroecological models. The approach integrates modern and fossil occurrence records, ancient DNA, spatiotemporal reconstructions of past climatic change, species-specific population ecology, and the growth and spread of anatomically modern humans. We show that accurately reconstructing inferences of past demographic changes for muskox over the last 21,000 years require high dispersal abilities, large maximum densities, and a small Allee effect. Analyses of validated process-explicit projections indicate that climatic change was the primary driver of muskox distribution shifts and demographic changes across its previously extensive (circumpolar) range, with populations responding negatively to rapid warming events. Regional analyses show that the range collapse and extinction of the muskox in Europe (~13,000 years ago) was likely caused by humans operating in synergy with climatic warming. In Canada and Greenland, climatic change and human activities probably combined to drive recent population sizes. The impact of past climatic change on the range and extinction dynamics of muskox during the Pleistocene-Holocene transition signals a vulnerability of this species to future increased warming. By better establishing the ecological processes that shaped the distribution of the muskox through space and time, we show that process-explicit macroecological models have important applications for the future conservation and management of this iconic species in a warming Arctic.
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Affiliation(s)
- Elisabetta Canteri
- The Environment Institute and School of Biological SciencesUniversity of AdelaideAdelaideSouth AustraliaAustralia
- Center for Macroecology, Evolution and ClimateGlobe Institute, University of CopenhagenCopenhagenDenmark
| | - Stuart C. Brown
- The Environment Institute and School of Biological SciencesUniversity of AdelaideAdelaideSouth AustraliaAustralia
- Section for Molecular Ecology and EvolutionGlobe Institute, University of CopenhagenCopenhagenDenmark
| | - Niels Martin Schmidt
- Department of Ecoscience and Arctic Research CentreAarhus UniversityRoskildeDenmark
| | - Rasmus Heller
- Department of Biology, Section of Computational and RNA BiologyUniversity of CopenhagenCopenhagenDenmark
| | - David Nogués‐Bravo
- Center for Macroecology, Evolution and ClimateGlobe Institute, University of CopenhagenCopenhagenDenmark
| | - Damien A. Fordham
- The Environment Institute and School of Biological SciencesUniversity of AdelaideAdelaideSouth AustraliaAustralia
- Center for Macroecology, Evolution and ClimateGlobe Institute, University of CopenhagenCopenhagenDenmark
- Center for Global Mountain BiodiversityGlobe Institute, University of CopenhagenCopenhagenDenmark
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21
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Westbury MV, Lorenzen ED. Iteratively mapping ancient
DNA
to reconstruct highly divergent mitochondrial genomes: An evaluation of software, parameters and bait reference. Methods Ecol Evol 2022. [DOI: 10.1111/2041-210x.13990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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22
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Leonardi M, Boschin F, Boscato P, Manica A. Following the niche: the differential impact of the last glacial maximum on four European ungulates. Commun Biol 2022; 5:1038. [PMID: 36175492 PMCID: PMC9523052 DOI: 10.1038/s42003-022-03993-7] [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: 02/02/2021] [Accepted: 09/14/2022] [Indexed: 11/09/2022] Open
Abstract
Predicting the effects of future global changes on species requires a better understanding of the ecological niche dynamics in response to climate; the large climatic fluctuations of the last 50,000 years can be used as a natural experiment to that aim. Here we test whether the realized niche of horse, aurochs, red deer, and wild boar changed between 47,000 and 7500 years ago using paleoecological modelling over an extensive archaeological database. We show that they all changed their niche, with species-specific responses to climate fluctuations. We also suggest that they survived the climatic turnovers thanks to their flexibility and by expanding their niche in response to the extinction of competitors and predators. Irrespective of the mechanism behind such processes, the fact that species with long generation times can change their niche over thousands of years cautions against assuming it to stay constant both when reconstructing the past and predicting the future. European megafaunal ungulates living in open habitats over the last 50,000 years showed evidence for niche change, possibly driven by climatic change and extinction of competitors and predators
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Affiliation(s)
- Michela Leonardi
- Evolutionary Ecology Group, Department of Zoology, University of Cambridge, Downing Street, Cambridge, CB2 3EJ, UK.
| | - Francesco Boschin
- U.R. Preistoria e Antropologia, Dipartimento di Scienze Fisiche della Terra e dell'Ambiente, Università degli Studi di Siena, Via Laterina 8, 53100, Siena, Italy.
| | - Paolo Boscato
- U.R. Preistoria e Antropologia, Dipartimento di Scienze Fisiche della Terra e dell'Ambiente, Università degli Studi di Siena, Via Laterina 8, 53100, Siena, Italy
| | - Andrea Manica
- Evolutionary Ecology Group, Department of Zoology, University of Cambridge, Downing Street, Cambridge, CB2 3EJ, UK
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23
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Vidal-Cordasco M, Ocio D, Hickler T, Marín-Arroyo AB. Ecosystem productivity affected the spatiotemporal disappearance of Neanderthals in Iberia. Nat Ecol Evol 2022; 6:1644-1657. [PMID: 36175541 DOI: 10.1038/s41559-022-01861-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 07/28/2022] [Indexed: 11/09/2022]
Abstract
What role did fluctuations play in biomass availability for secondary consumers in the disappearance of Neanderthals and the survival of modern humans? To answer this, we quantify the effects of stadial and interstadial conditions on ecosystem productivity and human spatiotemporal distribution patterns during the Middle to Upper Palaeolithic transition (50,000-30,000 calibrated years before the present) in Iberia. First, we used summed probability distribution, optimal linear estimation and Bayesian age modelling to reconstruct an updated timescale for the transition. Next, we executed a generalized dynamic vegetation model to estimate the net primary productivity. Finally, we developed a macroecological model validated with present-day observations to calculate herbivore abundance. The results indicate that, in the Eurosiberian region, the disappearance of Neanderthal groups was contemporaneous with a significant decrease in the available biomass for secondary consumers, and the arrival of the first Homo sapiens populations coincided with an increase in herbivore carrying capacity. During stadials, the Mediterranean region had the most stable conditions and the highest biomass of medium and medium-large herbivores. These outcomes support an ecological cause for the hiatus between the Mousterian and Aurignacian technocomplexes in Northern Iberia and the longer persistence of Neanderthals in southern latitudes.
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Affiliation(s)
- M Vidal-Cordasco
- Grupo I+D+i EvoAdapta (Evolución Humana y Adaptaciones Económicas y Ecológicas durante la Prehistoria), Departamento Ciencias Históricas, Universidad de Cantabria, Santander, Spain.
| | - D Ocio
- Mott MacDonald, Cambridge, UK
| | - T Hickler
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt am Main, Germany.,Department of Physical Geography, Goethe University, Frankfurt, Germany
| | - A B Marín-Arroyo
- Grupo I+D+i EvoAdapta (Evolución Humana y Adaptaciones Económicas y Ecológicas durante la Prehistoria), Departamento Ciencias Históricas, Universidad de Cantabria, Santander, Spain.
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24
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Bai D, Wan X, Zhang L, Campos-Arceiz A, Wei F, Zhang Z. The recent Asian elephant range expansion in Yunnan, China, is associated with climate change and enforced protection efforts in human-dominated landscapes. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.889077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Recently, the northward movement of Asian elephants (Elephas maximus) in Yunnan, China, has attracted international attention. Climate change or human disturbances have been proposed to be the key drivers, but these hypotheses have not been rigorously tested. In this study, we quantified the relationship between climate change and human impacts on the recent range expansion of Asian elephants in southwest China. We found that the first observation probability of this species in a new place during 1959–2021 had a significant and positive association with change in air temperature and human density, resulting in a movement toward a high-latitude region with a warmer climate and higher human density; however, its association with precipitation was scale-dependent in time: positive or negative during the past 10 or 5 years, respectively. Under the enforced protection policy, human-dominated areas became preferred habitats for elephants. Our results indicate that climate change and enforced protection efforts in human-dominated landscapes in the last few decades are significant drivers of the recent range expansion of Asian elephants in Yunnan, China. It is necessary to expand the current protected areas or habitat corridors toward the north or set up new reserves in the north and set up barriers between human settlements and elephant habitats to facilitate elephant movements and minimize human-elephant conflicts under accelerated global change.
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25
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Schwörer C, Leunda M, Alvarez N, Gugerli F, Sperisen C. The untapped potential of macrofossils in ancient plant DNA research. THE NEW PHYTOLOGIST 2022; 235:391-401. [PMID: 35306671 PMCID: PMC9322452 DOI: 10.1111/nph.18108] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 03/07/2022] [Indexed: 05/26/2023]
Abstract
The rapid development of ancient DNA analysis in the last decades has induced a paradigm shift in ecology and evolution. Driven by a combination of breakthroughs in DNA isolation techniques, high-throughput sequencing, and bioinformatics, ancient genome-scale data for a rapidly growing variety of taxa are now available, allowing researchers to directly observe demographic and evolutionary processes over time. However, the vast majority of paleogenomic studies still focus on human or animal remains. In this article, we make the case for a vast untapped resource of ancient plant material that is ideally suited for paleogenomic analyses: plant remains, such as needles, leaves, wood, seeds, or fruits, that are deposited in natural archives, such as lake sediments, permafrost, or even ice caves. Such plant remains are commonly found in large numbers and in stratigraphic sequence through time and have so far been used primarily to reconstruct past local species presences and abundances. However, they are also unique repositories of genetic information with the potential to revolutionize the fields of ecology and evolution by directly studying microevolutionary processes over time. Here, we give an overview of the current state-of-the-art, address important challenges, and highlight new research avenues to inspire future research.
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Affiliation(s)
- Christoph Schwörer
- Institute of Plant Sciences & Oeschger Centre for Climate Change ResearchUniversity of Bern3013BernSwitzerland
| | - Maria Leunda
- Institute of Plant Sciences & Oeschger Centre for Climate Change ResearchUniversity of Bern3013BernSwitzerland
- WSL Swiss Federal Research Institute8903BirmensdorfSwitzerland
| | - Nadir Alvarez
- Natural History Museum of Geneva1208GenevaSwitzerland
- Department of Genetics and EvolutionUniversity of Geneva1205GenevaSwitzerland
| | - Felix Gugerli
- WSL Swiss Federal Research Institute8903BirmensdorfSwitzerland
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26
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Verry AJF, Lubbe P, Mitchell KJ, Rawlence NJ. Thirty years of ancient DNA and the faunal biogeography of Aotearoa New Zealand: lessons and future directions. J R Soc N Z 2022. [DOI: 10.1080/03036758.2022.2093227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- Alexander J. F. Verry
- Otago Palaeogenetics Laboratory, Department of Zoology, University of Otago, Dunedin, New Zealand
- Centre for Anthropobiology and Genomics of Toulouse, Faculté de Médecine Purpan, Université de Toulouse, Université Paul Sabatier, Toulouse, France
| | - Pascale Lubbe
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - Kieren J. Mitchell
- Otago Palaeogenetics Laboratory, Department of Zoology, University of Otago, Dunedin, New Zealand
| | - Nicolas J. Rawlence
- Otago Palaeogenetics Laboratory, Department of Zoology, University of Otago, Dunedin, New Zealand
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27
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Birds adapted to cold conditions show greater changes in range size related to past climatic oscillations than temperate birds. Sci Rep 2022; 12:10813. [PMID: 35752649 PMCID: PMC9233688 DOI: 10.1038/s41598-022-14972-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 06/15/2022] [Indexed: 11/18/2022] Open
Abstract
Investigation of ecological responses of species to past climate oscillations provides crucial information to understand the effects of global warming. In this work, we investigated how past climate changes affected the distribution of six bird species with different climatic requirements and migratory behaviours in the Western Palearctic and in Africa. Species Distribution Models and Marine Isotopic Stage (MIS) 2 fossil occurrences of selected species were employed to evaluate the relation between changes in range size and species climatic tolerances. The Last Glacial Maximum (LGM) range predictions, generally well supported by the MIS 2 fossil occurrences, suggest that cold-dwelling species considerably expanded their distribution in the LGM, experiencing more pronounced net changes in range size compared to temperate species. Overall, the thermal niche proves to be a key ecological trait for explaining the impact of climate change in species distributions. Thermal niche is linked to range size variations due to climatic oscillations, with cold-adapted species currently suffering a more striking range reduction compared to temperate species. This work also supports the persistence of Afro-Palearctic migrations during the LGM due to the presence of climatically suitable wintering areas in Africa even during glacial maxima.
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28
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Stojak J, Jędrzejewska B. Extinction and replacement events shaped the historical biogeography of Arctic mammals in Europe: new models of species response. Mamm Rev 2022. [DOI: 10.1111/mam.12298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Joanna Stojak
- Mammal Research Institute, Polish Academy of Sciences ul. Stoczek 1, 17‐230 Białowieża Poland
- Department of Ecology and Evolutionary Biology, Paleogenomics Laboratory University of California Santa Cruz Santa Cruz CA 95064 USA
| | - Bogumiła Jędrzejewska
- Mammal Research Institute, Polish Academy of Sciences ul. Stoczek 1, 17‐230 Białowieża Poland
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29
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Speciation in a metapopulation model upon environmental changes. Ecol Modell 2022. [DOI: 10.1016/j.ecolmodel.2022.109958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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30
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Ye Z, Yuan J, Damgaard J, Berchi GM, Cianferoni F, Pintar MR, Olosutean H, Zhu X, Jiang K, Yang X, Fu S, Bu W. Climate Warming Since the Holocene Accelerates West-East Communication for the Eurasian Temperate Water Strider Species Aquarius paludum. Mol Biol Evol 2022; 39:6575397. [PMID: 35482393 PMCID: PMC9087890 DOI: 10.1093/molbev/msac089] [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: 12/02/2022] Open
Abstract
Holocene climate warming has dramatically altered biological diversity and distributions. Recent human-induced emissions of greenhouse gases will exacerbate global warming and thus induce threats to cold-adapted taxa. However, the impacts of this major climate change on transcontinental temperate species are still poorly understood. Here, we generated extensive genomic datasets for a water strider, Aquarius paludum, which was sampled across its entire distribution in Eurasia and used these datasets in combination with ecological niche modeling (ENM) to elucidate the influence of the Holocene and future climate warming on its population structure and demographic history. We found that A. paludum consisted of two phylogeographic lineages that diverged in the middle Pleistocene, which resulted in a “west–east component” genetic pattern that was probably triggered by Central Asia-Mongoxin aridification and Pleistocene glaciations. The diverged western and eastern lineages had a second contact in the Holocene, which shaped a temporary hybrid zone located at the boundary of the arid–semiarid regions of China. Future predictions detected a potentially novel northern corridor to connect the western and eastern populations, indicating west–east gene flow would possibly continue to intensify under future warming climate conditions. Further integrating phylogeographic and ENM analyses of multiple Eurasian temperate taxa based on published studies reinforced our findings on the “west–east component” genetic pattern and the predicted future northern corridor for A. paludum. Our study provided a detailed paradigm from a phylogeographic perspective of how transcontinental temperate species differ from cold-adapted taxa in their response to climate warming.
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Affiliation(s)
- Zhen Ye
- Institute of Entomology, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China
| | - Juanjuan Yuan
- College of Life Sciences, Zaozhuang University, 1 Beian Road, Shandong 277000, China
| | - Jakob Damgaard
- Natural History Museum of Denmark, Zoological Museum, Universitetsparken 15, 2100 Copenhagen Ø, Denmark
| | - Gavril Marius Berchi
- Department of Taxonomy & Ecology, Faculty of Biology & Geology, Babeş-Bolyai University, 5-7 Clinicilor Street, 400015 Cluj-Napoca, Romania.,Institute for Advanced Environmental Research, West University of Timișoara, 4 Oituz Street, 300086 Timișoara, Romania
| | - Fabio Cianferoni
- Research Institute on Terrestrial Ecosystems, National Research Council of Italy, Via Madonna del Piano 10, I-50019 Sesto Fiorentino, Italy.,Zoology, "La Specola", Natural History Museum, University of Florence, Via Romana 17, I-50125 Florence, Italy
| | - Matthew R Pintar
- Institute of Environment, Florida International University, Miami, FL, USA
| | - Horea Olosutean
- Applied Ecology Research Center, Lucian Blaga University of Sibiu, 5-7 Ion Ratiu Street, 550012 Sibiu, Romania
| | - Xiuxiu Zhu
- Institute of Entomology, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China
| | - Kun Jiang
- Institute of Entomology, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China
| | - Xin Yang
- School of Sports, Taiyuan University of Science and Technology, 66 Waliu Road, Shanxi 030024, China
| | - Siying Fu
- Institute of Entomology, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China
| | - Wenjun Bu
- Institute of Entomology, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China
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31
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Magyari EK, Gasparik M, Major I, Lengyel G, Pál I, Virág A, Korponai J, Haliuc A, Szabó Z, Pazonyi P. Mammal extinction facilitated biome shift and human population change during the last glacial termination in East-Central Europe. Sci Rep 2022; 12:6796. [PMID: 35474321 PMCID: PMC9043214 DOI: 10.1038/s41598-022-10714-x] [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: 08/03/2021] [Accepted: 04/01/2022] [Indexed: 11/16/2022] Open
Abstract
The study of local extinction times, together with the associated environmental and human population changes in the last glacial termination, provides insights into the causes of mega- and microfauna extinctions. In East-Central (EC) Europe, groups of Palaeolithic humans were present throughout the last glacial maximum, but disappeared suddenly around 15,200 cal BP. In this study cave sediment profiles dated using radiocarbon techniques and a large set of mammal bones dated directly by AMS 14C were used to determine local extinction times. These were, in turn, compared to changes in the total megafauna population of EC Europe derived from coprophilous fungi, the Epigravettian population decline, quantitative climate models, pollen and plant macrofossil inferred climate, as well as to biome reconstructions. The results suggest that the population size of large herbivores decreased in the area after 17,700 cal BP, when temperate tree abundance and warm continental steppe cover both increased in the lowlands. Boreal forest expansion started around 16,200 cal BP. Cave sediments show the decline of narrow-headed vole and arctic lemming populations specifically associated with a tundra environment at the same time and the expansion of the common vole, an inhabitant of steppes. The last dated appearance of arctic lemming was at ~ 16,640 cal BP, while that of the narrow-headed vole at ~ 13,340, and the estimated extinction time of woolly mammoth was either at 13,830 (GRIWM) or 15,210 (PHASE), and reindeer at 11,860 (GRIWM) or 12,550 cal BP (PHASE). The population decline of the large herbivore fauna slightly preceded changes in terrestrial vegetation, and likely facilitated it via a reduction in the intensity of grazing and the concomitant accumulation of plant biomass. Furthermore, it is possible to conclude that the Late Epigravettian population had high degree of quarry-fidelity; they left the basin when these mammals vanished.
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Affiliation(s)
- Enikő Katalin Magyari
- MTA-MTM-ELTE Research Group for Palaeontology, Budapest, Ludovika tér 2, 1083, Hungary. .,Department of Environmental and Landscape Geography, Eötvös Loránd University, Budapest, Pázmány Péter stny 1/c, 1117, Hungary. .,Isotope Climatology and Environmental Research Centre (ICER), Institute for Nuclear Research, Hungarian Academy of Science, Debrecen, Bem tér 18/c, 4026, Hungary.
| | - Mihály Gasparik
- Department of Palaeontology and Geology, Hungarian Natural History Museum, Budapest, Ludovika tér 2, 1083, Hungary
| | - István Major
- Isotope Climatology and Environmental Research Centre (ICER), Institute for Nuclear Research, Hungarian Academy of Science, Debrecen, Bem tér 18/c, 4026, Hungary
| | - György Lengyel
- Department of Prehistory and Archaeology, University of Miskolc, Miskolc-Egyetemváros, 3515, Hungary
| | - Ilona Pál
- Isotope Climatology and Environmental Research Centre (ICER), Institute for Nuclear Research, Hungarian Academy of Science, Debrecen, Bem tér 18/c, 4026, Hungary
| | - Attila Virág
- MTA-MTM-ELTE Research Group for Palaeontology, Budapest, Ludovika tér 2, 1083, Hungary.,Department of Mineralogy and Geology, University of Debrecen, Debrecen, Egyetem tér 1, 4032, Hungary
| | - János Korponai
- Department of Water Supply and Sewerage, University of Public Service, Baja, Bajcsy-Zsilinszky utca 12-14, 6500, Hungary.,Department of Environmental Sciences, Sapientia Hungarian University of Transylvania, Calea Turzii str. 4, 400193, Cluj-Napoca, Romania.,Department of Danube's Diversity, Institute of Aquatic Ecology, Centre for Ecological Research, Budapest, Karolina út 29, 1113, Hungary
| | - Aritina Haliuc
- Institute of Speleology, Romanian Academy, 5 Clinicilor str, 400006, Cluj-Napoca, Romania.,EPOC, UMR 5805, Université de Bordeaux, Allée Geoffroy St Hilaire Bat B18N, CS 50023, 33615, Pessac Cedex, France
| | - Zoltán Szabó
- Department of Environmental and Landscape Geography, Eötvös Loránd University, Budapest, Pázmány Péter stny 1/c, 1117, Hungary
| | - Piroska Pazonyi
- MTA-MTM-ELTE Research Group for Palaeontology, Budapest, Ludovika tér 2, 1083, Hungary
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32
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Cabrera AA, Schall E, Bérubé M, Anderwald P, Bachmann L, Berrow S, Best PB, Clapham PJ, Cunha H, Dalla Rosa L, Dias C, Findlay K, Haug T, Heide‐Jørgensen MP, Hoelzel A, Kovacs KM, Landry S, Larsen F, Lopes XM, Lydersen C, Mattila DK, Oosting T, Pace RM, Papetti C, Paspati A, Pastene LA, Prieto R, Ramp C, Robbins J, Sears R, Secchi ER, Silva MA, Simon M, Víkingsson G, Wiig Ø, Øien N, Palsbøll PJ. Strong and lasting impacts of past global warming on baleen whales and their prey. GLOBAL CHANGE BIOLOGY 2022; 28:2657-2677. [PMID: 35106859 PMCID: PMC9305191 DOI: 10.1111/gcb.16085] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 11/01/2021] [Accepted: 11/03/2021] [Indexed: 05/14/2023]
Abstract
Global warming is affecting the population dynamics and trophic interactions across a wide range of ecosystems and habitats. Translating these real-time effects into their long-term consequences remains a challenge. The rapid and extreme warming period that occurred after the Last Glacial Maximum (LGM) during the Pleistocene-Holocene transition (7-12 thousand years ago) provides an opportunity to gain insights into the long-term responses of natural populations to periods with global warming. The effects of this post-LGM warming period have been assessed in many terrestrial taxa, whereas insights into the impacts of rapid global warming on marine taxa remain limited, especially for megafauna. In order to understand how large-scale climate fluctuations during the post-LGM affected baleen whales and their prey, we conducted an extensive, large-scale analysis of the long-term effects of the post-LGM warming on abundance and inter-ocean connectivity in eight baleen whale and seven prey (fish and invertebrates) species across the Southern and the North Atlantic Ocean; two ocean basins that differ in key oceanographic features. The analysis was based upon 7032 mitochondrial DNA sequences as well as genome-wide DNA sequence variation in 100 individuals. The estimated temporal changes in genetic diversity during the last 30,000 years indicated that most baleen whale populations underwent post-LGM expansions in both ocean basins. The increase in baleen whale abundance during the Holocene was associated with simultaneous changes in their prey and climate. Highly correlated, synchronized and exponential increases in abundance in both baleen whales and their prey in the Southern Ocean were indicative of a dramatic increase in ocean productivity. In contrast, the demographic fluctuations observed in baleen whales and their prey in the North Atlantic Ocean were subtle, varying across taxa and time. Perhaps most important was the observation that the ocean-wide expansions and decreases in abundance that were initiated by the post-LGM global warming, continued for millennia after global temperatures stabilized, reflecting persistent, long-lasting impacts of global warming on marine fauna.
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Affiliation(s)
- Andrea A. Cabrera
- Groningen Institute for Evolutionary Life SciencesUniversity of GroningenGroningenThe Netherlands
- GLOBE InstituteUniversity of CopenhagenCopenhagenDenmark
| | - Elena Schall
- Groningen Institute for Evolutionary Life SciencesUniversity of GroningenGroningenThe Netherlands
| | - Martine Bérubé
- Groningen Institute for Evolutionary Life SciencesUniversity of GroningenGroningenThe Netherlands
- Center for Coastal StudiesProvincetownMassachusettsUSA
| | - Pia Anderwald
- Swiss National ParkChastè Planta‐WildenbergZernezSwitzerland
| | | | - Simon Berrow
- Marine and Freshwater Research CentreGalway‐Mayo Institute of TechnologyGalwayIreland
- Irish Whale and Dolphin GroupMerchants QuayKilrushCounty ClareIreland
| | - Peter B. Best
- Department of Zoology and EntomologyMammal Research InstituteUniversity of PretoriaHatfieldSouth Africa
| | | | - Haydée A. Cunha
- Aquatic Mammals and Bioindicators Laboratory (MAQUA)Faculty of OceanographyState University of Rio de Janeiro ‐ UERJMaracanãRio de JaneiroBrazil
- Genetics Department of the Biology InstituteState University of Rio de Janeiro ‐ UERJMaracanãRio de JaneiroBrazil
| | - Luciano Dalla Rosa
- Laboratory of Ecology and Conservation of Marine MegafaunaInstitute of OceanographyFederal University of Rio Grande‐FURGRio GrandeRio Grande do SulBrazil
| | - Carolina Dias
- Aquatic Mammals and Bioindicators Laboratory (MAQUA)Faculty of OceanographyState University of Rio de Janeiro ‐ UERJMaracanãRio de JaneiroBrazil
| | - Kenneth P. Findlay
- Department of Zoology and EntomologyMammal Research InstituteUniversity of PretoriaHatfieldSouth Africa
- Department Conservation and Marine SciencesCentre for Sustainable Oceans EconomyCape Peninsula University of TechnologyCape TownSouth Africa
| | - Tore Haug
- Research Group Marine MammalsInstitute of Marine ResearchTromsøNorway
| | | | | | | | - Scott Landry
- Center for Coastal StudiesProvincetownMassachusettsUSA
| | - Finn Larsen
- Section for Ecosystem based Marine ManagementNational Institute of Aquatic ResourcesTechnical University of DenmarkKongens LyngbyDenmark
| | - Xênia M. Lopes
- Groningen Institute for Evolutionary Life SciencesUniversity of GroningenGroningenThe Netherlands
| | | | | | - Tom Oosting
- Groningen Institute for Evolutionary Life SciencesUniversity of GroningenGroningenThe Netherlands
- School of Biological SciencesVictoria University of WellingtonWellingtonNew Zealand
| | - Richard M. Pace
- Northeast Fisheries Science CenterNational Marine Fisheries ServiceWoods HoleMassachusettsUSA
| | | | - Angeliki Paspati
- Groningen Institute for Evolutionary Life SciencesUniversity of GroningenGroningenThe Netherlands
- Hellenic Agricultural Organisation‐“DIMITRA”HerakleionCreteGreece
| | | | - Rui Prieto
- Institute of Marine Sciences – Okeanos & Institute of Marine Research ‐ IMARUniversity of the AzoresHortaPortugal
| | - Christian Ramp
- Sea Mammal Research UnitScottish Oceans InstituteUniversity of St. AndrewsScotlandUK
- Mingan Island Cetacean StudySaint LambertQuébecCanada
| | - Jooke Robbins
- Center for Coastal StudiesProvincetownMassachusettsUSA
| | - Richard Sears
- Greenland Climate Research CentreGreenland Institute of Natural ResourcesNuukGreenland
| | - Eduardo R. Secchi
- Laboratory of Ecology and Conservation of Marine MegafaunaInstitute of OceanographyFederal University of Rio Grande‐FURGRio GrandeRio Grande do SulBrazil
| | - Mónica A. Silva
- Institute of Marine Sciences – Okeanos & Institute of Marine Research ‐ IMARUniversity of the AzoresHortaPortugal
| | - Malene Simon
- Greenland Climate Research CentreGreenland Institute of Natural ResourcesNuukGreenland
| | | | - Øystein Wiig
- Natural History MuseumUniversity of OsloOsloNorway
| | - Nils Øien
- Marine Mammal DivisionInstitute of Marine ResearchBergenNorway
| | - Per J. Palsbøll
- Groningen Institute for Evolutionary Life SciencesUniversity of GroningenGroningenThe Netherlands
- Center for Coastal StudiesProvincetownMassachusettsUSA
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33
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Shadrina EG, Volpert YL, Okhlopkov IM. Introduction of Mammals in Yakutia: Analysis of Effectiveness, Prospects, and Negative Impacts. RUSSIAN JOURNAL OF BIOLOGICAL INVASIONS 2022. [DOI: 10.1134/s2075111722010131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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34
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Iijima M, Qiao Y, Lin W, Peng Y, Yoneda M, Liu J. An intermediate crocodylian linking two extant gharials from the Bronze Age of China and its human-induced extinction. Proc Biol Sci 2022; 289:20220085. [PMID: 35259993 PMCID: PMC8905159 DOI: 10.1098/rspb.2022.0085] [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] [Indexed: 01/09/2023] Open
Abstract
A solid phylogenetic framework is the basis of biological studies, yet higher level relationships are still unresolved in some major vertebrate lineages. One such group is Crocodylia, where the branching pattern of three major families (Alligatoridae, Crocodylidae and Gavialidae) has been disputed over decades due to the uncertain relationship of two slender-snouted lineages, gavialines and tomistomines. Here, we report a bizarre crocodylian from the Bronze Age of China, which shows a mosaic of gavialine and tomistomine features across the skeleton, rendering support to their sister taxon relationship as molecular works have consistently postulated. Gavialine characters of the new Chinese crocodylian include a novel configuration of the pterygoid bulla, a vocal structure known in mature male Indian gharials. Extinct gavialines have repeatedly evolved potentially male-only acoustic apparatus of various shapes, illuminating the deep history of sexual selection on acoustic signalling in a slender-snouted group of crocodylians. Lastly, a cutmark analysis combined with accelerator mass spectrometry (AMS) radiocarbon dating of bone remains demonstrated that two individuals from Shang and Zhou dynasties in Guangdong, China, suffered head injuries and decapitation. Archaeological evidence together with historical accounts suggests the human-induced extinction of this unique crocodylian only a few hundred years ago.
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Affiliation(s)
- Masaya Iijima
- School of Resource and Environmental Engineering, Hefei University of Technology, 193 Tunxi Road, Baohe, Hefei, Anhui 230009, People's Republic of China,Department of Biological Sciences, Clemson University, Clemson, SC 29634, USA,Nagoya University Museum, Furocho, Chikusa-Ku, Nagoya, Aichi 464-8601, Japan
| | - Yu Qiao
- School of Resource and Environmental Engineering, Hefei University of Technology, 193 Tunxi Road, Baohe, Hefei, Anhui 230009, People's Republic of China
| | - Wenbin Lin
- Xinhui Museum, 12 Gongyuan Road, Xinhui, Jiangmen, Guangdong 529199, People's Republic of China
| | - Youjie Peng
- Shunde Museum, Bishui Road, Shunde, Foshan, Guangdong 528300, People's Republic of China
| | - Minoru Yoneda
- The University Museum, The University of Tokyo, Hongo 7-3-1, Bunkyo, Tokyo 113-0033, Japan
| | - Jun Liu
- School of Resource and Environmental Engineering, Hefei University of Technology, 193 Tunxi Road, Baohe, Hefei, Anhui 230009, People's Republic of China
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35
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Puzachenko AY, Kirillova IV, Shidlovsky FK, Levchenko VA. Variability and Morphological Features of Woolly Rhinoceros Skulls (Coelodonta antiquitatis (Blumenbach 1799)) from Northeastern Asia in the Late Pleistocene. BIOL BULL+ 2022. [DOI: 10.1134/s1062359021140144] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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36
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Response of Iranian lizards to future climate change by poleward expansion, southern contraction, and elevation shifts. Sci Rep 2022; 12:2348. [PMID: 35149739 PMCID: PMC8837782 DOI: 10.1038/s41598-022-06330-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 01/27/2022] [Indexed: 11/28/2022] Open
Abstract
This study explores the relationships between recent Iranian lizard species distributions and the observed climate, as well as potential future distributions of species. For this purpose, an ensemble of seven algorithms was used to forecast the distributions of 30 species for the recent and future (2070) based on the averages of 14 global climate models under optimistic (RCP2.6) and pessimistic (RCP8.5) scenarios. Annual precipitation (n = 16) and annual mean temperature (n = 7) were identified as the most important variables in determining the distribution of 76.66% (23 out of 30) of the species. The consensus model predicts that the ranges of 83.33% of species (n = 25) have the potential to expand poleward at higher latitudes while preserving the majority of their recent distributions (except for four species). Furthermore, the ranges of the remaining species (n = 5) will be preserved at higher latitudes. However, they (n = 22) may contract slightly (n = 13) or excessively (n = 9) in the south of their distribution range at lower latitudes. These results indicate that species (N = 19) situated in mountainous areas such as the Zagros, Alborz, and Kopet Dagh may move or maintain their range at higher elevations as a result of future climate change. Finally, this study suggests that 30% of species (n = 9) may be threatened by future climate change and that they should be prioritized in conservation efforts.
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37
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Machado FA, Marroig G, Hubbe A. The pre-eminent role of directional selection in generating extreme morphological change in glyptodonts (Cingulata; Xenarthra). Proc Biol Sci 2022; 289:20212521. [PMID: 35042420 PMCID: PMC8767197 DOI: 10.1098/rspb.2021.2521] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 12/14/2021] [Indexed: 01/28/2023] Open
Abstract
The prevalence of stasis on macroevolution has been classically taken as evidence of the strong role of stabilizing selection in constraining morphological change. Rates of evolution calculated over longer timescales tend to fall below the expected under genetic drift, suggesting that directional selection signals are erased at longer timescales. Here, we investigated the rates of morphological evolution of the skull in a fossil lineage that underwent extreme morphological modification, the glyptodonts. Contrary to what was expected, we show here that directional selection was the primary process during the evolution of glyptodonts. Furthermore, the reconstruction of selection patterns shows that traits selected to generate a glyptodont morphology are markedly different from those operating on extant armadillos. Changes in both direction and magnitude of selection are probably tied to glyptodonts' invasion of a specialist-herbivore adaptive zone. These results suggest that directional selection might have played a more critical role in the evolution of extreme morphologies than previously imagined.
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Affiliation(s)
| | - Gabriel Marroig
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Alex Hubbe
- Departamento de Oceanografia, Instituto de Geociências, Universidade Federal da Bahia, Salvador, Brazil
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38
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Murchie TJ, Monteath AJ, Mahony ME, Long GS, Cocker S, Sadoway T, Karpinski E, Zazula G, MacPhee RDE, Froese D, Poinar HN. Collapse of the mammoth-steppe in central Yukon as revealed by ancient environmental DNA. Nat Commun 2021; 12:7120. [PMID: 34880234 PMCID: PMC8654998 DOI: 10.1038/s41467-021-27439-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Accepted: 11/22/2021] [Indexed: 12/30/2022] Open
Abstract
The temporal and spatial coarseness of megafaunal fossil records complicates attempts to to disentangle the relative impacts of climate change, ecosystem restructuring, and human activities associated with the Late Quaternary extinctions. Advances in the extraction and identification of ancient DNA that was shed into the environment and preserved for millennia in sediment now provides a way to augment discontinuous palaeontological assemblages. Here, we present a 30,000-year sedimentary ancient DNA (sedaDNA) record derived from loessal permafrost silts in the Klondike region of Yukon, Canada. We observe a substantial turnover in ecosystem composition between 13,500 and 10,000 calendar years ago with the rise of woody shrubs and the disappearance of the mammoth-steppe (steppe-tundra) ecosystem. We also identify a lingering signal of Equus sp. (North American horse) and Mammuthus primigenius (woolly mammoth) at multiple sites persisting thousands of years after their supposed extinction from the fossil record.
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Affiliation(s)
- Tyler J Murchie
- McMaster Ancient DNA Centre, McMaster University, Hamilton, Canada. .,Department of Anthropology, McMaster University, Hamilton, Canada.
| | - Alistair J Monteath
- Department of Earth and Atmospheric Sciences, University of Alberta, Edmonton, Canada.,School of Geography and Environmental Science, University of Southampton, Southampton, United Kingdom
| | - Matthew E Mahony
- Department of Earth and Atmospheric Sciences, University of Alberta, Edmonton, Canada
| | - George S Long
- McMaster Ancient DNA Centre, McMaster University, Hamilton, Canada.,Department of Biology, McMaster University, Hamilton, Canada
| | - Scott Cocker
- Department of Earth and Atmospheric Sciences, University of Alberta, Edmonton, Canada
| | - Tara Sadoway
- McMaster Ancient DNA Centre, McMaster University, Hamilton, Canada.,The Hospital for Sick Children, Toronto, Canada
| | - Emil Karpinski
- McMaster Ancient DNA Centre, McMaster University, Hamilton, Canada.,Department of Biology, McMaster University, Hamilton, Canada
| | - Grant Zazula
- Yukon Government, Palaeontology Program, Department of Tourism and Culture, Whitehorse, Canada.,Collections and Research, Canadian Museum of Nature, Ottawa, Canada
| | - Ross D E MacPhee
- Division of Vertebrate Zoology/Mammalogy, American Museum of Natural History, New York, United States
| | - Duane Froese
- Department of Earth and Atmospheric Sciences, University of Alberta, Edmonton, Canada.
| | - Hendrik N Poinar
- McMaster Ancient DNA Centre, McMaster University, Hamilton, Canada. .,Department of Anthropology, McMaster University, Hamilton, Canada. .,Department of Biochemistry, McMaster University, Hamilton, Canada. .,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Canada. .,CIFAR Humans and the Microbiome Program, Toronto, Canada.
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39
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Cappello L, Palacios JA. Adaptive Preferential Sampling in Phylodynamics With an Application to SARS-CoV-2. J Comput Graph Stat 2021; 31:541-552. [PMID: 36035966 PMCID: PMC9409340 DOI: 10.1080/10618600.2021.1987256] [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] [Indexed: 11/22/2022]
Abstract
Longitudinal molecular data of rapidly evolving viruses and pathogens provide information about disease spread and complement traditional surveillance approaches based on case count data. The coalescent is used to model the genealogy that represents the sample ancestral relationships. The basic assumption is that coalescent events occur at a rate inversely proportional to the effective population size Ne(t), a time-varying measure of genetic diversity. When the sampling process (collection of samples over time) depends on Ne(t), the coalescent and the sampling processes can be jointly modeled to improve estimation of Ne(t). Failing to do so can lead to bias due to model misspecification. However, the way that the sampling process depends on the effective population size may vary over time. We introduce an approach where the sampling process is modeled as an inhomogeneous Poisson process with rate equal to the product of Ne(t) and a time-varying coefficient, making minimal assumptions on their functional shapes via Markov random field priors. We provide efficient algorithms for inference, show the model performance vis-a-vis alternative methods in a simulation study, and apply our model to SARS-CoV-2 sequences from Los Angeles and Santa Clara counties. The methodology is implemented and available in the R package adapref. Supplementary files for this article are available online.
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Affiliation(s)
| | - Julia A. Palacios
- Department of Statistics, Stanford University, Stanford, CA
- Department of Biomedical Data Science, Stanford Medicine, Stanford, CA
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40
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Abstract
Natural history collections are invaluable repositories of biological information that provide an unrivaled record of Earth's biodiversity. Museum genomics-genomics research using traditional museum and cryogenic collections and the infrastructure supporting these investigations-has particularly enhanced research in ecology and evolutionary biology, the study of extinct organisms, and the impact of anthropogenic activity on biodiversity. However, leveraging genomics in biological collections has exposed challenges, such as digitizing, integrating, and sharing collections data; updating practices to ensure broadly optimal data extraction from existing and new collections; and modernizing collections practices, infrastructure, and policies to ensure fair, sustainable, and genomically manifold uses of museum collections by increasingly diverse stakeholders. Museum genomics collections are poised to address these challenges and, with increasingly sensitive genomics approaches, will catalyze a future era of reproducibility, innovation, and insight made possible through integrating museum and genome sciences.
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Affiliation(s)
- Daren C Card
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA; .,Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, California 95064, USA.,Howard Hughes Medical Institute, University of California, Santa Cruz, California 95064, USA
| | - Gonzalo Giribet
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA; .,Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Craig Moritz
- Centre for Biodiversity Analysis and Research School of Biology, The Australian National University, Canberra, Australian Capital Territory 0200, Australia
| | - Scott V Edwards
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA; .,Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts 02138, USA
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41
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Picin A, Benazzi S, Blasco R, Hajdinjak M, Helgen KM, Hublin JJ, Rosell J, Skoglund P, Stringer C, Talamo S. Comment on "A global environmental crisis 42,000 years ago". Science 2021; 374:eabi8330. [PMID: 34793212 PMCID: PMC7612203 DOI: 10.1126/science.abi8330] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Cooper et al. (Research Articles, 19 February 2021, p. 811) propose that the Laschamps geomagnetic inversion ~42 ka BP drove global climatic shifts, causing major behavioural changes within prehistoric groups, and events of human and megafaunal extinction. Other scientific studies indicate that this proposition is unproven from the current archaeological, paleoanthropological, and genetic records.
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Affiliation(s)
- Andrea Picin
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Stefano Benazzi
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.,Department of Cultural Heritage, University of Bologna, Ravenna 48121, Italy
| | - Ruth Blasco
- Institut Català de Paleoecologia Humana i Evolució Social (IPHES-CERCA), Zona Educacional 4, Campus Sescelades URV (Edifici W3), Tarragona 43007, Spain.,Departament d'Història i Història de l'Art, Universitat Rovira i Virgili, Tarragona 43002, Spain
| | - Mateja Hajdinjak
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.,Francis Crick Institute, London NW1 1AT, UK
| | | | - Jean-Jacques Hublin
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.,Chaire de Paléoanthropologie, Collège de France, Paris 75231, France
| | - Jordi Rosell
- Institut Català de Paleoecologia Humana i Evolució Social (IPHES-CERCA), Zona Educacional 4, Campus Sescelades URV (Edifici W3), Tarragona 43007, Spain.,Departament d'Història i Història de l'Art, Universitat Rovira i Virgili, Tarragona 43002, Spain
| | | | - Chris Stringer
- CHER, Department of Earth Sciences, Natural History Museum, London SW7 5BD, UK
| | - Sahra Talamo
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.,Department of Chemistry "G. Ciamician," University of Bologna, Bologna 40126, Italy
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Farrell MJ, Park AW, Cressler CE, Dallas T, Huang S, Mideo N, Morales-Castilla I, Davies TJ, Stephens P. The ghost of hosts past: impacts of host extinction on parasite specificity. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200351. [PMID: 34538147 PMCID: PMC8450631 DOI: 10.1098/rstb.2020.0351] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/11/2021] [Indexed: 11/29/2022] Open
Abstract
A growing body of research is focused on the extinction of parasite species in response to host endangerment and declines. Beyond the loss of parasite species richness, host extinction can impact apparent parasite host specificity, as measured by host richness or the phylogenetic distances among hosts. Such impacts on the distribution of parasites across the host phylogeny can have knock-on effects that may reshape the adaptation of both hosts and parasites, ultimately shifting the evolutionary landscape underlying the potential for emergence and the evolution of virulence across hosts. Here, we examine how the reshaping of host phylogenies through extinction may impact the host specificity of parasites, and offer examples from historical extinctions, present-day endangerment, and future projections of biodiversity loss. We suggest that an improved understanding of the impact of host extinction on contemporary host-parasite interactions may shed light on core aspects of disease ecology, including comparative studies of host specificity, virulence evolution in multi-host parasite systems, and future trajectories for host and parasite biodiversity. This article is part of the theme issue 'Infectious disease macroecology: parasite diversity and dynamics across the globe'.
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Affiliation(s)
- Maxwell J. Farrell
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | | | - Clayton E. Cressler
- School of Biological Sciences, University of Nebraska, Lincoln, NE 68588, USA
| | - Tad Dallas
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70806, USA
- Department of Biological Sciences, University of South Carolina, Columbia, SC, 29208, USA
| | - Shan Huang
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt am Main, Germany
| | - Nicole Mideo
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Ignacio Morales-Castilla
- Universidad de Alcalá, GloCEE - Global Change Ecology and Evolution Research Group, Departamento de Ciencias de la Vida, 28805 Alcalá de Henares, Madrid, Spain
| | - T. Jonathan Davies
- Department of Botany, University of British Columbia, Vancouver, BC, Canada, V6T 1Z4
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, Canada, V6T 1Z4
- Department of Botany and Plant Biotechnology, African Centre for DNA Barcoding, University of Johannesburg, Johannesburg 2092, South Africa
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43
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Fordham DA, Brown SC, Akçakaya HR, Brook BW, Haythorne S, Manica A, Shoemaker KT, Austin JJ, Blonder B, Pilowsky J, Rahbek C, Nogues-Bravo D. Process-explicit models reveal pathway to extinction for woolly mammoth using pattern-oriented validation. Ecol Lett 2021; 25:125-137. [PMID: 34738712 DOI: 10.1111/ele.13911] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 09/18/2021] [Accepted: 10/05/2021] [Indexed: 12/01/2022]
Abstract
Pathways to extinction start long before the death of the last individual. However, causes of early stage population declines and the susceptibility of small residual populations to extirpation are typically studied in isolation. Using validated process-explicit models, we disentangle the ecological mechanisms and threats that were integral in the initial decline and later extinction of the woolly mammoth. We show that reconciling ancient DNA data on woolly mammoth population decline with fossil evidence of location and timing of extinction requires process-explicit models with specific demographic and niche constraints, and a constrained synergy of climatic change and human impacts. Validated models needed humans to hasten climate-driven population declines by many millennia, and to allow woolly mammoths to persist in mainland Arctic refugia until the mid-Holocene. Our results show that the role of humans in the extinction dynamics of woolly mammoth began well before the Holocene, exerting lasting effects on the spatial pattern and timing of its range-wide extinction.
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Affiliation(s)
- Damien A Fordham
- The Environment Institute and School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia.,Center for Macroecology, Evolution, and Climate, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Stuart C Brown
- The Environment Institute and School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - H Reşit Akçakaya
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, USA
| | - Barry W Brook
- School of Natural Sciences and ARC Centre of Excellence for Australian Biodiversity and Heritage, University of Tasmania, Hobart, Tasmania, Australia
| | - Sean Haythorne
- The Environment Institute and School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Andrea Manica
- Department of Zoology, University of Cambridge, Cambridge, England
| | - Kevin T Shoemaker
- Department of Natural Resources and Environmental Science, University of Nevada, Reno, Nevada, USA
| | - Jeremy J Austin
- The Environment Institute and School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Benjamin Blonder
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, California, USA
| | - Julia Pilowsky
- The Environment Institute and School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia.,Center for Macroecology, Evolution, and Climate, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Carsten Rahbek
- Center for Macroecology, Evolution, and Climate, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,Department of Life Sciences, Imperial College London, Ascot, England.,Danish Institute for Advanced Study, University of Southern Denmark, Odense, Denmark.,Institute of Ecology, Peking University, Beijing, China
| | - David Nogues-Bravo
- Center for Macroecology, Evolution, and Climate, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
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44
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Baca M, Popović D, Lemanik A, Fewlass H, Talamo S, Zima J, Ridush B, Popov V, Nadachowski A. The Tien Shan vole ( Microtus ilaeus; Rodentia: Cricetidae) as a new species in the Late Pleistocene of Europe. Ecol Evol 2021; 11:16113-16125. [PMID: 34824815 PMCID: PMC8601874 DOI: 10.1002/ece3.8289] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 10/12/2021] [Indexed: 11/09/2022] Open
Abstract
Grey voles (subgenus Microtus) represent a complex of at least seven closely related and partly cryptic species. The range of these species extends from the Atlantic to the Altai Mountains, but most of them occur east of the Black Sea. Using ancient DNA analyses of the Late Pleistocene specimens, we identified a new mtDNA lineage of grey voles in Europe. Phylogenetic analysis of mitochondrial DNA cytochrome b sequences from 23 voles from three caves, namely, Emine-Bair-Khosar (Crimea, Ukraine), Cave 16 (Bulgaria), and Bacho Kiro (Bulgaria), showed that 14 specimens form a previously unrecognized lineage, sister to the Tien Shan vole. The average sequence divergence of this lineage and the extant Tien Shan vole was 4.8%, which is similar to the divergence of grey vole forms, which are considered distinct species or being on the verge of speciation; M. arvalis and M. obscurus or M. mystacinus and M. rossiaemeridionalis. We estimated the time to the most recent common ancestor of the grey voles to be 0.66 Ma, which is over twice the recent estimates, while the divergence of the extant Tien Shan vole and the new lineage to be 0.29 Ma. Our discovery suggests that grey voles may have been more diversified in the past and that their ranges may have differed substantially from current ones. It also underlines the utility of ancient DNA to decipher the evolutionary history of voles.
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Affiliation(s)
- Mateusz Baca
- Centre of New TechnologiesUniversity of WarsawWarszawaPoland
| | | | - Anna Lemanik
- Institute of Systematics and Evolution of AnimalsPolish Academy of SciencesKrakówPoland
| | - Helen Fewlass
- Department of Human EvolutionMax Planck Institute for Evolutionary AnthropologyLeipzigGermany
| | - Sahra Talamo
- Department of Human EvolutionMax Planck Institute for Evolutionary AnthropologyLeipzigGermany
- Department of Chemistry G. CiamicianUniversity of BolognaBolognaItaly
| | - Jan Zima
- Institute of Vertebrate BiologyAcademy of Sciences of Czech RepublicBrnoCzech Republic
| | - Bogdan Ridush
- Department of Physical Geography, Geomorphology and PaleogeographyYuriy Fedkovych Chernivtsi National UniversityChernivtsiUkraine
| | - Vasil Popov
- Institute of Biodiversity and Ecosystem ResearchBulgarian Academy of SciencesSophiaBulgaria
| | - Adam Nadachowski
- Institute of Systematics and Evolution of AnimalsPolish Academy of SciencesKrakówPoland
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45
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Brüniche-Olsen A, Kellner KF, Belant JL, DeWoody JA. Life-history traits and habitat availability shape genomic diversity in birds: implications for conservation. Proc Biol Sci 2021; 288:20211441. [PMID: 34702080 PMCID: PMC8548786 DOI: 10.1098/rspb.2021.1441] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 10/06/2021] [Indexed: 12/15/2022] Open
Abstract
More than 25% of species assessed by the International Union for Conservation of Nature (IUCN) are threatened with extinction. Understanding how environmental and biological processes have shaped genomic diversity may inform management practices. Using 68 extant avian species, we parsed the effects of habitat availability and life-history traits on genomic diversity over time to provide a baseline for conservation efforts. We used published whole-genome sequence data to estimate overall genomic diversity as indicated by historical long-term effective population sizes (Ne) and current genomic variability (H), then used environmental niche modelling to estimate Pleistocene habitat dynamics for each species. We found that Ne and H were positively correlated with habitat availability and related to key life-history traits (body mass and diet), suggesting the latter contribute to the overall genomic variation. We found that H decreased with increasing species extinction risk, suggesting that H may serve as a leading indicator of demographic trends related to formal IUCN conservation status in birds. Our analyses illustrate that genome-wide summary statistics estimated from sequence data reflect meaningful ecological attributes relevant to species conservation.
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Affiliation(s)
- Anna Brüniche-Olsen
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, 2200 KBH N Copenhagen, Denmark
| | - Kenneth F. Kellner
- Global Wildlife Conservation Center, State University of New York College of Environmental Science and Forestry, Syracuse, NY 13210, USA
| | - Jerrold L. Belant
- Global Wildlife Conservation Center, State University of New York College of Environmental Science and Forestry, Syracuse, NY 13210, USA
| | - J. Andrew DeWoody
- Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN 47905, USA
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47905, USA
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46
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Bacon AM, Bourgon N, Welker F, Cappellini E, Fiorillo D, Tombret O, Thi Mai Huong N, Anh Tuan N, Sayavonkhamdy T, Souksavatdy V, Sichanthongtip P, Antoine PO, Duringer P, Ponche JL, Westaway K, Joannes-Boyau R, Boesch Q, Suzzoni E, Frangeul S, Patole-Edoumba E, Zachwieja A, Shackelford L, Demeter F, Hublin JJ, Dufour É. A multi-proxy approach to exploring Homo sapiens' arrival, environments and adaptations in Southeast Asia. Sci Rep 2021; 11:21080. [PMID: 34702921 PMCID: PMC8548499 DOI: 10.1038/s41598-021-99931-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 10/05/2021] [Indexed: 01/29/2023] Open
Abstract
The capability of Pleistocene hominins to successfully adapt to different types of tropical forested environments has long been debated. In order to investigate environmental changes in Southeast Asia during a critical period for the turnover of hominin species, we analysed palaeoenvironmental proxies from five late Middle to Late Pleistocene faunas. Human teeth discoveries have been reported at Duoi U'Oi, Vietnam (70-60 ka) and Nam Lot, Laos (86-72 ka). However, the use of palaeoproteomics allowed us to discard the latter, and, to date, no human remains older than ~ 70 ka are documented in the area. Our findings indicate that tropical rainforests were highly sensitive to climatic changes over that period, with significant fluctuations of the canopy forests. Locally, large-bodied faunas were resilient to these fluctuations until the cooling period of the Marine Isotope Stage 4 (MIS 4; 74-59 ka) that transformed the overall biotope. Then, under strong selective pressures, populations with new phenotypic characteristics emerged while some other species disappeared. We argue that this climate-driven shift offered new foraging opportunities for hominins in a novel rainforest environment and was most likely a key factor in the settlement and dispersal of our species during MIS 4 in SE Asia.
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Affiliation(s)
- Anne-Marie Bacon
- grid.508487.60000 0004 7885 7602UMR 8045 BABEL, CNRS, Université de Paris, Faculté de Chirurgie dentaire, 1 rue Maurice Arnoux, 92120 Montrouge, France
| | - Nicolas Bourgon
- grid.419518.00000 0001 2159 1813Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany ,grid.5802.f0000 0001 1941 7111Applied and Analytical Palaeontology, Institute of Geosciences, Johannes Gutenberg University, Mainz, Germany
| | - Frido Welker
- grid.5254.60000 0001 0674 042XSection for Evolutionary Genomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Enrico Cappellini
- grid.5254.60000 0001 0674 042XSection for Evolutionary Genomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Denis Fiorillo
- UMR 7209 Archéozoologie, Archéobotanique: Sociétés, Pratiques, Environnements, Muséum National d’Histoire Naturelle, CNRS, Paris, France
| | - Olivier Tombret
- UMR 7209 Archéozoologie, Archéobotanique: Sociétés, Pratiques, Environnements, Muséum National d’Histoire Naturelle, CNRS, Paris, France
| | - Nguyen Thi Mai Huong
- Anthropological and Palaeoenvironmental Department, Institute of Archaeology, Hoan Kiem District, Ha Noi, Vietnam
| | - Nguyen Anh Tuan
- Anthropological and Palaeoenvironmental Department, Institute of Archaeology, Hoan Kiem District, Ha Noi, Vietnam
| | - Thongsa Sayavonkhamdy
- Department of Heritage, Ministry of Information, Culture and Tourism, Vientiane, Laos
| | - Viengkeo Souksavatdy
- Department of Heritage, Ministry of Information, Culture and Tourism, Vientiane, Laos
| | | | - Pierre-Olivier Antoine
- grid.121334.60000 0001 2097 0141Institut des Sciences de l’Évolution de Montpellier, Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | - Philippe Duringer
- grid.11843.3f0000 0001 2157 9291Ecole et Observatoire des Sciences de la Terre (EOST Géologie), Institut de Physique du Globe de Strasbourg (IPGS) (CNRS/UMR 7516), Institut de Géologie, Université de Strasbourg, Strasbourg, France
| | - Jean-Luc Ponche
- grid.463965.b0000 0004 0452 6077UMR 7362 Laboratoire Image Ville et Environnement, Institut de Géologie, Strasbourg, France
| | - Kira Westaway
- grid.1004.50000 0001 2158 5405Department of Earth and Environmental Sciences, Traps’ MQ Luminescence Dating Facility, Macquarie University, Sydney, Australia
| | - Renaud Joannes-Boyau
- grid.1031.30000000121532610Geoarchaeology & Archaeometry Research Group, Southern Cross University, Lismore, Australia ,grid.458456.e0000 0000 9404 3263Institute of Vertebrate Paleontology and Paleoanthropology (IVPP) of the Chinese Academy of Sciences, Beijing, China
| | - Quentin Boesch
- grid.11843.3f0000 0001 2157 9291Ecole et Observatoire des Sciences de la Terre (EOST Géologie), Institut de Physique du Globe de Strasbourg (IPGS) (CNRS/UMR 7516), Institut de Géologie, Université de Strasbourg, Strasbourg, France
| | - Eric Suzzoni
- Spitteurs Pan, Technical Cave Supervision and Exploration, La Chapelle-en-Vercors, France
| | - Sébastien Frangeul
- Spitteurs Pan, Technical Cave Supervision and Exploration, La Chapelle-en-Vercors, France
| | - Elise Patole-Edoumba
- grid.410350.30000 0001 2174 9334Muséum d’Histoire Naturelle, La Rochelle, France
| | - Alexandra Zachwieja
- grid.17635.360000000419368657Department of Biomedical Sciences, University of Minnesota Medical School, Duluth, MN USA
| | - Laura Shackelford
- grid.35403.310000 0004 1936 9991Department of Anthropology, University of Illinois at Urbana-Champaign, Urbana, IL USA
| | - Fabrice Demeter
- grid.452548.a0000 0000 9817 5300Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, Copenhagen, Denmark ,UMR 7206 Eco-Anthropologie, Muséum National d’Histoire Naturelle, CNRS, Paris, France
| | - Jean-Jacques Hublin
- grid.419518.00000 0001 2159 1813Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany ,grid.410533.00000 0001 2179 2236Collège de France, Chaire de Paléoanthropologie, Paris, France
| | - Élise Dufour
- UMR 7209 Archéozoologie, Archéobotanique: Sociétés, Pratiques, Environnements, Muséum National d’Histoire Naturelle, CNRS, Paris, France
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47
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Zeller U, Göttert T. Humans, megafauna and landscape structure – Rock engravings from Namibia encourage a comparative approach to central Europe and southern Africa. VERTEBRATE ZOOLOGY 2021. [DOI: 10.3897/vz.71.e72811] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
This paper deals with reflections that arose after observing prehistoric rock engravings at different locations in Namibia. These observations stimulated comparative considerations with focus on southern Africa and central Europe. Similar to the Aurignacian rock art of European origin, the most common motifs in the Namibian rock engravings are large animals. While in Europe, the species that served as a blueprint for the illustration of Aurignacian rock art have mostly disappeared, the megafauna illustrated on the rock engravings in Namibia can still be found in the immediate vicinity of the rock art. Against this background, we discuss and further develop a comparative regional approach. We reconstruct and evaluate the suitability of African savannas and still-existing megafauna communities as an appropriate reference-frame for natural European grassland systems and extinct associated warm-adapted megafauna (Eemian Interglacial megafauna). Special attention is laid on the unique situation in Africa in the light of a global extinction wave of megafauna following increasing human activity in the Late Quaternary. This leads us to discuss the use of domesticated ungulates as surrogate taxa to fulfill ecosystem functions in Europe as part of concepts termed “rewilding” or “naturalistic grazing”. After critically examining these concepts, we conclude that using domesticated forms as representatives of extinct or locally disappeared species in Europe has its justification to some extent. If, however, the naturally occurring megaherbivore community still exists (Africa), these naturally occurring species should be given priority due to their organismic abilities and limitations adapted to the harsh conditions in their specific environment. Finally, we discuss the application of (transboundary) protected areas as effective instruments to mitigate human-wildlife conflicts. A holistic approach, including nature conservation and preservation of cultural achievements (domesticated forms, grazing systems), appears promising for the effective protection of the natural African savanna ecosystems with their unique fauna elements, as illustrated in rock engravings that inspired us to write this paper.
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48
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Pedersen SH, Bentzen TW, Reinking AK, Liston GE, Elder K, Lenart EA, Prichard AK, Welker JM. Quantifying effects of snow depth on caribou winter range selection and movement in Arctic Alaska. MOVEMENT ECOLOGY 2021; 9:48. [PMID: 34551820 PMCID: PMC8456671 DOI: 10.1186/s40462-021-00276-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 07/18/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Caribou and reindeer across the Arctic spend more than two thirds of their lives moving in snow. Yet snow-specific mechanisms driving their winter ecology and potentially influencing herd health and movement patterns are not well known. Integrative research coupling snow and wildlife sciences using observations, models, and wildlife tracking technologies can help fill this knowledge void. METHODS Here, we quantified the effects of snow depth on caribou winter range selection and movement. We used location data of Central Arctic Herd (CAH) caribou in Arctic Alaska collected from 2014 to 2020 and spatially distributed and temporally evolving snow depth data produced by SnowModel. These landscape-scale (90 m), daily snow depth data reproduced the observed spatial snow-depth variability across typical areal extents occupied by a wintering caribou during a 24-h period. RESULTS We found that fall snow depths encountered by the herd north of the Brooks Range exerted a strong influence on selection of two distinct winter range locations. In winters with relatively shallow fall snow depth (2016/17, 2018/19, and 2019/20), the majority of the CAH wintered on the tundra north of the Brooks Range mountains. In contrast, during the winters with relatively deep fall snow depth (2014/15, 2015/16, and 2017/18), the majority of the CAH caribou wintered in the mountainous boreal forest south of the Brooks Range. Long-term (19 winters; 2001-2020) monitoring of CAH caribou winter distributions confirmed this relationship. Additionally, snow depth affected movement and selection differently within these two habitats: in the mountainous boreal forest, caribou avoided areas with deeper snow, but when on the tundra, snow depth did not trigger significant deep-snow avoidance. In both wintering habitats, CAH caribou selected areas with higher lichen abundance, and they moved significantly slower when encountering deeper snow. CONCLUSIONS In general, our findings indicate that regional-scale selection of winter range is influenced by snow depth at or prior to fall migration. During winter, daily decision-making within the winter range is driven largely by snow depth. This integrative approach of coupling snow and wildlife observations with snow-evolution and caribou-movement modeling to quantify the multi-facetted effects of snow on wildlife ecology is applicable to caribou and reindeer herds throughout the Arctic.
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Affiliation(s)
- Stine Højlund Pedersen
- Department of Biological Sciences, University of Alaska Anchorage, Anchorage, AK, 99508, USA.
- Cooperative Institute for Research in the Atmosphere, Colorado State University, Fort Collins, CO, 80523, USA.
| | | | - Adele K Reinking
- Cooperative Institute for Research in the Atmosphere, Colorado State University, Fort Collins, CO, 80523, USA
| | - Glen E Liston
- Cooperative Institute for Research in the Atmosphere, Colorado State University, Fort Collins, CO, 80523, USA
| | - Kelly Elder
- US Forest Service, Rocky Mountain Research Station, Fort Collins, CO, 80526, USA
| | | | | | - Jeffrey M Welker
- Department of Biological Sciences, University of Alaska Anchorage, Anchorage, AK, 99508, USA
- Ecology and Genetics Research Unit, University of Oulu, 90014, Oulu, Finland
- UArctic, University of the Arctic, 96101, Rovaniemi, Finland
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49
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Taylor RS, Manseau M, Klütsch CFC, Polfus JL, Steedman A, Hervieux D, Kelly A, Larter NC, Gamberg M, Schwantje H, Wilson PJ. Population dynamics of caribou shaped by glacial cycles before the last glacial maximum. Mol Ecol 2021; 30:6121-6143. [PMID: 34482596 PMCID: PMC9293238 DOI: 10.1111/mec.16166] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 08/18/2021] [Accepted: 08/23/2021] [Indexed: 12/04/2022]
Abstract
Pleistocene glacial cycles influenced the diversification of high‐latitude wildlife species through recurrent periods of range contraction, isolation, divergence, and expansion from refugia and subsequent admixture of refugial populations. We investigate population size changes and the introgressive history of caribou (Rangifer tarandus) in western Canada using 33 whole genome sequences coupled with larger‐scale mitochondrial data. We found that a major population expansion of caribou occurred starting around 110,000 years ago (kya), the start of the last glacial period. Additionally, we found effective population sizes of some caribou reaching ~700,000 to 1,000,000 individuals, one of the highest recorded historical effective population sizes for any mammal species thus far. Mitochondrial analyses dated introgression events prior to the LGM dating to 20–30 kya and even more ancient at 60 kya, coinciding with colder periods with extensive ice coverage, further demonstrating the importance of glacial cycles and events prior to the LGM in shaping demographic history. Reconstructing the origins and differential introgressive history has implications for predictions on species responses under climate change. Our results have implications for other whole genome analyses using pairwise sequentially Markovian coalescent (PSMC) analyses, as well as highlighting the need to investigate pre‐LGM demographic patterns to fully reconstruct the origin of species diversity, especially for high‐latitude species.
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Affiliation(s)
- Rebecca S Taylor
- Biology Department, Trent University, Peterborough, Ontario, Canada
| | - Micheline Manseau
- Biology Department, Trent University, Peterborough, Ontario, Canada.,Landscape Science and Technology, Environment and Climate Change Canada, Ottawa, Ontario, Canada
| | | | - Jean L Polfus
- Biology Department, Trent University, Peterborough, Ontario, Canada
| | - Audrey Steedman
- Parks Canada, Government of Canada, Winnipeg, Manitoba, Canada
| | - Dave Hervieux
- Department of Environment and Parks, Government of Alberta, Grande Prairie, Alberta, Canada
| | - Allicia Kelly
- Department of Environment and Natural Resources, Government of the Northwest Territories, Fort Smith, Northwest Territories, Canada
| | - Nicholas C Larter
- Department of Environment and Natural Resources, Government of the Northwest Territories, Fort Simpson, Northwest Territories, Canada
| | | | - Helen Schwantje
- BC Ministry of Forest, Lands, Natural Resource Operations, and Rural Development, Nanaimo, British Columbia, Canada
| | - Paul J Wilson
- Biology Department, Trent University, Peterborough, Ontario, Canada
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50
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Dussex N, Bergfeldt N, de Anca Prado V, Dehasque M, Díez-Del-Molino D, Ersmark E, Kanellidou F, Larsson P, Lemež Š, Lord E, Mármol-Sánchez E, Meleg IN, Måsviken J, Naidoo T, Studerus J, Vicente M, von Seth J, Götherström A, Dalén L, Heintzman PD. Integrating multi-taxon palaeogenomes and sedimentary ancient DNA to study past ecosystem dynamics. Proc Biol Sci 2021; 288:20211252. [PMID: 34428961 PMCID: PMC8385357 DOI: 10.1098/rspb.2021.1252] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Ancient DNA (aDNA) has played a major role in our understanding of the past. Important advances in the sequencing and analysis of aDNA from a range of organisms have enabled a detailed understanding of processes such as past demography, introgression, domestication, adaptation and speciation. However, to date and with the notable exception of microbiomes and sediments, most aDNA studies have focused on single taxa or taxonomic groups, making the study of changes at the community level challenging. This is rather surprising because current sequencing and analytical approaches allow us to obtain and analyse aDNA from multiple source materials. When combined, these data can enable the simultaneous study of multiple taxa through space and time, and could thus provide a more comprehensive understanding of ecosystem-wide changes. It is therefore timely to develop an integrative approach to aDNA studies by combining data from multiple taxa and substrates. In this review, we discuss the various applications, associated challenges and future prospects of such an approach.
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Affiliation(s)
- Nicolas Dussex
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Department of Zoology, Stockholm University, Stockholm, Sweden.,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Nora Bergfeldt
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Department of Zoology, Stockholm University, Stockholm, Sweden.,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | | | - Marianne Dehasque
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Department of Zoology, Stockholm University, Stockholm, Sweden.,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - David Díez-Del-Molino
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Erik Ersmark
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Foteini Kanellidou
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden
| | - Petter Larsson
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Špela Lemež
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden
| | - Edana Lord
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Department of Zoology, Stockholm University, Stockholm, Sweden.,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Emilio Mármol-Sánchez
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Ioana N Meleg
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.,'Emil Racoviță' Institute of Speleology of the Romanian Academy, Calea 13 Septembrie, nr. 13, 050711, Sector 5, Bucharest, Romania.,Emil. G. Racoviță Institute, Babeș-Bolyai University, Clinicilor 5-7, 400006 Cluj-Napoca, Romania
| | - Johannes Måsviken
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Department of Zoology, Stockholm University, Stockholm, Sweden.,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Thijessen Naidoo
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden.,Ancient DNA Unit, SciLifeLab, Stockholm and Uppsala, Sweden
| | - Jovanka Studerus
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden
| | - Mário Vicente
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Johanna von Seth
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Department of Zoology, Stockholm University, Stockholm, Sweden.,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Anders Götherström
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Love Dalén
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Department of Zoology, Stockholm University, Stockholm, Sweden.,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Peter D Heintzman
- The Arctic University Museum of Norway, The Arctic University of Norway, 9037 Tromsø, Norway
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