1
|
Hoffecker JF, Elias SA, Scott GR, O'Rourke DH, Hlusko LJ, Potapova O, Pitulko V, Pavlova E, Bourgeon L, Vachula RS. Beringia and the peopling of the Western Hemisphere. Proc Biol Sci 2023; 290:20222246. [PMID: 36629115 PMCID: PMC9832545 DOI: 10.1098/rspb.2022.2246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Did Beringian environments represent an ecological barrier to humans until less than 15 000 years ago or was access to the Americas controlled by the spatial-temporal distribution of North American ice sheets? Beringian environments varied with respect to climate and biota, especially in the two major areas of exposed continental shelf. The East Siberian Arctic Shelf ('Great Arctic Plain' (GAP)) supported a dry steppe-tundra biome inhabited by a diverse large-mammal community, while the southern Bering-Chukchi Platform ('Bering Land Bridge' (BLB)) supported mesic tundra and probably a lower large-mammal biomass. A human population with west Eurasian roots occupied the GAP before the Last Glacial Maximum (LGM) and may have accessed mid-latitude North America via an interior ice-free corridor. Re-opening of the corridor less than 14 000 years ago indicates that the primary ancestors of living First Peoples, who already had spread widely in the Americas at this time, probably dispersed from the NW Pacific coast. A genetic 'arctic signal' in non-arctic First Peoples suggests that their parent population inhabited the GAP during the LGM, before their split from the former. We infer a shift from GAP terrestrial to a subarctic maritime economy on the southern BLB coast before dispersal in the Americas from the NW Pacific coast.
Collapse
Affiliation(s)
- John F. Hoffecker
- Institute of Arctic and Alpine Research, University of Colorado, Boulder, CO 80309, USA,Department of Anthropology, University of Kansas, 622 Fraser Hall, 1415 Jayhawk Blvd, Lawrence, KS 66045, USA
| | - Scott A. Elias
- Institute of Arctic and Alpine Research, University of Colorado, Boulder, CO 80309, USA
| | - G. Richard Scott
- Department of Anthropology, University of Nevada-Reno, 1664 N. Virginia Street, Reno, NV 89557, USA
| | - Dennis H. O'Rourke
- Department of Anthropology, University of Kansas, 622 Fraser Hall, 1415 Jayhawk Blvd, Lawrence, KS 66045, USA
| | - Leslea J. Hlusko
- Human Evolution Research Center, University of California-Berkeley, 3101 Valley Life Sciences Building, Berkeley, CA 94720-3140, USA,Centro Nacional de Investigación sobre la Evolución Humana (CENIEH), Burgos, Spain
| | - Olga Potapova
- Pleistocene Park Foundation, Philadelphia, PA 19006, USA,Department of Mammoth Fauna Studies, Academy of Sciences of Sakha, Yakutsk, Russia,The Mammoth Site of Hot Springs, Hot Springs, SD 57747, USA
| | - Vladimir Pitulko
- Institute of the History of Material Culture, Russian Academy of Sciences, Dvortsovaya nab., 18, 191186 St Petersburg, Russia,Peter the Great Museum of Anthropology and Ethnography (Kunstkamera), Russian Academy of Sciences, 3, Universitetskaya nab., St Petersburg 199034, Russian Federation
| | - Elena Pavlova
- Arctic and Antarctic Research Institute, Russian Federal Service for Hydrometeorology and Environmental Monitoring, 38 Bering Street, 199397 St Petersburg, Russia
| | - Lauriane Bourgeon
- Kansas Geological Survey, University of Kansas, 1930 Constant Ave., Lawrence, KS 66047, USA
| | - Richard S. Vachula
- Department of Geosciences, Auburn University, 2050 Beard Eaves Coliseum, Auburn, AL 36849-5305, USA
| |
Collapse
|
2
|
Salis AT, Bray SCE, Lee MSY, Heiniger H, Barnett R, Burns JA, Doronichev V, Fedje D, Golovanova L, Harington CR, Hockett B, Kosintsev P, Lai X, Mackie Q, Vasiliev S, Weinstock J, Yamaguchi N, Meachen JA, Cooper A, Mitchell KJ. Lions and brown bears colonized North America in multiple synchronous waves of dispersal across the Bering Land Bridge. Mol Ecol 2022; 31:6407-6421. [PMID: 34748674 DOI: 10.1111/mec.16267] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 10/15/2021] [Accepted: 10/25/2021] [Indexed: 01/13/2023]
Abstract
The Bering Land Bridge connecting North America and Eurasia was periodically exposed and inundated by oscillating sea levels during the Pleistocene glacial cycles. This land connection allowed the intermittent dispersal of animals, including humans, between Western Beringia (far northeast Asia) and Eastern Beringia (northwest North America), changing the faunal community composition of both continents. The Pleistocene glacial cycles also had profound impacts on temperature, precipitation and vegetation, impacting faunal community structure and demography. While these palaeoenvironmental impacts have been studied in many large herbivores from Beringia (e.g., bison, mammoths, horses), the Pleistocene population dynamics of the diverse guild of carnivorans present in the region are less well understood, due to their lower abundances. In this study, we analyse mitochondrial genome data from ancient brown bears (Ursus arctos; n = 103) and lions (Panthera spp.; n = 39), two megafaunal carnivorans that dispersed into North America during the Pleistocene. Our results reveal striking synchronicity in the population dynamics of Beringian lions and brown bears, with multiple waves of dispersal across the Bering Land Bridge coinciding with glacial periods of low sea levels, as well as synchronous local extinctions in Eastern Beringia during Marine Isotope Stage 3. The evolutionary histories of these two taxa underline the crucial biogeographical role of the Bering Land Bridge in the distribution, turnover and maintenance of megafaunal populations in North America.
Collapse
Affiliation(s)
- Alexander T Salis
- Australian Centre for Ancient DNA (ACAD), School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia.,Division of Vertebrate Zoology, American Museum of Natural History, New York, New York, USA
| | - Sarah C E Bray
- Australian Centre for Ancient DNA (ACAD), School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia.,Registry of Senior Australians (ROSA), South Australian Health and Medical Research Institute (SAHMRI), Adelaide, South Australia, Australia
| | - Michael S Y Lee
- College of Science and Engineering, Flinders University, Bedford Park, South Australia, Australia.,South Australian Museum, Adelaide, South Australia, Australia
| | - Holly Heiniger
- Australian Centre for Ancient DNA (ACAD), School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Ross Barnett
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - James A Burns
- Curator Emeritus, Royal Alberta Museum, Edmonton, Alberta, Canada
| | | | - Daryl Fedje
- Department of Anthropology, University of Victoria, Victoria, B.C, Canada
| | | | - C Richard Harington
- Curator Emeritus and Research Associate, Research Division (Paleobiology), Canadian Museum of Nature, Ottawa, Canada
| | - Bryan Hockett
- US Department of Interior, Bureau of Land Management, Nevada State Office, Reno, Nevada, USA
| | - Pavel Kosintsev
- Institute of Plant and Animal Ecology, Ural Branch of the Russian Academy of Sciences, Yekaterinburg, Russia.,Department of History, Ural Federal University, Yekaterinburg, Russia
| | - Xulong Lai
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, Hubei, China
| | - Quentin Mackie
- Department of Anthropology, University of Victoria, Victoria, B.C, Canada
| | - Sergei Vasiliev
- Institute of Archaeology and Ethnography, Russian Academy of Sciences, Russia
| | - Jacobo Weinstock
- Faculty of Humanities (Archaeology), University of Southampton, UK
| | - Nobuyuki Yamaguchi
- Institute of Tropical Biodiversity and Sustainable Development, University Malaysia Terengganu, Kuala Nerus, Malaysia
| | - Julie A Meachen
- Anatomy Department, Des Moines University, Des Moines, Iowa, USA
| | - Alan Cooper
- South Australian Museum, Adelaide, South Australia, Australia
| | - Kieren J Mitchell
- Australian Centre for Ancient DNA (ACAD), School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia.,Department of Zoology, Otago Palaeogenetics Laboratory, University of Otago, Dunedin, New Zealand
| |
Collapse
|
3
|
Phylogeny and evolution of the genus Cervus (Cervidae, Mammalia) as revealed by complete mitochondrial genomes. Sci Rep 2022; 12:16381. [PMID: 36180508 PMCID: PMC9525267 DOI: 10.1038/s41598-022-20763-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 09/19/2022] [Indexed: 11/24/2022] Open
Abstract
Mitochondrial DNA (mtDNA) lineages are recognized as important components of intra- and interspecific biodiversity, and allow to reveal colonization routes and phylogeographic structure of many taxa. Among these is the genus Cervus that is widely distributed across the Holarctic. We obtained sequences of complete mitochondrial genomes from 13 Cervus taxa and included them in global phylogenetic analyses of 71 Cervinae mitogenomes. The well-resolved phylogenetic trees confirmed Cervus to be monophyletic. Molecular dating based on several fossil calibration points revealed that ca. 2.6 Mya two main mitochondrial lineages of Cervus separated in Central Asia, the Western (including C. hanglu and C. elaphus) and the Eastern (comprising C. albirostris, C. canadensis and C. nippon). We also observed convergent changes in the composition of some mitochondrial genes in C. hanglu of the Western lineage and representatives of the Eastern lineage. Several subspecies of C. nippon and C. hanglu have accumulated a large portion of deleterious substitutions in their mitochondrial protein-coding genes, probably due to drift in the wake of decreasing population size. In contrast to previous studies, we found that the relic haplogroup B of C. elaphus was sister to all other red deer lineages and that the Middle-Eastern haplogroup E shared a common ancestor with the Balkan haplogroup C. Comparison of the mtDNA phylogenetic tree with a published nuclear genome tree may imply ancient introgressions of mtDNA between different Cervus species as well as from the common ancestor of South Asian deer, Rusa timorensis and R. unicolor, to the Cervus clade.
Collapse
|
4
|
Groves P, Mann DH, Kunz ML. Prehistoric perspectives can help interpret the present: 14,000 years of moose (Alces alces L) in the Western Arctic. CAN J ZOOL 2022. [DOI: 10.1139/cjz-2022-0079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Rapidly changing climate at high latitudes has triggered a search for bellwethers of ecological change there. If the initial signs of change can be identified, perhaps we can predict where these changes will lead. Large-bodied, terrestrial, herbivores are potential candidates for bellwether taxa because of the key roles they play in some ecological communities. Here we assemble historical, archaeological and paleontological records of moose (<i>Alces alces</i> Linnaeus, 1758.) from the western Arctic and Subarctic. Results show that rather than having recently invaded tundra regions in response to post-Little Ice Age warming, moose have inhabited river corridors several hundred kilometers north of the closed, boreal forest since they first colonized North America across the Bering Land Bridge ca. 14,000 years ago. The combination of high mobility, fluctuation-prone metapopulations, and reliance on early successional vegetation makes changes in the northern range limits of moose undependable bellwethers for other biotic responses to changing climate. The history of moose at high latitudes illustrates how understanding what happened in prehistory is useful for correctly assigning significance and cause to present-day ecological changes.
Collapse
Affiliation(s)
- Pamela Groves
- University of Alaska Fairbanks, Institute of Arctic Biology, Fairbanks, Alaska, United States
| | - Daniel H Mann
- University of Alaska Fairbanks, Institute of Arctic Biology, Fairbanks, Alaska, United States
| | - Mike L Kunz
- University of Alaska Fairbanks, Museum of the North, Fairbanks, Alaska, United States
| |
Collapse
|
5
|
Niedbalski SD, Long JC. Novel alleles gained during the Beringian isolation period. Sci Rep 2022; 12:4289. [PMID: 35277570 PMCID: PMC8917172 DOI: 10.1038/s41598-022-08212-1] [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: 08/27/2021] [Accepted: 02/09/2022] [Indexed: 01/23/2023] Open
Abstract
During the Last Glacial Maximum, a small band of Siberians entered the Beringian corridor, where they persisted, isolated from gene flow, for several thousand years before expansion into the Americas. The ecological features of the Beringian environment, coupled with an extended period of isolation at small population size, would have provided evolutionary opportunity for novel genetic variation to arise as both rare standing variants and new mutations were driven to high frequency through both neutral and directed processes. Here we perform a full genome investigation of Native American populations in the Thousand Genomes Project Phase 3 to identify unique high frequency alleles that can be dated to an origin in Beringia. Our analyses demonstrate that descendant populations of Native Americans harbor 20,424 such variants, which is on a scale comparable only to Africa and the Out of Africa bottleneck. This is consistent with simulations of a serial founder effects model. Tests for selection reveal that some of these Beringian variants were likely driven to high frequency by adaptive processes, and bioinformatic analyses suggest possible phenotypic pathways that were under selection during the Beringian Isolation period. Specifically, pathways related to cardiac processes and melanocyte function appear to be enriched for selected Beringian variants.
Collapse
Affiliation(s)
- Sara D Niedbalski
- Human Evolutionary Genetics Unit, UMR 2000, CNRS, Institut Pasteur, Paris, France.,Department of Anthropology, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Jeffrey C Long
- Department of Anthropology, University of New Mexico, Albuquerque, NM, 87131, USA.
| |
Collapse
|
6
|
Oyundelger K, Harpke D, Herklotz V, Troeva E, Zheng Z, Li Z, Oyuntsetseg B, Wagner V, Wesche K, Ritz CM. Phylogeography of Artemisia frigida (Anthemideae, Asteraceae) based on genotyping-by-sequencing and plastid DNA data: Migration through Beringia. J Evol Biol 2021; 35:64-80. [PMID: 34792226 DOI: 10.1111/jeb.13960] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 11/03/2021] [Accepted: 11/10/2021] [Indexed: 12/20/2022]
Abstract
Artemisia frigida is a temperate grassland species that has the largest natural range among its genus, with occurrences across the temperate grassland biomes of Eurasia and North America. Despite its wide geographic range, we know little about the species' distribution history. Hence, we conducted a phylogeographical study to test the hypothesis that the species' distribution pattern is related to a potential historical migration over the 'Bering land bridge'. We applied two molecular approaches: genotyping-by-sequencing (GBS) and Sanger sequencing of the plastid intergenic spacer region (rpl32 - trnL) to investigate genetic differentiation and relatedness among 21 populations from North America, Middle Asia, Central Asia and the Russian Far East. Furthermore, we identified the ploidy level of individuals based on GBS data. Our results indicate that A. frigida originated in Asia, spread northwards to the Far East and then to North America across the Bering Strait. We found a pronounced genetic structuring between Middle and Central Asian populations with mixed ploidy levels, tetraploids in the Far East, and nearly exclusively diploids in North America except for one individual. According to phylogenetic analysis, two populations of Kazakhstan (KZ2 and KZ3) represent the most likely ancestral diploids that constitute the basally branching lineages, and subsequent polyploidization has occurred on several occasions independently. Mantel tests revealed weak correlations between genetic distance and geographical distance and climatic conditions, which indicates that paleoclimatic fluctuations may have more profoundly influenced A. frigida's spatial genetic structure and distribution than the current environment.
Collapse
Affiliation(s)
- Khurelpurev Oyundelger
- Chair of Biodiversity of Higher Plants, International Institute (IHI) Zittau, Technische Universität Dresden, Zittau, Germany.,Department of Botany, Senckenberg Museum of Natural History Görlitz, Görlitz, Germany
| | - Dörte Harpke
- Leibniz Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK), Seeland, Germany
| | - Veit Herklotz
- Department of Botany, Senckenberg Museum of Natural History Görlitz, Görlitz, Germany
| | - Elena Troeva
- Institute for Biological Problems of Cryolithozone, Siberian Branch of the Russian Academy of Sciences, Yakutsk, Russia
| | - Zhenzhen Zheng
- College of Life Sciences, University of the Chinese Academy of Sciences, Beijing, China
| | - Zheng Li
- School of Life Sciences, Henan University, Kaifeng, China
| | - Batlai Oyuntsetseg
- Department of Biology, School of Arts and Sciences, National University of Mongolia, Ulaanbaatar, Mongolia
| | - Viktoria Wagner
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Karsten Wesche
- Chair of Biodiversity of Higher Plants, International Institute (IHI) Zittau, Technische Universität Dresden, Zittau, Germany.,Department of Botany, Senckenberg Museum of Natural History Görlitz, Görlitz, Germany
| | - Christiane M Ritz
- Chair of Biodiversity of Higher Plants, International Institute (IHI) Zittau, Technische Universität Dresden, Zittau, Germany.,Department of Botany, Senckenberg Museum of Natural History Görlitz, Görlitz, Germany
| |
Collapse
|
7
|
Ferrante JA, Smith CH, Thompson LM, Hunter ME. Genome-wide SNP analysis of three moose subspecies at the southern range limit in the contiguous United States. CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01402-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
AbstractGenome-wide evaluations of genetic diversity and population structure are important for informing management and conservation of trailing-edge populations. North American moose (Alces alces) are declining along portions of the southern edge of their range due to disease, species interactions, and marginal habitat, all of which may be exacerbated by climate change. We employed a genotyping by sequencing (GBS) approach in an effort to collect baseline information on the genetic variation of moose inhabiting the species’ southern range periphery in the contiguous United States. We identified 1920 single nucleotide polymorphisms (SNPs) from 155 moose representing three subspecies from five states: A. a. americana (New Hampshire), A. a. andersoni (Minnesota), and A. a. shirasi (Idaho, Montana, and Wyoming). Molecular analyses supported three geographically isolated clusters, congruent with currently recognized subspecies. Additionally, while moderately low genetic diversity was observed, there was little evidence of inbreeding. Results also indicated > 20% shared ancestry proportions between A. a. shirasi samples from northern Montana and A. a. andersoni samples from Minnesota, indicating a putative hybrid zone warranting further investigation. GBS has proven to be a simple and effective method for genome-wide SNP discovery in moose and provides robust data for informing herd management and conservation priorities. With increasing disease, predation, and climate related pressure on range edge moose populations in the United States, the use of SNP data to identify gene flow between subspecies may prove a powerful tool for moose management and recovery, particularly if hybrid moose are more able to adapt.
Collapse
|
8
|
Doan K, Niedziałkowska M, Stefaniak K, Sykut M, Jędrzejewska B, Ratajczak-Skrzatek U, Piotrowska N, Ridush B, Zachos FE, Popović D, Baca M, Mackiewicz P, Kosintsev P, Makowiecki D, Charniauski M, Boeskorov G, Bondarev AA, Danila G, Kusak J, Rannamäe E, Saarma U, Arakelyan M, Manaseryan N, Krasnodębski D, Titov V, Hulva P, Bălășescu A, Trantalidou K, Dimitrijević V, Shpansky A, Kovalchuk O, Klementiev AM, Foronova I, Malikov DG, Juras A, Nikolskiy P, Grigoriev SE, Cheprasov MY, Novgorodov GP, Sorokin AD, Wilczyński J, Protopopov AV, Lipecki G, Stanković A. Phylogenetics and phylogeography of red deer mtDNA lineages during the last 50 000 years in Eurasia. Zool J Linn Soc 2021. [DOI: 10.1093/zoolinnean/zlab025] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
The present phylogeographic pattern of red deer in Eurasia is not only a result of the contraction of their distribution range into glacial refugia and postglacial expansion, but probably also an effect of replacement of some red deer s.l. mtDNA lineages by others during the last 50 000 years. To better recognize this process, we analysed 501 sequences of mtDNA cytochrome b, including 194 ancient and 75 contemporary samples newly obtained for this study. The inclusion of 161 radiocarbon-dated samples enabled us to study the phylogeny in a temporal context and conduct divergence-time estimation and molecular dating. Depending on methodology, our estimate of divergence between Cervus elaphus and Cervus canadensis varied considerably (370 000 or 1.37 million years BP, respectively). The divergence times of genetic lineages and haplogroups corresponded to large environmental changes associated with stadials and interstadials of the Late Pleistocene. Due to the climatic oscillations, the distribution of C. elaphus and C. canadensis fluctuated in north–south and east–west directions. Some haplotypes dated to pre-Last Glacial Maximum periods were not detected afterwards, representing possibly extinct populations. We indicated with a high probability the presence of red deer sensu lato in south-eastern Europe and western Asia during the Last Glacial Maximum.
Collapse
Affiliation(s)
- Karolina Doan
- College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, S. Banacha 2C, 02-097 Warsaw, Poland
- Museum and Institute of Zoology, Polish Academy of Sciences, Wilcza 64, 00-679 Warsaw, Poland
| | | | - Krzysztof Stefaniak
- Department of Palaeozoology, University of Wrocław, Sienkiewicza 21, 50-335 Wrocław, Poland
| | - Maciej Sykut
- Mammal Research Institute Polish Academy of Sciences, Stoczek 1c, 17-230 Białowieża, Poland
| | - Bogumiła Jędrzejewska
- Mammal Research Institute Polish Academy of Sciences, Stoczek 1c, 17-230 Białowieża, Poland
| | | | - Natalia Piotrowska
- Radiocarbon Laboratory Institute of Physics–Center for Science and Education, Silesian University of Technology, Konarskiego 22b,44-100 Gliwice, Poland
| | - Bogdan Ridush
- Department of Physical Geography, Geomorphology and Paleogeography, Yuriy Fedkovych Chernivtsi National University, Kotsubynskogo 2, Chernivtsi 58012, Ukraine
| | - Frank E Zachos
- Natural History Museum Vienna, 1010 Vienna, Austria
- Department of Genetics, University of the Free State, 9301 Bloemfontein, South Africa
- Department of Evolutionary Biology, University of Vienna, 1090 Vienna, Austria
| | - Danijela Popović
- Centre of New Technologies, University of Warsaw, S. Banacha 2c, 02-097 Warsaw, Poland
| | - Mateusz Baca
- Centre of New Technologies, University of Warsaw, S. Banacha 2c, 02-097 Warsaw, Poland
| | - Paweł Mackiewicz
- Department of Bioinformatics and Genomics, Faculty of Biotechnology, University of Wrocław, Joliot-Curie 14a, 50-383 Wrocław, Poland
| | - Pavel Kosintsev
- Institute of Plant and Animal Ecology, Ural Branch of the Russian Academy of Sciences, 8 Marta 202, Yekaterinburg 620144, Russia
| | - Daniel Makowiecki
- Nicolaus Copernicus University, Institute of Archaeology, Department of Historical Sciences, Szosa Bydgoska 44/48, 87-100 Toruń, Poland
| | - Maxim Charniauski
- Institute of History of the National Academy of Sciences of Belarus, Academic 1, 220072 Minsk, Belarus
| | - Gennady Boeskorov
- Institute of Diamond and Precious Metals Geology, Siberian Branch of Russian Academy of Sciences, Yakutsk, Yakutia, Russian Federation
| | | | - Gabriel Danila
- Universitatea Stefan cel Mare Suceava, Facultatea de Silvicultura, Suceava, Romania
| | - Josip Kusak
- Veterinary Faculty, University of Zagreb, 10000 Zagreb, Croatia
| | - Eve Rannamäe
- Department of Archaeology, Institute of History and Archaeology, University of Tartu, Jakobi 2, 51005 Tartu, Estonia
| | - Urmas Saarma
- Department of Zoology, Institute of Ecology and Earth Sciences, University of Tartu, Vanemuise 46, 51003 Tartu, Estonia
| | - Marine Arakelyan
- Yerevan State University, Faculty of Biology, Department of Zoology, Alex Manoogian 1, 0025 Yerevan, Republic of Armenia
| | - Ninna Manaseryan
- The Scientific Center of Zoology and Hydroecology of National Academy of Sciences of Armenia, P. Sevak 7, Yerevan 0014, Republic of Armenia
| | - Dariusz Krasnodębski
- Institute of Archaeology and Ethnology Polish Academy of Sciences, Al. Solidarności 105, 00-140 Warsaw, Poland
| | - Vadim Titov
- Southern Scientific Centre Russian Academy of Sciences, Chekhov 41, Rostov-on-Don 344006, Russian Federation
| | - Pavel Hulva
- Charles University in Prague, Department of Zoology, Viničná 1594/7, 128 00 Nové Město, Prague, Czech Republic
- University of Ostrava, Department of Biology and Ecology, Chittussiho 10, 710 00 Slezská Ostrava, Czech Republic
| | - Adrian Bălășescu
- ’Vasile Pârvan’ Institute of Archaeology, Romanian Academy, Henri Coandă 11, 010667 Bucharest, Romania
| | | | - Vesna Dimitrijević
- Laboratory for Bioarchaeology, Department of Archaeology, Faculty of Philosophy, University of Belgrade, Čika Ljubina 18-20, 11000 Belgrade, Serbia
| | - Andrey Shpansky
- Department of Palaeontology and Historical Geology, Tomsk State University, 634050 Tomsk, Russian Federation
| | - Oleksandr Kovalchuk
- Department of Paleontology, National Museum of Natural History National Academy of Sciences of Ukraine, 15 B. Khmelnytsky 15, Kyiv 01030Ukraine
| | - Alexey M Klementiev
- Institute of the Earth’s Crust, Siberian Branch of the Russian Academy of Sciences, 664033 Irkutsk, Russian Federation
| | - Irina Foronova
- V. S. Sobolev Institute of Geology and Mineralogy, Siberian Branch of the Russian Academy of Sciences, Koptyuga pr. 3, Novosibirsk, Russian Federation
| | - Dmitriy G Malikov
- V. S. Sobolev Institute of Geology and Mineralogy, Siberian Branch of the Russian Academy of Sciences, Koptyuga pr. 3, Novosibirsk, Russian Federation
| | - Anna Juras
- Institute of Human Biology & Evolution, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland
| | - Pavel Nikolskiy
- Laboratory of Quaternary Stratigraphy, Geological Institute, Russian Academy of Sciences, 119017 Moscow, Russia
| | - Semyon Egorovich Grigoriev
- Laboratory of P. A. Lazarev Mammoth Museum of the Research Institute of Applied Ecology of the North, North-Eastern Federal University named after M. K. Ammosov, Building of Faculties of Natural Sciences (KFEN), 48 Kulakovsky Str., 677000 Yakutsk, Republic of Sakha (Yakutia), Russian Federation
| | - Maksim Yurievich Cheprasov
- Laboratory of P. A. Lazarev Mammoth Museum of the Research Institute of Applied Ecology of the North, North-Eastern Federal University named after M. K. Ammosov, Building of Faculties of Natural Sciences (KFEN), 48 Kulakovsky Str., 677000 Yakutsk, Republic of Sakha (Yakutia), Russian Federation
| | - Gavril Petrovich Novgorodov
- Laboratory of P. A. Lazarev Mammoth Museum of the Research Institute of Applied Ecology of the North, North-Eastern Federal University named after M. K. Ammosov, Building of Faculties of Natural Sciences (KFEN), 48 Kulakovsky Str., 677000 Yakutsk, Republic of Sakha (Yakutia), Russian Federation
| | | | - Jarosław Wilczyński
- Institute of Systematics and Evolution of Animals, Polish Academy of Sciences, Sławkowska 17, 31-016 Cracow, Poland
| | - Albert Vasilievich Protopopov
- Department of Study of Mammoth Fauna, Academy of Science of Sakha Republic (Yakutia), Lenin Avenue 33, Yakutsk, 677027, Republic of Sakha (Yakutia), Russian Federation
| | - Grzegorz Lipecki
- Institute of Systematics and Evolution of Animals, Polish Academy of Sciences, Sławkowska 17, 31-016 Cracow, Poland
| | - Ana Stanković
- Institute of Genetics and Biotechnology, University of Warsaw, Pawińskiego 5a, 02-106, Warsaw, Poland
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, Pawińskiego 5a, 02-106, Warsaw, Poland
- The Antiquity of Southeastern Europe Research Centre, University of Warsaw, Krakowskie Przedmieście 32, 00-927 Warsaw, Poland
| |
Collapse
|
9
|
Willerslev E, Meltzer DJ. Peopling of the Americas as inferred from ancient genomics. Nature 2021; 594:356-364. [PMID: 34135521 DOI: 10.1038/s41586-021-03499-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 03/26/2021] [Indexed: 02/05/2023]
Abstract
In less than a decade, analyses of ancient genomes have transformed our understanding of the Indigenous peopling and population history of the Americas. These studies have shown that this history, which began in the late Pleistocene epoch and continued episodically into the Holocene epoch, was far more complex than previously thought. It is now evident that the initial dispersal involved the movement from northeast Asia of distinct and previously unknown populations, including some for whom there are no currently known descendants. The first peoples, once south of the continental ice sheets, spread widely, expanded rapidly and branched into multiple populations. Their descendants-over the next fifteen millennia-experienced varying degrees of isolation, admixture, continuity and replacement, and their genomes help to illuminate the relationships among major subgroups of Native American populations. Notably, all ancient individuals in the Americas, save for later-arriving Arctic peoples, are more closely related to contemporary Indigenous American individuals than to any other population elsewhere, which challenges the claim-which is based on anatomical evidence-that there was an early, non-Native American population in the Americas. Here we review the patterns revealed by ancient genomics that help to shed light on the past peoples who created the archaeological landscape, and together lead to deeper insights into the population and cultural history of the Americas.
Collapse
Affiliation(s)
- Eske Willerslev
- GeoGenetics Group, Department of Zoology, University of Cambridge, Cambridge, UK. .,Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark. .,Wellcome Trust Sanger Institute, Cambridge, UK.
| | - David J Meltzer
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark. .,Department of Anthropology, Southern Methodist University, Dallas, TX, USA.
| |
Collapse
|
10
|
Vershinina AO, Heintzman PD, Froese DG, Zazula G, Cassatt-Johnstone M, Dalén L, Der Sarkissian C, Dunn SG, Ermini L, Gamba C, Groves P, Kapp JD, Mann DH, Seguin-Orlando A, Southon J, Stiller M, Wooller MJ, Baryshnikov G, Gimranov D, Scott E, Hall E, Hewitson S, Kirillova I, Kosintsev P, Shidlovsky F, Tong HW, Tiunov MP, Vartanyan S, Orlando L, Corbett-Detig R, MacPhee RD, Shapiro B. Ancient horse genomes reveal the timing and extent of dispersals across the Bering Land Bridge. Mol Ecol 2021; 30:6144-6161. [PMID: 33971056 DOI: 10.1111/mec.15977] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Revised: 03/24/2021] [Accepted: 04/27/2021] [Indexed: 01/02/2023]
Abstract
The Bering Land Bridge (BLB) last connected Eurasia and North America during the Late Pleistocene. Although the BLB would have enabled transfers of terrestrial biota in both directions, it also acted as an ecological filter whose permeability varied considerably over time. Here we explore the possible impacts of this ecological corridor on genetic diversity within, and connectivity among, populations of a once wide-ranging group, the caballine horses (Equus spp.). Using a panel of 187 mitochondrial and eight nuclear genomes recovered from present-day and extinct caballine horses sampled across the Holarctic, we found that Eurasian horse populations initially diverged from those in North America, their ancestral continent, around 1.0-0.8 million years ago. Subsequent to this split our mitochondrial DNA analysis identified two bidirectional long-range dispersals across the BLB ~875-625 and ~200-50 thousand years ago, during the Middle and Late Pleistocene. Whole genome analysis indicated low levels of gene flow between North American and Eurasian horse populations, which probably occurred as a result of these inferred dispersals. Nonetheless, mitochondrial and nuclear diversity of caballine horse populations retained strong phylogeographical structuring. Our results suggest that barriers to gene flow, currently unidentified but possibly related to habitat distribution across Beringia or ongoing evolutionary divergence, played an important role in shaping the early genetic history of caballine horses, including the ancestors of living horses within Equus ferus.
Collapse
Affiliation(s)
- Alisa O Vershinina
- Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Peter D Heintzman
- The Arctic University Museum of Norway, UiT - The Arctic University of Norway, Tromsø, Norway
| | - Duane G Froese
- Department of Earth and Atmospheric Sciences, University of Alberta, Edmonton, AB, Canada
| | - Grant Zazula
- Collections and Research, Canadian Museum of Nature, Station D, Ottawa, ON, Canada.,Government of Yukon, Department of Tourism and Culture, Palaeontology Program, Whitehorse, YT, Canada
| | | | - Love Dalén
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.,Centre for Palaeogenetics, Stockholm, Sweden
| | - Clio Der Sarkissian
- Centre d'Anthropobiologie et de Génomique de Toulouse UMR5288, Faculté de Médecine Purpan, Université Paul Sabatier, Toulouse, France
| | - Shelby G Dunn
- Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Luca Ermini
- Lundbeck Foundation GeoGenetics Center, University of Copenhagen, Copenhagen, Denmark
| | - Cristina Gamba
- Lundbeck Foundation GeoGenetics Center, University of Copenhagen, Copenhagen, Denmark
| | - Pamela Groves
- Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, CA, USA
| | - Joshua D Kapp
- Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Daniel H Mann
- Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, CA, USA
| | - Andaine Seguin-Orlando
- Centre d'Anthropobiologie et de Génomique de Toulouse UMR5288, Faculté de Médecine Purpan, Université Paul Sabatier, Toulouse, France
| | - John Southon
- Keck-CCAMS Group, Earth System Science Department, University of California, Irvine, CA, USA
| | - Mathias Stiller
- Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA.,Division Molecular Pathology, Institute of Pathology, University Hospital Leipzig, Leipzig, Germany
| | - Matthew J Wooller
- Alaska Stable Isotope Facility, Water and Environmental Research Center, Institute of Northern Engineering, University of Alaska Fairbanks, Fairbanks, AK, USA.,Department of Marine Biology, College of Fisheries and Ocean Sciences, University of Alaska Fairbanks, Fairbanks, AK, USA
| | - Gennady Baryshnikov
- Laboratory of Theriology, Zoological Institute of the Russian Academy of Sciences, St. Petersburg, Russia
| | - Dmitry Gimranov
- Institute of Plant & Animal Ecology of the Russian Academy of Sciences, Ural Branch, Ekaterinburg, Russia.,Ural Federal University named after the first President of Russia B. N. Yeltsin, Ekaterinburg, Russia
| | - Eric Scott
- California State University, San Bernardino, CA, USA
| | - Elizabeth Hall
- Government of Yukon, Department of Tourism and Culture, Palaeontology Program, Whitehorse, YT, Canada
| | - Susan Hewitson
- Government of Yukon, Department of Tourism and Culture, Palaeontology Program, Whitehorse, YT, Canada
| | - Irina Kirillova
- Institute of Geography, Russian Academy of Sciences, Moscow, Russia
| | - Pavel Kosintsev
- Institute of Plant & Animal Ecology of the Russian Academy of Sciences, Ural Branch, Ekaterinburg, Russia
| | | | - Hao-Wen Tong
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, China.,CAS Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, China
| | - Mikhail P Tiunov
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of Russian Academy of Sciences, Vladivostok, Russia
| | - Sergey Vartanyan
- North-East Interdisciplinary Scientific Research Institute N.A. Shilo, Far East Branch, Russian Academy of Sciences, Magadan, Russia
| | - Ludovic Orlando
- Centre d'Anthropobiologie et de Génomique de Toulouse UMR5288, Faculté de Médecine Purpan, Université Paul Sabatier, Toulouse, France
| | | | | | - Beth Shapiro
- Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA.,Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| |
Collapse
|
11
|
Halffman CM, Potter BA, McKinney HJ, Tsutaya T, Finney BP, Kemp BM, Bartelink EJ, Wooller MJ, Buckley M, Clark CT, Johnson JJ, Bingham BL, Lanoë FB, Sattler RA, Reuther JD. Ancient Beringian paleodiets revealed through multiproxy stable isotope analyses. SCIENCE ADVANCES 2020; 6:6/36/eabc1968. [PMID: 32917621 PMCID: PMC7473743 DOI: 10.1126/sciadv.abc1968] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 07/16/2020] [Indexed: 06/04/2023]
Abstract
The earliest Native Americans have often been portrayed as either megafaunal specialists or generalist foragers, but this debate cannot be resolved by studying the faunal record alone. Stable isotope analysis directly reveals the foods consumed by individuals. We present multi-tissue isotope analyses of two Ancient Beringian infants from the Upward Sun River site (USR), Alaska (~11,500 years ago). Models of fetal bone turnover combined with seasonally-sensitive taxa show that the carbon and nitrogen isotope composition of USR infant bone collagen reflects maternal diets over the summer. Using comparative faunal isotope data, we demonstrate that although terrestrial sources dominated maternal diets, salmon was also important, supported by carbon isotope analysis of essential amino acids and bone bioapatite. Tooth enamel samples indicate increased salmon use between spring and summer. Our results do not support either strictly megafaunal specialists or generalized foragers but indicate that Ancient Beringian diets were complex and seasonally structured.
Collapse
Affiliation(s)
- Carrin M Halffman
- Department of Anthropology, University of Alaska Fairbanks, Fairbanks, AK, USA.
| | - Ben A Potter
- Arctic Studies Center, Liaocheng University, Liaocheng City, Shandong Province, China.
| | - Holly J McKinney
- Department of Anthropology, University of Alaska Fairbanks, Fairbanks, AK, USA
| | - Takumi Tsutaya
- Japan Agency for Marine-Earth Science and Technology, Research Institute for Marine Resources Utilization, Yokosuka, Kanagawa, Japan
| | - Bruce P Finney
- Departments of Biological Sciences and Geosciences, Idaho State University, Pocatello, ID, USA
| | - Brian M Kemp
- Laboratories of Molecular Anthropology and Microbiome Research, Norman, OK, USA
- Department of Anthropology, University of Oklahoma, Norman, OK, USA
| | - Eric J Bartelink
- Department of Anthropology, California State University, Chico, CA, USA
| | - Matthew J Wooller
- Alaska Stable Isotope Facility, Water and Environmental Research Center, Institute of Northern Engineering, University of Alaska Fairbanks, Fairbanks, AK, USA
- Marine Biology Department, College of Fisheries and Ocean Sciences, University of Alaska Fairbanks, Fairbanks, AK, USA
| | - Michael Buckley
- Department of Earth and Environmental Sciences Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
| | - Casey T Clark
- Joint Institute for the Study of Atmosphere and Ocean, University of Washington, Seattle, WA, USA
- Water and Environmental Research Center, University of Alaska Fairbanks, Fairbanks, AK, USA
| | - Jessica J Johnson
- Department of Biology and Wildlife/Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, AK, USA
| | - Brittany L Bingham
- Laboratories of Molecular Anthropology and Microbiome Research, Norman, OK, USA
| | - François B Lanoë
- Bureau of Applied Research in Anthropology, University of Arizona, Tucson AZ, USA
- Archaeology Department, University of Alaska Museum of the North, Fairbanks, AK, USA
| | | | - Joshua D Reuther
- Department of Anthropology, University of Alaska Fairbanks, Fairbanks, AK, USA
- Archaeology Department, University of Alaska Museum of the North, Fairbanks, AK, USA
| |
Collapse
|
12
|
Affiliation(s)
- John F. Hoffecker
- Institute of Arctic and Alpine Research, University of Colorado at Boulder, Boulder, CO, USA
| | - Scott A. Elias
- Institute of Arctic and Alpine Research, University of Colorado at Boulder, Boulder, CO, USA
| | - Olga Potapova
- Pleistocene Park Foundation, Philadelphia, PA, USA
- Department of Mammoth Fauna Studies, Academy of Sciences of Sakha, Yakutsk, Russian Federation
- The Mammoth Site of Hot Springs, SD, Inc., Hot Springs, SD, USA
| |
Collapse
|
13
|
Gibbs AJ, Hajizadeh M, Ohshima K, Jones RA. The Potyviruses: An Evolutionary Synthesis Is Emerging. Viruses 2020; 12:E132. [PMID: 31979056 PMCID: PMC7077269 DOI: 10.3390/v12020132] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 01/16/2020] [Accepted: 01/20/2020] [Indexed: 12/28/2022] Open
Abstract
In this review, encouraged by the dictum of Theodosius Dobzhansky that "Nothing in biology makes sense except in the light of evolution", we outline the likely evolutionary pathways that have resulted in the observed similarities and differences of the extant molecules, biology, distribution, etc. of the potyvirids and, especially, its largest genus, the potyviruses. The potyvirids are a family of plant-infecting RNA-genome viruses. They had a single polyphyletic origin, and all share at least three of their genes (i.e., the helicase region of their CI protein, the RdRp region of their NIb protein and their coat protein) with other viruses which are otherwise unrelated. Potyvirids fall into 11 genera of which the potyviruses, the largest, include more than 150 distinct viruses found worldwide. The first potyvirus probably originated 15,000-30,000 years ago, in a Eurasian grass host, by acquiring crucial changes to its coat protein and HC-Pro protein, which enabled it to be transmitted by migrating host-seeking aphids. All potyviruses are aphid-borne and, in nature, infect discreet sets of monocotyledonous or eudicotyledonous angiosperms. All potyvirus genomes are under negative selection; the HC-Pro, CP, Nia, and NIb genes are most strongly selected, and the PIPO gene least, but there are overriding virus specific differences; for example, all turnip mosaic virus genes are more strongly conserved than those of potato virus Y. Estimates of dN/dS (ω) indicate whether potyvirus populations have been evolving as one or more subpopulations and could be used to help define species boundaries. Recombinants are common in many potyvirus populations (20%-64% in five examined), but recombination seems to be an uncommon speciation mechanism as, of 149 distinct potyviruses, only two were clear recombinants. Human activities, especially trade and farming, have fostered and spread both potyviruses and their aphid vectors throughout the world, especially over the past five centuries. The world distribution of potyviruses, especially those found on islands, indicates that potyviruses may be more frequently or effectively transmitted by seed than experimental tests suggest. Only two meta-genomic potyviruses have been recorded from animal samples, and both are probably contaminants.
Collapse
Affiliation(s)
- Adrian J. Gibbs
- Emeritus Faculty, Australian National University, Canberra, ACT 2601, Australia
| | - Mohammad Hajizadeh
- Department of Plant Protection, Faculty of Agriculture, University of Kurdistan, P.O. Box 416, Sanandaj, Iran
| | - Kazusato Ohshima
- Laboratory of Plant Virology, Department of Applied Biological Sciences, Faculty of Agriculture, Saga University, 1-banchi, Honjo-machi, Saga 840-8502, Japan;
- The United Graduate School of Agricultural Sciences, Kagoshima University, 1-21-2410 Korimoto, Kagoshima 890-0065, Japan
| | - Roger A.C. Jones
- Institute of Agriculture, University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
| |
Collapse
|
14
|
Stigall AL. The Invasion Hierarchy: Ecological and Evolutionary Consequences of Invasions in the Fossil Record. ANNUAL REVIEW OF ECOLOGY, EVOLUTION, AND SYSTEMATICS 2019. [DOI: 10.1146/annurev-ecolsys-110617-062638] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Species invasions are pervasive in Earth history, yet the ecological and evolutionary consequences vary greatly. Ancient invasion events can be organized in a hierarchy of increasing invasion intensity from ephemeral invasions to globally pervasive invasive regimes. Each level exhibits emergent properties exceeding the sum of interactions at lower levels. Hierarchy levels correspond to, but do not always exactly correlate with, geographic extent of invasion success. The ecological impacts of lower-level impacts can be negligible or result in temporary community accommodation. Invasion events at moderate to high levels of the hierarchy permanently alter ecological communities, regional faunas, and global ecosystems. The prevalence of invasive species results in evolutionary changes by fostering niche evolution, differential survival of ecologically generalized taxa, faunal homogenization, and suppressing speciation. These impacts can contribute to mass extinctions and biodiversity crises that alter the trajectory of ecological and evolutionary patterns of life. The fossil record provides a long-term record of how invasion impacts may scale up through time, which can augment ecological studies of modern species invasions.
Collapse
Affiliation(s)
- Alycia L. Stigall
- Department of Geological Sciences, and OHIO Center for Ecology and Evolutionary Studies, Ohio University, Athens, Ohio 45701, USA
| |
Collapse
|
15
|
Kunz F, Gamauf A, Zachos FE, Haring E. Mitochondrial phylogenetics of the goshawk
Accipiter
[
gentilis
] superspecies. J ZOOL SYST EVOL RES 2019. [DOI: 10.1111/jzs.12285] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Florian Kunz
- Central Research Laboratories Natural History Museum Vienna Vienna Austria
- Institute of Wildlife Biology and Game Management University of Natural Resources and Life Sciences Vienna Vienna Austria
| | - Anita Gamauf
- 1st Zoological Department Natural History Museum Vienna Vienna Austria
- Department of Integrative Zoology University of Vienna Vienna Austria
| | - Frank E. Zachos
- 1st Zoological Department Natural History Museum Vienna Vienna Austria
- Department of Integrative Zoology University of Vienna Vienna Austria
| | - Elisabeth Haring
- Central Research Laboratories Natural History Museum Vienna Vienna Austria
- Department of Integrative Zoology University of Vienna Vienna Austria
| |
Collapse
|
16
|
Abstract
Null hypothesis significance testing (NHST) is the most common statistical framework used by scientists, including archaeologists. Owing to increasing dissatisfaction, however, Bayesian inference has become an alternative to these methods. In this article, we review the application of Bayesian statistics to archaeology. We begin with a simple example to demonstrate the differences in applying NHST and Bayesian inference to an archaeological problem. Next, we formally define NHST and Bayesian inference, provide a brief historical overview of their development, and discuss the advantages and limitations of each method. A review of Bayesian inference and archaeology follows, highlighting the applications of Bayesian methods to chronological, bioarchaeological, zooarchaeological, ceramic, lithic, and spatial analyses. We close by considering the future applications of Bayesian statistics to archaeological research.
Collapse
Affiliation(s)
| | - Melissa G. Torquato
- Department of Anthropology, Purdue University, West Lafayette, Indiana 47907, USA;,
| |
Collapse
|
17
|
Wooller MJ, Saulnier-Talbot É, Potter BA, Belmecheri S, Bigelow N, Choy K, Cwynar LC, Davies K, Graham RW, Kurek J, Langdon P, Medeiros A, Rawcliffe R, Wang Y, Williams JW. A new terrestrial palaeoenvironmental record from the Bering Land Bridge and context for human dispersal. ROYAL SOCIETY OPEN SCIENCE 2018; 5:180145. [PMID: 30110451 PMCID: PMC6030284 DOI: 10.1098/rsos.180145] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 05/01/2018] [Indexed: 06/08/2023]
Abstract
Palaeoenvironmental records from the now-submerged Bering Land Bridge (BLB) covering the Last Glacial Maximum (LGM) to the present are needed to document changing environments and connections with the dispersal of humans into North America. Moreover, terrestrially based records of environmental changes are needed in close proximity to the re-establishment of circulation between Pacific and Atlantic Oceans following the end of the last glaciation to test palaeo-climate models for the high latitudes. We present the first terrestrial temperature and hydrologic reconstructions from the LGM to the present from the BLB's south-central margin. We find that the timing of the earliest unequivocal human dispersals into Alaska, based on archaeological evidence, corresponds with a shift to warmer/wetter conditions on the BLB between 14 700 and 13 500 years ago associated with the early Bølling/Allerød interstadial (BA). These environmental changes could have provided the impetus for eastward human dispersal at that time, from Western or central Beringia after a protracted human population standstill. Our data indicate substantial climate-induced environmental changes on the BLB since the LGM, which would potentially have had significant influences on megafaunal and human biogeography in the region.
Collapse
Affiliation(s)
- Matthew J. Wooller
- Water and Environmental Research Center, Institute of Northern Engineering, Fairbanks, AK, USA
- Alaska Stable Isotope Facility, College of Fisheries and Ocean Sciences, Fairbanks, AK, USA
| | - Émilie Saulnier-Talbot
- Water and Environmental Research Center, Institute of Northern Engineering, Fairbanks, AK, USA
- Alaska Stable Isotope Facility, College of Fisheries and Ocean Sciences, Fairbanks, AK, USA
| | | | - Soumaya Belmecheri
- Laboratory of Tree Ring Research, University of Arizona, Tucson, AZ, USA
| | - Nancy Bigelow
- Alaska Quaternary Center, University of Alaska Fairbanks, Fairbanks, AK, USA
| | - Kyungcheol Choy
- Water and Environmental Research Center, Institute of Northern Engineering, Fairbanks, AK, USA
- Alaska Stable Isotope Facility, College of Fisheries and Ocean Sciences, Fairbanks, AK, USA
| | - Les C. Cwynar
- Department of Biology, University of New Brunswick, Fredericton, New Brunswick, Canada
| | - Kimberley Davies
- Department of Geography and Environment, University of Southampton, Southampton, Hampshire, UK
- School of Geography, Earth and Environmental Sciences, Plymouth University, Plymouth, UK
| | - Russell W. Graham
- Department of Geosciences and Earth and Mineral Sciences Museum & Art Gallery, The Pennsylvania State University, University Park, PA, USA
| | - Joshua Kurek
- Department of Geography and Environment, Mount Allison University, Sackville, New Brunswick, Canada
| | - Peter Langdon
- Department of Geography and Environment, University of Southampton, Southampton, Hampshire, UK
| | | | - Ruth Rawcliffe
- Water and Environmental Research Center, Institute of Northern Engineering, Fairbanks, AK, USA
- Alaska Stable Isotope Facility, College of Fisheries and Ocean Sciences, Fairbanks, AK, USA
| | - Yue Wang
- Department of Geography, University of Wisconsin-Madison, Madison, WI, USA
| | - John W. Williams
- Department of Geography, University of Wisconsin-Madison, Madison, WI, USA
- Center for Climatic Research, University of Wisconsin-Madison, Madison, WI, USA
| |
Collapse
|
18
|
Doan K, Mackiewicz P, Sandoval-Castellanos E, Stefaniak K, Ridush B, Dalén L, Węgleński P, Stankovic A. The history of Crimean red deer population and Cervus phylogeography in Eurasia. Zool J Linn Soc 2017. [DOI: 10.1093/zoolinnean/zlx065] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Karolina Doan
- College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, Banacha, Warsaw, Poland
| | - Paweł Mackiewicz
- Department of Genomics, Faculty of Biotechnology, University of Wrocław, Joliot-Curie, Wrocław, Poland
| | - Edson Sandoval-Castellanos
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
- Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Krzysztof Stefaniak
- Department of Palaeozoology, University of Wrocław, Sienkiewicza, Wrocław, Poland
| | - Bogdan Ridush
- Department of Physical Geography, Geomorphology and Paleogeography, Yuriy Fedkovych Chernivtsi National University, Kotsubynskogo, Chernivtsi, Ukraine
| | - Love Dalén
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Piotr Węgleński
- Centre of New Technologies, University of Warsaw, Banacha, Warsaw, Poland
| | - Ana Stankovic
- Institute of Genetics and Biotechnology, University of Warsaw, Pawińskiego, Warsaw, Poland
| |
Collapse
|
19
|
Abstract
When humans moved from Asia toward the Americas over 18,000 y ago and eventually peopled the New World they encountered a new environment with extreme climate conditions and distinct dietary resources. These environmental and dietary pressures may have led to instances of genetic adaptation with the potential to influence the phenotypic variation in extant Native American populations. An example of such an event is the evolution of the fatty acid desaturases (FADS) genes, which have been claimed to harbor signals of positive selection in Inuit populations due to adaptation to the cold Greenland Arctic climate and to a protein-rich diet. Because there was evidence of intercontinental variation in this genetic region, with indications of positive selection for its variants, we decided to compare the Inuit findings with other Native American data. Here, we use several lines of evidence to show that the signal of FADS-positive selection is not restricted to the Arctic but instead is broadly observed throughout the Americas. The shared signature of selection among populations living in such a diverse range of environments is likely due to a single and strong instance of local adaptation that took place in the common ancestral population before their entrance into the New World. These first Americans peopled the whole continent and spread this adaptive variant across a diverse set of environments.
Collapse
|
20
|
Brace S, Ruddy M, Miller R, Schreve DC, Stewart JR, Barnes I. The colonization history of British water vole (Arvicola amphibius (Linnaeus, 1758)): origins and development of the Celtic fringe. Proc Biol Sci 2017; 283:rspb.2016.0130. [PMID: 27122559 DOI: 10.1098/rspb.2016.0130] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 04/06/2016] [Indexed: 12/13/2022] Open
Abstract
The terminal Pleistocene and Early Holocene, a period from 15 000 to 18 000 Before Present (BP), was critical in establishing the current Holarctic fauna, with temperate-climate species largely replacing cold-adapted ones at mid-latitudes. However, the timing and nature of this process remain unclear for many taxa, a point that impacts on current and future management strategies. Here, we use an ancient DNA dataset to test more directly postglacial histories of the water vole (Arvicola amphibius, formerly A terrestris), a species that is both a conservation priority and a pest in different parts of its range. We specifically examine colonization of Britain, where a complex genetic structure can be observed today. Although we focus on population history at the limits of the species' range, the inclusion of additional European samples allows insights into European postglacial colonization events and provides a molecular perspective on water vole taxonomy.
Collapse
Affiliation(s)
- Selina Brace
- Department of Earth Sciences, Natural History Museum, London SW7 5BD, UK
| | | | - Rebecca Miller
- Service of Prehistory, University of Liège, Liège 4000, Belgium
| | - Danielle C Schreve
- Department of Geography, Royal Holloway University of London, Egham, Surrey TW20 0EX, UK
| | - John R Stewart
- School of Applied Sciences, Bournemouth University, Poole, Dorset BH12 5BB, UK
| | - Ian Barnes
- Department of Earth Sciences, Natural History Museum, London SW7 5BD, UK
| |
Collapse
|
21
|
Postglacial viability and colonization in North America's ice-free corridor. Nature 2016; 537:45-49. [PMID: 27509852 DOI: 10.1038/nature19085] [Citation(s) in RCA: 118] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 07/07/2016] [Indexed: 02/07/2023]
Abstract
During the Last Glacial Maximum, continental ice sheets isolated Beringia (northeast Siberia and northwest North America) from unglaciated North America. By around 15 to 14 thousand calibrated radiocarbon years before present (cal. kyr bp), glacial retreat opened an approximately 1,500-km-long corridor between the ice sheets. It remains unclear when plants and animals colonized this corridor and it became biologically viable for human migration. We obtained radiocarbon dates, pollen, macrofossils and metagenomic DNA from lake sediment cores in a bottleneck portion of the corridor. We find evidence of steppe vegetation, bison and mammoth by approximately 12.6 cal. kyr bp, followed by open forest, with evidence of moose and elk at about 11.5 cal. kyr bp, and boreal forest approximately 10 cal. kyr bp. Our findings reveal that the first Americans, whether Clovis or earlier groups in unglaciated North America before 12.6 cal. kyr bp, are unlikely to have travelled by this route into the Americas. However, later groups may have used this north-south passageway.
Collapse
|
22
|
Pieper KE, Dyer KA. Occasional recombination of a selfish X-chromosome may permit its persistence at high frequencies in the wild. J Evol Biol 2016; 29:2229-2241. [PMID: 27423061 DOI: 10.1111/jeb.12948] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Revised: 07/12/2016] [Accepted: 07/13/2016] [Indexed: 01/07/2023]
Abstract
The sex-ratio X-chromosome (SR) is a selfish chromosome that promotes its own transmission to the next generation by destroying Y-bearing sperm in the testes of carrier males. In some natural populations of the fly Drosophila neotestacea, up to 30% of the X-chromosomes are SR chromosomes. To investigate the molecular evolutionary history and consequences of SR, we sequenced SR and standard (ST) males at 11 X-linked loci that span the ST X-chromosome and at seven arbitrarily chosen autosomal loci from a sample of D. neotestacea males from throughout the species range. We found that the evolutionary relationship between ST and SR varies among individual markers, but genetic differentiation between SR and ST is chromosome-wide and likely due to large chromosomal inversions that suppress recombination. However, SR does not consist of a single multilocus haplotype: we find evidence for gene flow between ST and SR at every locus assayed. Furthermore, we do not find long-distance linkage disequilibrium within SR chromosomes, suggesting that recombination occurs in females homozygous for SR. Finally, polymorphism on SR is reduced compared to that on ST, and loci displaying signatures of selection on ST do not show similar patterns on SR. Thus, even if selection is less effective on SR, our results suggest that gene flow with ST and recombination between SR chromosomes may prevent the accumulation of deleterious mutations and allow its long-term persistence at relatively high frequencies.
Collapse
Affiliation(s)
- K E Pieper
- Department of Genetics, University of Georgia, Athens, GA, USA.
| | - K A Dyer
- Department of Genetics, University of Georgia, Athens, GA, USA
| |
Collapse
|
23
|
Hoffecker JF, Elias SA, O'Rourke DH, Scott GR, Bigelow NH. Beringia and the global dispersal of modern humans. Evol Anthropol 2016; 25:64-78. [DOI: 10.1002/evan.21478] [Citation(s) in RCA: 119] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
|
24
|
Abstract
Clovis groups in Late Pleistocene North America occasionally hunted several now extinct large mammals. But whether their hunting drove 37 genera of animals to extinction has been disputed, largely for want of kill sites. Overkill proponents argue that there is more archaeological evidence than we ought to expect, that humans had the wherewithal to decimate what may have been millions of animals, and that the appearance of humans and the disappearance of the fauna is too striking to be a mere coincidence. Yet, there is less to these claims than meets the eye. Moreover, extinctions took place amid sweeping climatic and environmental changes as the Pleistocene came to an end. It has long been difficult to link those changes to mammalian extinctions, but the advent of ancient DNA, coupled with high-resolution paleoecological, radiocarbon, and archeological records, should help disentangle the relative role of changing climates and people in mammalian extinctions.
Collapse
Affiliation(s)
- David J. Meltzer
- Department of Anthropology, Southern Methodist University, Dallas, Texas 75275
| |
Collapse
|
25
|
Mitochondrial genome diversity at the Bering Strait area highlights prehistoric human migrations from Siberia to northern North America. Eur J Hum Genet 2015; 23:1399-404. [PMID: 25564040 DOI: 10.1038/ejhg.2014.286] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Revised: 11/12/2014] [Accepted: 12/02/2014] [Indexed: 11/09/2022] Open
Abstract
The patterns of prehistoric migrations across the Bering Land Bridge are far from being completely understood: there still exists a significant gap in our knowledge of the population history of former Beringia. Here, through comprehensive survey of mitochondrial DNA genomes retained in 'relic' populations, the Maritime Chukchi, Siberian Eskimos, and Commander Aleuts, we explore genetic contribution of prehistoric Siberians/Asians to northwestern Native Americans. Overall, 201 complete mitochondrial sequences (52 new and 149 published) were selected in the reconstruction of trees encompassing mtDNA lineages that are restricted to Coastal Chukotka and Alaska, the Canadian Arctic, Greenland, and the Aleutian chain. Phylogeography of the resulting mtDNA genomes (mitogenomes) considerably extends the range and intrinsic diversity of haplogroups (eg, A2a, A2b, D2a, and D4b1a2a1) that emerged and diversified in postglacial central Beringia, defining independent origins of Neo-Eskimos versus Paleo-Eskimos, Aleuts, and Tlingit (Na-Dene). Specifically, Neo-Eskimos, ancestral to modern Inuit, not only appear to be of the High Arctic origin but also to harbor Altai/Sayan-related ancestry. The occurrence of the haplogroup D2a1b haplotypes in Chukotka (Sireniki) introduces the possibility that the traces of Paleo-Eskimos have not been fully erased by spread of the Neo-Eskimos or their descendants. Our findings are consistent with the recurrent gene flow model of multiple streams of expansions to northern North America from northeastern Eurasia in late Pleistocene-early Holocene.
Collapse
|
26
|
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.
Collapse
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
| |
Collapse
|
27
|
Speller C, Kooyman B, Rodrigues A, Langemann E, Jobin R, Yang D. Assessing prehistoric genetic structure and diversity of North American elk ( Cervus elaphus) populations in Alberta, Canada. CAN J ZOOL 2014. [DOI: 10.1139/cjz-2013-0253] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
North American elk (Cervus elaphus L., 1758) are an important component of Canada’s natural ecosystems. Overhunting and habitat decline in the 19th century led to the near eradication of Rocky Mountain elk (Cervus elaphus nelsoni Bailey, 1935) and Manitoban elk (Cervus elaphus manitobensis Millais, 1915) within Alberta. Though elk populations have been restored within provincial and national parks, it is unknown to what degree historic population declines affected overall genetic diversity and population structuring of the two subspecies. This study targeted 551 bp of mitochondrial D-loop DNA from 50 elk remains recovered from 16 archaeological sites (2260 BCE (before common era) to 1920 CE (common era)) to examine the former genetic diversity and population structure of Alberta’s historic elk populations. Comparisons of ancient and modern haplotype and nucleotide diversity suggest that historic population declines reduced the mitochondrial diversity of Manitoban elk, while translocation of animals from Yellowstone National Park in the early 20th century served to maintain the diversity of Rocky Mountain populations. Gene flow between the two subspecies was significantly higher in the past than today, suggesting that the two subspecies previously formed a continuous population. These data on precontact genetic diversity and gene flow in Alberta elk provide essential baseline data integral for elk management and conservation in the province.
Collapse
Affiliation(s)
- C.F. Speller
- Department of Archaeology, University of Calgary, Calgary, AB T2N 1N4, Canada
- Ancient DNA Laboratory, Department of Archaeology, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - B. Kooyman
- Department of Archaeology, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - A.T. Rodrigues
- Ancient DNA Laboratory, Department of Archaeology, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - E.G. Langemann
- Cultural Resource Services, Western and Northern Service Centre, Parks Canada, Calgary, AB T2P 3M3, Canada
| | - R.M. Jobin
- Special Investigations and Forensic Services Section, Fish and Wildlife Enforcement Branch, Justice and Solicitor General, Government of Alberta, 7th Floor, OS Longman Building, 6909-116 Street, Edmonton, AB T6H 4P2, Canada
| | - D.Y. Yang
- Ancient DNA Laboratory, Department of Archaeology, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| |
Collapse
|