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Velli E, Caniglia R, Mattucci F. Phylogenetic History and Phylogeographic Patterns of the European Wildcat ( Felis silvestris) Populations. Animals (Basel) 2023; 13:ani13050953. [PMID: 36899811 PMCID: PMC10000227 DOI: 10.3390/ani13050953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 02/27/2023] [Accepted: 03/02/2023] [Indexed: 03/09/2023] Open
Abstract
Disentangling phylogenetic and phylogeographic patterns is fundamental to reconstruct the evolutionary histories of taxa and assess their actual conservation status. Therefore, in this study, for the first time, the most exhaustive biogeographic history of European wildcat (Felis silvestris) populations was reconstructed by typing 430 European wildcats, 213 domestic cats, and 72 putative admixed individuals, collected across the entire species' distribution range, at a highly diagnostic portion of the mitochondrial ND5 gene. Phylogenetic and phylogeographic analyses identified two main ND5 lineages (D and W) roughly associated with domestic and wild polymorphisms. Lineage D included all domestic cats, 83.3% of putative admixed individuals, and also 41.4% of wildcats; these latter mostly showed haplotypes belonging to sub-clade Ia, that diverged about 37,700 years ago, long pre-dating any evidence for cat domestication. Lineage W included all the remaining wildcats and putative admixed individuals, spatially clustered into four main geographic groups, which started to diverge about 64,200 years ago, corresponding to (i) the isolated Scottish population, (ii) the Iberian population, (iii) a South-Eastern European cluster, and (iv) a Central European cluster. Our results suggest that the last Pleistocene glacial isolation and subsequent re-expansion from Mediterranean and extra-Mediterranean glacial refugia were pivotal drivers in shaping the extant European wildcat phylogenetic and phylogeographic patterns, which were further modeled by both historical natural gene flow among wild lineages and more recent wild x domestic anthropogenic hybridization, as confirmed by the finding of F. catus/lybica shared haplotypes. The reconstructed evolutionary histories and the wild ancestry contents detected in this study could be used to identify adequate Conservation Units within European wildcat populations and help to design appropriate long-term management actions.
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2
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Loog L. Sometimes hidden but always there: the assumptions underlying genetic inference of demographic histories. Philos Trans R Soc Lond B Biol Sci 2020; 376:20190719. [PMID: 33250022 DOI: 10.1098/rstb.2019.0719] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Demographic processes directly affect patterns of genetic variation within contemporary populations as well as future generations, allowing for demographic inference from patterns of both present-day and past genetic variation. Advances in laboratory procedures, sequencing and genotyping technologies in the past decades have resulted in massive increases in high-quality genome-wide genetic data from present-day populations and allowed retrieval of genetic data from archaeological material, also known as ancient DNA. This has resulted in an explosion of work exploring past changes in population size, structure, continuity and movement. However, as genetic processes are highly stochastic, patterns of genetic variation only indirectly reflect demographic histories. As a result, past demographic processes need to be reconstructed using an inferential approach. This usually involves comparing observed patterns of variation with model expectations from theoretical population genetics. A large number of approaches have been developed based on different population genetic models that each come with assumptions about the data and underlying demography. In this article I review some of the key models and assumptions underlying the most commonly used approaches for past demographic inference and their consequences for our ability to link the inferred demographic processes to the archaeological and climate records. This article is part of the theme issue 'Cross-disciplinary approaches to prehistoric demography'.
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Affiliation(s)
- Liisa Loog
- Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
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3
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Kelly LJ, Mack RN, Novak SJ. Genetic analysis of Bromus tectorum (Poaceae) in the Mediterranean region: biogeographical pattern of native populations. Heredity (Edinb) 2020; 126:178-193. [PMID: 32814871 DOI: 10.1038/s41437-020-00354-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 07/27/2020] [Accepted: 08/01/2020] [Indexed: 11/09/2022] Open
Abstract
Genetic diversity within and among 42 native populations of Bromus tectorum (cheatgrass) was characterized within two regions, the eastern Mediterranean and the western Mediterranean. Two hypotheses were tested for the genetic diversity of these populations: (1) populations from the eastern Mediterranean are more genetically diverse compared with populations to the west, a potential consequence of the species' westward dispersal with the spread of agriculture, and (2) populations across the Mediterranean contain comparable genetic diversity but display high genetic differentiation, a potential consequence of both regions having served as refugia during glacial advances in the late Quaternary Period. Populations in the eastern Mediterranean possess 16 polymorphic loci and 37 multilocus genotypes. In contrast, populations from the western Mediterranean include a subset of these polymorphic loci (9) and fewer multilocus genotypes (19), consistent with the dispersal of B. tectorum with the east-west Holocene spread of agriculture. Among the 19 multilocus genotypes identified in populations from the western Mediterranean, 13 are undetected among eastern Mediterranean populations. Average genetic diversity within populations from the eastern Mediterranean is nonetheless comparable to the genetic diversity in populations from the Iberian Peninsula, whereas diversity is the lowest in the populations from southern France. Our results suggest a prominent role for agriculture in the grass's western spread, although glacial history and environmental heterogeneity also could have influenced the grass's genetic diversity. The exceptionally high level of self-pollination (>99%) in B. tectorum has contributed to preserving the genetic signature associated with the species' biogeographical history across the Mediterranean region.
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Affiliation(s)
- Lauren J Kelly
- School of Biological Sciences, Washington State University, Pullman, WA, 99164, USA
| | - Richard N Mack
- School of Biological Sciences, Washington State University, Pullman, WA, 99164, USA
| | - Stephen J Novak
- Department of Biological Sciences, Boise State University, 1910 University Dr., Boise, ID, 83725-1515, USA.
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4
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Mizumachi K, Spassov N, Kostov D, Raichev EG, Peeva S, Hirata D, Nishita Y, Kaneko Y, Masuda R. Mitochondrial haplogrouping of the ancient brown bears (Ursus arctos) in Bulgaria, revealed by the APLP method. MAMMAL RES 2020. [DOI: 10.1007/s13364-020-00482-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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5
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Lynch LM. Fossil Calibration of Mitochondrial Phylogenetic Relationships of North American Pine Martens, Martes, Suggests an Older Divergence of M. americana and M. caurina than Previously Hypothesized. J MAMM EVOL 2019. [DOI: 10.1007/s10914-019-09476-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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6
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Ersmark E, Baryshnikov G, Higham T, Argant A, Castaños P, Döppes D, Gasparik M, Germonpré M, Lidén K, Lipecki G, Marciszak A, Miller R, Moreno‐García M, Pacher M, Robu M, Rodriguez‐Varela R, Rojo Guerra M, Sabol M, Spassov N, Storå J, Valdiosera C, Villaluenga A, Stewart JR, Dalén L. Genetic turnovers and northern survival during the last glacial maximum in European brown bears. Ecol Evol 2019; 9:5891-5905. [PMID: 31161006 PMCID: PMC6540696 DOI: 10.1002/ece3.5172] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 03/08/2019] [Accepted: 03/15/2019] [Indexed: 12/03/2022] Open
Abstract
The current phylogeographic pattern of European brown bears (Ursus arctos) has commonly been explained by postglacial recolonization out of geographically distinct refugia in southern Europe, a pattern well in accordance with the expansion/contraction model. Studies of ancient DNA from brown bear remains have questioned this pattern, but have failed to explain the glacial distribution of mitochondrial brown bear clades and their subsequent expansion across the European continent. We here present 136 new mitochondrial sequences generated from 346 remains from Europe, ranging in age between the Late Pleistocene and historical times. The genetic data show a high Late Pleistocene diversity across the continent and challenge the strict confinement of bears to traditional southern refugia during the last glacial maximum (LGM). The mitochondrial data further suggest a genetic turnover just before this time, as well as a steep demographic decline starting in the mid-Holocene. Levels of stable nitrogen isotopes from the remains confirm a previously proposed shift toward increasing herbivory around the LGM in Europe. Overall, these results suggest that in addition to climate, anthropogenic impact and inter-specific competition may have had more important effects on the brown bear's ecology, demography, and genetic structure than previously thought.
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Affiliation(s)
- Erik Ersmark
- Department of Bioinformatics and GeneticsSwedish Museum of Natural HistoryStockholmSweden
- Department of ZoologyStockholm UniversityStockholmSweden
| | | | - Thomas Higham
- Research Laboratory for Archaeology and the History of ArtUniversity of OxfordOxfordUK
| | - Alain Argant
- CNRS, Minist. Culture, LAMPEA, UMR 7269Aix Marseille UniversityAix‐en‐ProvenceFrance
| | | | | | - Mihaly Gasparik
- Department of Palaeontology and GeologyHungarian Natural History MuseumBudapestHungary
| | - Mietje Germonpré
- Operational Direction “Earth and History of Life”Royal Belgian Institute of Natural SciencesBrusselBelgium
| | - Kerstin Lidén
- Department of Archaeology and Classical StudiesStockholm UniversityStockholmSweden
| | - Grzegorz Lipecki
- Institute of Systematics and Evolution of AnimalsPolish Academy of SciencesKrakówPoland
| | - Adrian Marciszak
- Department of Paleozoology, Institute of Evolutionary Biology and Ecology, Faculty of Biological SciencesUniversity of WrocławWrocławPoland
| | | | - Marta Moreno‐García
- GI Arqueobiología, Instituto de HistoriaConsejo Superior de Investigaciones CientíficasMadridSpain
| | - Martina Pacher
- Institute of PalaeontologyUniversity of ViennaViennaAustria
| | - Marius Robu
- “Emil Racoviţă” Institute of SpeleologyRomanian AcademyBucharestRomania
| | | | - Manuel Rojo Guerra
- Department of Prehistory and ArchaeologyUniversity of ValladolidValladolidSpain
| | - Martin Sabol
- Department of Geology and Palaeontology, Faculty of Natural SciencesComenius UniversityBratislavaSlovak Republic
| | - Nikolai Spassov
- National Museum of Natural History at the Bulgarian Academy of SciencesSofiaBulgaria
| | - Jan Storå
- Department of Archaeology and Classical StudiesStockholm UniversityStockholmSweden
| | - Christina Valdiosera
- Department of Archaeology and HistoryLa Trobe UniversityMelbourneVictoriaAustralia
| | - Aritza Villaluenga
- Aranzadi Society of SciencesDonostia‐San SebastianSpain
- Facultad de Letras, High Yield Research Group on PrehistoryUniversity of the Basque Country (UPV‐EHU)Vitoria‐GasteizSpain
| | - John R. Stewart
- Faculty of Science and TechnologyBournemouth UniversityDorsetUK
| | - Love Dalén
- Department of Bioinformatics and GeneticsSwedish Museum of Natural HistoryStockholmSweden
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7
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Ancient DNA from Giant Panda (Ailuropoda melanoleuca) of South-Western China Reveals Genetic Diversity Loss during the Holocene. Genes (Basel) 2018; 9:genes9040198. [PMID: 29642393 PMCID: PMC5924540 DOI: 10.3390/genes9040198] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Revised: 03/26/2018] [Accepted: 03/27/2018] [Indexed: 02/02/2023] Open
Abstract
The giant panda was widely distributed in China and south-eastern Asia during the middle to late Pleistocene, prior to its habitat becoming rapidly reduced in the Holocene. While conservation reserves have been established and population numbers of the giant panda have recently increased, the interpretation of its genetic diversity remains controversial. Previous analyses, surprisingly, have indicated relatively high levels of genetic diversity raising issues concerning the efficiency and usefulness of reintroducing individuals from captive populations. However, due to a lack of DNA data from fossil specimens, it is unknown whether genetic diversity was even higher prior to the most recent population decline. We amplified complete cytb and 12s rRNA, partial 16s rRNA and ND1, and control region sequences from the mitochondrial genomes of two Holocene panda specimens. We estimated genetic diversity and population demography by analyzing the ancient mitochondrial DNA sequences alongside those from modern giant pandas, as well as from other members of the bear family (Ursidae). Phylogenetic analyses show that one of the ancient haplotypes is sister to all sampled modern pandas and the second ancient individual is nested among the modern haplotypes, suggesting that genetic diversity may indeed have been higher earlier during the Holocene. Bayesian skyline plot analysis supports this view and indicates a slight decline in female effective population size starting around 6000 years B.P., followed by a recovery around 2000 years ago. Therefore, while the genetic diversity of the giant panda has been affected by recent habitat contraction, it still harbors substantial genetic diversity. Moreover, while its still low population numbers require continued conservation efforts, there seem to be no immediate threats from the perspective of genetic evolutionary potential.
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8
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Kühne G, Kosuch J, Hochkirch A, Schmitt T. Extra-Mediterranean glacial refugia in a Mediterranean faunal element: the phylogeography of the chalk-hill blue Polyommatus coridon (Lepidoptera, Lycaenidae). Sci Rep 2017. [PMCID: PMC5353669 DOI: 10.1038/srep43533] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Most warm-adapted Central European species are thought to have survived ice ages exclusively in Mediterranean refugia. During recent years, this point of view has been questioned. Therefore, we tested the hypothesis that extra-Mediterranean refugia also played a role in warm-adapted insect species and selected the chalk-hill blue, Polyommatus coridon. We sequenced two mitochondrial loci (COI, CR) in 150 individuals from 30 populations covering nearly the complete range. Minimum spanning networks and other statistical analyses concordantly revealed four genetic lineages with strong phylogeographic signal: a western group in Italy, France and western/central Germany, an eastern lineage in the Balkan Peninsula, the Carpathian Basin and eastern Central Europe, an Alpine group with populations in the Alps and southern Germany and a Pyrenean group. Our results are generally consistent with previous analyses for P. coridon based on allozymes and DNA sequences, but provide additional insights. We propose that these four lineages have evolved during allopatry in different glacial refugia, two in typical Mediterranean refugia (Apennines and Balkan Peninsulas), but two in extra-Mediterranean areas south of the Alps and Pyrenees. This supports survival of warm-adapted organisms in these regions in close geographic proximity to the refugia of high mountain species.
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9
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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.
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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
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10
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Stojak J, McDevitt AD, Herman JS, Kryštufek B, Uhlíková J, Purger JJ, Lavrenchenko LA, Searle JB, Wójcik JM. Between the Balkans and the Baltic: Phylogeography of a Common Vole Mitochondrial DNA Lineage Limited to Central Europe. PLoS One 2016; 11:e0168621. [PMID: 27992546 PMCID: PMC5161492 DOI: 10.1371/journal.pone.0168621] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Accepted: 12/02/2016] [Indexed: 11/30/2022] Open
Abstract
The common vole (Microtus arvalis) has been a model species of small mammal for studying end-glacial colonization history. In the present study we expanded the sampling from central and eastern Europe, analyzing contemporary genetic structure to identify the role of a potential 'northern glacial refugium', i.e. a refugium at a higher latitude than the traditional Mediterranean refugia. Altogether we analyzed 786 cytochrome b (cytb) sequences (representing mitochondrial DNA; mtDNA) from the whole of Europe, adding 177 new sequences from central and eastern Europe, and we conducted analyses on eight microsatellite loci for 499 individuals (representing nuclear DNA) from central and eastern Europe, adding data on 311 new specimens. Our new data fill gaps in the vicinity of the Carpathian Mountains, the potential northern refugium, such that there is now dense sampling from the Balkans to the Baltic Sea. Here we present evidence that the Eastern mtDNA lineage of the common vole was present in the vicinity of this Carpathian refugium during the Last Glacial Maximum and the Younger Dryas. The Eastern lineage expanded from this refugium to the Baltic and shows low cytb nucleotide diversity in those most northerly parts of the distribution. Analyses of microsatellites revealed a similar pattern but also showed little differentiation between all of the populations sampled in central and eastern Europe.
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Affiliation(s)
- Joanna Stojak
- Mammal Research Institute, Polish Academy of Sciences, Białowieża, Poland
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, United States of America
| | - Allan D. McDevitt
- Ecosystems and Environment Research Centre, School of Environment and Life Sciences, University of Salford, Salford, United Kingdom
| | - Jeremy S. Herman
- Department of Natural Sciences, National Museums Scotland, Edinburgh, United Kingdom
| | - Boris Kryštufek
- Vertebrate Department, Slovenian Museum of Natural History, Ljubljana, Slovenia
| | - Jitka Uhlíková
- Nature Conservation Agency of the Czech Republic, Prague, Czech Republic
| | - Jenő J. Purger
- Department of Ecology, Institute of Biology, University in Pécs, Pécs, Hungary
| | - Leonid A. Lavrenchenko
- Department of Mammalian Microevolution, A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia
| | - Jeremy B. Searle
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, United States of America
| | - Jan M. Wójcik
- Mammal Research Institute, Polish Academy of Sciences, Białowieża, Poland
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11
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Ersmark E, Klütsch CFC, Chan YL, Sinding MHS, Fain SR, Illarionova NA, Oskarsson M, Uhlén M, Zhang YP, Dalén L, Savolainen P. From the Past to the Present: Wolf Phylogeography and Demographic History Based on the Mitochondrial Control Region. Front Ecol Evol 2016. [DOI: 10.3389/fevo.2016.00134] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
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12
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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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13
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Rodríguez‐Varela R, García N, Nores C, Álvarez‐Lao D, Barnett R, Arsuaga JL, Valdiosera C. Ancient
DNA
reveals past existence of
E
urasian lynx in
S
pain. J Zool (1987) 2015. [DOI: 10.1111/jzo.12289] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- R. Rodríguez‐Varela
- Centro Mixto Universidad Complutense de Madrid–Instituto de Salud Carlos III de Evolución y Comportamiento Humanos Madrid Spain
- Departamento de Paleontología Universidad Complutense de Madrid Madrid Spain
| | - N. García
- Centro Mixto Universidad Complutense de Madrid–Instituto de Salud Carlos III de Evolución y Comportamiento Humanos Madrid Spain
- Departamento de Paleontología Universidad Complutense de Madrid Madrid Spain
| | - C. Nores
- INDUROT University of Oviedo Oviedo Spain
| | - D. Álvarez‐Lao
- Departamento de Geología Universidad de Oviedo Oviedo Spain
| | - R. Barnett
- Centre for GeoGenetics Natural History Museum of Denmark Copenhagen Denmark
| | - J. L. Arsuaga
- Centro Mixto Universidad Complutense de Madrid–Instituto de Salud Carlos III de Evolución y Comportamiento Humanos Madrid Spain
- Departamento de Paleontología Universidad Complutense de Madrid Madrid Spain
| | - C. Valdiosera
- Centro Mixto Universidad Complutense de Madrid–Instituto de Salud Carlos III de Evolución y Comportamiento Humanos Madrid Spain
- Department of Archaeology Environment and Community Planning Faculty of Humanities and Social Sciences La Trobe University Melbourne Vic. Australia
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14
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Çilingir FG, Akın Pekşen Ç, Ambarlı H, Beerli P, Bilgin CC. Exceptional maternal lineage diversity in brown bears (Ursus arctos) from Turkey. Zool J Linn Soc 2015. [DOI: 10.1111/zoj.12322] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- F. Gözde Çilingir
- Department of Biology; Middle East Technical University; Ankara Turkey
- Department of Biological Sciences; National University of Singapore; Singapore
| | - Çiğdem Akın Pekşen
- Department of Biology; Middle East Technical University; Ankara Turkey
- Deparment of Biology; Yüzüncüyıl University; Van Turkey
| | - Hüseyin Ambarlı
- Department of Biology; Middle East Technical University; Ankara Turkey
- Department of Wildlife Ecology and Management; Düzce University; Düzce Turkey
| | - Peter Beerli
- Department of Scientific Computing; Florida State University; Tallahassee FL USA
| | - C. Can Bilgin
- Department of Biology; Middle East Technical University; Ankara Turkey
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15
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Parks M, Subramanian S, Baroni C, Salvatore MC, Zhang G, Millar CD, Lambert DM. Ancient population genomics and the study of evolution. Philos Trans R Soc Lond B Biol Sci 2015; 370:20130381. [PMID: 25487332 DOI: 10.1098/rstb.2013.0381] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Recently, the study of ancient DNA (aDNA) has been greatly enhanced by the development of second-generation DNA sequencing technologies and targeted enrichment strategies. These developments have allowed the recovery of several complete ancient genomes, a result that would have been considered virtually impossible only a decade ago. Prior to these developments, aDNA research was largely focused on the recovery of short DNA sequences and their use in the study of phylogenetic relationships, molecular rates, species identification and population structure. However, it is now possible to sequence a large number of modern and ancient complete genomes from a single species and thereby study the genomic patterns of evolutionary change over time. Such a study would herald the beginnings of ancient population genomics and its use in the study of evolution. Species that are amenable to such large-scale studies warrant increased research effort. We report here progress on a population genomic study of the Adélie penguin (Pygoscelis adeliae). This species is ideally suited to ancient population genomic research because both modern and ancient samples are abundant in the permafrost conditions of Antarctica. This species will enable us to directly address many of the fundamental questions in ecology and evolution.
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Affiliation(s)
- M Parks
- Environmental Futures Research Institute, Griffith University, Nathan, Australia
| | - S Subramanian
- Environmental Futures Research Institute, Griffith University, Nathan, Australia
| | - C Baroni
- Dipartimento di Scienze della Terra, Universita di Pisa, Pisa, Italy
| | - M C Salvatore
- Dipartimento di Scienze della Terra, Universita di Pisa, Pisa, Italy
| | - G Zhang
- China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen, Republic of China Centre for Social Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - C D Millar
- Allan Wilson Centre for Molecular Ecology and Evolution, School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - D M Lambert
- Environmental Futures Research Institute, Griffith University, Nathan, Australia
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16
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Kumar V, Kutschera VE, Nilsson MA, Janke A. Genetic signatures of adaptation revealed from transcriptome sequencing of Arctic and red foxes. BMC Genomics 2015; 16:585. [PMID: 26250829 PMCID: PMC4528681 DOI: 10.1186/s12864-015-1724-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 06/26/2015] [Indexed: 11/17/2022] Open
Abstract
Background The genus Vulpes (true foxes) comprises numerous species that inhabit a wide range of habitats and climatic conditions, including one species, the Arctic fox (Vulpes lagopus) which is adapted to the arctic region. A close relative to the Arctic fox, the red fox (Vulpes vulpes), occurs in subarctic to subtropical habitats. To study the genetic basis of their adaptations to different environments, transcriptome sequences from two Arctic foxes and one red fox individual were generated and analyzed for signatures of positive selection. In addition, the data allowed for a phylogenetic analysis and divergence time estimate between the two fox species. Results The de novo assembly of reads resulted in more than 160,000 contigs/transcripts per individual. Approximately 17,000 homologous genes were identified using human and the non-redundant databases. Positive selection analyses revealed several genes involved in various metabolic and molecular processes such as energy metabolism, cardiac gene regulation, apoptosis and blood coagulation to be under positive selection in foxes. Branch site tests identified four genes to be under positive selection in the Arctic fox transcriptome, two of which are fat metabolism genes. In the red fox transcriptome eight genes are under positive selection, including molecular process genes, notably genes involved in ATP metabolism. Analysis of the three transcriptomes and five Sanger re-sequenced genes in additional individuals identified a lower genetic variability within Arctic foxes compared to red foxes, which is consistent with distribution range differences and demographic responses to past climatic fluctuations. A phylogenomic analysis estimated that the Arctic and red fox lineages diverged about three million years ago. Conclusions Transcriptome data are an economic way to generate genomic resources for evolutionary studies. Despite not representing an entire genome, this transcriptome analysis identified numerous genes that are relevant to arctic adaptation in foxes. Similar to polar bears, fat metabolism seems to play a central role in adaptation of Arctic foxes to the cold climate, as has been identified in the polar bear, another arctic specialist. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1724-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Vikas Kumar
- Senckenberg Biodiversity and Climate Research Center, Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, D-60325, Frankfurt am Main, Germany.
| | - Verena E Kutschera
- Senckenberg Biodiversity and Climate Research Center, Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, D-60325, Frankfurt am Main, Germany. .,Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-75236, Uppsala, Sweden.
| | - Maria A Nilsson
- Senckenberg Biodiversity and Climate Research Center, Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, D-60325, Frankfurt am Main, Germany.
| | - Axel Janke
- Senckenberg Biodiversity and Climate Research Center, Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, D-60325, Frankfurt am Main, Germany. .,Evolution & Diversity, Goethe University Frankfurt, Institute for Ecology, Biologicum, Max-von-Laue-Str.13, D-60439, Frankfurt am Main, Germany.
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17
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Xenikoudakis G, Ersmark E, Tison JL, Waits L, Kindberg J, Swenson JE, Dalén L. Consequences of a demographic bottleneck on genetic structure and variation in the Scandinavian brown bear. Mol Ecol 2015; 24:3441-54. [PMID: 26042479 DOI: 10.1111/mec.13239] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Revised: 05/07/2015] [Accepted: 05/08/2015] [Indexed: 11/30/2022]
Abstract
The Scandinavian brown bear went through a major decline in population size approximately 100 years ago, due to intense hunting. After being protected, the population subsequently recovered and today numbers in the thousands. The genetic diversity in the contemporary population has been investigated in considerable detail, and it has been shown that the population consists of several subpopulations that display relatively high levels of genetic variation. However, previous studies have been unable to resolve the degree to which the demographic bottleneck impacted the contemporary genetic structure and diversity. In this study, we used mitochondrial and microsatellite DNA markers from pre- and postbottleneck Scandinavian brown bear samples to investigate the effect of the bottleneck. Simulation and multivariate analysis suggested the same genetic structure for the historical and modern samples, which are clustered into three subpopulations in southern, central and northern Scandinavia. However, the southern subpopulation appears to have gone through a marked change in allele frequencies. When comparing the mitochondrial DNA diversity in the whole population, we found a major decline in haplotype numbers across the bottleneck. However, the loss of autosomal genetic diversity was less pronounced, although a significant decline in allelic richness was observed in the southern subpopulation. Approximate Bayesian computations provided clear support for a decline in effective population size during the bottleneck, in both the southern and northern subpopulations. These results have implications for the future management of the Scandinavian brown bear because they indicate a recent loss in genetic diversity and also that the current genetic structure may have been caused by historical ecological processes rather than recent anthropogenic persecution.
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Affiliation(s)
- G Xenikoudakis
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, SE-10405, Stockholm, Sweden.,Department of Zoology, Stockholm University, SE-106 91, Stockholm, Sweden
| | - E Ersmark
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, SE-10405, Stockholm, Sweden.,Department of Zoology, Stockholm University, SE-106 91, Stockholm, Sweden
| | - J-L Tison
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, SE-10405, Stockholm, Sweden
| | - L Waits
- Department of Fish and Wildlife Sciences, University of Idaho, 875 Perimeter Drive MS 1136, Moscow, ID, 83844, USA
| | - J Kindberg
- Department of Wildlife, Fish, and Environmental Studies, Swedish University of Agricultural Sciences, SE-90183, Umeå, Sweden
| | - J E Swenson
- Department of Ecology and Natural Resource Management, Norwegian University of Life Sciences, NO-1432, Ås, Norway.,Norwegian Institute for Nature Research, PO Box 5685 Sluppen, NO-7485, Trondheim, Norway
| | - L Dalén
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, SE-10405, Stockholm, Sweden
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18
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Bogdanowicz W, Hulva P, Černá Bolfíková B, Buś MM, Rychlicka E, Sztencel-Jabłonka A, Cistrone L, Russo D. Cryptic diversity of Italian bats and the role of the Apennine refugium in the phylogeography of the western Palaearctic. Zool J Linn Soc 2015. [DOI: 10.1111/zoj.12248] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Wiesław Bogdanowicz
- Museum and Institute of Zoology; Polish Academy of Sciences; Wilcza 64 00-679 Warszawa Poland
| | - Pavel Hulva
- Department of Zoology; Charles University in Prague; Viničná 7 12843 Prague Czech Republic
- Department of Biology and Ecology; University of Ostrava; Chittussiho 10 71000 Ostrava Czech Republic
| | - Barbora Černá Bolfíková
- Faculty of Tropical AgriSciences; Czech University of Life Sciences Prague; Kamýcká 129 16500 Prague Czech Republic
| | - Magdalena M. Buś
- Museum and Institute of Zoology; Polish Academy of Sciences; Wilcza 64 00-679 Warszawa Poland
| | - Edyta Rychlicka
- Museum and Institute of Zoology; Polish Academy of Sciences; Wilcza 64 00-679 Warszawa Poland
| | - Anna Sztencel-Jabłonka
- Museum and Institute of Zoology; Polish Academy of Sciences; Wilcza 64 00-679 Warszawa Poland
| | - Luca Cistrone
- Forestry and Conservation; Via Botticelli n°14 03043 Cassino Frosinone Italy
| | - Danilo Russo
- Wildlife Research Unit; Laboratorio di Ecologia Applicata; Sezione di Biologia e Protezione dei Sistemi Agrari e Forestali; Dipartimento di Agraria; Università degli Studi di Napoli Federico II; via Università, 100 80055 Portici Napoli Italy
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19
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Cahill JA, Stirling I, Kistler L, Salamzade R, Ersmark E, Fulton TL, Stiller M, Green RE, Shapiro B. Genomic evidence of geographically widespread effect of gene flow from polar bears into brown bears. Mol Ecol 2015; 24:1205-17. [PMID: 25490862 PMCID: PMC4409089 DOI: 10.1111/mec.13038] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Revised: 11/15/2014] [Accepted: 11/26/2014] [Indexed: 12/16/2022]
Abstract
Polar bears are an arctic, marine adapted species that is closely related to brown bears. Genome analyses have shown that polar bears are distinct and genetically homogeneous in comparison to brown bears. However, these analyses have also revealed a remarkable episode of polar bear gene flow into the population of brown bears that colonized the Admiralty, Baranof and Chichagof islands (ABC islands) of Alaska. Here, we present an analysis of data from a large panel of polar bear and brown bear genomes that includes brown bears from the ABC islands, the Alaskan mainland and Europe. Our results provide clear evidence that gene flow between the two species had a geographically wide impact, with polar bear DNA found within the genomes of brown bears living both on the ABC islands and in the Alaskan mainland. Intriguingly, while brown bear genomes contain up to 8.8% polar bear ancestry, polar bear genomes appear to be devoid of brown bear ancestry, suggesting the presence of a barrier to gene flow in that direction.
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Affiliation(s)
- James A Cahill
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, 95064, USA
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20
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Ratkiewicz M, Matosiuk M, Saveljev AP, Sidorovich V, Ozolins J, Männil P, Balciauskas L, Kojola I, Okarma H, Kowalczyk R, Schmidt K. Long-range gene flow and the effects of climatic and ecological factors on genetic structuring in a large, solitary carnivore: the Eurasian lynx. PLoS One 2014; 9:e115160. [PMID: 25551216 PMCID: PMC4281111 DOI: 10.1371/journal.pone.0115160] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Accepted: 11/19/2014] [Indexed: 11/26/2022] Open
Abstract
Due to their high mobility, large terrestrial predators are potentially capable of maintaining high connectivity, and therefore low genetic differentiation among populations. However, previous molecular studies have provided contradictory findings in relation to this. To elucidate patterns of genetic structure in large carnivores, we studied the genetic variability of the Eurasian lynx, Lynx lynx throughout north-eastern Europe using microsatellite, mitochondrial DNA control region and Y chromosome-linked markers. Using SAMOVA we found analogous patterns of genetic structure based on both mtDNA and microsatellites, which coincided with a relatively little evidence for male-biased dispersal. No polymorphism for the cytochrome b and ATP6 mtDNA genes and Y chromosome-linked markers were found. Lynx inhabiting a large area encompassing Finland, the Baltic countries and western Russia formed a single genetic unit, while some marginal populations were clearly divergent from others. The existence of a migration corridor was suggested to correspond with distribution of continuous forest cover. The lowest variability (in both markers) was found in lynx from Norway and Białowieża Primeval Forest (BPF), which coincided with a recent demographic bottleneck (Norway) or high habitat fragmentation (BPF). The Carpathian population, being monomorphic for the control region, showed relatively high microsatellite diversity, suggesting the effect of a past bottleneck (e.g. during Last Glacial Maximum) on its present genetic composition. Genetic structuring for the mtDNA control region was best explained by latitude and snow cover depth. Microsatellite structuring correlated with the lynx's main prey, especially the proportion of red deer (Cervus elaphus) in its diet. Eurasian lynx are capable of maintaining panmictic populations across eastern Europe unless they are severely limited by habitat continuity or a reduction in numbers. Different correlations of mtDNA and microsatellite population divergence patterns with climatic and ecological factors may suggest separate selective pressures acting on males and females in this solitary carnivore.
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Affiliation(s)
| | - Maciej Matosiuk
- Institute of Biology, University of Białystok, Białystok, Poland
| | - Alexander P. Saveljev
- B. M. Zhitkov Russian Research Institute of Game Management and Fur Farming, Russian Academy of Sciences, Kirov, Russia
| | - Vadim Sidorovich
- Centre for Biological Resources (former Institute of Zoology) of National Academy of Sciences, Minsk, Belarus
| | - Janis Ozolins
- Latvian State Forest Research Institute “Silava”, Salaspils, Latvia
| | | | | | - Ilpo Kojola
- Finnish Game and Fisheries Research Institute, Oulu Game and Fisheries Research, University of Oulu, Finland
| | - Henryk Okarma
- Institute of Nature Conservation, Polish Academy of Sciences, Kraków, Poland
| | - Rafał Kowalczyk
- Mammal Research Institute, Polish Academy of Sciences, Białowieża, Poland
| | - Krzysztof Schmidt
- Mammal Research Institute, Polish Academy of Sciences, Białowieża, Poland
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21
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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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22
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Frosch C, Dutsov A, Zlatanova D, Valchev K, Reiners TE, Steyer K, Pfenninger M, Nowak C. Noninvasive genetic assessment of brown bear population structure in Bulgarian mountain regions. Mamm Biol 2014. [DOI: 10.1016/j.mambio.2014.04.001] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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23
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Horn S, Prost S, Stiller M, Makowiecki D, Kuznetsova T, Benecke N, Pucher E, Hufthammer AK, Schouwenburg C, Shapiro B, Hofreiter M. Ancient mitochondrial DNA and the genetic history of Eurasian beaver (Castor fiber) in Europe. Mol Ecol 2014; 23:1717-29. [DOI: 10.1111/mec.12691] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Susanne Horn
- Max Planck Institute for Evolutionary Anthropology; Deutscher Platz 6 Leipzig Germany
| | - Stefan Prost
- Department of Anatomy; Allan Wilson Centre for Molecular Ecology and Evolution; University of Otago; 270 Great King Street Dunedin 9054 New Zealand
- Department of Integrative Biology; University of California; 1005 Valley Life Sciences Bldg. #3140 Berkeley CA 94720-3140 USA
- Department of Biodiversity Informatics and Genetics; Swedish Museum of Natural History; Box 50007 10405 Stockholm Sweden
| | - Mathias Stiller
- Department of Ecology and Evolutionary Biology; University of California Santa Cruz; 1156 High Street Santa Cruz CA 95064 USA
| | - Daniel Makowiecki
- Institute of Archaeology; Nicolaus Copernicus University; Szosa Bydgoska 44/48 PL 87-100 Toruń Poland
| | - Tatiana Kuznetsova
- Department of Paleontology; Faculty of Geology; Moscow State University; Leninskie Gory 1 MSU Moscow 119991 Russia
| | - Norbert Benecke
- Scientific Department of the Head Office; German Archaeological Institute; Im Dol 2-6 (Haus I) D-14195 Berlin Germany
| | - Erich Pucher
- Department for Zooarchaeology; Natural History Museum Vienna; Burgring 7 A-1010 Vienna Austria
| | - Anne K. Hufthammer
- University Museum Bergen; University of Bergen; Post box 7800 5020 Bergen Norway
| | | | - Beth Shapiro
- Department of Ecology and Evolutionary Biology; University of California Santa Cruz; 1156 High Street Santa Cruz CA 95064 USA
| | - Michael Hofreiter
- Department of Biology; University of York; Wentworth Way; Heslington York YO31 7SG UK
- Evolutionary and Adaptive Genomics; Institute of Biochemistry and Biology; Faculty of Mathematics and Life Sciences; University of Potsdam; Karl-Liebknecht-Straße 24-25; 14476 Potsdam Germany
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24
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Buś MM, Allen M. Collecting and Preserving Biological Samples from Challenging Environments for DNA Analysis. Biopreserv Biobank 2014; 12:17-22. [DOI: 10.1089/bio.2013.0060] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Affiliation(s)
- Magdalena M. Buś
- Department of Immunology, Genetics, and Pathology (IGP), Uppsala Biomedical Centre (BMC), Uppsala University, Uppsala, Sweden
| | - Marie Allen
- Department of Immunology, Genetics, and Pathology (IGP), Uppsala Biomedical Centre (BMC), Uppsala University, Uppsala, Sweden
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25
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Meiri M, Huchon D, Bar-Oz G, Boaretto E, Horwitz LK, Maeir AM, Sapir-Hen L, Larson G, Weiner S, Finkelstein I. Ancient DNA and population turnover in southern levantine pigs--signature of the sea peoples migration? Sci Rep 2013; 3:3035. [PMID: 24186332 PMCID: PMC3816294 DOI: 10.1038/srep03035] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Accepted: 07/23/2013] [Indexed: 11/20/2022] Open
Abstract
Near Eastern wild boars possess a characteristic DNA signature. Unexpectedly, wild boars from Israel have the DNA sequences of European wild boars and domestic pigs. To understand how this anomaly evolved, we sequenced DNA from ancient and modern pigs from Israel. Pigs from Late Bronze Age (until ca. 1150 BCE) in Israel shared haplotypes of modern and ancient Near Eastern pigs. European haplotypes became dominant only during the Iron Age (ca. 900 BCE). This raises the possibility that European pigs were brought to the region by the Sea Peoples who migrated to the Levant at that time. Then, a complete genetic turnover took place, most likely because of repeated admixture between local and introduced European domestic pigs that went feral. Severe population bottlenecks likely accelerated this process. Introductions by humans have strongly affected the phylogeography of wild animals, and interpretations of phylogeography based on modern DNA alone should be taken with caution.
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Affiliation(s)
- Meirav Meiri
- 1] Institute of Archaeology, Tel Aviv University, Tel Aviv 69978, Israel [2] Department of Zoology, Tel Aviv University, Tel Aviv 69978, Israel
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26
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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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Salvi D, Harris DJ, Kaliontzopoulou A, Carretero MA, Pinho C. Persistence across Pleistocene ice ages in Mediterranean and extra-Mediterranean refugia: phylogeographic insights from the common wall lizard. BMC Evol Biol 2013; 13:147. [PMID: 23841475 PMCID: PMC3711914 DOI: 10.1186/1471-2148-13-147] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Accepted: 07/08/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Pleistocene climatic oscillations have played a major role in structuring present-day biodiversity. The southern Mediterranean peninsulas have long been recognized as major glacial refugia, from where Northern Europe was post-glacially colonized. However, recent studies have unravelled numerous additional refugia also in northern regions. We investigated the phylogeographic pattern of the widespread Western Palaearctic lizard Podarcis muralis, using a range-wide multilocus approach, to evaluate whether it is concordant with a recent expansion from southern glacial refugia or alternatively from a combination of Mediterranean and northern refugia. RESULTS We analyzed DNA sequences of two mitochondrial (cytb and nd4) and three nuclear (acm4, mc1r, and pdc) gene fragments in individuals from 52 localities across the species range, using phylogenetic and phylogeographic methods. The complex phylogeographic pattern observed, with 23 reciprocally monophyletic allo- parapatric lineages having a Pleistocene divergence, suggests a scenario of long-term isolation in multiple ice-age refugia across the species distribution range. Multiple lineages were identified within the three Mediterranean peninsulas - Iberia, Italy and the Balkans - where the highest genetic diversity was observed. Such an unprecedented phylogeographic pattern - here called "refugia within all refugia" - compasses the classical scenario of multiple southern refugia. However, unlike the southern refugia model, various distinct lineages were also found in northern regions, suggesting that additional refugia in France, Northern Italy, Eastern Alps and Central Balkans allowed the long-term persistence of this species throughout Pleistocene glaciations. CONCLUSIONS The phylogeography of Podarcis muralis provides a paradigm of temperate species survival in Mediterranean and extra-Mediterranean glacial refugia. Such refugia acted as independent biogeographic compartments for the long-term persistence of this species, for the differentiation of its genetic lineages, and for the short-distance post-glacial re-colonization of neighbouring areas. This finding echoes previous findings from recent phylogeographic studies on species from temperate ecoregions, thus suggesting the need for a reappraisal of the role of northern refugia for glacial persistence and post-glacial assembly of Holarctic biota.
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Affiliation(s)
- Daniele Salvi
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal.
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Kutschera VE, Lecomte N, Janke A, Selva N, Sokolov AA, Haun T, Steyer K, Nowak C, Hailer F. A range-wide synthesis and timeline for phylogeographic events in the red fox (Vulpes vulpes). BMC Evol Biol 2013; 13:114. [PMID: 23738594 PMCID: PMC3689046 DOI: 10.1186/1471-2148-13-114] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Accepted: 05/29/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Many boreo-temperate mammals have a Pleistocene fossil record throughout Eurasia and North America, but only few have a contemporary distribution that spans this large area. Examples of Holarctic-distributed carnivores are the brown bear, grey wolf, and red fox, all three ecological generalists with large dispersal capacity and a high adaptive flexibility. While the two former have been examined extensively across their ranges, no phylogeographic study of the red fox has been conducted across its entire Holarctic range. Moreover, no study included samples from central Asia, leaving a large sampling gap in the middle of the Eurasian landmass. RESULTS Here we provide the first mitochondrial DNA sequence data of red foxes from central Asia (Siberia), and new sequences from several European populations. In a range-wide synthesis of 729 red fox mitochondrial control region sequences, including 677 previously published and 52 newly obtained sequences, this manuscript describes the pattern and timing of major phylogeographic events in red foxes, using a Bayesian coalescence approach with multiple fossil tip and root calibration points. In a 335 bp alignment we found in total 175 unique haplotypes. All newly sequenced individuals belonged to the previously described Holarctic lineage. Our analyses confirmed the presence of three Nearctic- and two Japan-restricted lineages that were formed since the Mid/Late Pleistocene. CONCLUSIONS The phylogeographic history of red foxes is highly similar to that previously described for grey wolves and brown bears, indicating that climatic fluctuations and habitat changes since the Pleistocene had similar effects on these highly mobile generalist species. All three species originally diversified in Eurasia and later colonized North America and Japan. North American lineages persisted through the last glacial maximum south of the ice sheets, meeting more recent colonizers from Beringia during postglacial expansion into the northern Nearctic. Both brown bears and red foxes colonized Japan's northern island Hokkaido at least three times, all lineages being most closely related to different mainland lineages. Red foxes, grey wolves, and brown bears thus represent an interesting case where species that occupy similar ecological niches also exhibit similar phylogeographic histories.
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Ruiz-González A, Madeira MJ, Randi E, Abramov AV, Davoli F, Gómez-Moliner BJ. Phylogeography of the forest-dwelling European pine marten (Martes martes): new insights into cryptic northern glacial refugia. Biol J Linn Soc Lond 2013. [DOI: 10.1111/bij.12046] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | | | | | - Alexei V. Abramov
- Laboratory of Mammalogy; Zoological Institute; Russian Academy of Sciences; Universitetskaya nab. 1; Saint-Petersburg; 199034; Russia
| | - Francesca Davoli
- Laboratorio di genetica; Istituto Superiore per la Protezione e la Ricerca Ambientale (ISPRA); Via Cà Fornacetta 9; 40064; Ozzano dell'Emilia; Bologna; Italy
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Porretta D, Mastrantonio V, Mona S, Epis S, Montagna M, Sassera D, Bandi C, Urbanelli S. The integration of multiple independent data reveals an unusual response to Pleistocene climatic changes in the hard tick Ixodes ricinus. Mol Ecol 2013; 22:1666-82. [PMID: 23398505 DOI: 10.1111/mec.12203] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2012] [Revised: 11/29/2012] [Accepted: 11/29/2012] [Indexed: 11/29/2022]
Abstract
In the last few years, improved analytical tools and the integration of genetic data with multiple sources of information have shown that temperate species exhibited more complex responses to ice ages than previously thought. In this study, we investigated how Pleistocene climatic changes affected the current distribution and genetic diversity of European populations of the tick Ixodes ricinus, an ectoparasite with high ecological plasticity. We first used mitochondrial and nuclear genetic markers to investigate the phylogeographic structure of the species and its Pleistocene history using coalescent-based methods; then we used species distribution modelling to infer the climatic niche of the species at last glacial maximum; finally, we reviewed the literature on the I. ricinus hosts to identify the locations of their glacial refugia. Our results support the scenario that during the last glacial phase, I. ricinus never experienced a prolonged allopatric divergence in separate glacial refugia, but persisted with interconnected populations across Southern and Central Europe. The generalist behaviour in host choice of I. ricinus would have played a major role in maintaining connections between its populations. Although most of the hosts persisted in separate refugia, from the point of view of I. ricinus, they represented a continuity of 'bridges' among populations. Our study highlights the importance of species-specific ecology in affecting responses to Pleistocene glacial-interglacial cycles. Together with other cases in Europe and elsewhere, it contributes to setting new hypotheses on how species with wide ecological plasticity coped with Pleistocene climatic changes.
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Affiliation(s)
- Daniele Porretta
- Department of Ecological and Biological Sciences, Tuscia University, Viterbo, Italy.
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Edwards CJ, Soulsbury CD, Statham MJ, Ho SY, Wall D, Dolf G, Iossa G, Baker PJ, Harris S, Sacks BN, Bradley DG. Temporal genetic variation of the red fox, Vulpes vulpes, across western Europe and the British Isles. QUATERNARY SCIENCE REVIEWS 2012; 57:95-104. [PMID: 24068852 PMCID: PMC3778924 DOI: 10.1016/j.quascirev.2012.10.010] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2012] [Accepted: 10/09/2012] [Indexed: 06/02/2023]
Abstract
Quaternary climatic fluctuations have had profound effects on the phylogeographic structure of many species. Classically, species were thought to have become isolated in peninsular refugia, but there is limited evidence that large, non-polar species survived outside traditional refugial areas. We examined the phylogeographic structure of the red fox (Vulpes vulpes), a species that shows high ecological adaptability in the western Palaearctic region. We compared mitochondrial DNA sequences (cytochrome b and control region) from 399 modern and 31 ancient individuals from across Europe. Our objective was to test whether red foxes colonised the British Isles from mainland Europe in the late Pleistocene, or whether there is evidence that they persisted in the region through the Last Glacial Maximum. We found red foxes to show a high degree of phylogeographic structuring across Europe and, consistent with palaeontological and ancient DNA evidence, confirmed via phylogenetic indicators that red foxes were persistent in areas outside peninsular refugia during the last ice age. Bayesian analyses and tests of neutrality indicated population expansion. We conclude that there is evidence that red foxes from the British Isles derived from central European populations that became isolated after the closure of the landbridge with Europe.
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Affiliation(s)
- Ceiridwen J. Edwards
- Smurfit Institute of Genetics, Trinity College, Dublin 2, Ireland
- Research Laboratory for Archaeology, University of Oxford, Dyson Perrins Building, South Parks Road, Oxford OX1 3QY, UK
| | - Carl D. Soulsbury
- School of Biological Sciences, University of Bristol, Woodland Road, Bristol BS8 1UG, UK
- School of Life Sciences, University of Lincoln, Brayford Pool, Lincoln LN6 7TS, UK
| | - Mark J. Statham
- Canid Diversity and Conservation Laboratory, Center for Veterinary Genetics, University of California, One Shields Avenue/Old Davis Road, Davis, CA 95616-8744, USA
| | - Simon Y.W. Ho
- School of Biological Sciences, University of Sydney, NSW 2006, Sydney, Australia
| | - Dave Wall
- UCD School of Biology and Environmental Science, University College Dublin, Ireland
| | - Gaudenz Dolf
- Institute of Genetics, Vetsuisse Faculty, University of Berne, 3001 Berne, Switzerland
| | - Graziella Iossa
- School of Biological Sciences, University of Bristol, Woodland Road, Bristol BS8 1UG, UK
| | - Phillip J. Baker
- School of Biological Sciences, University of Bristol, Woodland Road, Bristol BS8 1UG, UK
| | - Stephen Harris
- School of Biological Sciences, University of Bristol, Woodland Road, Bristol BS8 1UG, UK
| | - Benjamin N. Sacks
- Canid Diversity and Conservation Laboratory, Center for Veterinary Genetics, University of California, One Shields Avenue/Old Davis Road, Davis, CA 95616-8744, USA
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, One Shields Avenue/Old Davis Road, Davis, CA 95616-8744, USA
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Glacial history of a modern invader: phylogeography and species distribution modelling of the Asian tiger mosquito Aedes albopictus. PLoS One 2012; 7:e44515. [PMID: 22970238 PMCID: PMC3435282 DOI: 10.1371/journal.pone.0044515] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2012] [Accepted: 08/03/2012] [Indexed: 11/19/2022] Open
Abstract
Background The tiger mosquito, Aedes albopictus, is one of the 100 most invasive species in the world and a vector of human diseases. In the last 30 years, it has spread from its native range in East Asia to Africa, Europe, and the Americas. Although this modern invasion has been the focus of many studies, the history of the species’ native populations remains poorly understood. Here, we aimed to assess the role of Pleistocene climatic changes in shaping the current distribution of the species in its native range. Methodology/Principal Findings We investigated the phylogeography, historical demography, and species distribution of Ae. albopictus native populations at the Last Glacial Maximum (LGM). Individuals from 16 localities from East Asia were analyzed for sequence variation at two mitochondrial genes. No phylogeographic structure was observed across the study area. Demographic analyses showed a signature of population expansion that started roughly 70,000 years BP. The occurrence of a continuous and climatically suitable area comprising Southeast China, Indochinese Peninsula, and Sundaland during LGM was indicated by species distribution modelling. Conclusions/Significance Our results suggest an evolutionary scenario in which, during the last glacial phase, Ae. albopictus did not experience a fragmentation phase but rather persisted in interconnected populations and experienced demographic growth. The wide ecological flexibility of the species probably played a crucial role in its response to glacial-induced environmental changes. Currently, there is little information on the impact of Pleistocene climatic changes on animal species in East Asia. Most of the studies focused on forest-associated species and suggested cycles of glacial fragmentation and post-glacial expansion. The case of Ae. albopictus, which exhibits a pattern not previously observed in the study area, adds an important piece to our understanding of the Pleistocene history of East Asian biota.
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Schmitt T, Varga Z. Extra-Mediterranean refugia: The rule and not the exception? Front Zool 2012; 9:22. [PMID: 22953783 PMCID: PMC3462695 DOI: 10.1186/1742-9994-9-22] [Citation(s) in RCA: 145] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2012] [Accepted: 08/28/2012] [Indexed: 11/23/2022] Open
Abstract
Some decades ago, biogeographers distinguished three major faunal types of high importance for Europe: (i) Mediterranean elements with exclusive glacial survival in the Mediterranean refugia, (ii) Siberian elements with glacial refugia in the eastern Palearctic and only postglacial expansion to Europe and (iii) arctic and/or alpine elements with large zonal distributions in the periglacial areas and postglacial retreat to the North and/or into the high mountain systems. Genetic analyses have unravelled numerous additional refugia both of continental and Mediterranean species, thus strongly modifying the biogeographical view of Europe. This modified notion is particularly true for the so-called Siberian species, which in many cases have not immigrated into Europe during the postglacial period, but most likely have survived the last, or even several glacial phases, in extra-Mediterranean refugia in some climatically favourable but geographically limited areas of southern Central and Eastern Europe. Recently, genetic analyses revealed that typical Mediterranean species have also survived the Last Glacial Maximum in cryptic northern refugia (e.g. in the Carpathians or even north of the Alps) in addition to their Mediterranean refuge areas.
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Affiliation(s)
- Thomas Schmitt
- Biogeography, Trier University, D - 54 286, Trier, Germany.
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COLANGELO PAOLO, LOY ANNA, HUBER DJURO, GOMERČIĆ TOMISLAV, VIGNA TAGLIANTI AUGUSTU, CIUCCI PAOLO. Cranial distinctiveness in the Apennine brown bear: genetic drift effect or ecophenotypic adaptation? Biol J Linn Soc Lond 2012. [DOI: 10.1111/j.1095-8312.2012.01926.x] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Bray SC, Austin JJ, Metcalf JL, Østbye K, Østbye E, Lauritzen SE, Aaris-Sørensen K, Valdiosera C, Adler CJ, Cooper A. Ancient DNA identifies post-glacial recolonisation, not recent bottlenecks, as the primary driver of contemporary mtDNA phylogeography and diversity in Scandinavian brown bears. DIVERS DISTRIB 2012. [DOI: 10.1111/j.1472-4642.2012.00923.x] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Affiliation(s)
- Sarah C.E. Bray
- Australian Centre for Ancient DNA, School of Earth and Environmental Sciences; University of Adelaide; Adelaide; SA; 5005; Australia
| | | | | | | | - Eivind Østbye
- Department of Biology; University of Oslo; PO Box 1066; Blindern, NO-0316; Oslo; Norway
| | - Stein-Erik Lauritzen
- Department of Earth Science; University of Bergen; Allegaten 41, NO-5007; Bergen; Norway
| | - Kim Aaris-Sørensen
- Centre for GeoGenetics, Natural History Museum of Copenhagen; University of Copenhagen; Universitetsparken 15, DK-2100; Copenhagen Ø; Denmark
| | - Cristina Valdiosera
- Centro Mixto; Universidad Complutense de Madrid-Instituto de Salud Carlos III de Evolucion y Comportamiento Humanos; c/Sinesio Delgado 4 Pabellon 14; 28029; Madrid; Spain
| | | | - Alan Cooper
- Australian Centre for Ancient DNA, School of Earth and Environmental Sciences; University of Adelaide; Adelaide; SA; 5005; Australia
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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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Rodríguez R, Ramírez O, Valdiosera CE, García N, Alda F, Madurell-Malapeira J, Marmi J, Doadrio I, Willerslev E, Götherström A, Arsuaga JL, Thomas MG, Lalueza-Fox C, Dalén L. 50,000 years of genetic uniformity in the critically endangered Iberian lynx. Mol Ecol 2011; 20:3785-95. [PMID: 21864323 DOI: 10.1111/j.1365-294x.2011.05231.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Low genetic diversity in the endangered Iberian lynx, including lack of mitochondrial control region variation, is thought to result from historical or Pleistocene/Holocene population bottlenecks, and to indicate poor long-term viability. We find no variability in control region sequences from 19 Iberian lynx remains from across the Iberian Peninsula and spanning the last 50,000 years. This is best explained by continuously small female effective population size through time. We conclude that low genetic variability in the Iberian lynx is not in itself a threat to long-term viability, and so should not preclude conservation efforts.
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Affiliation(s)
- Ricardo Rodríguez
- Centro Mixto, Universidad Complutense de Madrid-Instituto de Salud Carlos III de Evolución y Comportamiento Humanos, Avda. Monforte de Lemos 5, Pabellón 14. 28029 Madrid, Spain.
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de Bruyn M, Hoelzel AR, Carvalho GR, Hofreiter M. Faunal histories from Holocene ancient DNA. Trends Ecol Evol 2011; 26:405-13. [PMID: 21529992 DOI: 10.1016/j.tree.2011.03.021] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2011] [Revised: 03/24/2011] [Accepted: 03/28/2011] [Indexed: 02/05/2023]
Abstract
Recent studies using ancient DNA have been instrumental in advancing understanding of the impact of Holocene climate change on biodiversity. Ancient DNA has been used to track demography, migration and diversity, and is providing new insights into the long-term dynamics of species and population distributions. The Holocene is key to understanding how the past has impacted on the present, as it bridges the gap between contemporary phylogeographic studies and those with inference on Pleistocene patterns, based on ancient DNA studies. Here, we examine the major patterns of Holocene faunal population dynamics and connectivity; highlighting the dynamic nature of species and population responses to Holocene climatic change, thereby providing an 'analogue' for understanding potential impacts of future change.
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Affiliation(s)
- Mark de Bruyn
- Molecular Ecology & Fisheries Genetics Laboratory, Environment Centre for Wales, School of Biological Sciences, Bangor University, Bangor, UK, LL57 2UW.
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Teacher AGF, Thomas JA, Barnes I. Modern and ancient red fox (Vulpes vulpes) in Europe show an unusual lack of geographical and temporal structuring, and differing responses within the carnivores to historical climatic change. BMC Evol Biol 2011; 11:214. [PMID: 21774815 PMCID: PMC3154186 DOI: 10.1186/1471-2148-11-214] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2011] [Accepted: 07/20/2011] [Indexed: 11/16/2022] Open
Abstract
Background Despite phylogeographical patterns being well characterised in a large number of species, and generalised patterns emerging, the carnivores do not all appear to show consistent trends. While some species tend to fit with standard theoretical phylogeographic expectations (e.g. bears), others show little obvious modern phylogeographic structure (e.g. wolves). In this study we briefly review these studies, and present a new phylogeographical study of the red fox (Vulpes vulpes) throughout Europe, using a combination of ancient DNA sequences obtained from museum specimens, and modern sequences collated from GenBank. We used cytochrome b (250 bp) and the mitochondrial control region (268 bp) to elucidate both current and historical phylogeographical patterning. Results We found evidence for slight isolation by distance in modern populations, as well as differentiation associated with time, both of which can likely be attributed to random genetic drift. Despite high sequence diversity (11.2% cytochrome b, 16.4% control region), no evidence for spatial structure (from Bayesian trees) is found either in modern samples or ancient samples for either gene, and Bayesian skyline plots suggested little change in the effective population size over the past 40,000 years. Conclusions It is probable that the high dispersal ability and adaptability of the red fox has contributed to the lack of observable differentiation, which appears to have remained consistent over tens of thousands of years. Generalised patterns of how animals are thought to have responded to historical climatic change are not necessarily valid for all species, and so understanding the differences between species will be critical for predicting how species will be affected by future climatic change.
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Affiliation(s)
- Amber G F Teacher
- Royal Holloway University of London, Egham Hill, Egham, Surrey TW20 0EX, UK.
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Edwards CJ, Suchard MA, Lemey P, Welch JJ, Barnes I, Fulton TL, Barnett R, O'Connell TC, Coxon P, Monaghan N, Valdiosera CE, Lorenzen ED, Willerslev E, Baryshnikov GF, Rambaut A, Thomas MG, Bradley DG, Shapiro B. Ancient hybridization and an Irish origin for the modern polar bear matriline. Curr Biol 2011; 21:1251-8. [PMID: 21737280 DOI: 10.1016/j.cub.2011.05.058] [Citation(s) in RCA: 153] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2011] [Revised: 05/19/2011] [Accepted: 05/26/2011] [Indexed: 11/16/2022]
Abstract
BACKGROUND Polar bears (Ursus maritimus) are among those species most susceptible to the rapidly changing arctic climate, and their survival is of global concern. Despite this, little is known about polar bear species history. Future conservation strategies would significantly benefit from an understanding of basic evolutionary information, such as the timing and conditions of their initial divergence from brown bears (U. arctos) or their response to previous environmental change. RESULTS We used a spatially explicit phylogeographic model to estimate the dynamics of 242 brown bear and polar bear matrilines sampled throughout the last 120,000 years and across their present and past geographic ranges. Our results show that the present distribution of these matrilines was shaped by a combination of regional stability and rapid, long-distance dispersal from ice-age refugia. In addition, hybridization between polar bears and brown bears may have occurred multiple times throughout the Late Pleistocene. CONCLUSIONS The reconstructed matrilineal history of brown and polar bears has two striking features. First, it is punctuated by dramatic and discrete climate-driven dispersal events. Second, opportunistic mating between these two species as their ranges overlapped has left a strong genetic imprint. In particular, a likely genetic exchange with extinct Irish brown bears forms the origin of the modern polar bear matriline. This suggests that interspecific hybridization not only may be more common than previously considered but may be a mechanism by which species deal with marginal habitats during periods of environmental deterioration.
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Affiliation(s)
- Ceiridwen J Edwards
- Smurfit Institute of Genetics, Trinity College, University of Dublin, Dublin, Ireland
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NAVASCUÉS MIGUEL, DEPAULIS FRANTZ, EMERSON BRENTC. Combining contemporary and ancient DNA in population genetic and phylogeographical studies. Mol Ecol Resour 2010; 10:760-72. [DOI: 10.1111/j.1755-0998.2010.02895.x] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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MURTSKHVALADZE MARINE, GAVASHELISHVILI ALEXANDER, TARKHNISHVILI DAVID. Geographic and genetic boundaries of brown bear (Ursus arctos) population in the Caucasus. Mol Ecol 2010; 19:1829-41. [DOI: 10.1111/j.1365-294x.2010.04610.x] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Pilot M, Branicki W, Jedrzejewski W, Goszczyński J, Jedrzejewska B, Dykyy I, Shkvyrya M, Tsingarska E. Phylogeographic history of grey wolves in Europe. BMC Evol Biol 2010; 10:104. [PMID: 20409299 PMCID: PMC2873414 DOI: 10.1186/1471-2148-10-104] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2009] [Accepted: 04/21/2010] [Indexed: 02/06/2023] Open
Abstract
Background While it is generally accepted that patterns of intra-specific genetic differentiation are substantially affected by glacial history, population genetic processes occurring during Pleistocene glaciations are still poorly understood. In this study, we address the question of the genetic consequences of Pleistocene glaciations for European grey wolves. Combining our data with data from published studies, we analysed phylogenetic relationships and geographic distribution of mitochondrial DNA haplotypes for 947 contemporary European wolves. We also compared the contemporary wolf sequences with published sequences of 24 ancient European wolves. Results We found that haplotypes representing two haplogroups, 1 and 2, overlap geographically, but substantially differ in frequency between populations from south-western and eastern Europe. A comparison between haplotypes from Europe and other continents showed that both haplogroups are spread throughout Eurasia, while only haplogroup 1 occurs in contemporary North American wolves. All ancient wolf samples from western Europe that dated from between 44,000 and 1,200 years B.P. belonged to haplogroup 2, suggesting the long-term predominance of this haplogroup in this region. Moreover, a comparison of current and past frequencies and distributions of the two haplogroups in Europe suggested that haplogroup 2 became outnumbered by haplogroup 1 during the last several thousand years. Conclusions Parallel haplogroup replacement, with haplogroup 2 being totally replaced by haplogroup 1, has been reported for North American grey wolves. Taking into account the similarity of diets reported for the late Pleistocene wolves from Europe and North America, the correspondence between these haplogroup frequency changes may suggest that they were associated with ecological changes occurring after the Last Glacial Maximum.
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Affiliation(s)
- Małgorzata Pilot
- Museum and Institute of Zoology, Polish Academy of Sciences, 00-679 Warszawa, Poland.
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Mona S, Catalano G, Lari M, Larson G, Boscato P, Casoli A, Sineo L, Di Patti C, Pecchioli E, Caramelli D, Bertorelle G. Population dynamic of the extinct European aurochs: genetic evidence of a north-south differentiation pattern and no evidence of post-glacial expansion. BMC Evol Biol 2010; 10:83. [PMID: 20346116 PMCID: PMC2858146 DOI: 10.1186/1471-2148-10-83] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2009] [Accepted: 03/26/2010] [Indexed: 11/17/2022] Open
Abstract
Background The aurochs (Bos primigenius) was a large bovine that ranged over almost the entirety of the Eurasian continent and North Africa. It is the wild ancestor of the modern cattle (Bos taurus), and went extinct in 1627 probably as a consequence of human hunting and the progressive reduction of its habitat. To investigate in detail the genetic history of this species and to compare the population dynamics in different European areas, we analysed Bos primigenius remains from various sites across Italy. Results Fourteen samples provided ancient DNA fragments from the mitochondrial hypervariable region. Our data, jointly analysed with previously published sequences, support the view that Italian aurochsen were genetically similar to modern bovine breeds, but very different from northern/central European aurochsen. Bayesian analyses and coalescent simulations indicate that the genetic variation pattern in both Italian and northern/central European aurochsen is compatible with demographic stability after the last glaciation. We provide evidence that signatures of population expansion can erroneously arise in stable aurochsen populations when the different ages of the samples are not taken into account. Conclusions Distinct groups of aurochsen probably inhabited Italy and northern/central Europe after the last glaciation, respectively. On the contrary, Italian and Fertile Crescent aurochsen likely shared several mtDNA sequences, now common in modern breeds. We argue that a certain level of genetic homogeneity characterized aurochs populations in Southern Europe and the Middle East, and also that post-glacial recolonization of northern and central Europe advanced, without major demographic expansions, from eastern, and not southern, refugia.
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Affiliation(s)
- Stefano Mona
- Dipartimento di Biologia ed Evoluzione, Università di Ferrara, Ferrara, Italy
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KITCHENER AC. Taxonomic issues in bears: impacts on conservation in zoos and the wild, and gaps in current knowledge. ACTA ACUST UNITED AC 2010. [DOI: 10.1111/j.1748-1090.2009.00087.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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BUCKLEY THOMASR, MARSKE KATHARINEA, ATTANAYAKE DILINI. Identifying glacial refugia in a geographic parthenogen using palaeoclimate modelling and phylogeography: the New Zealand stick insectArgosarchus horridus(White). Mol Ecol 2009; 18:4650-63. [DOI: 10.1111/j.1365-294x.2009.04396.x] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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O’KEEFE KIM, RAMAKRISHNAN UMA, VAN TUINEN MARCEL, HADLY ELIZABETHA. Source-sink dynamics structure a common montane mammal. Mol Ecol 2009; 18:4775-89. [DOI: 10.1111/j.1365-294x.2009.04382.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Molecular evidence of conspecificity of South African hares conventionally considered Lepus capensis L., 1758. Mamm Biol 2009. [DOI: 10.1016/j.mambio.2009.05.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Calvignac S, Hughes S, Hänni C. Genetic diversity of endangered brown bear (Ursus arctos) populations at the crossroads of Europe, Asia and Africa. DIVERS DISTRIB 2009. [DOI: 10.1111/j.1472-4642.2009.00586.x] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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