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Ancient Faunal History Revealed by Interdisciplinary Biomolecular Approaches. DIVERSITY 2021. [DOI: 10.3390/d13080370] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Starting four decades ago, studies have examined the ecology and evolutionary dynamics of populations and species using short mitochondrial DNA fragments and stable isotopes. Through technological and analytical advances, the methods and biomolecules at our disposal have increased significantly to now include lipids, whole genomes, proteomes, and even epigenomes. At an unprecedented resolution, the study of ancient biomolecules has made it possible for us to disentangle the complex processes that shaped the ancient faunal diversity across millennia, with the potential to aid in implicating probable causes of species extinction and how humans impacted the genetics and ecology of wild and domestic species. However, even now, few studies explore interdisciplinary biomolecular approaches to reveal ancient faunal diversity dynamics in relation to environmental and anthropogenic impact. This review will approach how biomolecules have been implemented in a broad variety of topics and species, from the extinct Pleistocene megafauna to ancient wild and domestic stocks, as well as how their future use has the potential to offer an enhanced understanding of drivers of past faunal diversity on Earth.
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2
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Fry E, Kim SK, Chigurapti S, Mika KM, Ratan A, Dammermann A, Mitchell BJ, Miller W, Lynch VJ. Functional Architecture of Deleterious Genetic Variants in the Genome of a Wrangel Island Mammoth. Genome Biol Evol 2021; 12:48-58. [PMID: 32031213 PMCID: PMC7094797 DOI: 10.1093/gbe/evz279] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/18/2019] [Indexed: 12/21/2022] Open
Abstract
Woolly mammoths were among the most abundant cold-adapted species during the Pleistocene. Their once-large populations went extinct in two waves, an end-Pleistocene extinction of continental populations followed by the mid-Holocene extinction of relict populations on St. Paul Island ∼5,600 years ago and Wrangel Island ∼4,000 years ago. Wrangel Island mammoths experienced an episode of rapid demographic decline coincident with their isolation, leading to a small population, reduced genetic diversity, and the fixation of putatively deleterious alleles, but the functional consequences of these processes are unclear. Here, we show that a Wrangel Island mammoth genome had many putative deleterious mutations that are predicted to cause diverse behavioral and developmental defects. Resurrection and functional characterization of several genes from the Wrangel Island mammoth carrying putatively deleterious substitutions identified both loss and gain of function mutations in genes associated with developmental defects (HYLS1), oligozoospermia and reduced male fertility (NKD1), diabetes (NEUROG3), and the ability to detect floral scents (OR5A1). These data suggest that at least one Wrangel Island mammoth may have suffered adverse consequences from reduced population size and isolation.
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Affiliation(s)
- Erin Fry
- Department of Human Genetics, The University of Chicago
| | - Sun K Kim
- Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern University
| | | | | | - Aakrosh Ratan
- Center for Public Health Genomics, University of Virginia
| | | | - Brian J Mitchell
- Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern University
| | - Webb Miller
- Center for Comparative Genomics and Bioinformatics, Pennsylvania State University
| | - Vincent J Lynch
- Department of Biological Sciences, University at Buffalo, SUNY
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3
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Bessa-Silva A, Vallinoto M, Sampaio I, Flores-Villela OA, Smith EN, Sequeira F. The roles of vicariance and dispersal in the differentiation of two species of the Rhinella marina species complex. Mol Phylogenet Evol 2019; 145:106723. [PMID: 31891757 DOI: 10.1016/j.ympev.2019.106723] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 12/23/2019] [Accepted: 12/23/2019] [Indexed: 11/19/2022]
Abstract
The high levels of Neotropical biodiversity are commonly associated with the intense Neogene-Quaternary geological events and climate dynamics. Here, we investigate the evolutionary history of two species of Neotropical closely related amphibians (R. horribilis and R. marina). We combine published data with new mitochondrial DNA sequences and multiple nuclear markers, including 12 microsatellites. The phylogenetic analyses showed support for grouping the samples in two main clades; R. horribilis (Central America and Mexico) and R. marina (South America east of the Andes). However, the phylogenetic inferences also show an evident mito-nuclear discordance. We use Approximate Bayesian Computation (ABC) to test the role of different events in the diversification between the two groups recovered. We found that both species were affected primarily by a recent Pleistocene divergence, which was similar to the divergence estimate revealed by the Isolation-with-Migration model, under persistent bidirectional gene flow through time. We provide the first evidence that R. horribilis is differentiated from the South American R. marina at the nuclear level supporting the taxonomic status of R. horribilis, which has been controversial for more than a century.
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Affiliation(s)
- Adam Bessa-Silva
- Laboratório de Evolução (LEVO), Instituto de Estudos Costeiros (IECOS), Universidade Federal do Pará, Campus de Bragança, 68 600-000 Pará, Brazil; CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus Agrário de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
| | - Marcelo Vallinoto
- Laboratório de Evolução (LEVO), Instituto de Estudos Costeiros (IECOS), Universidade Federal do Pará, Campus de Bragança, 68 600-000 Pará, Brazil; CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus Agrário de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal.
| | - Iracilda Sampaio
- Laboratório de Evolução (LEVO), Instituto de Estudos Costeiros (IECOS), Universidade Federal do Pará, Campus de Bragança, 68 600-000 Pará, Brazil
| | - Oscar A Flores-Villela
- Museo de Zoología, Department of Evolutionary Biology, Facultad de Ciencias, Universidad Nacional Autónoma de México, External Circuit of Ciudad Universitaria, Mexico City 04510, Mexico
| | - Eric N Smith
- Department of Biology, The University of Texas at Arlington, Arlington, TX, USA; The Amphibian and Reptile Diversity Research Center, University of Texas at Arlington, Arlington, TX, USA
| | - Fernando Sequeira
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus Agrário de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
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4
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Fenderson LE, Kovach AI, Llamas B. Spatiotemporal landscape genetics: Investigating ecology and evolution through space and time. Mol Ecol 2019; 29:218-246. [DOI: 10.1111/mec.15315] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 09/22/2019] [Accepted: 11/13/2019] [Indexed: 12/22/2022]
Affiliation(s)
- Lindsey E. Fenderson
- Australian Centre for Ancient DNA School of Biological Sciences Environment Institute University of Adelaide Adelaide South Australia Australia
- Department of Natural Resources and the Environment University of New Hampshire Durham NH USA
| | - Adrienne I. Kovach
- Department of Natural Resources and the Environment University of New Hampshire Durham NH USA
| | - Bastien Llamas
- Australian Centre for Ancient DNA School of Biological Sciences Environment Institute University of Adelaide Adelaide South Australia Australia
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5
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Cossu G, Terrier LM, Destrieux C, Velut S, François P, Zemmoura I, Amelot A. Arcuate foramen: "Anatomical variation shape or adaptation legacy?". Surg Radiol Anat 2019; 41:583-588. [PMID: 30656416 DOI: 10.1007/s00276-019-02186-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 01/11/2019] [Indexed: 12/12/2022]
Abstract
PURPOSE The groove of the vertebral artery on the posterior arch of the atlas (sulcus arteriae vertebralis) may become a complete or partial osseous foramen: the arcuate foramen. The presence of a complete or partial arcuate foramen is a rare anatomical variant described in a minority of patients and it seems to be associated with vertigo, vertebro-basilar insufficiency, posterior circulation strokes, and musculoskeletal pain. As the number and morphology of cervical vertebrae is highly preserved, we questioned about its significance from an evolutionary point of view. We thus investigated through an extensive literature review if the arcuate foramen is a pure anatomical variation shape or if it might represent an adaptation legacy. METHODS We observed five atlas of an extinct species, the Late Pleistocene Mammoths (M. primigenius), and we compared them with five atlas of a closely related existent species, the African elephant (L. africana). RESULTS All the mammoths' atlas had an arcuate foramen through which the vertebral artery passed before turning anteriorly and becoming intradural. This foramen was not present in elephants' atlas, where only a groove was observed, such as in the majority of patients. CONCLUSION We would like to raise the hypothesis that this peculiar morphology of mammoths' atlas might have contributed, in association with other factors, to their precocious extinction and that the arcuate foramen might represent a disadvantage in the evolutionary process, with a low prevalence in humans being the result of a natural selection.
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Affiliation(s)
- Giulia Cossu
- Department of Neurosurgery, Bretonneau University Hospital, Tonnellé Boulevard 2, Tours, France.,Department of Neurosurgery, Lausanne University Hospital, Lausanne, Switzerland
| | - Louis-Marie Terrier
- Department of Neurosurgery, Bretonneau University Hospital, Tonnellé Boulevard 2, Tours, France
| | - Christophe Destrieux
- Department of Neurosurgery, Bretonneau University Hospital, Tonnellé Boulevard 2, Tours, France
| | - Stephane Velut
- Department of Neurosurgery, Bretonneau University Hospital, Tonnellé Boulevard 2, Tours, France
| | - Patrick François
- Department of Neurosurgery, Bretonneau University Hospital, Tonnellé Boulevard 2, Tours, France
| | - Ilyess Zemmoura
- Department of Neurosurgery, Bretonneau University Hospital, Tonnellé Boulevard 2, Tours, France
| | - Aymeric Amelot
- Department of Neurosurgery, Bretonneau University Hospital, Tonnellé Boulevard 2, Tours, France. .,Department of Neurosurgery, La Pitié-Salpétrière University Hospital, Paris, France.
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6
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Pečnerová P, Palkopoulou E, Wheat CW, Skoglund P, Vartanyan S, Tikhonov A, Nikolskiy P, van der Plicht J, Díez-Del-Molino D, Dalén L. Mitogenome evolution in the last surviving woolly mammoth population reveals neutral and functional consequences of small population size. Evol Lett 2017; 1:292-303. [PMID: 30283657 PMCID: PMC6121868 DOI: 10.1002/evl3.33] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 11/06/2017] [Indexed: 01/25/2023] Open
Abstract
The onset of the Holocene was associated with a global temperature increase, which led to a rise in sea levels and isolation of the last surviving population of woolly mammoths on Wrangel Island. Understanding what happened with the population's genetic diversity at the time of the isolation and during the ensuing 6000 years can help clarify the effects of bottlenecks and subsequent limited population sizes in species approaching extinction. Previous genetic studies have highlighted questions about how the Holocene Wrangel population was established and how the isolation event affected genetic diversity. Here, we generated high‐quality mitogenomes from 21 radiocarbon‐dated woolly mammoths to compare the ancestral large and genetically diverse Late Pleistocene Siberian population and the small Holocene Wrangel population. Our results indicate that mitogenome diversity was reduced to one single haplotype at the time of the isolation, and thus that the Holocene Wrangel Island population was established by a single maternal lineage. Moreover, we show that the ensuing small effective population size coincided with fixation of a nonsynonymous mutation, and a comparative analysis of mutation rates suggests that the evolutionary rate was accelerated in the Holocene population. These results suggest that isolation on Wrangel Island led to an increase in the frequency of deleterious genetic variation, and thus are consistent with the hypothesis that strong genetic drift in small populations leads to purifying selection being less effective in removing deleterious mutations.
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Affiliation(s)
- Patrícia Pečnerová
- Department of Bioinformatics and Genetics Swedish Museum of Natural History Stockholm Sweden.,Department of Zoology Stockholm University Stockholm Sweden
| | - Eleftheria Palkopoulou
- Department of Bioinformatics and Genetics Swedish Museum of Natural History Stockholm Sweden.,Department of Zoology Stockholm University Stockholm Sweden.,Department of Genetics Harvard Medical School Boston Massachusetts 02115
| | | | - Pontus Skoglund
- Department of Genetics Harvard Medical School Boston Massachusetts 02115.,Broad Institute of Harvard and MIT Cambridge Massachusetts 02142
| | - Sergey Vartanyan
- North-East Interdisciplinary Scientific Research Institute N.A.N.A. Shilo Far East Branch, Russian Academy of Sciences (NEISRI FEB RAS) Magadan Russia
| | - Alexei Tikhonov
- Zoological Institute of Russian Academy of Sciences Saint-Petersburg Russia.,Institute of Applied Ecology of the North North-Eastern Federal University Yakutsk Russia
| | - Pavel Nikolskiy
- Geological Institute of the Russian Academy of Sciences Moscow Russia
| | - Johannes van der Plicht
- Centre for Isotope Research Groningen University Groningen The Netherlands.,Faculty of Archaeology Leiden University Leiden The Netherlands
| | - David Díez-Del-Molino
- Department of Bioinformatics and Genetics Swedish Museum of Natural History Stockholm Sweden
| | - Love Dalén
- Department of Bioinformatics and Genetics Swedish Museum of Natural History Stockholm Sweden
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7
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van der Geer AAE, Galis F. High incidence of cervical ribs indicates vulnerable condition in Late Pleistocene woolly rhinoceroses. PeerJ 2017; 5:e3684. [PMID: 28875067 PMCID: PMC5580387 DOI: 10.7717/peerj.3684] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2017] [Accepted: 07/22/2017] [Indexed: 11/20/2022] Open
Abstract
Mammals as a rule have seven cervical vertebrae, a number that remains remarkably constant. Changes of this number are associated with major congenital abnormalities (pleiotropic effects) that are, at least in humans, strongly selected against. Recently, it was found that Late Pleistocene mammoths (Mammuthus primigenius) from the North Sea have an unusually high incidence of abnormal cervical vertebral numbers, approximately ten times higher than that of extant elephants. Abnormal numbers were due to the presence of large cervical ribs on the seventh vertebra, indicating a homeotic change from a cervical rib-less vertebra into a thoracic rib-bearing vertebra. The high incidence of cervical ribs indicates a vulnerable condition and is thought to be due to inbreeding and adverse conditions that may have impacted early pregnancies in declining populations. In this study we investigated the incidence of cervical ribs in another extinct Late Pleistocene megaherbivore from the North Sea and the Netherlands, the woolly rhinoceros (Coelodonta antiquitatis). We show that the incidence of abnormal cervical vertebral numbers in the woolly rhinoceros is unusually high for mammals (15,6%, n = 32) and much higher than in extant Rhinoceratidae (0%, n = 56). This indicates that woolly rhinoceros lived under vulnerable conditions, just like woolly mammoths. The vulnerable condition may well have contributed to their eventual extinction.
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Affiliation(s)
- Alexandra A E van der Geer
- Naturalis Biodiversity Center, Leiden, the Netherlands.,Department of Geology and Geoenvironment, National and Kapodistrian University of Athens, Zografou, Greece
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8
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Pečnerová P, Díez-del-Molino D, Vartanyan S, Dalén L. Changes in variation at the MHC class II DQA locus during the final demise of the woolly mammoth. Sci Rep 2016; 6:25274. [PMID: 27143688 PMCID: PMC4855147 DOI: 10.1038/srep25274] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 04/13/2016] [Indexed: 12/28/2022] Open
Abstract
According to the nearly-neutral theory of evolution, the relative strengths of selection and drift shift in favour of drift at small population sizes. Numerous studies have analysed the effect of bottlenecks and small population sizes on genetic diversity in the MHC, which plays a central role in pathogen recognition and immune defense and is thus considered a model example for the study of adaptive evolution. However, to understand changes in genetic diversity at loci under selection, it is necessary to compare the genetic diversity of a population before and after the bottleneck. In this study, we analyse three fragments of the MHC DQA gene in woolly mammoth samples radiocarbon dated to before and after a well-documented bottleneck that took place about ten thousand years ago. Our results indicate a decrease in observed heterozygosity and number of alleles, suggesting that genetic drift had an impact on the variation on MHC. Based on coalescent simulations, we found no evidence of balancing selection maintaining MHC diversity during the Holocene. However, strong trans-species polymorphism among mammoths and elephants points to historical effects of balancing selection on the woolly mammoth lineage.
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Affiliation(s)
- Patrícia Pečnerová
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, SE-10405 Stockholm, Sweden
- Department of Zoology, Stockholm University, SE-10691 Stockholm, Sweden
| | - David Díez-del-Molino
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, SE-10405 Stockholm, Sweden
| | - Sergey Vartanyan
- North-East Interdisciplinary Scientific Research Institute N.A.N.A. Shilo, Far East Branch, Russian Academy of Sciences (NEISRI FEB RAS), Magadan, Russia
| | - Love Dalén
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, SE-10405 Stockholm, Sweden
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9
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10
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Pacioni C, Hunt H, Allentoft ME, Vaughan TG, Wayne AF, Baynes A, Haouchar D, Dortch J, Bunce M. Genetic diversity loss in a biodiversity hotspot: ancient
DNA
quantifies genetic decline and former connectivity in a critically endangered marsupial. Mol Ecol 2015; 24:5813-28. [DOI: 10.1111/mec.13430] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Revised: 10/07/2015] [Accepted: 10/13/2015] [Indexed: 11/30/2022]
Affiliation(s)
- Carlo Pacioni
- Ancient DNA Laboratory School of Veterinary and Life Sciences Murdoch University Murdoch WA 6150 Australia
| | - Helen Hunt
- Ancient DNA Laboratory School of Veterinary and Life Sciences Murdoch University Murdoch WA 6150 Australia
| | - Morten E. Allentoft
- Ancient DNA Laboratory School of Veterinary and Life Sciences Murdoch University Murdoch WA 6150 Australia
- Centre for GeoGenetics Natural History Museum University of Copenhagen Øster Voldgade 5‐7 1350 Copenhagen K Denmark
| | - Timothy G. Vaughan
- Department of Computer Science University of Auckland Private Bag 92019 Auckland 1142 New Zealand
| | | | - Alexander Baynes
- Western Australian Museum Locked Bag 49 Welshpool DC WA 6986 Australia
| | - Dalal Haouchar
- Ancient DNA Laboratory School of Veterinary and Life Sciences Murdoch University Murdoch WA 6150 Australia
| | - Joe Dortch
- Archaeology M257 The University of Western Australia 35 Stirling Highway Nedlands WA 6009 Australia
| | - Michael Bunce
- Ancient DNA Laboratory School of Veterinary and Life Sciences Murdoch University Murdoch WA 6150 Australia
- Department of Environment and Agriculture Trace and Environmental DNA Laboratory Kent Street, Bentley Perth WA 6845 Australia
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Abstract
Clovis groups in Late Pleistocene North America occasionally hunted several now extinct large mammals. But whether their hunting drove 37 genera of animals to extinction has been disputed, largely for want of kill sites. Overkill proponents argue that there is more archaeological evidence than we ought to expect, that humans had the wherewithal to decimate what may have been millions of animals, and that the appearance of humans and the disappearance of the fauna is too striking to be a mere coincidence. Yet, there is less to these claims than meets the eye. Moreover, extinctions took place amid sweeping climatic and environmental changes as the Pleistocene came to an end. It has long been difficult to link those changes to mammalian extinctions, but the advent of ancient DNA, coupled with high-resolution paleoecological, radiocarbon, and archeological records, should help disentangle the relative role of changing climates and people in mammalian extinctions.
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Affiliation(s)
- David J. Meltzer
- Department of Anthropology, Southern Methodist University, Dallas, Texas 75275
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12
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Norén K, Statham MJ, Ågren EO, Isomursu M, Flagstad Ø, Eide NE, Berg TBG, Bech-Sanderhoff L, Sacks BN. Genetic footprints reveal geographic patterns of expansion in Fennoscandian red foxes. GLOBAL CHANGE BIOLOGY 2015; 21:3299-3312. [PMID: 26058388 DOI: 10.1111/gcb.12922] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Accepted: 01/29/2015] [Indexed: 06/04/2023]
Abstract
Population expansions of boreal species are among the most substantial ecological consequences of climate change, potentially transforming both structure and processes of northern ecosystems. Despite their importance, little is known about expansion dynamics of boreal species. Red foxes (Vulpes vulpes) are forecasted to become a keystone species in northern Europe, a process stemming from population expansions that began in the 19th century. To identify the relative roles of geographic and demographic factors and the sources of northern European red fox population expansion, we genotyped 21 microsatellite loci in modern and historical (1835-1941) Fennoscandian red foxes. Using Bayesian clustering and Bayesian inference of migration rates, we identified high connectivity and asymmetric migration rates across the region, consistent with source-sink dynamics, whereby more recently colonized sampling regions received immigrants from multiple sources. There were no clear clines in allele frequency or genetic diversity as would be expected from a unidirectional range expansion from south to north. Instead, migration inferences, demographic models and comparison to historical red fox genotypes suggested that the population expansion of the red fox is a consequence of dispersal from multiple sources, as well as in situ demographic growth. Together, these findings provide a rare glimpse into the anatomy of a boreal range expansion and enable informed predictions about future changes in boreal communities.
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Affiliation(s)
- Karin Norén
- Mammalian Ecology and Conservation Unit, Center for Veterinary Genetics, University of California Davis, Davis, CA, USA
- Department of Zoology, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Mark J Statham
- Mammalian Ecology and Conservation Unit, Center for Veterinary Genetics, University of California Davis, Davis, CA, USA
| | - Erik O Ågren
- National Veterinary Institute, Department of Pathology and Wildlife Diseases, SE-751 89, Uppsala, Sweden
| | - Marja Isomursu
- Finnish Food Safety Authority Evira, Production Animal and Wildlife Health Research Unit, Elektroniikkatie 5, FIN-90590, Oulu, Finland
| | - Øystein Flagstad
- Norwegian Institute for Nature Research, N-7485, Trondheim, Norway
| | - Nina E Eide
- Norwegian Institute for Nature Research, N-7485, Trondheim, Norway
| | | | - Lene Bech-Sanderhoff
- Naturama - Modern Natural History, Dronningemaen 30, DK-5700, Svendborg, Denmark
| | - Benjamin N Sacks
- Mammalian Ecology and Conservation Unit, Center for Veterinary Genetics, University of California Davis, Davis, CA, USA
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Abstract
The Bronze Age of Eurasia (around 3000-1000 BC) was a period of major cultural changes. However, there is debate about whether these changes resulted from the circulation of ideas or from human migrations, potentially also facilitating the spread of languages and certain phenotypic traits. We investigated this by using new, improved methods to sequence low-coverage genomes from 101 ancient humans from across Eurasia. We show that the Bronze Age was a highly dynamic period involving large-scale population migrations and replacements, responsible for shaping major parts of present-day demographic structure in both Europe and Asia. Our findings are consistent with the hypothesized spread of Indo-European languages during the Early Bronze Age. We also demonstrate that light skin pigmentation in Europeans was already present at high frequency in the Bronze Age, but not lactose tolerance, indicating a more recent onset of positive selection on lactose tolerance than previously thought.
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14
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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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15
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Allentoft ME, Heller R, Holdaway RN, Bunce M. Ancient DNA microsatellite analyses of the extinct New Zealand giant moa (Dinornis robustus) identify relatives within a single fossil site. Heredity (Edinb) 2015; 115:481-7. [PMID: 26039408 DOI: 10.1038/hdy.2015.48] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 04/27/2015] [Indexed: 12/26/2022] Open
Abstract
By analysing ancient DNA (aDNA) from 74 (14)C-dated individuals of the extinct South Island giant moa (Dinornis robustus) of New Zealand, we identified four dyads of closely related adult females. Although our total sample included bones from four fossil deposits located within a 10 km radius, these eight individuals had all been excavated from the same locality. Indications of kinship were based on high pairwise genetic relatedness (rXY) in six microsatellite markers genotyped from aDNA, coupled with overlapping radiocarbon ages. The observed rXY values in the four dyads exceeded a conservative cutoff value for potential relatives obtained from simulated data. In three of the four dyads, the kinship was further supported by observing shared and rare mitochondrial haplotypes. Simulations demonstrated that the proportion of observed dyads above the cutoff value was at least 20 times higher than expected in a randomly mating population with temporal sampling, also when introducing population structure in the simulations. We conclude that the results must reflect social structure in the moa population and we discuss the implications for future aDNA research.
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Affiliation(s)
- M E Allentoft
- Centre for GeoGenetics, Natural History Museum, University of Copenhagen, Copenhagen, Denmark
| | - R Heller
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - R N Holdaway
- Palaecol Research Ltd, Christchurch, New Zealand.,School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - M Bunce
- Trace and Environmental DNA (TrEnD) laboratory, Department of Environment and Agriculture, Curtin University, Perth, Western Australia, Australia
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16
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Palkopoulou E, Mallick S, Skoglund P, Enk J, Rohland N, Li H, Omrak A, Vartanyan S, Poinar H, Götherström A, Reich D, Dalén L. Complete genomes reveal signatures of demographic and genetic declines in the woolly mammoth. Curr Biol 2015; 25:1395-400. [PMID: 25913407 DOI: 10.1016/j.cub.2015.04.007] [Citation(s) in RCA: 159] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Revised: 03/12/2015] [Accepted: 04/03/2015] [Indexed: 11/24/2022]
Abstract
The processes leading up to species extinctions are typically characterized by prolonged declines in population size and geographic distribution, followed by a phase in which populations are very small and may be subject to intrinsic threats, including loss of genetic diversity and inbreeding. However, whether such genetic factors have had an impact on species prior to their extinction is unclear; examining this would require a detailed reconstruction of a species' demographic history as well as changes in genome-wide diversity leading up to its extinction. Here, we present high-quality complete genome sequences from two woolly mammoths (Mammuthus primigenius). The first mammoth was sequenced at 17.1-fold coverage and dates to ∼4,300 years before present, representing one of the last surviving individuals on Wrangel Island. The second mammoth, sequenced at 11.2-fold coverage, was obtained from an ∼44,800-year-old specimen from the Late Pleistocene population in northeastern Siberia. The demographic trajectories inferred from the two genomes are qualitatively similar and reveal a population bottleneck during the Middle or Early Pleistocene, and a more recent severe decline in the ancestors of the Wrangel mammoth at the end of the last glaciation. A comparison of the two genomes shows that the Wrangel mammoth has a 20% reduction in heterozygosity as well as a 28-fold increase in the fraction of the genome that comprises runs of homozygosity. We conclude that the population on Wrangel Island, which was the last surviving woolly mammoth population, was subject to reduced genetic diversity shortly before it became extinct.
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Affiliation(s)
- Eleftheria Palkopoulou
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, 10405 Stockholm, Sweden; Department of Zoology, Stockholm University, 10691 Stockholm, Sweden.
| | - Swapan Mallick
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Pontus Skoglund
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden
| | - Jacob Enk
- McMaster Ancient DNA Centre, Departments of Anthropology and Biology, and the Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L9, Canada; MYcroarray, 5692 Plymouth Road, Ann Arbor, MI 48105, USA
| | - Nadin Rohland
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Heng Li
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ayça Omrak
- Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden
| | - Sergey Vartanyan
- N.A. Shilo North-East Interdisciplinary Scientific Research Institute, Far East Branch, Russian Academy of Sciences (NEISRI FEB RAS), Magadan 685000, Russia
| | - Hendrik Poinar
- McMaster Ancient DNA Centre, Departments of Anthropology and Biology, and the Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L9, Canada
| | - Anders Götherström
- Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Love Dalén
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, 10405 Stockholm, Sweden.
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17
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Gargani M, Pariset L, Lenstra JA, De Minicis E, Valentini A. Microsatellite genotyping of medieval cattle from central Italy suggests an old origin of Chianina and Romagnola cattle. Front Genet 2015; 6:68. [PMID: 25788902 PMCID: PMC4349168 DOI: 10.3389/fgene.2015.00068] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Accepted: 02/10/2015] [Indexed: 12/02/2022] Open
Abstract
Analysis of DNA from archeological remains is a valuable tool to interpret the history of ancient animal populations. So far most studies of ancient DNA target mitochondrial DNA (mtDNA), which reveals maternal lineages, but only partially the relationships of current breeds and ancient populations. In this study we explore the feasibility of nuclear DNA analysis. DNA was extracted from 1000-years old cattle bone collected from Ferento, an archeological site in central Italy. Amplification of 15 microsatellite FAO-recommended markers with PCR products yielded genotypes for four markers. Expected heterozygosity was comparable with values of modern breeds, but observed heterozygosity was underestimated due to allelic loss. Genetic distances suggested a position intermediate between (1) Anatolian, Balkan, Sicilian and South-Italian cattle and (2) the Iberian, North-European and Central-European cattle, but also a clear relationship with two central-Italian breeds, Chianina and Romagnola. This suggests that these breeds are derived from medieval cattle living in the same area. Our results illustrate the potential of ancient DNA for reconstructing the history of local cattle husbandry.
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Affiliation(s)
- Maria Gargani
- Department for Innovation in Biological, Agro-food and Forest systems, University of Tuscia Viterbo, Italy
| | - Lorraine Pariset
- Department for Innovation in Biological, Agro-food and Forest systems, University of Tuscia Viterbo, Italy
| | | | - Elisabetta De Minicis
- Department of Sciences of Cultural Heritage (DISBEC), University of Tuscia Viterbo, Italy
| | | | - Alessio Valentini
- Department for Innovation in Biological, Agro-food and Forest systems, University of Tuscia Viterbo, Italy
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18
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Roca AL, Ishida Y, Brandt AL, Benjamin NR, Zhao K, Georgiadis NJ. Elephant Natural History: A Genomic Perspective. Annu Rev Anim Biosci 2015; 3:139-67. [DOI: 10.1146/annurev-animal-022114-110838] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Alfred L. Roca
- Department of Animal Sciences,
- Institute for Genomic Biology, and
| | | | | | - Neal R. Benjamin
- Department of Animal Sciences,
- College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801; , , , , ,
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19
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Sandom C, Faurby S, Sandel B, Svenning JC. Global late Quaternary megafauna extinctions linked to humans, not climate change. Proc Biol Sci 2015; 281:rspb.2013.3254. [PMID: 24898370 PMCID: PMC4071532 DOI: 10.1098/rspb.2013.3254] [Citation(s) in RCA: 143] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The late Quaternary megafauna extinction was a severe global-scale event. Two factors, climate change and modern humans, have received broad support as the primary drivers, but their absolute and relative importance remains controversial. To date, focus has been on the extinction chronology of individual or small groups of species, specific geographical regions or macroscale studies at very coarse geographical and taxonomic resolution, limiting the possibility of adequately testing the proposed hypotheses. We present, to our knowledge, the first global analysis of this extinction based on comprehensive country-level data on the geographical distribution of all large mammal species (more than or equal to 10 kg) that have gone globally or continentally extinct between the beginning of the Last Interglacial at 132 000 years BP and the late Holocene 1000 years BP, testing the relative roles played by glacial–interglacial climate change and humans. We show that the severity of extinction is strongly tied to hominin palaeobiogeography, with at most a weak, Eurasia-specific link to climate change. This first species-level macroscale analysis at relatively high geographical resolution provides strong support for modern humans as the primary driver of the worldwide megafauna losses during the late Quaternary.
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Affiliation(s)
- Christopher Sandom
- Ecoinformatics and Biodiversity, Department of Bioscience, Aarhus University, Ny Munkegade 114, Aarhus C 8000, Denmark
| | - Søren Faurby
- Ecoinformatics and Biodiversity, Department of Bioscience, Aarhus University, Ny Munkegade 114, Aarhus C 8000, Denmark
| | - Brody Sandel
- Ecoinformatics and Biodiversity, Department of Bioscience, Aarhus University, Ny Munkegade 114, Aarhus C 8000, Denmark
| | - Jens-Christian Svenning
- Ecoinformatics and Biodiversity, Department of Bioscience, Aarhus University, Ny Munkegade 114, Aarhus C 8000, Denmark
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20
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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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21
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Tison JL, Blennow V, Palkopoulou E, Gustafsson P, Roos A, Dalén L. Population structure and recent temporal changes in genetic variation in Eurasian otters from Sweden. CONSERV GENET 2014. [DOI: 10.1007/s10592-014-0664-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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22
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Skoglund P, Sjödin P, Skoglund T, Lascoux M, Jakobsson M. Investigating population history using temporal genetic differentiation. Mol Biol Evol 2014; 31:2516-27. [PMID: 24939468 PMCID: PMC4137715 DOI: 10.1093/molbev/msu192] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The rapid advance of sequencing technology, coupled with improvements in molecular methods for obtaining genetic data from ancient sources, holds the promise of producing a wealth of genomic data from time-separated individuals. However, the population-genetic properties of time-structured samples have not been extensively explored. Here, we consider the implications of temporal sampling for analyses of genetic differentiation and use a temporal coalescent framework to show that complex historical events such as size reductions, population replacements, and transient genetic barriers between populations leave a footprint of genetic differentiation that can be traced through history using temporal samples. Our results emphasize explicit consideration of the temporal structure when making inferences and indicate that genomic data from ancient individuals will greatly increase our ability to reconstruct population history.
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Affiliation(s)
- Pontus Skoglund
- Department of Evolutionary Biology, Uppsala University, Uppsala, Sweden
| | - Per Sjödin
- Department of Evolutionary Biology, Uppsala University, Uppsala, Sweden
| | - Tobias Skoglund
- Department of Evolutionary Biology, Uppsala University, Uppsala, SwedenDepartment of Information Technology, Uppsala University, Uppsala, Sweden
| | - Martin Lascoux
- Department of Ecology and Genetics, Program in Plant Ecology and Evolution, Uppsala University, Uppsala, SwedenScience for Life Laboratory, Uppsala, Sweden
| | - Mattias Jakobsson
- Department of Evolutionary Biology, Uppsala University, Uppsala, SwedenScience for Life Laboratory, Uppsala, Sweden
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23
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Sandoval-Castellanos E, Palkopoulou E, Dalén L. Back to BaySICS: a user-friendly program for Bayesian Statistical Inference from Coalescent Simulations. PLoS One 2014; 9:e98011. [PMID: 24865457 PMCID: PMC4035278 DOI: 10.1371/journal.pone.0098011] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Accepted: 04/28/2014] [Indexed: 12/02/2022] Open
Abstract
Inference of population demographic history has vastly improved in recent years due to a number of technological and theoretical advances including the use of ancient DNA. Approximate Bayesian computation (ABC) stands among the most promising methods due to its simple theoretical fundament and exceptional flexibility. However, limited availability of user-friendly programs that perform ABC analysis renders it difficult to implement, and hence programming skills are frequently required. In addition, there is limited availability of programs able to deal with heterochronous data. Here we present the software BaySICS: Bayesian Statistical Inference of Coalescent Simulations. BaySICS provides an integrated and user-friendly platform that performs ABC analyses by means of coalescent simulations from DNA sequence data. It estimates historical demographic population parameters and performs hypothesis testing by means of Bayes factors obtained from model comparisons. Although providing specific features that improve inference from datasets with heterochronous data, BaySICS also has several capabilities making it a suitable tool for analysing contemporary genetic datasets. Those capabilities include joint analysis of independent tables, a graphical interface and the implementation of Markov-chain Monte Carlo without likelihoods.
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Affiliation(s)
- Edson Sandoval-Castellanos
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden; Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Eleftheria Palkopoulou
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden; Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Love Dalén
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
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24
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Reumer JWF, Ten Broek CMA, Galis F. Extraordinary incidence of cervical ribs indicates vulnerable condition in Late Pleistocene mammoths. PeerJ 2014; 2:e318. [PMID: 24711969 PMCID: PMC3970796 DOI: 10.7717/peerj.318] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Accepted: 03/03/2014] [Indexed: 11/26/2022] Open
Abstract
The number of cervical vertebrae in mammals is highly conserved at seven. We have shown that changes of this number are selected against due to a coupling with major congenital abnormalities (pleiotropic effects). Here we show that the incidence of abnormal cervical vertebral numbers in Late Pleistocene mammoths from the North Sea is high (33.3%) and approximately 10 times higher than that of extant elephants (3.6%). Abnormal numbers were due to the presence of large cervical ribs on the seventh vertebra, which we deduced from the presence of rib articulation facets on sixth (posterior side) and seventh (anterior side) cervical vertebrae. The incidence of abnormal cervical vertebral numbers in mammoths appears to be much higher than in other mammalian species, apart from exceptional sloths, manatees and dugongs and indicates a vulnerable condition. We argue that the increased incidence of cervical ribs in mammoths is probably caused by inbreeding and adverse conditions that impact early pregnancies in declining populations close to extinction in the Late Pleistocene.
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Affiliation(s)
- Jelle W F Reumer
- Natural History Museum , Rotterdam , The Netherlands ; Faculty of Geosciences, Utrecht University , Utrecht , The Netherlands
| | - Clara M A Ten Broek
- Naturalis Biodiversity Center, Terrestrial Zoology/Geology , Leiden , The Netherlands ; University Antwerp, Evolutionary Ecology Group , Antwerp , Belgium
| | - Frietson Galis
- Naturalis Biodiversity Center, Terrestrial Zoology/Geology , Leiden , The Netherlands
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25
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Gold DA, Robinson J, Farrell AB, Harris JM, Thalmann O, Jacobs DK. Attempted DNA extraction from a Rancho La Brea Columbian mammoth (Mammuthus columbi): prospects for ancient DNA from asphalt deposits. Ecol Evol 2014; 4:329-36. [PMID: 24634719 PMCID: PMC3936381 DOI: 10.1002/ece3.928] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Accepted: 12/01/2013] [Indexed: 11/30/2022] Open
Abstract
Fossil-bearing asphalt deposits are an understudied and potentially significant source of ancient DNA. Previous attempts to extract DNA from skeletons preserved at the Rancho La Brea tar pits in Los Angeles, California, have proven unsuccessful, but it is unclear whether this is due to a lack of endogenous DNA, or if the problem is caused by asphalt-mediated inhibition. In an attempt to test these hypotheses, a recently recovered Columbian mammoth (Mammuthus columbi) skeleton with an unusual pattern of asphalt impregnation was studied. Ultimately, none of the bone samples tested successfully amplified M. columbi DNA. Our work suggests that reagents typically used to remove asphalt from ancient samples also inhibit DNA extraction. Ultimately, we conclude that the probability of recovering ancient DNA from fossils in asphalt deposits is strongly (perhaps fatally) hindered by the organic compounds that permeate the bones and that at the Rancho La Brea tar pits, environmental conditions might not have been ideal for the general preservation of genetic material.
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Affiliation(s)
- David A Gold
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, California 90095
| | - Jacqueline Robinson
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, California 90095
| | - Aisling B Farrell
- The George C. Page Museum of La Brea Discoveries 5801 Wilshire Boulevard, Los Angeles, California 90036
| | - John M Harris
- The George C. Page Museum of La Brea Discoveries 5801 Wilshire Boulevard, Los Angeles, California 90036
| | - Olaf Thalmann
- Department of Biology, Division of Genetics and Physiology, University of Turku Itäinen Pitkäkatu 4, Turku 20014, Finland
| | - David K Jacobs
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, California 90095
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26
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Extinct New Zealand megafauna were not in decline before human colonization. Proc Natl Acad Sci U S A 2014; 111:4922-7. [PMID: 24639531 DOI: 10.1073/pnas.1314972111] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The extinction of New Zealand's moa (Aves: Dinornithiformes) followed the arrival of humans in the late 13th century and was the final event of the prehistoric Late Quaternary megafauna extinctions. Determining the state of the moa populations in the pre-extinction period is fundamental to understanding the causes of the event. We sampled 281 moa individuals and combined radiocarbon dating with ancient DNA analyses to help resolve the extinction debate and gain insights into moa biology. The samples, which were predominantly from the last 4,000 years preceding the extinction, represent four sympatric moa species excavated from five adjacent fossil deposits. We characterized the moa assemblage using mitochondrial DNA and nuclear microsatellite markers developed specifically for moa. Although genetic diversity differed significantly among the four species, we found that the millennia preceding the extinction were characterized by a remarkable degree of genetic stability in all species, with no loss of heterozygosity and no shifts in allele frequencies over time. The extinction event itself was too rapid to be manifested in the moa gene pools. Contradicting previous claims of a decline in moa before Polynesian settlement in New Zealand, our findings indicate that the populations were large and stable before suddenly disappearing. This interpretation is supported by approximate Bayesian computation analyses. Our analyses consolidate the disappearance of moa as the most rapid, human-facilitated megafauna extinction documented to date.
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27
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Sjödin P, Skoglund P, Jakobsson M. Assessing the maximum contribution from ancient populations. Mol Biol Evol 2014; 31:1248-60. [PMID: 24497031 DOI: 10.1093/molbev/msu059] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Ancestral relationships between populations separated by time represent an often neglected dimension in population genetics, a field which historically has focused on analysis of spatially distributed samples from the same point in time. Models are usually straightforward when two time-separated populations are assumed to be completely isolated from all other populations. However, this is usually an unrealistically stringent assumption when there is gene flow with other populations. Here, we investigate continuity in the presence of gene flow from unknown populations. This setup allows a more nuanced treatment of questions regarding population continuity in terms of "level of contribution" from a particular ancient population to a more recent population. We propose a statistical framework which makes use of a biallelic marker sampled at two different points in time to assess population contribution, and present two different interpretations of the concept. We apply the approach to published data from a prehistoric human population in Scandinavia (Malmström H, Gilbert MTP, Thomas MG, Brandström M, Storå J, Molnar P, Andersen PK, Bendixen C, Holmlund G, Götherström A, et al. 2009. Ancient DNA reveals lack of continuity between Neolithic hunter-gatherers and contemporary Scandinavians. Curr Biol. 19:1758-1762) and Pleistocene woolly mammoth (Barnes I, Shapiro B, Lister A, Kuznetsova T, Sher A, Guthrie D, Thomas MG. 2007. Genetic structure and extinction of the woolly mammoth, Mammuthus primigenius. Curr Biol. 17:1072-1075; Debruyne R, Chu G, King CE, Bos K, Kuch M, Schwarz C, Szpak P, Gröcke DR, Matheus P, Zazula G, et al. 2008. Out of America: ancient DNA evidence for a new world origin of late quaternary woolly mammoths. Curr Biol. 18:1320-1326).
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Affiliation(s)
- Per Sjödin
- Department of Evolutionary Biology, Uppsala University, Norbyvägen, Sweden
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28
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Palkopoulou E, Dalén L, Lister AM, Vartanyan S, Sablin M, Sher A, Edmark VN, Brandström MD, Germonpré M, Barnes I, Thomas JA. Holarctic genetic structure and range dynamics in the woolly mammoth. Proc Biol Sci 2013; 280:20131910. [PMID: 24026825 PMCID: PMC3779339 DOI: 10.1098/rspb.2013.1910] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
Ancient DNA analyses have provided enhanced resolution of population histories in many Pleistocene taxa. However, most studies are spatially restricted, making inference of species-level biogeographic histories difficult. Here, we analyse mitochondrial DNA (mtDNA) variation in the woolly mammoth from across its Holarctic range to reconstruct its history over the last 200 thousand years (kyr). We identify a previously undocumented major mtDNA lineage in Europe, which was replaced by another major mtDNA lineage 32–34 kyr before present (BP). Coalescent simulations provide support for demographic expansions at approximately 121 kyr BP, suggesting that the previous interglacial was an important driver for demography and intraspecific genetic divergence. Furthermore, our results suggest an expansion into Eurasia from America around 66 kyr BP, coinciding with the first exposure of the Bering Land Bridge during the Late Pleistocene. Bayesian inference indicates Late Pleistocene demographic stability until 20–15 kyr BP, when a severe population size decline occurred.
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Affiliation(s)
- Eleftheria Palkopoulou
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, , 10405 Stockholm, Sweden, Department of Zoology, Stockholm University, , Stockholm 10691, Sweden, Department of Earth Sciences, Natural History Museum, , London SW7 5BD, UK, Northeast Interdisciplinary Research Institute, Far East Branch, Russian Academy of Sciences, , Magadan 685000, Russia, Zoological Institute of Russian Academy of Sciences, Saint-Petersburg 199034, Russia, Institute of Ecology and Evolution, Russian Academy of Sciences, , Moscow 119071, Russia, Department of Forest Mycology and Pathology, Swedish University of Agricultural Sciences, , 10691 Uppsala, Sweden, Operational Direction 'Earth and History of Life', Royal Belgian Institute of Natural Sciences, , Vautierstraat 29, 1000 Brussels, Belgium, School of Biological Sciences, Royal Holloway University of London, , Egham, Surrey TW20 0EX, UK
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29
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Rieseberg L, Vines T, Kane N. Editorial 2013. Mol Ecol 2012; 22:1-14. [PMID: 23252575 DOI: 10.1111/mec.12145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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30
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Abstract
Woolly mammoths, Mammuthus primigenius, are arguably the most iconic of the extinct Pleistocene megafauna, and an abundance of large permafrost-embedded bone and ivory material (Fig. 1) means they were also among the first to yield credible DNA sequences (Hagelberg et al. 1994; Hoss et al. 1994). Despite mammoth remains being numerous throughout northern Eurasia and North America, both the earliest and most recent fossils are found in northeast Siberia, with the last known population being confined to Wrangel Island in the Arctic Ocean from around 10,000 years ago until their extinction around 4,000 years ago. The extent to which these Holocene mammoths were descended from the Pleistocene populations of Wrangel Island and the demographic nature of their terminal decline have, until now, remained something of a mystery. In this issue of Molecular Ecology, Nyström et al. (2012) report the first use of autosomal variation to track the decline of the last mammoths and, in doing so, take a significant step towards resolving these questions. The authors genotyped four microsatellite loci in 59 Pleistocene and Holocene mammoths from Wrangel Island and Chukotka in mainland northeastern Siberia and showed that while the Pleistocene-to-Holocene transition is associated with a significant reduction in genetic diversity, subsequent levels of variation remain constant until extinction. Such a pattern is somewhat surprising as it indicates that while the last mammoths were confined to only a few Arctic islands, their final extinction on Wrangel Island was not a gradual process resulting from loss of genetic diversity/inbreeding. Instead, it seems they maintained a viable effective population size of around 500 until near their presumably rapid extinction. While the ultimate agent of mammoth extinction remains unknown, the work of Nyström et al. (2012). suggests that we should be looking for something sudden, like a rapid change in climate/ecology or perhaps the arrival of humans.
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Affiliation(s)
- M G Thomas
- Research Department of Genetics, Evolution and Environment, University College London, Gower street, London WC1E 6BT, UK.
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