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Wang X, Pei J, Xiong L, Bao P, Chu M, Ma X, La Y, Liang C, Yan P, Guo X. Genetic diversity, phylogeography, and maternal origin of yak (Bos grunniens). BMC Genomics 2024; 25:481. [PMID: 38750421 PMCID: PMC11097540 DOI: 10.1186/s12864-024-10378-z] [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: 12/26/2023] [Accepted: 05/06/2024] [Indexed: 05/18/2024] Open
Abstract
BACKGROUND There is no consensus as to the origin of the domestic yak (Bos grunniens). Previous studies on yak mitochondria mainly focused on mitochondrial displacement loop (D-loop), a region with low phylogenetic resolution. Here, we analyzed the entire mitochondrial genomes of 509 yaks to obtain greater phylogenetic resolution and a comprehensive picture of geographical diversity. RESULTS A total of 278 haplotypes were defined in 509 yaks from 21 yak breeds. Among them, 28 haplotypes were shared by different varieties, and 250 haplotypes were unique to specific varieties. The overall haplotype diversity and nucleotide diversity of yak were 0.979 ± 0.0039 and 0.00237 ± 0.00076, respectively. Phylogenetic tree and network analysis showed that yak had three highly differentiated genetic branches with high support rate. The differentiation time of clades I and II were about 0.4328 Ma, and the differentiation time of clades (I and II) and III were 0.5654 Ma. Yushu yak is shared by all haplogroups. Most (94.70%) of the genetic variation occurred within populations, and only 5.30% of the genetic variation occurred between populations. The classification showed that yaks and wild yaks were first clustered together, and yaks were clustered with American bison as a whole. Altitude had the highest impact on the distribution of yaks. CONCLUSIONS Yaks have high genetic diversity and yak populations have experienced population expansion and lack obvious phylogeographic structure. During the glacial period, yaks had at least three or more glacial refugia.
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Affiliation(s)
- Xingdong Wang
- Key Laboratory of Yak Breeding in Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, 730050, P.R. China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou, 730050, P.R. China
| | - Jie Pei
- Key Laboratory of Yak Breeding in Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, 730050, P.R. China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou, 730050, P.R. China
| | - Lin Xiong
- Key Laboratory of Yak Breeding in Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, 730050, P.R. China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou, 730050, P.R. China
| | - Pengjia Bao
- Key Laboratory of Yak Breeding in Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, 730050, P.R. China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou, 730050, P.R. China
| | - Min Chu
- Key Laboratory of Yak Breeding in Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, 730050, P.R. China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou, 730050, P.R. China
| | - Xiaoming Ma
- Key Laboratory of Yak Breeding in Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, 730050, P.R. China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou, 730050, P.R. China
| | - Yongfu La
- Key Laboratory of Yak Breeding in Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, 730050, P.R. China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou, 730050, P.R. China
| | - Chunnian Liang
- Key Laboratory of Yak Breeding in Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, 730050, P.R. China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou, 730050, P.R. China
| | - Ping Yan
- Key Laboratory of Yak Breeding in Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, 730050, P.R. China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou, 730050, P.R. China
| | - Xian Guo
- Key Laboratory of Yak Breeding in Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, 730050, P.R. China.
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou, 730050, P.R. China.
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2
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Santoro A, Santolamazza F, Cacciò SM, La Rosa G, Antolová D, Auer H, Bagrade G, Bandelj P, Basso W, Beck R, Citterio CV, Davidson RK, Deksne G, Frey CF, Fuglei E, Glawischnig W, Gottstein B, Harna J, Huus Petersen H, Karamon J, Jansen F, Jarošová J, Jokelainen P, Lundström-Stadelmann B, Maksimov P, Miljević M, Miterpáková M, Moks E, Origgi F, Ozolina Z, Ryser MP, Romig T, Šarkūnas M, Scorrano N, Saarma U, Šnábel V, Sréter T, Umhang G, Vengušt G, Žele Vengušt D, Casulli A. Mitochondrial genetic diversity and phylogenetic relationships of Echinococcus multilocularis in Europe. Int J Parasitol 2024; 54:233-245. [PMID: 38246405 DOI: 10.1016/j.ijpara.2024.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 11/09/2023] [Accepted: 01/14/2024] [Indexed: 01/23/2024]
Abstract
The cestode Echinococcus multilocularis is the causative agent of alveolar echinococcosis, a fatal zoonotic parasitic disease of the northern hemisphere. Red foxes are the main reservoir hosts and, likely, the main drivers of the geographic spread of the disease in Europe. Knowledge of genetic relationships among E. multilocularis isolates at a European scale is key to understanding the dispersal characteristics of E. multilocularis. Hence, the present study aimed to describe the genetic diversity of E. multilocularis isolates obtained from different host species in 19 European countries. Based on the analysis of complete nucleotide sequences of the cob, atp6, nad2, nad1 and cox1 mitochondrial genes (4,968 bp), 43 haplotypes were inferred. Four haplotypes represented 62.56 % of the examined isolates (142/227), and one of these four haplotypes was found in each country investigated, except Svalbard, Norway. While the haplotypes from Svalbard were markedly different from all the others, mainland Europe appeared to be dominated by two main clusters, represented by most western, central and eastern European countries, and the Baltic countries and northeastern Poland, respectively. Moreover, one Asian-like haplotype was identified in Latvia and northeastern Poland. To better elucidate the presence of Asian genetic variants of E. multilocularis in Europe, and to obtain a more comprehensive Europe-wide coverage, further studies, including samples from endemic regions not investigated in the present study, especially some eastern European countries, are needed. Further, the present work proposes historical causes that may have contributed to shaping the current genetic variability of E. multilocularis in Europe.
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Affiliation(s)
- Azzurra Santoro
- European Union Reference Laboratory for Parasites, Department of Infectious Diseases, Istituto Superiore Di Sanità, Viale Regina Elena 299, 00161 Rome, Italy; WHO Collaborating Centre for the Epidemiology, Detection and Control of Cystic and Alveolar Echinococcosis, Department of Infectious Diseases, Istituto Superiore Di Sanità, Viale Regina Elena 299, 00161 Rome, Italy.
| | - Federica Santolamazza
- European Union Reference Laboratory for Parasites, Department of Infectious Diseases, Istituto Superiore Di Sanità, Viale Regina Elena 299, 00161 Rome, Italy; WHO Collaborating Centre for the Epidemiology, Detection and Control of Cystic and Alveolar Echinococcosis, Department of Infectious Diseases, Istituto Superiore Di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - Simone M Cacciò
- European Union Reference Laboratory for Parasites, Department of Infectious Diseases, Istituto Superiore Di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - Giuseppe La Rosa
- European Union Reference Laboratory for Parasites, Department of Infectious Diseases, Istituto Superiore Di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - Daniela Antolová
- Institute of Parasitology, Slovak Academy of Sciences, Košice, Hlinkova 3, 040 01 Košice, Slovakia
| | - Herbert Auer
- Medical Parasitology, Institute of Specific Prophylaxis and Tropical Medicine, Center of Pathophysiology, Infectiology and Immunology, Medical University Vienna, Kinderspitalgasse 15, 1090 Vienna, Austria
| | - Guna Bagrade
- Latvian State Forest Research Institute "Silava", Wildlife Management Research Group, Salaspils, Rigas Street 111, LV-2169 Salaspils, Latvia
| | - Petra Bandelj
- Institute of Microbiology and Parasitology, Veterinary Faculty, University of Ljubljana, Gerbičeva 60, 1000 Ljubljana, Slovenia
| | - Walter Basso
- Institute of Parasitology, Vetsuisse Faculty, University of Bern, Länggassstrasse 122, CH-3012 Bern, Switzerland
| | - Relja Beck
- Croatian Veterinary Institute, Laboratory for Parasitology, 10000 Zagreb, Croatia
| | - Carlo V Citterio
- Centro Specialistico Fauna Selvatica, SCT2-Belluno, Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Via Cappellari 44/A, 32100 Belluno, Italy
| | | | - Gunita Deksne
- Institute of Food Safety, Animal Health and Environment "BIOR", Lejupes Street 3, Riga LV-1076, Latvia; Faculty of Biology, University of Lavia, Jelgavas Street 1, Riga LV-1004, Latvia
| | - Caroline F Frey
- Institute of Parasitology, Vetsuisse Faculty, University of Bern, Länggassstrasse 122, CH-3012 Bern, Switzerland
| | - Eva Fuglei
- Norwegian Polar Institute, Fram Centre, NO-9296 Tromsø, Norway
| | - Walter Glawischnig
- Institute for Veterinary Disease Control Innsbruck, Austrian Agency for Health and Food Safety, Technikerstraße 70, 6020 Innsbruck, Austria
| | - Bruno Gottstein
- Institute of Parasitology, Vetsuisse Faculty, University of Bern, Länggassstrasse 122, CH-3012 Bern, Switzerland; Institute of Infectious Diseases, Faculty of Medicine, University of Bern, CH-3012 Bern, Switzerland
| | - Jiří Harna
- State Veterinary Institute Olomouc, Jakoubka ze Stribra 1, 779 00 Olomouc, Czech Republic
| | - Heidi Huus Petersen
- Danish Veterinary and Food Administration, Ministry of Food, Agriculture and Fisheries of Denmark, Stationsparken 31-33 2600, Glostrup, Denmark
| | - Jacek Karamon
- National Veterinary Research Institute, Department of Parasitology and Invasive Diseases, Partyzantow Avenue 57, 24-100 Pulawy, Poland
| | - Famke Jansen
- Institute of Tropical Medicine (ITM), Department of Biomedical Sciences, 155 Nationalestraat, B-2000 Antwerp, Belgium
| | - Júlia Jarošová
- Institute of Parasitology, Slovak Academy of Sciences, Košice, Hlinkova 3, 040 01 Košice, Slovakia
| | - Pikka Jokelainen
- Infectious Disease Preparedness, Statens Serum Institut, Artillerivej 5, DK-2300 Copenhagen S, Denmark
| | - Britta Lundström-Stadelmann
- Institute of Parasitology, Vetsuisse Faculty, University of Bern, Länggassstrasse 122, CH-3012 Bern, Switzerland; Multidisciplinary Center for Infectious Diseases, University of Bern, Länggass-Strasse 122, 3012 Bern, Switzerland
| | - Pavlo Maksimov
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Epidemiology, Südufer 10, 17493 Greifswald‑Insel Riems, Germany
| | - Milan Miljević
- Department of Genetic Research, Institute for Biological Research "Siniša Stanković", National Institute of Republic of Serbia, University of Belgrade, Bulevar Despota Stefana 142, 11000 Belgrade, Serbia
| | - Martina Miterpáková
- Institute of Parasitology, Slovak Academy of Sciences, Košice, Hlinkova 3, 040 01 Košice, Slovakia
| | - Epp Moks
- National Centre for Laboratory Research and Risk Assessment, Fr. R. Kreutzwaldi 30, Tartu, Estonia
| | - Francesco Origgi
- Institute for Fish and Wildlife Health (FIWI), Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Längassstrasse 122, 3012 Bern, Switzerland
| | - Zanda Ozolina
- Institute of Food Safety, Animal Health and Environment "BIOR", Lejupes Street 3, Riga LV-1076, Latvia
| | - Marie-Pierre Ryser
- Institute for Fish and Wildlife Health (FIWI), Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Längassstrasse 122, 3012 Bern, Switzerland
| | - Thomas Romig
- Parasitology Unit, Institute of Biology, University of Hohenheim, 70593 Stuttgart, Germany
| | - Mindaugas Šarkūnas
- Department of Veterinary Pathobiology, Veterinary Academy, Lithuanian University of Health Sciences, Tilžės str. 18, 47181 Kaunas, Lithuania
| | - Nathalie Scorrano
- Institute of Parasitology, Vetsuisse Faculty, University of Bern, Länggassstrasse 122, CH-3012 Bern, Switzerland
| | - Urmas Saarma
- Department of Zoology, Institute of Ecology and Earth Sciences, University of Tartu, J. Liivi 2, 50409 Tartu, Estonia
| | - Viliam Šnábel
- Institute of Parasitology, Slovak Academy of Sciences, Košice, Hlinkova 3, 040 01 Košice, Slovakia
| | - Tamás Sréter
- National Reference Laboratory of Medical Parasitology, National Public Health Center, Albert Flórián út 2-6, Budapest, Hungary
| | - Gèrald Umhang
- Anses, Nancy Laboratory for Rabies and Wildlife, National Reference Laboratory Echinococcus spp, 54220 Malzéville, France
| | - Gorazd Vengušt
- Institute of Microbiology and Parasitology, Veterinary Faculty, University of Ljubljana, Gerbičeva 60, 1000 Ljubljana, Slovenia
| | - Diana Žele Vengušt
- Institute of Microbiology and Parasitology, Veterinary Faculty, University of Ljubljana, Gerbičeva 60, 1000 Ljubljana, Slovenia
| | - Adriano Casulli
- European Union Reference Laboratory for Parasites, Department of Infectious Diseases, Istituto Superiore Di Sanità, Viale Regina Elena 299, 00161 Rome, Italy; WHO Collaborating Centre for the Epidemiology, Detection and Control of Cystic and Alveolar Echinococcosis, Department of Infectious Diseases, Istituto Superiore Di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
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3
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Segawa T, Rey-Iglesia A, Lorenzen ED, Westbury MV. The origins and diversification of Holarctic brown bear populations inferred from genomes of past and present populations. Proc Biol Sci 2024; 291:20232411. [PMID: 38264778 PMCID: PMC10806438 DOI: 10.1098/rspb.2023.2411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Accepted: 12/20/2023] [Indexed: 01/25/2024] Open
Abstract
The brown bear (Ursus arctos) is one of the survivors of the Late Quaternary megafauna extinctions. However, despite being widely distributed across the Holarctic, brown bears have experienced extensive range reductions, and even extirpations in some geographical regions. Previous research efforts using genetic data have provided valuable insights into their evolutionary history. However, most studies have been limited to contemporary individuals or mitochondrial DNA, limiting insights into population processes that preceded the present. Here, we present genomic data from two Late Pleistocene brown bears from Honshu, Japan and eastern Siberia, and combine them with published contemporary and ancient genomes from across the Holarctic range of brown bears to investigate the evolutionary relationships among brown bear populations through time and space. By including genomic data from Late Pleistocene and Holocene individuals sampled outside the current distribution range, we uncover diversity not present in contemporary populations. Notably, although contemporary individuals display geographically structured populations most likely driven by isolation-by-distance, this pattern varies among the ancient samples across different regions. The inclusion of ancient brown bears in our analysis provides novel insights into the evolutionary history of brown bears and contributes to understanding the populations and diversity lost during the Late Quaternary.
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Affiliation(s)
- Takahiro Segawa
- Center for Life Science Research, University of Yamanashi, Chuo, Yamanashi, Japan
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4
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Panitsina VA, Bodrov SY, Boulygina ES, Slobodova NV, Kosintsev PA, Abramson NI. In Search of the Elusive North: Evolutionary History of the Arctic Fox ( Vulpes lagopus) in the Palearctic from the Late Pleistocene to the Recent Inferred from Mitogenomic Data. BIOLOGY 2023; 12:1517. [PMID: 38132343 PMCID: PMC10740874 DOI: 10.3390/biology12121517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 12/07/2023] [Accepted: 12/09/2023] [Indexed: 12/23/2023]
Abstract
Despite the high level of interest, the population history of arctic foxes during the Late Pleistocene and Holocene remains poorly understood. Here we aimed to fill gaps in the demographic and colonization history of the arctic fox by analyzing new ancient DNA data from fossil specimens aged from 50 to 1 thousand years from the Northern and Polar Urals, historic DNA from museum specimens from the Novaya Zemlya Archipelago and the Taymyr Peninsula and supplementing these data by previously published sequences of recent and extinct arctic foxes from other regions. This dataset was used for reconstruction of a time-calibrated phylogeny and a temporal haplotype network covering four time intervals: Late Pleistocene (ranging from 30 to 13 thousand years bp), Holocene (ranging from 4 to 1 thousand years bp), historical (approximately 150 years), and modern. Our results revealed that Late Pleistocene specimens showed no genetic similarity to either modern or historical specimens, thus supporting the earlier hypothesis on local extinction rather than habitat tracking.
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Affiliation(s)
- Valentina A. Panitsina
- Zoological Institute, Russian Academy of Sciences, 199034 Saint-Petersburg, Russia; (V.A.P.); (S.Y.B.)
| | - Semyon Yu. Bodrov
- Zoological Institute, Russian Academy of Sciences, 199034 Saint-Petersburg, Russia; (V.A.P.); (S.Y.B.)
| | | | | | - Pavel A. Kosintsev
- Institute of Plant and Animal Ecology, Ural Branch, Russian Academy of Sciences, 620144 Yekaterinburg, Russia
| | - Natalia I. Abramson
- Zoological Institute, Russian Academy of Sciences, 199034 Saint-Petersburg, Russia; (V.A.P.); (S.Y.B.)
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5
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Plis K, Niedziałkowska M, Borowik T, Lang J, Heddergott M, Tiainen J, Bunevich A, Šprem N, Paule L, Danilkin A, Kholodova M, Zvychaynaya E, Kashinina N, Pokorny B, Flajšman K, Paulauskas A, Djan M, Ristić Z, Novák L, Kusza S, Miller C, Tsaparis D, Stoyanov S, Shkvyria M, Suchentrunk F, Kutal M, Lavadinović V, Šnjegota D, Krapal A, Dănilă G, Veeroja R, Dulko E, Jędrzejewska B. Pan‐European phylogeography of the European roe deer (
Capreolus capreolus
). Ecol Evol 2022; 12:e8931. [PMID: 35600675 PMCID: PMC9120558 DOI: 10.1002/ece3.8931] [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: 10/09/2021] [Revised: 04/13/2022] [Accepted: 04/25/2022] [Indexed: 11/18/2022] Open
Abstract
To provide the most comprehensive picture of species phylogeny and phylogeography of European roe deer (Capreolus capreolus), we analyzed mtDNA control region (610 bp) of 1469 samples of roe deer from Central and Eastern Europe and included into the analyses additional 1541 mtDNA sequences from GenBank from other regions of the continent. We detected two mtDNA lineages of the species: European and Siberian (an introgression of C. pygargus mtDNA into C. capreolus). The Siberian lineage was most frequent in the eastern part of the continent and declined toward Central Europe. The European lineage contained three clades (Central, Eastern, and Western) composed of several haplogroups, many of which were separated in space. The Western clade appeared to have a discontinuous range from Portugal to Russia. Most of the haplogroups in the Central and the Eastern clades were under expansion during the Weichselian glacial period before the Last Glacial Maximum (LGM), while the expansion time of the Western clade overlapped with the Eemian interglacial. The high genetic diversity of extant roe deer is the result of their survival during the LGM probably in a large, contiguous range spanning from the Iberian Peninsula to the Caucasus Mts and in two northern refugia.
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Affiliation(s)
- Kamila Plis
- Mammal Research Institute Polish Academy of Sciences Białowieża Poland
| | | | - Tomasz Borowik
- Mammal Research Institute Polish Academy of Sciences Białowieża Poland
| | - Johannes Lang
- Working Group for Wildlife Research at Clinic for Birds, Reptiles, Amphibians and Fish Justus‐Liebig‐University Giessen Gießen Germany
| | - Mike Heddergott
- Department of Zoology Musée National d’Histoire Naturelle Luxembourg City Luxembourg
| | - Juha Tiainen
- Lammi Biological Station University of Helsinki Lammi Finland
- Natural Resources Institute Finland (Luke) Helsinki Finland
| | - Aleksey Bunevich
- State National Park Belovezhskaya Pushcha Kamenyuki Republic of Belarus
| | - Nikica Šprem
- Department of Fisheries, Apiculture, Wildlife Management and Special Zoology Faculty of Agriculture University of Zagreb Zagreb Croatia
| | - Ladislav Paule
- Department of Phytology Technical University in Zvolen Zvolen Slovak Republic
| | - Aleksey Danilkin
- A.N. Severtsov Institute of Ecology and Evolution Russian Academy of Sciences Moscow Russia
| | - Marina Kholodova
- A.N. Severtsov Institute of Ecology and Evolution Russian Academy of Sciences Moscow Russia
| | - Elena Zvychaynaya
- A.N. Severtsov Institute of Ecology and Evolution Russian Academy of Sciences Moscow Russia
| | - Nadezhda Kashinina
- A.N. Severtsov Institute of Ecology and Evolution Russian Academy of Sciences Moscow Russia
| | - Boštjan Pokorny
- Faculty of Environmental Protection Velenje Slovenia
- Department of Forest Ecology Slovenian Forestry Institute Ljubljana Slovenia
| | - Katarina Flajšman
- Department of Forest Ecology Slovenian Forestry Institute Ljubljana Slovenia
| | | | - Mihajla Djan
- Department of Biology and Ecology Faculty of Sciences University of Novi Sad Novi Sad Republic of Serbia
| | - Zoran Ristić
- Department of Geography, Tourism and Hotel Management Faculty of Sciences University of Novi Sad Novi Sad Serbia
| | - Luboš Novák
- Department of Forest Protection and Wildlife Management Mendel University in Brno Brno Czech Republic
| | - Szilvia Kusza
- Centre for Agricultural Genomics and Biotechnology Faculty of Agricultural and Food Sciences and Environmental Management University of Debrecen Debrecen Hungary
| | | | - Dimitris Tsaparis
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC) Hellenic Centre for Marine Research Heraklion, Crete Greece
| | - Stoyan Stoyanov
- Wildlife Management Department University of Forestry Sofia Bulgaria
| | | | - Franz Suchentrunk
- Research Institute of Wildlife Ecology University of Veterinary Medicine Vienna Vienna Austria
| | - Miroslav Kutal
- Department of Forest Ecology Faculty of Forestry and Wood Technology Mendel University in Brno Brno Czech Republic
| | | | - Dragana Šnjegota
- Faculty of Natural Sciences and Mathematics University of Banja Luka Banja Luka Bosnia and Herzegovina
| | - Ana‐Maria Krapal
- "Grigore Antipa" National Museum of Natural History Bucharest Romania
| | - Gabriel Dănilă
- Faculty of Forestry Stefan cel Mare University of Suceava Suceava Romania
| | - Rauno Veeroja
- Department of Wildlife Monitoring Estonian Environment Agency Tallin Estonia
| | - Elżbieta Dulko
- Department of Anesthesiology University of Virginia Health System Charlottesville Virginia USA
- Faculty of Biology University of Warsaw Warszawa Poland
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6
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van der Zee JP, Christianen MJA, Bérubé M, Nava M, van der Wal S, Berkel J, Bervoets T, Meijer Zu Schlochtern M, Becking LE, Palsbøll PJ. Demographic changes in Pleistocene sea turtles were driven by past sea level fluctuations affecting feeding habitat availability. Mol Ecol 2021; 31:1044-1056. [PMID: 34861074 PMCID: PMC9299637 DOI: 10.1111/mec.16302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 11/18/2021] [Accepted: 11/22/2021] [Indexed: 11/28/2022]
Abstract
Pleistocene environmental changes are generally assumed to have dramatically affected species’ demography via changes in habitat availability, but this is challenging to investigate due to our limited knowledge of how Pleistocene ecosystems changed through time. Here, we tracked changes in shallow marine habitat availability resulting from Pleistocene sea level fluctuations throughout the last glacial cycle (120–14 thousand years ago; kya) and assessed correlations with past changes in genetic diversity inferred from genome‐wide SNPs, obtained via ddRAD sequencing, in Caribbean hawksbill turtles, which feed in coral reefs commonly found in shallow tropical waters. We found sea level regression resulted in an average 75% reduction in shallow marine habitat availability during the last glacial cycle. Changes in shallow marine habitat availability correlated strongly with past changes in hawksbill turtle genetic diversity, which gradually declined to ~1/4th of present‐day levels during the Last Glacial Maximum (LGM; 26–19 kya). Shallow marine habitat availability and genetic diversity rapidly increased after the LGM, signifying a population expansion in response to warming environmental conditions. Our results suggest a positive correlation between Pleistocene environmental changes, habitat availability and species’ demography, and that demographic changes in hawksbill turtles were potentially driven by feeding habitat availability. However, we also identified challenges associated with disentangling the potential environmental drivers of past demographic changes, which highlights the need for integrative approaches. Our conclusions underline the role of habitat availability on species’ demography and biodiversity, and that the consequences of ongoing habitat loss should not be underestimated.
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Affiliation(s)
- Jurjan P van der Zee
- Marine Evolution and Conservation, Groningen Institute for Evolutionary Life Sciences, University of Groningen, AG Groningen, the Netherlands.,Wageningen Marine Research, Den Helder, the Netherlands
| | - Marjolijn J A Christianen
- Marine Evolution and Conservation, Groningen Institute for Evolutionary Life Sciences, University of Groningen, AG Groningen, the Netherlands.,Aquatic Ecology and Water Quality Management Group, Wageningen University & Research, Wageningen, the Netherlands
| | - Martine Bérubé
- Marine Evolution and Conservation, Groningen Institute for Evolutionary Life Sciences, University of Groningen, AG Groningen, the Netherlands.,Center for Coastal Studies, Provincetown, Massachusetts, USA
| | - Mabel Nava
- Sea Turtle Conservation Bonaire, Kralendijk, Bonaire, Caribbean Netherlands
| | | | - Jessica Berkel
- Sint Eustatius National Parks Foundation, Sint Eustatius, Caribbean Netherlands
| | - Tadzio Bervoets
- Sint Maarten Nature Foundation, Cole Bay, Sint Maarten.,Dutch Caribbean Nature Alliance, Kralendijk, Bonaire, Caribbean Netherlands
| | | | - Leontine E Becking
- Wageningen Marine Research, Den Helder, the Netherlands.,Marine Animal Ecology Group, Wageningen University & Research, Wageningen, the Netherlands
| | - Per J Palsbøll
- Marine Evolution and Conservation, Groningen Institute for Evolutionary Life Sciences, University of Groningen, AG Groningen, the Netherlands.,Center for Coastal Studies, Provincetown, Massachusetts, USA
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7
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Levicoy D, Flores K, Rosenfeld S, Cárdenas L. Phylogeography and genetic diversity of the microbivalve Kidderia subquadrata, reveals new data from West Antarctic Peninsula. Sci Rep 2021; 11:5705. [PMID: 33707560 PMCID: PMC7952419 DOI: 10.1038/s41598-021-85042-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Accepted: 02/19/2021] [Indexed: 12/14/2022] Open
Abstract
It is well established that Antarctic biodiversity has been strongly influenced by rapid climatic fluctuations during the Quaternary. Marine invertebrates from Antarctica constitute an interesting lens through which to study the impacts of the last glacial periods as glaciation impacted the distribution and intraspecific genetic variation of these animals. However, the impact on the spatial genetic distribution and historical demography of local processes in areas adjacent to the West Antarctic Peninsula (WAP) is less clear. Here we present new genetic information on the bivalve Kidderia subquadrata, a small mollusk that inhabits intertidal rocky island ecosystems throughout the WAP. Using a phylogeographical approach, we examined the spatial patterns of genetic diversity in this brooder species to test the hypothesis of strong genetic structure in incubating organisms and the hypothesis of glacial refugia in organisms with limited dispersion. We found evidence of strong genetic structure among populations of the WAP and a recent expansion in the South Shetland Islands. Our findings are concordant with the predictions that incubating organisms, abundant in Antarctica, present a strong genetic structure among their populations and also support the hypothesis of glacial refugia in organisms with limited dispersion. The effect of the coastal current pattern in the WAP is suggested as a driver to the local spatial dynamics of the genetic diversity distribution. Although genetic information about this microbivalve is still scarce, the knowledge reported here has increased our understanding of the evolutionary patterns of this organism that is endemic to the Southern Ocean.
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Affiliation(s)
- Daniela Levicoy
- Centro FONDAP- IDEAL, Instituto de Ciencias Ambientales and Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Independencia 641, P.O. Box 567, Valdivia, Punta Arenas, Chile
| | - Kamilla Flores
- Centro FONDAP- IDEAL, Instituto de Ciencias Ambientales and Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Independencia 641, P.O. Box 567, Valdivia, Punta Arenas, Chile
| | - Sebastián Rosenfeld
- Laboratorio de Ecosistemas Marinos Antárticos Y Subantárticos, Universidad de Magallanes, Casilla 113-D, Punta Arenas, Chile.,Laboratorio de Ecología Molecular, Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Las Palmeras # 3425, Ñuñoa, Santiago, Chile.,Instituto de Ecología y Biodiversidad (IEB), Las Palmeras # 3425, Ñuñoa, Santiago, Chile
| | - Leyla Cárdenas
- Centro FONDAP- IDEAL, Instituto de Ciencias Ambientales and Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Independencia 641, P.O. Box 567, Valdivia, Punta Arenas, Chile.
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8
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Fordham DA, Jackson ST, Brown SC, Huntley B, Brook BW, Dahl-Jensen D, Gilbert MTP, Otto-Bliesner BL, Svensson A, Theodoridis S, Wilmshurst JM, Buettel JC, Canteri E, McDowell M, Orlando L, Pilowsky J, Rahbek C, Nogues-Bravo D. Using paleo-archives to safeguard biodiversity under climate change. Science 2020; 369:369/6507/eabc5654. [PMID: 32855310 DOI: 10.1126/science.abc5654] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 06/30/2020] [Indexed: 12/29/2022]
Abstract
Strategies for 21st-century environmental management and conservation under global change require a strong understanding of the biological mechanisms that mediate responses to climate- and human-driven change to successfully mitigate range contractions, extinctions, and the degradation of ecosystem services. Biodiversity responses to past rapid warming events can be followed in situ and over extended periods, using cross-disciplinary approaches that provide cost-effective and scalable information for species' conservation and the maintenance of resilient ecosystems in many bioregions. Beyond the intrinsic knowledge gain such integrative research will increasingly provide the context, tools, and relevant case studies to assist in mitigating climate-driven biodiversity losses in the 21st century and beyond.
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Affiliation(s)
- Damien A Fordham
- The Environment Institute and School of Biological Sciences, University of Adelaide, South Australia 5005, Australia. .,Center for Macroecology, Evolution, and Climate, GLOBE Institute, University of Copenhagen, Copenhagen Ø 2100, Denmark
| | - Stephen T Jackson
- Southwest and South Central Climate Adaptation Science Centers, U.S. Geological Survey, Tucson, AZ 85721, USA.,Department of Geosciences and School of Natural Resources and the Environment, University of Arizona, Tucson, AZ 85721, USA
| | - Stuart C Brown
- The Environment Institute and School of Biological Sciences, University of Adelaide, South Australia 5005, Australia
| | - Brian Huntley
- Department of Biosciences, Durham University, Durham, DH1 3LE, UK
| | - Barry W Brook
- School of Natural Sciences and ARC Centre of Excellence for Australian Biodiversity and Heritage, University of Tasmania, Hobart, Tasmania 7001, Australia
| | - Dorthe Dahl-Jensen
- Centre for Ice and Climate, Niels Bohr Institute, University of Copenhagen, Juliane Maries Vej 30, 2100 Copenhagen Ø 2100, Denmark.,Centre for Earth Observation Science, University of Manitoba, Winnipeg MB R3T 2N2, Canada
| | - M Thomas P Gilbert
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, Copenhagen Ø 2100, Denmark.,University Museum, Norwegian University of Science and Technology, Trondheim, Norway
| | - Bette L Otto-Bliesner
- Climate and Global Dynamics Laboratory, National Center for Atmospheric Research, Boulder, CO 80307-3000, USA
| | - Anders Svensson
- Centre for Ice and Climate, Niels Bohr Institute, University of Copenhagen, Juliane Maries Vej 30, 2100 Copenhagen Ø 2100, Denmark
| | - Spyros Theodoridis
- Center for Macroecology, Evolution, and Climate, GLOBE Institute, University of Copenhagen, Copenhagen Ø 2100, Denmark
| | - Janet M Wilmshurst
- Long-Term Ecology Laboratory, Manaaki Whenua-Landcare Research, Lincoln 7640, New Zealand.,School of Environment, The University of Auckland, Auckland 1142, New Zealand
| | - Jessie C Buettel
- School of Natural Sciences and ARC Centre of Excellence for Australian Biodiversity and Heritage, University of Tasmania, Hobart, Tasmania 7001, Australia
| | - Elisabetta Canteri
- The Environment Institute and School of Biological Sciences, University of Adelaide, South Australia 5005, Australia.,Center for Macroecology, Evolution, and Climate, GLOBE Institute, University of Copenhagen, Copenhagen Ø 2100, Denmark
| | - Matthew McDowell
- School of Natural Sciences and ARC Centre of Excellence for Australian Biodiversity and Heritage, University of Tasmania, Hobart, Tasmania 7001, Australia
| | - Ludovic Orlando
- Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse UMR 5288, Université de Toulouse, CNRS, Université Paul Sabatier, France.,Section for GeoGenetics, GLOBE Institute, University of Copenhagen, Copenhagen Ø 2100, Denmark
| | - Julia Pilowsky
- The Environment Institute and School of Biological Sciences, University of Adelaide, South Australia 5005, Australia.,Center for Macroecology, Evolution, and Climate, GLOBE Institute, University of Copenhagen, Copenhagen Ø 2100, Denmark
| | - Carsten Rahbek
- Center for Macroecology, Evolution, and Climate, GLOBE Institute, University of Copenhagen, Copenhagen Ø 2100, Denmark.,Department of Life Sciences, Imperial College London, Ascot SL5 7PY, UK.,Danish Institute for Advanced Study, University of Southern Denmark, Odense, Denmark.,Institute of Ecology, Peking University, Beijing 100871, China
| | - David Nogues-Bravo
- Center for Macroecology, Evolution, and Climate, GLOBE Institute, University of Copenhagen, Copenhagen Ø 2100, Denmark
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9
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Large mammal faunas of the European part of Russia in Anthropocene. RUSSIAN JOURNAL OF THERIOLOGY 2020. [DOI: 10.15298/rusjtheriol.19.1.05] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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10
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Szuma E, Germonpré M. Were ancient foxes far more carnivorous than recent ones?-Carnassial morphological evidence. PLoS One 2020; 15:e0227001. [PMID: 31923224 PMCID: PMC6953794 DOI: 10.1371/journal.pone.0227001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 12/09/2019] [Indexed: 11/18/2022] Open
Abstract
Crown shape variation of the first lower molar in the arctic (Vulpes lagopus) and red foxes (Vulpes vulpes) was analyzed using five groups of morphotypes. Carnassial morphologies were compared between the species and between spatially and temporally distant populations: one Late Pleistocene (n = 45) and seven modern populations of the arctic fox (n = 259), and one Late Pleistocene (n = 35) and eight modern populations of the red fox (n = 606). The dentition of Holocene red foxes had larger morphotype variability than that of arctic foxes. The lower carnassials of the red fox kept have some primitive characters (additional cusps and stylids, complex shape of transverse cristid), whereas the first lower molars of the arctic fox have undergone crown shape simplification, with the occlusal part of the tooth undergoing a more pronounced adaptation to a more carnivorous diet. From the Late Pleistocene of Belgium to the present days, the arctic fox’s crown shape has been simplified and some primitive characters have disappeared. In the red fox chronological changes in the morphology of the lower carnassials were not clearly identified. The phyletic tree based on morphotype carnassial characteristics indicated the distinctiveness of both foxes: in the arctic fox line, the ancient population from Belgium and recent Greenland made separate branches, whereas in the red foxes the ancient population from Belgium was most similar to modern red foxes from Belgium and Italy.
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Affiliation(s)
- Elwira Szuma
- Mammal Research Institute Polish Academy of Sciences, Białowieża, Poland
- * E-mail:
| | - Mietje Germonpré
- Operational Direction “Earth and History of Life”, Royal Belgian Institute of Natural Sciences, Brussels, Belgium
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11
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Fenderson LE, Kovach AI, Llamas B. Spatiotemporal landscape genetics: Investigating ecology and evolution through space and time. Mol Ecol 2019; 29:218-246. [DOI: 10.1111/mec.15315] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 09/22/2019] [Accepted: 11/13/2019] [Indexed: 12/22/2022]
Affiliation(s)
- Lindsey E. Fenderson
- Australian Centre for Ancient DNA School of Biological Sciences Environment Institute University of Adelaide Adelaide South Australia Australia
- Department of Natural Resources and the Environment University of New Hampshire Durham NH USA
| | - Adrienne I. Kovach
- Department of Natural Resources and the Environment University of New Hampshire Durham NH USA
| | - Bastien Llamas
- Australian Centre for Ancient DNA School of Biological Sciences Environment Institute University of Adelaide Adelaide South Australia Australia
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12
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Size of the lower carnassial in the arctic and the red fox from Late Pleistocene in Belgium compared to other ancient and extant populations. MAMMAL RES 2019. [DOI: 10.1007/s13364-019-00459-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
AbstractLengths, widths, and size proportions (length to width) of the lower carnassial were measured in 45 teeth of the arctic fox and 35 teeth of the red fox from Belgium radiocarbon dated to 46 640–14 120 ka BP. Data the Late Pleistocene foxes from Belgium were compared to 20 ancient and extant populations form Europe, Asia, and North America. The Pleistocene arctic fox from Belgium showed larger carnassial than in all recent samples of this species, whereas the Belgian fossil red foxes were characterized by the carnassial size comparable to that of the recent Siberian red foxes. Both fox species from the Pleistocene of Belgium showed the highest index of the carnassials length to width, which means increase in carnivorous adaptation. We conclude that the higher level of carnivorous specialization reached by the Belgian arctic and red foxes at the end of the Late Pleistocene reflected their scavenging on kills of large carnivores and human hunters (remains of megafauna). Harsh environmental conditions of that period and specific composition of ecosystems led to adapting to a more carnivorous food niche in both foxes.
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13
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Larsson P, von Seth J, Hagen IJ, Götherström A, Androsov S, Germonpré M, Bergfeldt N, Fedorov S, Eide NE, Sokolova N, Berteaux D, Angerbjörn A, Flagstad Ø, Plotnikov V, Norén K, Díez-Del-Molino D, Dussex N, Stanton DWG, Dalén L. Consequences of past climate change and recent human persecution on mitogenomic diversity in the arctic fox. Philos Trans R Soc Lond B Biol Sci 2019; 374:20190212. [PMID: 31679495 PMCID: PMC6863501 DOI: 10.1098/rstb.2019.0212] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Ancient DNA provides a powerful means to investigate the timing, rate and extent of population declines caused by extrinsic factors, such as past climate change and human activities. One species probably affected by both these factors is the arctic fox, which had a large distribution during the last glaciation that subsequently contracted at the start of the Holocene. More recently, the arctic fox population in Scandinavia went through a demographic bottleneck owing to human persecution. To investigate the consequences of these processes, we generated mitogenome sequences from a temporal dataset comprising Pleistocene, historical and modern arctic fox samples. We found no evidence that Pleistocene populations in mid-latitude Europe or Russia contributed to the present-day gene pool of the Scandinavian population, suggesting that postglacial climate warming led to local population extinctions. Furthermore, during the twentieth-century bottleneck in Scandinavia, at least half of the mitogenome haplotypes were lost, consistent with a 20-fold reduction in female effective population size. In conclusion, these results suggest that the arctic fox in mainland Western Europe has lost genetic diversity as a result of both past climate change and human persecution. Consequently, it might be particularly vulnerable to the future challenges posed by climate change. This article is part of a discussion meeting issue 'The past is a foreign country: how much can the fossil record actually inform conservation?'
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Affiliation(s)
- Petter Larsson
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.,Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Johanna von Seth
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.,Department of Zoology, Stockholm University, Stockholm, Sweden
| | | | - Anders Götherström
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | | | - Mietje Germonpré
- Operational Direction 'Earth and History of Life', Royal Belgian Institute of Natural Sciences, Brussels, Belgium
| | - Nora Bergfeldt
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.,Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Sergey Fedorov
- Mammoth Museum of Institute of Applied Ecology of the North, North-Eastern Federal University, Yakutsk, Republic Sakha (Yakutia), Russia
| | - Nina E Eide
- Norwegian Institute for Nature Research, Trondheim, Norway
| | - Natalia Sokolova
- Arctic Research Station of Institute of Plant and Animal Ecology, Ural Branch of Russian Academy of Sciences, Yamal-Nenets Autonomous District, Russia.,Arctic Research Center of Yamal-Nenets Autonomous District, Salekhard, Russia
| | - Dominique Berteaux
- Canada Research Chair on Northern Biodiversity and Centre for Northern Studies, Université du Québec à Rimouski, Rimouski, Canada
| | | | | | - Valeri Plotnikov
- Academy of Sciences of Sakha Republic, Lenin Avenue 33, Republic of Sakha, Yakutia, Russia
| | - Karin Norén
- Department of Zoology, Stockholm University, Stockholm, Sweden
| | - David Díez-Del-Molino
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.,Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Nicolas Dussex
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - David W G Stanton
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Love Dalén
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.,Department of Zoology, Stockholm University, Stockholm, Sweden
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14
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Oosting T, Star B, Barrett JH, Wellenreuther M, Ritchie PA, Rawlence NJ. Unlocking the potential of ancient fish DNA in the genomic era. Evol Appl 2019; 12:1513-1522. [PMID: 31462911 PMCID: PMC6708421 DOI: 10.1111/eva.12811] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Revised: 04/11/2019] [Accepted: 04/29/2019] [Indexed: 12/17/2022] Open
Abstract
Fish are the most diverse group of vertebrates, fulfil important ecological functions and are of significant economic interest for aquaculture and wild fisheries. Advances in DNA extraction methods, sequencing technologies and bioinformatic applications have advanced genomic research for nonmodel organisms, allowing the field of fish ancient DNA (aDNA) to move into the genomics era. This move is enabling researchers to investigate a multitude of new questions in evolutionary ecology that could not, until now, be addressed. In many cases, these new fields of research have relevance to evolutionary applications, such as the sustainable management of fisheries resources and the conservation of aquatic animals. Here, we focus on the application of fish aDNA to (a) highlight new research questions, (b) outline methodological advances and current challenges, (c) discuss how our understanding of fish ecology and evolution can benefit from aDNA applications and (d) provide a future perspective on how the field will help answer key questions in conservation and management. We conclude that the power of fish aDNA will be unlocked through the application of continually improving genomic resources and methods to well-chosen taxonomic groups represented by well-dated archaeological samples that can provide temporally and/or spatially extensive data sets.
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Affiliation(s)
- Tom Oosting
- School of Biological SciencesVictoria University of WellingtonWellingtonNew Zealand
| | - Bastiaan Star
- Department of Biosciences, Centre for Ecological and Evolutionary SynthesisUniversity of OsloOsloNorway
| | - James H. Barrett
- Department of ArchaeologyUniversity of CambridgeCambridgeUK
- Department of Archaeology and Cultural HistoryNTNU University MuseumTrondheimNorway
- Trinity Centre for Environmental HumanitiesTrinity College DublinDublinIreland
| | - Maren Wellenreuther
- Nelson Seafood Research UnitPlant and Food ResearchNelsonNew Zealand
- School of Biological SciencesUniversity of AucklandAucklandNew Zealand
| | - Peter A. Ritchie
- School of Biological SciencesVictoria University of WellingtonWellingtonNew Zealand
| | - Nicolas J. Rawlence
- Otago Palaeogenetics Laboratory, Department of ZoologyUniversity of OtagoDunedinNew Zealand
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15
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Joordens JC, Feibel CS, Vonhof HB, Schulp AS, Kroon D. Relevance of the eastern African coastal forest for early hominin biogeography. J Hum Evol 2019; 131:176-202. [DOI: 10.1016/j.jhevol.2019.03.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 03/10/2019] [Accepted: 03/13/2019] [Indexed: 12/25/2022]
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16
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Garrison EG, Morgan GS, McGrath K, Speller C, Cherkinsky A. Recent dating of extinct Atlantic gray whale fossils, (Eschrichtius robustus), Georgia Bight and Florida, western Atlantic Ocean. PeerJ 2019; 7:e6381. [PMID: 30746309 PMCID: PMC6368218 DOI: 10.7717/peerj.6381] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 12/28/2018] [Indexed: 11/20/2022] Open
Abstract
The Atlantic gray whale (Eschrichtius robustus) presents an interesting case study of climate related dispersal and extinction. While (limited) fossil records confirm its presence in the Atlantic up until the 18th Century, its abundance and distribution within the Eastern and Western basins are still not well understood. The discovery of presumed gray whale fossil remains from the Georgia Bight and the Atlantic coast of Florida, from the mid-1980s to late-2000s, provides a new opportunity to recover additional data regarding their chronology within the Western basin. Here, we apply accelerator mass spectrometry radiocarbon techniques to six fossil whale finds, identifying dates within marine isotope stage 3 (59-24 ka) and the late Holocene, ∼2,000 yr BP. We additionally confirm the taxonomic identification of two fossil bone samples as E. robustus using collagen peptide mass fingerprinting (ZooMS). The obtained dates, when combined with a larger corpus of previously published Atlantic gray whale fossil dates, support the hypothesis for the decline of the Atlantic gray whale in the late Pleistocene and the late Holocene. These new data augment the findings of the Eastern Atlantic Basin and better incorporate the Western Atlantic Basin into a pan-ocean understanding for the species.
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Affiliation(s)
| | - Gary S Morgan
- New Mexico Museum of Natural History & Science, Albuquerque, NM, USA
| | | | - Camilla Speller
- University of York, BioArch Centre, York, UK.,Department of Anthropology, University of British Columbia, Vancouver, BC, Canada
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17
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Wallén J, Statham MJ, Ågren E, Isomursu M, Flagstad Ø, Bjørneboe-Berg T, Sacks BN, Norén K. Multiple recolonization routes towards the north: population history of the Fennoscandian red fox (Vulpes vulpes). Biol J Linn Soc Lond 2018. [DOI: 10.1093/biolinnean/bly060] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Johan Wallén
- Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Mark J Statham
- Mammalian Ecology and Conservation Unit, Center for Veterinary Genetics, University of California Davis, Davis, CA, USA
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California Davis, Davis, CA, USA
| | - Erik Ågren
- National Veterinary Institute, Department of Pathology and Wildlife Diseases, Uppsala, Sweden
| | - Marja Isomursu
- Finnish Food Safety Authority Evira, Production Animal and Wildlife Health Research Unit, Elektroniikkatie, Oulu, Finland
| | | | | | - Benjamin N Sacks
- Mammalian Ecology and Conservation Unit, Center for Veterinary Genetics, University of California Davis, Davis, CA, USA
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California Davis, Davis, CA, USA
| | - Karin Norén
- Department of Zoology, Stockholm University, Stockholm, Sweden
- Mammalian Ecology and Conservation Unit, Center for Veterinary Genetics, University of California Davis, Davis, CA, USA
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18
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Johnson BM, Kemp BM, Thorgaard GH. Increased mitochondrial DNA diversity in ancient Columbia River basin Chinook salmon Oncorhynchus tshawytscha. PLoS One 2018; 13:e0190059. [PMID: 29320518 PMCID: PMC5761847 DOI: 10.1371/journal.pone.0190059] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 12/07/2017] [Indexed: 01/20/2023] Open
Abstract
The Columbia River and its tributaries provide essential spawning and rearing habitat for many salmonid species, including Chinook salmon (Oncorhynchus tshawytscha). Chinook salmon were historically abundant throughout the basin and Native Americans in the region relied heavily on these fish for thousands of years. Following the arrival of Europeans in the 1800s, salmon in the basin experienced broad declines linked to overfishing, water diversion projects, habitat destruction, connectivity reduction, introgression with hatchery-origin fish, and hydropower development. Despite historical abundance, many native salmonids are now at risk of extinction. Research and management related to Chinook salmon is usually explored under what are termed "the four H's": habitat, harvest, hatcheries, and hydropower; here we explore a fifth H, history. Patterns of prehistoric and contemporary mitochondrial DNA variation from Chinook salmon were analyzed to characterize and compare population genetic diversity prior to recent alterations and, thus, elucidate a deeper history for this species. A total of 346 ancient and 366 contemporary samples were processed during this study. Species was determined for 130 of the ancient samples and control region haplotypes of 84 of these were sequenced. Diversity estimates from these 84 ancient Chinook salmon were compared to 379 contemporary samples. Our analysis provides the first direct measure of reduced genetic diversity for Chinook salmon from the ancient to the contemporary period, as measured both in direct loss of mitochondrial haplotypes and reductions in haplotype and nucleotide diversity. However, these losses do not appear equal across the basin, with higher losses of diversity in the mid-Columbia than in the Snake subbasin. The results are unexpected, as the two groups were predicted to share a common history as parts of the larger Columbia River Basin, and instead indicate that Chinook salmon in these subbasins may have divergent demographic histories.
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Affiliation(s)
- Bobbi M. Johnson
- School of Biological Sciences, Washington State University, Pullman, Washington, United States of America
- * E-mail:
| | - Brian M. Kemp
- School of Biological Sciences, Washington State University, Pullman, Washington, United States of America
- Department of Anthropology, Washington State University, Pullman, Washington, United States of America
| | - Gary H. Thorgaard
- School of Biological Sciences, Washington State University, Pullman, Washington, United States of America
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19
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Landvik M, Miraldo A, Niemelä P, Valainis U, Cibuļskis R, Roslin T. Evidence for geographic substructuring of mtDNA variation in the East European Hermit beetle (Osmoderma barnabita). NATURE CONSERVATION 2017. [DOI: 10.3897/natureconservation.19.12877] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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20
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Lagerholm VK, Sandoval-Castellanos E, Vaniscotte A, Potapova OR, Tomek T, Bochenski ZM, Shepherd P, Barton N, Van Dyck MC, Miller R, Höglund J, Yoccoz NG, Dalén L, Stewart JR. Range shifts or extinction? Ancient DNA and distribution modelling reveal past and future responses to climate warming in cold-adapted birds. GLOBAL CHANGE BIOLOGY 2017; 23:1425-1435. [PMID: 27762483 DOI: 10.1111/gcb.13522] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 08/13/2016] [Indexed: 06/06/2023]
Abstract
Global warming is predicted to cause substantial habitat rearrangements, with the most severe effects expected to occur in high-latitude biomes. However, one major uncertainty is whether species will be able to shift their ranges to keep pace with climate-driven environmental changes. Many recent studies on mammals have shown that past range contractions have been associated with local extinctions rather than survival by habitat tracking. Here, we have used an interdisciplinary approach that combines ancient DNA techniques, coalescent simulations and species distribution modelling, to investigate how two common cold-adapted bird species, willow and rock ptarmigan (Lagopus lagopus and Lagopus muta), respond to long-term climate warming. Contrary to previous findings in mammals, we demonstrate a genetic continuity in Europe over the last 20 millennia. Results from back-casted species distribution models suggest that this continuity may have been facilitated by uninterrupted habitat availability and potentially also the greater dispersal ability of birds. However, our predictions show that in the near future, some isolated regions will have little suitable habitat left, implying a future decrease in local populations at a scale unprecedented since the last glacial maximum.
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Affiliation(s)
- Vendela K Lagerholm
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
- Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Edson Sandoval-Castellanos
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
- Department of Zoology, Stockholm University, Stockholm, Sweden
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Amélie Vaniscotte
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Tromsø, Norway
| | | | - Teresa Tomek
- Institute of Systematics and Evolution of Animals, Polish Academy of Sciences, Kraków, Poland
| | - Zbigniew M Bochenski
- Institute of Systematics and Evolution of Animals, Polish Academy of Sciences, Kraków, Poland
| | | | - Nick Barton
- Institute of Archaeology, University of Oxford, Oxford, UK
| | - Marie-Claire Van Dyck
- Institute for the Analysis of Change in Contemporary and Historical Societies, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Rebecca Miller
- Service of Prehistory, University of Liège, Liège, Belgium
| | - Jacob Höglund
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Nigel G Yoccoz
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Love Dalén
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - John R Stewart
- School of Applied Sciences, Bournemouth University, Dorset House, Talbot Campus, Poole, UK
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Smith S, Sandoval-Castellanos E, Lagerholm VK, Napierala H, Sablin M, Von Seth J, Fladerer FA, Germonpré M, Wojtal P, Miller R, Stewart JR, Dalén L. Nonreceding hare lines: genetic continuity since the Late Pleistocene in European mountain hares (Lepus timidus). Biol J Linn Soc Lond 2017. [DOI: 10.1093/biolinnean/blw009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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22
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Tougard C. Did the Quaternary climatic fluctuations really influence the tempo and mode of diversification in European rodents? J ZOOL SYST EVOL RES 2016. [DOI: 10.1111/jzs.12152] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Christelle Tougard
- Institut des Sciences de l'Evolution de Montpellier; UMR CNRS-UM-EPHE 5554, IRD 226 and CIRAD 117; Université de Montpellier; Eugéne Bataillon, CC065 34095 Montpellier Cedex 05 France
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Splendiani A, Fioravanti T, Giovannotti M, Negri A, Ruggeri P, Olivieri L, Nisi Cerioni P, Lorenzoni M, Caputo Barucchi V. The Effects of Paleoclimatic Events on Mediterranean Trout: Preliminary Evidences from Ancient DNA. PLoS One 2016; 11:e0157975. [PMID: 27331397 PMCID: PMC4917132 DOI: 10.1371/journal.pone.0157975] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 06/08/2016] [Indexed: 11/19/2022] Open
Abstract
In this pilot study for the first time, ancient DNA has been extracted from bone remains of Salmo trutta. These samples were from a stratigraphic succession located in a coastal cave of Calabria (southern Italy) inhabited by humans from upper Palaeolithic to historical times. Seven pairs of primers were used to PCR-amplify and sequence from 128 to 410 bp of the mtDNA control region of eleven samples. Three haplotypes were observed: two (ADcs-1 and MEcs-1) already described in rivers from the Italian peninsula; one (ATcs-33) belonging to the southern Atlantic clade of the AT Salmo trutta mtDNA lineage (sensu Bernatchez). The prehistoric occurrence of this latter haplotype in the water courses of the Italian peninsula has been detected for the first time in this study. Finally, we observed a correspondence between frequency of trout remains and variation in haplotype diversity that we related with ecological and demographic changes resulting from a period of rapid cooling known as the Younger Dryas.
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Affiliation(s)
- Andrea Splendiani
- Dipartimento di Scienze della Vita e dell'Ambiente (DiSVA), Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Tatiana Fioravanti
- Dipartimento di Scienze della Vita e dell'Ambiente (DiSVA), Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Massimo Giovannotti
- Dipartimento di Scienze della Vita e dell'Ambiente (DiSVA), Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Alessandra Negri
- Dipartimento di Scienze della Vita e dell'Ambiente (DiSVA), Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Paolo Ruggeri
- Dipartimento di Scienze della Vita e dell'Ambiente (DiSVA), Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Luigi Olivieri
- Dipartimento di Scienze della Vita e dell'Ambiente (DiSVA), Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Paola Nisi Cerioni
- Dipartimento di Scienze della Vita e dell'Ambiente (DiSVA), Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Massimo Lorenzoni
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, Via Elce di Sotto, 06123 Perugia, Italy
| | - Vincenzo Caputo Barucchi
- Dipartimento di Scienze della Vita e dell'Ambiente (DiSVA), Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona, Italy
- Istituto Italiano di Paleontologia Umana, Is.I.P.U., Convitto Nazionale Regina Margherita, Piazza Ruggero Bonghi 2. 03012 Anagni, Italy
- * E-mail:
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Fuentes-Hurtado M, Hof AR, Jansson R. Paleodistribution modeling suggests glacial refugia in Scandinavia and out-of-Tibet range expansion of the Arctic fox. Ecol Evol 2016; 6:170-80. [PMID: 26811782 PMCID: PMC4716496 DOI: 10.1002/ece3.1859] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Revised: 11/04/2015] [Accepted: 11/06/2015] [Indexed: 11/08/2022] Open
Abstract
Quaternary glacial cycles have shaped the geographic distributions and evolution of numerous species in the Arctic. Ancient DNA suggests that the Arctic fox went extinct in Europe at the end of the Pleistocene and that Scandinavia was subsequently recolonized from Siberia, indicating inability to track its habitat through space as climate changed. Using ecological niche modeling, we found that climatically suitable conditions for Arctic fox were found in Scandinavia both during the last glacial maximum (LGM) and the mid-Holocene. Our results are supported by fossil occurrences from the last glacial. Furthermore, the model projection for the LGM, validated with fossil records, suggested an approximate distance of 2000 km between suitable Arctic conditions and the Tibetan Plateau well within the dispersal distance of the species, supporting the recently proposed hypothesis of range expansion from an origin on the Tibetan Plateau to the rest of Eurasia. The fact that the Arctic fox disappeared from Scandinavia despite suitable conditions suggests that extant populations may be more sensitive to climate change than previously thought.
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Affiliation(s)
- Marcelo Fuentes-Hurtado
- Departamento de Ecosistemas y Medio Ambiente Pontificia Universidad Católica de Chile Santiago Chile
| | - Anouschka R Hof
- Landscape Ecology Group Department of Ecology and Environmental Science Umeå University Umeå Sweden; Department of Wildlife Fish and Environmental Studies Swedish University of Agricultural Sciences (SLU) Umeå Sweden
| | - Roland Jansson
- Landscape Ecology Group Department of Ecology and Environmental Science Umeå University Umeå Sweden
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25
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Rawlence NJ, Kennedy M, Anderson CNK, Prost S, Till CE, Smith IWG, Scofield RP, Tennyson AJD, Hamel J, Lalas C, Matisoo-Smith EA, Waters JM. Geographically contrasting biodiversity reductions in a widespread New Zealand seabird. Mol Ecol 2015; 24:4605-16. [DOI: 10.1111/mec.13338] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2014] [Revised: 07/22/2015] [Accepted: 07/27/2015] [Indexed: 02/06/2023]
Affiliation(s)
- Nicolas J. Rawlence
- Allan Wilson Centre; Department of Zoology; University of Otago; Dunedin New Zealand
| | - Martyn Kennedy
- Allan Wilson Centre; Department of Zoology; University of Otago; Dunedin New Zealand
| | | | - Stefan Prost
- Department of Integrative Biology; University of California; Berkeley CA 94720-3140 USA
- Allan Wilson Centre; Department of Anatomy; University of Otago; Dunedin New Zealand
| | - Charlotte E. Till
- Allan Wilson Centre; Department of Zoology; University of Otago; Dunedin New Zealand
- School of Human Evolution and Social Change; Arizona State University; Tempe AZ USA
| | - Ian W. G. Smith
- Department of Anthropology and Archaeology; University of Otago; Dunedin New Zealand
| | | | | | | | - Chris Lalas
- Department of Marine Science; University of Otago; Dunedin New Zealand
| | | | - Jonathan M. Waters
- Allan Wilson Centre; Department of Zoology; University of Otago; Dunedin New Zealand
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26
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Neiva J, Assis J, Coelho NC, Fernandes F, Pearson GA, Serrão EA. Genes Left Behind: Climate Change Threatens Cryptic Genetic Diversity in the Canopy-Forming Seaweed Bifurcaria bifurcata. PLoS One 2015; 10:e0131530. [PMID: 26177545 PMCID: PMC4503591 DOI: 10.1371/journal.pone.0131530] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Accepted: 06/03/2015] [Indexed: 11/30/2022] Open
Abstract
The global redistribution of biodiversity will intensify in the coming decades of climate change, making projections of species range shifts and of associated genetic losses important components of conservation planning. Highly-structured marine species, notably brown seaweeds, often harbor unique genetic variation at warmer low-latitude rear edges and thus are of particular concern. Here, a combination of Ecological Niche Models (ENMs) and molecular data is used to forecast the potential near-future impacts of climate change for a warm-temperate, canopy forming seaweed, Bifurcaria bifurcata. ENMs for B. bifurcata were developed using marine and terrestrial climatic variables, and its range projected for 2040-50 and 2090-2100 under two greenhouse emission scenarios. Geographical patterns of genetic diversity were assessed by screening 18 populations spawning the entire distribution for two organelle genes and 6 microsatellite markers. The southern limit of B. bifurcata was predicted to shift northwards to central Morocco by the mid-century. By 2090-2100, depending on the emission scenario, it could either retreat further north to western Iberia or be relocated back to Western Sahara. At the opposing margin, B. bifurcata was predicted to expand its range to Scotland or even Norway. Microsatellite diversity and endemism were highest in Morocco, where a unique and very restricted lineage was also identified. Our results imply that B. bifurcata will maintain a relatively broad latitudinal distribution. Although its persistence is not threatened, the predicted extirpation of a unique southern lineage or even the entire Moroccan diversity hotspot will erase a rich evolutionary legacy and shrink global diversity to current (low) European levels. NW Africa and similarly understudied southern regions should receive added attention if expected range changes and diversity loss of warm-temperate species is not to occur unnoticed.
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Affiliation(s)
- João Neiva
- Centro de Ciências do Mar da Universidade do Algarve, Faro, Portugal
| | - Jorge Assis
- Centro de Ciências do Mar da Universidade do Algarve, Faro, Portugal
| | - Nelson C. Coelho
- Centro de Ciências do Mar da Universidade do Algarve, Faro, Portugal
| | | | - Gareth A. Pearson
- Centro de Ciências do Mar da Universidade do Algarve, Faro, Portugal
| | - Ester A. Serrão
- Centro de Ciências do Mar da Universidade do Algarve, Faro, Portugal
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Glynn F, Houghton JDR, Provan J. Population genetic analyses reveal distinct geographical blooms of the jellyfishRhizostoma octopus(Scyphozoa). Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12614] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Fergal Glynn
- School of Biological Sciences; Queen's University Belfast; 97 Lisburn Road BT9 7BL Belfast UK
- Institute for Global Food Security; Queen's University Belfast; Belfast UK
| | - Jonathan D. R. Houghton
- School of Biological Sciences; Queen's University Belfast; 97 Lisburn Road BT9 7BL Belfast UK
- Institute for Global Food Security; Queen's University Belfast; Belfast UK
- Queen's Marine Laboratory; 12-13 The Strand BT22 1PF Portaferry UK
| | - Jim Provan
- School of Biological Sciences; Queen's University Belfast; 97 Lisburn Road BT9 7BL Belfast UK
- Institute for Global Food Security; Queen's University Belfast; Belfast UK
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28
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Druzhkova AS, Vorobieva NV, Trifonov VA, Graphodatsky AS. Ancient DNA: Results and prospects (The 30th anniversary). RUSS J GENET+ 2015. [DOI: 10.1134/s1022795415060046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Gill JL, Blois JL, Benito B, Dobrowski S, Hunter ML, McGuire JL. A 2.5-million-year perspective on coarse-filter strategies for conserving nature's stage. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2015; 29:640-648. [PMID: 25924205 DOI: 10.1111/cobi.12504] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2014] [Accepted: 11/25/2014] [Indexed: 06/04/2023]
Abstract
Climate change will require novel conservation strategies. One such tactic is a coarse-filter approach that focuses on conserving nature's stage (CNS) rather than the actors (individual species). However, there is a temporal mismatch between the long-term goals of conservation and the short-term nature of most ecological studies, which leaves many assumptions untested. Paleoecology provides a valuable perspective on coarse-filter strategies by marshaling the natural experiments of the past to contextualize extinction risk due to the emerging impacts of climate change and anthropogenic threats. We reviewed examples from the paleoecological record that highlight the strengths, opportunities, and caveats of a CNS approach. We focused on the near-time geological past of the Quaternary, during which species were subjected to widespread changes in climate and concomitant changes in the physical environment in general. Species experienced a range of individualistic responses to these changes, including community turnover and novel associations, extinction and speciation, range shifts, changes in local richness and evenness, and both equilibrium and disequilibrium responses. Due to the dynamic nature of species responses to Quaternary climate change, a coarse-filter strategy may be appropriate for many taxa because it can accommodate dynamic processes. However, conservationists should also consider that the persistence of landforms varies across space and time, which could have potential long-term consequences for geodiversity and thus biodiversity.
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Affiliation(s)
- Jacquelyn L Gill
- School of Biology & Ecology, University of Maine, Orono, ME, U.S.A..
- Climate Change Institute, University of Maine, Orono, ME, U.S.A..
| | - Jessica L Blois
- School of Natural Sciences, University of California-Merced, Merced, CA, U.S.A
| | - Blas Benito
- Department of Bioscience, Ecoinformatics & Biodiversity, Aarhus University, Aarhus, Denmark
| | - Solomon Dobrowski
- Department of Forest Management, College of Forestry and Conservation, University of Montana, Missoula, MT, U.S.A
| | - Malcolm L Hunter
- Department of Wildlife, Fisheries, and Conservation Biology, University of Maine, Orono, ME, U.S.A
| | - Jenny L McGuire
- Department of Biology, Georgia Institute of Technology, Atlanta, GA, U.S.A
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30
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Stewart JR, Jacobi RM. The long term response of birds to climate change: new results from a cold stage avifauna in northern England. PLoS One 2015; 10:e0122617. [PMID: 25992609 PMCID: PMC4439125 DOI: 10.1371/journal.pone.0122617] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Accepted: 02/23/2015] [Indexed: 11/22/2022] Open
Abstract
The early MIS 3 (55–40 Kyr BP associated with Middle Palaeolithic archaeology) bird remains from Pin Hole, Creswell Crags, Derbyshire, England are analysed in the context of the new dating of the site’s stratigraphy. The analysis is restricted to the material from the early MIS 3 level of the cave because the upper fauna is now known to include Holocene material as well as that from the Late Glacial. The results of the analysis confirm the presence of the taxa, possibly unexpected for a Late Pleistocene glacial deposit including records such as Alpine swift, demoiselle crane and long-legged buzzard with southern and/or eastern distributions today. These taxa are accompanied by more expected ones such as willow ptarmigan /red grouse and rock ptarmigan living today in northern and montane areas. Finally, there are temperate taxa normally requiring trees for nesting such as wood pigeon and grey heron. Therefore, the result of the analysis is that the avifauna of early MIS 3 in England included taxa whose ranges today do not overlap making it a non-analogue community similar to the many steppe-tundra mammalian faunas of the time. The inclusion of more temperate and woodland taxa is discussed in the light that parts of northern Europe may have acted as cryptic northern refugia for some such taxa during the last glacial. These records showing former ranges of taxa are considered in the light of modern phylogeographic studies as these often assume former ranges without considering the fossil record of those taxa. In addition to the anomalous combination of taxa during MIS 3 living in Derbyshire, the individuals of a number of the taxa are different in size and shape to members of the species today probably due to the high carrying capacity of the steppe-tundra.
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Affiliation(s)
- John R. Stewart
- Faculty of Science and Technology, Bournemouth University, Talbot Campus, Fern Barrow, Poole, Dorset, BH12 5BB, United Kingdom
- * E-mail:
| | - Roger M. Jacobi
- Department of Earth Sciences, Natural History Museum, Cromwell Road, London, SW7 5BD, United Kingdom
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Orlando L, Cooper A. Using Ancient DNA to Understand Evolutionary and Ecological Processes. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2014. [DOI: 10.1146/annurev-ecolsys-120213-091712] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Ancient DNA provides a unique means to record genetic change through time and directly observe evolutionary and ecological processes. Although mostly based on mitochondrial DNA, the increasing availability of genomic sequences is leading to unprecedented levels of resolution. Temporal studies of population genetics have revealed dynamic patterns of change in many large vertebrates, featuring localized extinctions, migrations, and population bottlenecks. The pronounced climate cycles of the Late Pleistocene have played a key role, reducing the taxonomic and genetic diversity of many taxa and shaping modern populations. Importantly, the complex series of events revealed by ancient DNA data is seldom reflected in current biogeographic patterns. DNA preserved in ancient sediments and coprolites has been used to characterize a range of paleoenvironments and reconstruct functional relationships in paleoecological systems. In the near future, genome-level surveys of ancient populations will play an increasingly important role in revealing, calibrating, and testing evolutionary processes.
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Affiliation(s)
- Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350K Copenhagen, Denmark;,
| | - Alan Cooper
- Australian Center for Ancient DNA, University of Adelaide, Adelaide, South Australia
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Collins CJ, Rawlence NJ, Prost S, Anderson CNK, Knapp M, Scofield RP, Robertson BC, Smith I, Matisoo-Smith EA, Chilvers BL, Waters JM. Extinction and recolonization of coastal megafauna following human arrival in New Zealand. Proc Biol Sci 2014; 281:20140097. [PMID: 24827440 PMCID: PMC4046402 DOI: 10.1098/rspb.2014.0097] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Accepted: 04/14/2014] [Indexed: 11/12/2022] Open
Abstract
Extinctions can dramatically reshape biological communities. As a case in point, ancient mass extinction events apparently facilitated dramatic new evolutionary radiations of surviving lineages. However, scientists have yet to fully understand the consequences of more recent biological upheaval, such as the megafaunal extinctions that occurred globally over the past 50 kyr. New Zealand was the world's last large landmass to be colonized by humans, and its exceptional archaeological record documents a vast number of vertebrate extinctions in the immediate aftermath of Polynesian arrival approximately AD 1280. This recently colonized archipelago thus presents an outstanding opportunity to test for rapid biological responses to extinction. Here, we use ancient DNA (aDNA) analysis to show that extinction of an endemic sea lion lineage (Phocarctos spp.) apparently facilitated a subsequent northward range expansion of a previously subantarctic-limited lineage. This finding parallels a similar extinction-replacement event in penguins (Megadyptes spp.). In both cases, an endemic mainland clade was completely eliminated soon after human arrival, and then replaced by a genetically divergent clade from the remote subantarctic region, all within the space of a few centuries. These data suggest that ecological and demographic processes can play a role in constraining lineage distributions, even for highly dispersive species, and highlight the potential for dynamic biological responses to extinction.
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Affiliation(s)
- Catherine J Collins
- Allan Wilson Centre for Molecular Ecology and Evolution, Department of Zoology, University of Otago, Dunedin 9016, New Zealand
| | - Nicolas J Rawlence
- Allan Wilson Centre for Molecular Ecology and Evolution, Department of Zoology, University of Otago, Dunedin 9016, New Zealand
| | - Stefan Prost
- Allan Wilson Centre for Molecular Ecology and Evolution, Department of Anatomy, University of Otago, Dunedin 9016, New Zealand Department of Bioinformatics and Genetics, Swedish Museum of Natural History, 10405 Stockholm, Sweden Department of Integrative Biology, University of California, Berkeley, CA 94720-3140, USA
| | | | - Michael Knapp
- Allan Wilson Centre for Molecular Ecology and Evolution, Department of Anatomy, University of Otago, Dunedin 9016, New Zealand School of Biological Sciences, Bangor University, Bangor, LL57 2UW, Wales, UK
| | | | - Bruce C Robertson
- Allan Wilson Centre for Molecular Ecology and Evolution, Department of Zoology, University of Otago, Dunedin 9016, New Zealand
| | - Ian Smith
- Department of Anthropology and Archaeology, University of Otago, Dunedin 9016, New Zealand
| | - Elizabeth A Matisoo-Smith
- Allan Wilson Centre for Molecular Ecology and Evolution, Department of Anatomy, University of Otago, Dunedin 9016, New Zealand
| | - B Louise Chilvers
- Department of Conservation, Marine Species and Threats, Wellington 6011, New Zealand
| | - Jonathan M Waters
- Allan Wilson Centre for Molecular Ecology and Evolution, Department of Zoology, University of Otago, Dunedin 9016, New Zealand
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Barnett R, Yamaguchi N, Shapiro B, Ho SYW, Barnes I, Sabin R, Werdelin L, Cuisin J, Larson G. Revealing the maternal demographic history of Panthera leo using ancient DNA and a spatially explicit genealogical analysis. BMC Evol Biol 2014; 14:70. [PMID: 24690312 PMCID: PMC3997813 DOI: 10.1186/1471-2148-14-70] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Accepted: 03/13/2014] [Indexed: 11/15/2022] Open
Abstract
Background Understanding the demographic history of a population is critical to conservation and to our broader understanding of evolutionary processes. For many tropical large mammals, however, this aim is confounded by the absence of fossil material and by the misleading signal obtained from genetic data of recently fragmented and isolated populations. This is particularly true for the lion which as a consequence of millennia of human persecution, has large gaps in its natural distribution and several recently extinct populations. Results We sequenced mitochondrial DNA from museum-preserved individuals, including the extinct Barbary lion (Panthera leo leo) and Iranian lion (P. l. persica), as well as lions from West and Central Africa. We added these to a broader sample of lion sequences, resulting in a data set spanning the historical range of lions. Our Bayesian phylogeographical analyses provide evidence for highly supported, reciprocally monophyletic lion clades. Using a molecular clock, we estimated that recent lion lineages began to diverge in the Late Pleistocene. Expanding equatorial rainforest probably separated lions in South and East Africa from other populations. West African lions then expanded into Central Africa during periods of rainforest contraction. Lastly, we found evidence of two separate incursions into Asia from North Africa, first into India and later into the Middle East. Conclusions We have identified deep, well-supported splits within the mitochondrial phylogeny of African lions, arguing for recognition of some regional populations as worthy of independent conservation. More morphological and nuclear DNA data are now needed to test these subdivisions.
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Affiliation(s)
- Ross Barnett
- Durham Evolution and Ancient DNA, Department of Archaeology, Durham University, Durham DH1 3LE, UK.
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Lagerholm VK, Sandoval-Castellanos E, Ehrich D, Abramson NI, Nadachowski A, Kalthoff DC, Germonpré M, Angerbjörn A, Stewart JR, Dalén L. On the origin of the Norwegian lemming. Mol Ecol 2014; 23:2060-71. [DOI: 10.1111/mec.12698] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2013] [Revised: 01/31/2014] [Accepted: 02/07/2014] [Indexed: 11/28/2022]
Affiliation(s)
- Vendela K. Lagerholm
- Department of Bioinformatics and Genetics; Swedish Museum of Natural History; 10405 Stockholm Sweden
- Department of Zoology; Stockholm University; 10405 Stockholm Sweden
| | - Edson Sandoval-Castellanos
- Department of Bioinformatics and Genetics; Swedish Museum of Natural History; 10405 Stockholm Sweden
- Department of Zoology; Stockholm University; 10405 Stockholm Sweden
| | - Dorothee Ehrich
- Department of Arctic and Marine Biology; The Arctic University of Norway UiT; Tromsø 9037 Norway
| | - Natalia I. Abramson
- Zoological Institute; Russian Academy of Sciences; St. Petersburg 199034 Russia
| | - Adam Nadachowski
- Institute of Systematics and Evolution of Animals; Polish Academy of Sciences; Kraków 31-016 Poland
| | - Daniela C. Kalthoff
- Department of Zoology; Swedish Museum of Natural History; 10405 Stockholm Sweden
| | - Mietje Germonpré
- Operational Direction “Earth and History of Life”; Royal Belgian Institute of Natural Sciences; 1000 Brussels Belgium
| | | | - John R. Stewart
- Faculty of Science and Technology; Bournemouth University; Dorset BH12 5BB UK
| | - Love Dalén
- Department of Bioinformatics and Genetics; Swedish Museum of Natural History; 10405 Stockholm Sweden
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Dynesius M, Jansson R. Persistence of within-species lineages: a neglected control of speciation rates. Evolution 2013; 68:923-34. [PMID: 24329123 DOI: 10.1111/evo.12316] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Accepted: 11/07/2013] [Indexed: 11/30/2022]
Abstract
We present a framework distinguishing three principal controls of speciation rate: rate of splitting, level of persistence, and length of speciation duration. We contend that discussions on diversification become clearer in the light of this framework, because speciation rate variation could be attributed to any of these controls. In particular, we claim that the role of persistence of within-species lineages in controlling speciation rates has been greatly underappreciated. More emphasis on the persistence control would change expectations of the role of several biological traits and environmental factors, because they may drive speciation rate in one direction through the persistence control and in the opposite direction through the other two controls. Traits and environments have been little studied regarding their influence on speciation rate through the persistence control, with climatic fluctuations being a relatively well-studied exception. Considering the recent advances in genomic and phylogenetic analysis, we think that the time is ripe for applying the framework in empirical research. Variation among clades and areas (and thus among traits and environments) in the importance of the three rate controls could be addressed for example by dating splitting events, detecting within-species lineages, and scanning genomes for evidence of divergent selection.
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Affiliation(s)
- Mats Dynesius
- Department of Ecology and Environmental Science, Umeå University, SE-901 87 Umeå, Sweden.
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Rödder D, Lawing AM, Flecks M, Ahmadzadeh F, Dambach J, Engler JO, Habel JC, Hartmann T, Hörnes D, Ihlow F, Schidelko K, Stiels D, Polly PD. Evaluating the significance of paleophylogeographic species distribution models in reconstructing quaternary range-shifts of nearctic chelonians. PLoS One 2013; 8:e72855. [PMID: 24130664 PMCID: PMC3794015 DOI: 10.1371/journal.pone.0072855] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Accepted: 07/14/2013] [Indexed: 12/27/2022] Open
Abstract
The climatic cycles of the Quaternary, during which global mean annual temperatures have regularly changed by 5-10°C, provide a special opportunity for studying the rate, magnitude, and effects of geographic responses to changing climates. During the Quaternary, high- and mid-latitude species were extirpated from regions that were covered by ice or otherwise became unsuitable, persisting in refugial retreats where the environment was compatible with their tolerances. In this study we combine modern geographic range data, phylogeny, Pleistocene paleoclimatic models, and isotopic records of changes in global mean annual temperature, to produce a temporally continuous model of geographic changes in potential habitat for 59 species of North American turtles over the past 320 Ka (three full glacial-interglacial cycles). These paleophylogeographic models indicate the areas where past climates were compatible with the modern ranges of the species and serve as hypotheses for how their geographic ranges would have changed in response to Quaternary climate cycles. We test these hypotheses against physiological, genetic, taxonomic and fossil evidence, and we then use them to measure the effects of Quaternary climate cycles on species distributions. Patterns of range expansion, contraction, and fragmentation in the models are strongly congruent with (i) phylogeographic differentiation; (ii) morphological variation; (iii) physiological tolerances; and (iv) intraspecific genetic variability. Modern species with significant interspecific differentiation have geographic ranges that strongly fluctuated and repeatedly fragmented throughout the Quaternary. Modern species with low genetic diversity have geographic distributions that were highly variable and at times exceedingly small in the past. Our results reveal the potential for paleophylogeographic models to (i) reconstruct past geographic range modifications, (ii) identify geographic processes that result in genetic bottlenecks; and (iii) predict threats due to anthropogenic climate change in the future.
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Affiliation(s)
- Dennis Rödder
- Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany
| | - A. Michelle Lawing
- National Institute for Mathematical and Biological Synthesis (NIMBioS), University of Tennessee, Knoxville, Tennessee, United States of America
| | - Morris Flecks
- Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany
| | | | | | - Jan O. Engler
- Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany
- Department of Biogeography, Trier University, Trier, Germany
| | | | - Timo Hartmann
- Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany
| | - David Hörnes
- Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany
| | - Flora Ihlow
- Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany
| | | | - Darius Stiels
- Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany
| | - P. David Polly
- Department of Geological Sciences, Indiana University, Bloomington, Indiana, United States of America
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38
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Razgour O, Juste J, Ibáñez C, Kiefer A, Rebelo H, Puechmaille SJ, Arlettaz R, Burke T, Dawson DA, Beaumont M, Jones G, Wiens J. The shaping of genetic variation in edge-of-range populations under past and future climate change. Ecol Lett 2013; 16:1258-66. [PMID: 23890483 PMCID: PMC4015367 DOI: 10.1111/ele.12158] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2013] [Revised: 05/08/2013] [Accepted: 06/27/2013] [Indexed: 11/29/2022]
Abstract
With rates of climate change exceeding the rate at which many species are able to shift their range or adapt, it is important to understand how future changes are likely to affect biodiversity at all levels of organisation. Understanding past responses and extent of niche conservatism in climatic tolerance can help predict future consequences. We use an integrated approach to determine the genetic consequences of past and future climate changes on a bat species, Plecotus austriacus. Glacial refugia predicted by palaeo-modelling match those identified from analyses of extant genetic diversity and model-based inference of demographic history. Former refugial populations currently contain disproportionately high genetic diversity, but niche conservatism, shifts in suitable areas and barriers to migration mean that these hotspots of genetic diversity are under threat from future climate change. Evidence of population decline despite recent northward migration highlights the need to conserve leading-edge populations for spearheading future range shifts.
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Affiliation(s)
- Orly Razgour
- School of Biological Sciences, University of BristolWoodland Rd., Bristol, BS8 1UG, UK
- NERC Biomolecular Analysis Facility, Animal and Plant Sciences, University of SheffieldWestern Bank, Sheffield, S10 2TN, UK
| | - Javier Juste
- Estación Biológica de Doñana (CSIC)Apdo 1056, 41080, Sevilla, Spain
| | - Carlos Ibáñez
- Estación Biológica de Doñana (CSIC)Apdo 1056, 41080, Sevilla, Spain
| | - Andreas Kiefer
- Department of Biogeography, Trier UniversityD-54286, Trier, Germany
| | - Hugo Rebelo
- School of Biological Sciences, University of BristolWoodland Rd., Bristol, BS8 1UG, UK
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do PortoCampus Agrário de Vairão, R. Padre Armando Quintas, 4485-661, Vairão, Portugal
| | - Sébastien J Puechmaille
- School of Biology and Environmental Sciences, University College DublinBelfield, Dublin, Ireland
| | - Raphael Arlettaz
- Institute of Ecology and Evolution, Division of Conservation Biology, University of Bern3012, Bern, Switzerland
| | - Terry Burke
- NERC Biomolecular Analysis Facility, Animal and Plant Sciences, University of SheffieldWestern Bank, Sheffield, S10 2TN, UK
| | - Deborah A Dawson
- NERC Biomolecular Analysis Facility, Animal and Plant Sciences, University of SheffieldWestern Bank, Sheffield, S10 2TN, UK
| | - Mark Beaumont
- School of Biological Sciences, University of BristolWoodland Rd., Bristol, BS8 1UG, UK
| | - Gareth Jones
- School of Biological Sciences, University of BristolWoodland Rd., Bristol, BS8 1UG, UK
| | - John Wiens
- School of Biological Sciences, University of BristolWoodland Rd., Bristol, BS8 1UG, UK
- NERC Biomolecular Analysis Facility, Animal and Plant Sciences, University of SheffieldWestern Bank, Sheffield, S10 2TN, UK
- Estación Biológica de Doñana (CSIC)Apdo 1056, 41080, Sevilla, Spain
- Department of Biogeography, Trier UniversityD-54286, Trier, Germany
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do PortoCampus Agrário de Vairão, R. Padre Armando Quintas, 4485-661, Vairão, Portugal
- School of Biology and Environmental Sciences, University College DublinBelfield, Dublin, Ireland
- Institute of Ecology and Evolution, Division of Conservation Biology, University of Bern3012, Bern, Switzerland
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39
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Palkopoulou E, Dalén L, Lister AM, Vartanyan S, Sablin M, Sher A, Edmark VN, Brandström MD, Germonpré M, Barnes I, Thomas JA. Holarctic genetic structure and range dynamics in the woolly mammoth. Proc Biol Sci 2013; 280:20131910. [PMID: 24026825 PMCID: PMC3779339 DOI: 10.1098/rspb.2013.1910] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
Ancient DNA analyses have provided enhanced resolution of population histories in many Pleistocene taxa. However, most studies are spatially restricted, making inference of species-level biogeographic histories difficult. Here, we analyse mitochondrial DNA (mtDNA) variation in the woolly mammoth from across its Holarctic range to reconstruct its history over the last 200 thousand years (kyr). We identify a previously undocumented major mtDNA lineage in Europe, which was replaced by another major mtDNA lineage 32–34 kyr before present (BP). Coalescent simulations provide support for demographic expansions at approximately 121 kyr BP, suggesting that the previous interglacial was an important driver for demography and intraspecific genetic divergence. Furthermore, our results suggest an expansion into Eurasia from America around 66 kyr BP, coinciding with the first exposure of the Bering Land Bridge during the Late Pleistocene. Bayesian inference indicates Late Pleistocene demographic stability until 20–15 kyr BP, when a severe population size decline occurred.
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Affiliation(s)
- Eleftheria Palkopoulou
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, , 10405 Stockholm, Sweden, Department of Zoology, Stockholm University, , Stockholm 10691, Sweden, Department of Earth Sciences, Natural History Museum, , London SW7 5BD, UK, Northeast Interdisciplinary Research Institute, Far East Branch, Russian Academy of Sciences, , Magadan 685000, Russia, Zoological Institute of Russian Academy of Sciences, Saint-Petersburg 199034, Russia, Institute of Ecology and Evolution, Russian Academy of Sciences, , Moscow 119071, Russia, Department of Forest Mycology and Pathology, Swedish University of Agricultural Sciences, , 10691 Uppsala, Sweden, Operational Direction 'Earth and History of Life', Royal Belgian Institute of Natural Sciences, , Vautierstraat 29, 1000 Brussels, Belgium, School of Biological Sciences, Royal Holloway University of London, , Egham, Surrey TW20 0EX, UK
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40
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Leonard SA, Risley CL, Turvey ST. Could brown bears (Ursus arctos) have survived in Ireland during the Last Glacial Maximum? Biol Lett 2013; 9:20130281. [PMID: 23676655 PMCID: PMC3730640 DOI: 10.1098/rsbl.2013.0281] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Accepted: 04/22/2013] [Indexed: 11/12/2022] Open
Abstract
Brown bears are recorded from Ireland during both the Late Pleistocene and early-mid Holocene. Although most of the Irish landmass was covered by an ice sheet during the Last Glacial Maximum (LGM), Irish brown bears are known to have hybridized with polar bears during the Late Pleistocene, and it is suggested that the Irish brown bear population did not become extinct but instead persisted in situ through the LGM in a southwestern ice-free refugium. We use historical population modelling to demonstrate that brown bears are highly unlikely to have survived through the LGM in Ireland under any combination of life-history parameters shown by living bear populations, but instead would have rapidly become extinct following advance of the British-Irish ice sheet, and probably recolonized Ireland during the end-Pleistocene Woodgrange Interstadial from a closely related nearby source population. The time available for brown bear-polar bear hybridization was therefore restricted to narrow periods at the beginning or end of the LGM. Brown bears would have been extremely vulnerable to extinction in Quaternary habitat refugia and required areas substantially larger than southwestern Ireland to survive adverse glacial conditions.
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Affiliation(s)
- Saoirse A. Leonard
- Institute of Zoology, Zoological Society of London, Regent's Park, London NW1 4RY, UK
| | - Claire L. Risley
- University of Liverpool, Leahurst Campus, Neston, Cheshire CH64 7TE, UK
| | - Samuel T. Turvey
- Institute of Zoology, Zoological Society of London, Regent's Park, London NW1 4RY, UK
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41
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Meiri M, Lister AM, Higham TFG, Stewart JR, Straus LG, Obermaier H, González Morales MR, Marín-Arroyo AB, Barnes I. Late-glacial recolonization and phylogeography of European red deer (Cervus elaphusL.). Mol Ecol 2013; 22:4711-22. [DOI: 10.1111/mec.12420] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Revised: 06/09/2013] [Accepted: 06/11/2013] [Indexed: 11/27/2022]
Affiliation(s)
- Meirav Meiri
- Department of Zoology; Institute of Archaeology; Tel Aviv University; Tel Aviv 69978 Israel
| | - Adrian M. Lister
- Department of Earth Sciences; Natural History Museum; Cromwell Road London SW7 5BD UK
| | - Thomas F. G. Higham
- Research Lab for Archaeology and the History of Art; University of Oxford; Oxford OX1 3QY UK
| | - John R. Stewart
- School of Applied Sciences; Bournemouth University; Poole Dorset BH12 5BB UK
| | - Lawrence G. Straus
- Department of Anthropology; University of New Mexico; Albuquerque NM 87131-0001 USA
- Instituto Internacional de Investigaciones Prehistóricas de Cantabria; Universidad de Cantabria; Santander 39005 Spain
| | - Henriette Obermaier
- Bavarian State Collection for Anthropology and Palaeoanatomy Munich; Munich 80539 Germany
| | - Manuel R. González Morales
- Instituto Internacional de Investigaciones Prehistóricas de Cantabria; Universidad de Cantabria; Santander 39005 Spain
| | - Ana B. Marín-Arroyo
- Instituto Internacional de Investigaciones Prehistóricas de Cantabria; Universidad de Cantabria; Santander 39005 Spain
| | - Ian Barnes
- School of Biological Sciences; Royal Holloway; University of London; Egham Surrey TW20 0EX UK
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42
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Foote AD, Kaschner K, Schultze SE, Garilao C, Ho SY, Post K, Higham TF, Stokowska C, van der Es H, Embling CB, Gregersen K, Johansson F, Willerslev E, Gilbert MTP. Ancient DNA reveals that bowhead whale lineages survived Late Pleistocene climate change and habitat shifts. Nat Commun 2013; 4:1677. [DOI: 10.1038/ncomms2714] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2012] [Accepted: 03/07/2013] [Indexed: 11/09/2022] Open
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43
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Hung CM, Lin RC, Chu JH, Yeh CF, Yao CJ, Li SH. The de novo assembly of mitochondrial genomes of the extinct passenger pigeon (Ectopistes migratorius) with next generation sequencing. PLoS One 2013; 8:e56301. [PMID: 23437111 PMCID: PMC3577829 DOI: 10.1371/journal.pone.0056301] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2012] [Accepted: 01/11/2013] [Indexed: 11/18/2022] Open
Abstract
The information from ancient DNA (aDNA) provides an unparalleled opportunity to infer phylogenetic relationships and population history of extinct species and to investigate genetic evolution directly. However, the degraded and fragmented nature of aDNA has posed technical challenges for studies based on conventional PCR amplification. In this study, we present an approach based on next generation sequencing to efficiently sequence the complete mitochondrial genome (mitogenome) of two extinct passenger pigeons (Ectopistes migratorius) using de novo assembly of massive short (90 bp), paired-end or single-end reads. Although varying levels of human contamination and low levels of postmortem nucleotide lesion were observed, they did not impact sequencing accuracy. Our results demonstrated that the de novo assembly of shotgun sequence reads could be a potent approach to sequence mitogenomes, and offered an efficient way to infer evolutionary history of extinct species.
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Affiliation(s)
- Chih-Ming Hung
- Bell Museum and Department of Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, Minnesota, United States of America
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Rong-Chien Lin
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Jui-Hua Chu
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Chia-Fen Yeh
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Chiou-Ju Yao
- Department of Biology, National Museum of Natural Science, Taichung, Taiwan
| | - Shou-Hsien Li
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
- * E-mail:
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44
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Brace S, Palkopoulou E, Dalén L, Lister AM, Miller R, Otte M, Germonpré M, Blockley SPE, Stewart JR, Barnes I. Serial population extinctions in a small mammal indicate Late Pleistocene ecosystem instability. Proc Natl Acad Sci U S A 2012; 109:20532-6. [PMID: 23185018 PMCID: PMC3528586 DOI: 10.1073/pnas.1213322109] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The Late Pleistocene global extinction of many terrestrial mammal species has been a subject of intensive scientific study for over a century, yet the relative contributions of environmental changes and the global expansion of humans remain unresolved. A defining component of these extinctions is a bias toward large species, with the majority of small-mammal taxa apparently surviving into the present. Here, we investigate the population-level history of a key tundra-specialist small mammal, the collared lemming (Dicrostonyx torquatus), to explore whether events during the Late Pleistocene had a discernible effect beyond the large mammal fauna. Using ancient DNA techniques to sample across three sites in North-West Europe, we observe a dramatic reduction in genetic diversity in this species over the last 50,000 y. We further identify a series of extinction-recolonization events, indicating a previously unrecognized instability in Late Pleistocene small-mammal populations, which we link with climatic fluctuations. Our results reveal climate-associated, repeated regional extinctions in a keystone prey species across the Late Pleistocene, a pattern likely to have had an impact on the wider steppe-tundra community, and one that is concordant with environmental change as a major force in structuring Late Pleistocene biodiversity.
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Affiliation(s)
| | - Eleftheria Palkopoulou
- Department of Molecular Systematics, Swedish Museum of Natural History, 104 05 Stockholm, Sweden
- Department of Zoology, Stockholm University, 106 91 Stockholm, Sweden
| | - Love Dalén
- Department of Molecular Systematics, Swedish Museum of Natural History, 104 05 Stockholm, Sweden
| | - Adrian M. Lister
- Department of Earth Sciences, Natural History Museum, London SW7 5BD, United Kingdom
| | - Rebecca Miller
- Service of Prehistory, University of Liège, 4000 Liège, Belgium
| | - Marcel Otte
- Service of Prehistory, University of Liège, 4000 Liège, Belgium
| | - Mietje Germonpré
- Department of Palaeontology, Royal Belgian Institute of Natural Sciences, 1000 Brussels, Belgium; and
| | - Simon P. E. Blockley
- Department of Geography, Royal Holloway University of London, Egham, Surrey TW20 0EX, United Kingdom
| | - John R. Stewart
- School of Applied Sciences, Bournemouth University, Poole, Dorset BH12 5BB, United Kingdom
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45
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Elizabeth Alter S, Rosenbaum HC, Postma LD, Whitridge P, Gaines C, Weber D, Egan MG, Lindsay M, Amato G, Dueck L, Brownell RL, Heide-Jørgensen MP, Laidre KL, Caccone G, Hancock BL. Gene flow on ice: the role of sea ice and whaling in shaping Holarctic genetic diversity and population differentiation in bowhead whales (Balaena mysticetus). Ecol Evol 2012; 2:2895-911. [PMID: 23170222 PMCID: PMC3501639 DOI: 10.1002/ece3.397] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2012] [Revised: 08/21/2012] [Accepted: 08/27/2012] [Indexed: 11/10/2022] Open
Abstract
Sea ice is believed to be a major factor shaping gene flow for polar marine organisms, but it remains unclear to what extent it represents a true barrier to dispersal for arctic cetaceans. Bowhead whales are highly adapted to polar sea ice and were targeted by commercial whalers throughout Arctic and subarctic seas for at least four centuries, resulting in severe reductions in most areas. Both changing ice conditions and reductions due to whaling may have affected geographic distribution and genetic diversity throughout their range, but little is known about range-wide genetic structure or whether it differed in the past. This study represents the first examination of genetic diversity and differentiation across all five putative stocks, including Baffin Bay-Davis Strait, Hudson Bay-Foxe Basin, Bering-Beaufort-Chukchi, Okhotsk, and Spitsbergen. We also utilized ancient specimens from Prince Regent Inlet (PRI) in the Canadian Arctic and compared them with modern stocks. Results from analysis of molecular variance and demographic simulations are consistent with recent and high gene flow between Atlantic and Pacific stocks in the recent past. Significant genetic differences between ancient and modern populations suggest PRI harbored unique maternal lineages in the past that have been recently lost, possibly due to loss of habitat during the Little Ice Age and/or whaling. Unexpectedly, samples from this location show a closer genetic relationship with modern Pacific stocks than Atlantic, supporting high gene flow between the central Canadian Arctic and Beaufort Sea over the past millennium despite extremely heavy ice cover over much of this period.
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Affiliation(s)
- S Elizabeth Alter
- Department of Biology, York College, City University of New York 94-20 Guy R. Brewer Blvd, Jamaica, New York, 11415 ; CUNY Graduate Center, 365 Fifth Avenue New York city, New York, 10016 ; American Museum of Natural History, Sackler Institute for Comparative Genomics 79th St and Central Park West, New York city, New York, 10024
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46
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Molak M, Lorenzen ED, Shapiro B, Ho SY. Phylogenetic Estimation of Timescales Using Ancient DNA: The Effects of Temporal Sampling Scheme and Uncertainty in Sample Ages. Mol Biol Evol 2012; 30:253-62. [DOI: 10.1093/molbev/mss232] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Abstract
In recent years, ancient DNA has increasingly been used for estimating molecular timescales, particularly in studies of substitution rates and demographic histories. Molecular clocks can be calibrated using temporal information from ancient DNA sequences. This information comes from the ages of the ancient samples, which can be estimated by radiocarbon dating the source material or by dating the layers in which the material was deposited. Both methods involve sources of uncertainty. The performance of Bayesian phylogenetic inference depends on the information content of the data set, which includes variation in the DNA sequences and the structure of the sample ages. Various sources of estimation error can reduce our ability to estimate rates and timescales accurately and precisely. We investigated the impact of sample-dating uncertainties on the estimation of evolutionary timescale parameters using the software BEAST. Our analyses involved 11 published data sets and focused on estimates of substitution rate and root age. We show that, provided that samples have been accurately dated and have a broad temporal span, it might be unnecessary to account for sample-dating uncertainty in Bayesian phylogenetic analyses of ancient DNA. We also investigated the sample size and temporal span of the ancient DNA sequences needed to estimate phylogenetic timescales reliably. Our results show that the range of sample ages plays a crucial role in determining the quality of the results but that accurate and precise phylogenetic estimates of timescales can be made even with only a few ancient sequences. These findings have important practical consequences for studies of molecular rates, timescales, and population dynamics.
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Affiliation(s)
- Martyna Molak
- School of Biological Sciences, University of Sydney, Sydney, Australia
| | - Eline D. Lorenzen
- Department of Integrative Biology, University of California, Berkeley
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Beth Shapiro
- Department of Biology, Pennsylvania State University
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz
| | - Simon Y.W. Ho
- School of Biological Sciences, University of Sydney, Sydney, Australia
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47
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Ploshnitsa AI, Goltsman ME, Happ GM, Macdonald DW, Kennedy LJ. Historical and modern neutral genetic variability in
M
ednyi
A
rctic foxes passed through a severe bottleneck. J Zool (1987) 2012. [DOI: 10.1111/j.1469-7998.2012.00964.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- A. I. Ploshnitsa
- Biology Faculty, Department of Vertebrate Zoology Lomonosov Moscow State University Moscow Russia
| | - M. E. Goltsman
- Biology Faculty, Department of Vertebrate Zoology Lomonosov Moscow State University Moscow Russia
| | - G. M. Happ
- Institute of Arctic Biology University of Alaska Fairbanks AK USA
| | - D. W. Macdonald
- Wildlife Conservation Research Unit, Department of Zoology, The Recananti‐Kaplan Centre, Tubney House University of Oxford Tubney UK
| | - L. J. Kennedy
- Centre for Integrated Genomic Medical Research The University of Manchester Manchester UK
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48
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Rizzi E, Lari M, Gigli E, De Bellis G, Caramelli D. Ancient DNA studies: new perspectives on old samples. Genet Sel Evol 2012; 44:21. [PMID: 22697611 PMCID: PMC3390907 DOI: 10.1186/1297-9686-44-21] [Citation(s) in RCA: 129] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2011] [Accepted: 06/14/2012] [Indexed: 11/24/2022] Open
Abstract
In spite of past controversies, the field of ancient DNA is now a reliable research area due to recent methodological improvements. A series of recent large-scale studies have revealed the true potential of ancient DNA samples to study the processes of evolution and to test models and assumptions commonly used to reconstruct patterns of evolution and to analyze population genetics and palaeoecological changes. Recent advances in DNA technologies, such as next-generation sequencing make it possible to recover DNA information from archaeological and paleontological remains allowing us to go back in time and study the genetic relationships between extinct organisms and their contemporary relatives. With the next-generation sequencing methodologies, DNA sequences can be retrieved even from samples (for example human remains) for which the technical pitfalls of classical methodologies required stringent criteria to guaranty the reliability of the results. In this paper, we review the methodologies applied to ancient DNA analysis and the perspectives that next-generation sequencing applications provide in this field.
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Affiliation(s)
- Ermanno Rizzi
- Institute for Biomedical Technologies, National Research Council, Via F.lli Cervi 93, Segrate, Milan 20090, Italy
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49
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50
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Stewart JR, Stringer CB. Human Evolution Out of Africa: The Role of Refugia and Climate Change. Science 2012; 335:1317-21. [DOI: 10.1126/science.1215627] [Citation(s) in RCA: 195] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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