1
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Lobo D, López-Bao JV, Godinho R. The population bottleneck of the Iberian wolf impacted genetic diversity but not admixture with domestic dogs: A temporal genomic approach. Mol Ecol 2023; 32:5986-5999. [PMID: 37855673 DOI: 10.1111/mec.17171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 09/25/2023] [Accepted: 10/06/2023] [Indexed: 10/20/2023]
Abstract
After decades of intense persecution, the Iberian wolf subspecies faced a severe bottleneck in the 1970s that considerably reduced its range and population size, nearly leading to its extinction in central and southern Iberian Peninsula. Such population decline could have impacted the genetic diversity of Iberian wolves through different processes, namely genetic drift and dynamics of hybridization with domestic dogs. By contrasting the genomes of 68 contemporary with 54 historical samples spanning the periods before and immediately after the 1970s bottleneck, we found evidence of its impact on genetic diversity and dynamics of wolf-dog hybridization. Our genome-wide assessment revealed that wolves and dogs form two well-differentiated genetic groups in Iberia and that hybridization rates did not increase during the bottleneck. However, an increased number of hybrid individuals was found over time during the population re-expansion, particularly at the edge of the wolf range. We estimated a low percentage of dog ancestry (~1.4%) in historical samples, suggesting that dog introgression was not a key driver for wolf extinction in central and southern Iberia. Our findings also unveil a significant decline in genetic diversity in contemporary samples, with the highest proportion of homozygous segments in the genome being recently inherited. Overall, our study provides unprecedented insight into the impact of a sharp decline on the Iberian wolf genome and refines our understanding of the ecological and evolutionary drivers of wolf-dog hybridization in the wild.
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Affiliation(s)
- Diana Lobo
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
- BIOPOLIS, Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
| | - José Vicente López-Bao
- Biodiversity Research Institute (CSIC - Oviedo University - Principality of Asturias) Oviedo University, Mieres, Spain
| | - Raquel Godinho
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
- BIOPOLIS, Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
- Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, Johannesburg, South Africa
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2
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Anderson LA. Biomolecular histology as a novel proxy for ancient DNA and protein sequence preservation. Ecol Evol 2022; 12:e9518. [PMCID: PMC9743065 DOI: 10.1002/ece3.9518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 10/03/2022] [Accepted: 10/17/2022] [Indexed: 12/14/2022] Open
Abstract
Researchers' ability to accurately screen fossil and subfossil specimens for preservation of DNA and protein sequences remains limited. Thermal exposure and geologic age are usable proxies for sequence preservation on a broad scale but are of nominal use for specimens of similar depositional environments. Cell and tissue biomolecular histology is thus proposed as a novel proxy for determining sequence preservation potential of ancient specimens with improved accuracy. Biomolecular histology as a proxy is hypothesized to elucidate why fossils/subfossils of some depositional environments preserve sequences while others do not and to facilitate selection of ancient specimens for use in molecular studies.
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Affiliation(s)
- Landon A. Anderson
- Department of BiologyNorth Carolina State UniversityRaleighNorth CarolinaUSA
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3
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A decade of genetic monitoring reveals increased inbreeding for the Endangered western leopard toad, Sclerophrys pantherina. CONSERV GENET 2022. [DOI: 10.1007/s10592-022-01463-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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4
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Abstract
Archaeological and paleontological records offer tremendous yet often untapped potential for examining long-term biodiversity trends and the impact of climate change and human activity on ecosystems. Yet, zooarchaeological and fossil remains suffer various limitations, including that they are often highly fragmented and morphologically unidentifiable, preventing them from being optimally leveraged for addressing fundamental research questions in archaeology, paleontology, and conservation paleobiology. Here, we explore the potential of palaeoproteomics—the study of ancient proteins—to serve as a critical tool for creating richer, more informative datasets about biodiversity change that can be leveraged to generate more realistic, constructive, and effective conservation and restoration strategies into the future.
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5
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Salado I, Fernández-Gil A, Vilà C, Leonard JA. Automated genotyping of microsatellite loci from feces with high throughput sequences. PLoS One 2021; 16:e0258906. [PMID: 34695152 PMCID: PMC8544849 DOI: 10.1371/journal.pone.0258906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 10/07/2021] [Indexed: 11/18/2022] Open
Abstract
Ecological and conservation genetic studies often use noninvasive sampling, especially with elusive or endangered species. Because microsatellites are generally short in length, they can be amplified from low quality samples such as feces. Microsatellites are highly polymorphic so few markers are enough for reliable individual identification, kinship determination, or population characterization. However, the genotyping process from feces is expensive and time consuming. Given next-generation sequencing (NGS) and recent software developments, automated microsatellite genotyping from NGS data may now be possible. These software packages infer the genotypes directly from sequence reads, increasing throughput. Here we evaluate the performance of four software packages to genotype microsatellite loci from Iberian wolf (Canis lupus) feces using NGS. We initially combined 46 markers in a single multiplex reaction for the first time, of which 19 were included in the final analyses. Megasat was the software that provided genotypes with fewer errors. Coverage over 100X provided little additional information, but a relatively high number of PCR replicates were necessary to obtain a high quality genotype from highly unoptimized, multiplexed reactions (10 replicates for 18 of the 19 loci analyzed here). This could be reduced through optimization. The use of new bioinformatic tools and next-generation sequencing data to genotype these highly informative markers may increase throughput at a reasonable cost and with a smaller amount of laboratory work. Thus, high throughput sequencing approaches could facilitate the use of microsatellites with fecal DNA to address ecological and conservation questions.
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Affiliation(s)
- Isabel Salado
- Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana (EBD-CSIC), Seville, Spain
- * E-mail: (JAL); (IS)
| | - Alberto Fernández-Gil
- Department of Conservation Biology, Estación Biológica de Doñana (EBD-CSIC), Seville, Spain
| | - Carles Vilà
- Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana (EBD-CSIC), Seville, Spain
| | - Jennifer A. Leonard
- Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana (EBD-CSIC), Seville, Spain
- * E-mail: (JAL); (IS)
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6
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Andrews AJ, Puncher GN, Bernal-Casasola D, Di Natale A, Massari F, Onar V, Toker NY, Hanke A, Pavey SA, Savojardo C, Martelli PL, Casadio R, Cilli E, Morales-Muñiz A, Mantovani B, Tinti F, Cariani A. Ancient DNA SNP-panel data suggests stability in bluefin tuna genetic diversity despite centuries of fluctuating catches in the eastern Atlantic and Mediterranean. Sci Rep 2021; 11:20744. [PMID: 34671077 PMCID: PMC8528830 DOI: 10.1038/s41598-021-99708-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 09/25/2021] [Indexed: 11/10/2022] Open
Abstract
Atlantic bluefin tuna (Thunnus thynnus; BFT) abundance was depleted in the late 20th and early 21st century due to overfishing. Historical catch records further indicate that the abundance of BFT in the Mediterranean has been fluctuating since at least the 16th century. Here we build upon previous work on ancient DNA of BFT in the Mediterranean by comparing contemporary (2009–2012) specimens with archival (1911–1926) and archaeological (2nd century BCE–15th century CE) specimens that represent population states prior to these two major periods of exploitation, respectively. We successfully genotyped and analysed 259 contemporary and 123 historical (91 archival and 32 archaeological) specimens at 92 SNP loci that were selected for their ability to differentiate contemporary populations or their association with core biological functions. We found no evidence of genetic bottlenecks, inbreeding or population restructuring between temporal sample groups that might explain what has driven catch fluctuations since the 16th century. We also detected a putative adaptive response, involving the cytoskeletal protein synemin which may be related to muscle stress. However, these results require further investigation with more extensive genome-wide data to rule out demographic changes due to overfishing, and other natural and anthropogenic factors, in addition to elucidating the adaptive drivers related to these.
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Affiliation(s)
- Adam J Andrews
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Ravenna, Italy. .,Department of Cultural Heritage, University of Bologna, Ravenna, Italy.
| | - Gregory N Puncher
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Ravenna, Italy. .,Department of Biological Sciences, Canadian Rivers Institute, University of New Brunswick, Saint John, NB, Canada.
| | - Darío Bernal-Casasola
- Department of History, Geography and Philosophy, Faculty of Philosophy and Letters, University of Cádiz, Cádiz, Spain
| | | | - Francesco Massari
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Ravenna, Italy
| | - Vedat Onar
- Osteoarcheology Practice and Research Centre and Faculty of Veterinary Medicine, Istanbul University-Cerrahpaşa, Avcılar, Istanbul, Turkey
| | - Nezir Yaşar Toker
- Osteoarcheology Practice and Research Centre and Faculty of Veterinary Medicine, Istanbul University-Cerrahpaşa, Avcılar, Istanbul, Turkey
| | - Alex Hanke
- St. Andrews Biological Station, Fisheries and Oceans Canada, St. Andrews, NB, Canada
| | - Scott A Pavey
- Department of Biological Sciences, Canadian Rivers Institute, University of New Brunswick, Saint John, NB, Canada
| | | | | | - Rita Casadio
- Biocomputing Group, University of Bologna, Bologna, Italy
| | - Elisabetta Cilli
- Department of Cultural Heritage, University of Bologna, Ravenna, Italy
| | | | - Barbara Mantovani
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Fausto Tinti
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Ravenna, Italy
| | - Alessia Cariani
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Ravenna, Italy
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7
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Ababaikeri B, Abduriyim S, Tohetahong Y, Mamat T, Ahmat A, Halik M. Whole-genome sequencing of Tarim red deer ( Cervus elaphus yarkandensis) reveals demographic history and adaptations to an arid-desert environment. Front Zool 2020; 17:31. [PMID: 33072165 PMCID: PMC7565370 DOI: 10.1186/s12983-020-00379-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 10/02/2020] [Indexed: 01/08/2023] Open
Abstract
Background The initiation of desert conditions in the Tarim Basin in China since the late Miocene has led to the significant genetic structuring of local organisms. Tarim Red Deer (Cervus elaphus yarkandensis, TRD) have adapted to the harsh environmental conditions in this basin, including high solar radiation and temperature, aridity, and poor nutritional conditions. However, the underlying genetic basis of this adaptation is poorly understood. Results We sequenced the whole genomes of 13 TRD individuals, conducted comparative genomic analyses, and estimated demographic fluctuation. The ∂a∂i model estimated that the TRD and Tule elk (Cervus canadensis nannodes) populations diverged approximately 0.98 Mya. Analyses revealed a substantial influence of the Earth’s climate on the effective population size of TRD, associated with glacial advances and retreat, and human activities likely underlie a recent serious decline in population. A marked bottleneck may have profoundly affected the genetic diversity of TRD populations. We detected a set of candidate genes, pathways, and GO categories related to oxidative stress, water reabsorption, immune regulation, energy metabolism, eye protection, heat stress, respiratory system adaptation, prevention of high blood pressure, and DNA damage and repair that may directly or indirectly be involved in the adaptation of TRD to an arid-desert environment. Conclusions Our analyses highlight the role of historical global climates in the population dynamics of TRD. In light of ongoing global warming and the increasing incidence of droughts, our study offers insights into the genomic adaptations of animals, especially TRD, to extreme arid-desert environments and provides a valuable resource for future research on conservation design and biological adaptations to environmental change.
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Affiliation(s)
- Buweihailiqiemu Ababaikeri
- College of Life Sciences and Technology, Xinjiang University, Urumqi, 830046 Xinjiang China.,College of Xinjiang Uyghur Medicine, Hoten, 848000 Xinjiang China
| | - Shamshidin Abduriyim
- College of Life Science, Shihezi University, Shihezi, 832003 Xinjiang China.,Department of Ecology, Hubei Key Laboratory of Cell Homeostasis, College of Life Science, Wuhan University, Wuhan, 430072 Hubei China
| | - Yilamujiang Tohetahong
- College of Life Sciences and Technology, Xinjiang University, Urumqi, 830046 Xinjiang China
| | - Tayerjan Mamat
- College of Life Sciences and Technology, Xinjiang University, Urumqi, 830046 Xinjiang China
| | - Adil Ahmat
- College of Life Sciences and Technology, Xinjiang University, Urumqi, 830046 Xinjiang China
| | - Mahmut Halik
- College of Life Sciences and Technology, Xinjiang University, Urumqi, 830046 Xinjiang China
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8
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Vershinina AO, Kapp JD, Baryshnikov GF, Shapiro B. The case of an arctic wild ass highlights the utility of ancient DNA for validating problematic identifications in museum collections. Mol Ecol Resour 2020; 20:1182-1190. [DOI: 10.1111/1755-0998.13130] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 11/25/2019] [Accepted: 12/10/2019] [Indexed: 12/20/2022]
Affiliation(s)
- Alisa O. Vershinina
- Department of Ecology and Evolutionary Biology University of California Santa Cruz Santa Cruz CA USA
| | - Joshua D. Kapp
- Department of Ecology and Evolutionary Biology University of California Santa Cruz Santa Cruz CA USA
| | - Gennady F. Baryshnikov
- Laboratory of Theriology Zoological Institute of the Russian Academy of Sciences St. Petersburg Russia
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology University of California Santa Cruz Santa Cruz CA USA
- Howard Hughes Medical InstituteUniversity of California Santa Cruz Santa Cruz CA USA
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9
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Sugita N, Ebihara A, Hosoya T, Jinbo U, Kaneko S, Kurosawa T, Nakae M, Yukawa T. Non-destructive DNA extraction from herbarium specimens: a method particularly suitable for plants with small and fragile leaves. JOURNAL OF PLANT RESEARCH 2020; 133:133-141. [PMID: 31760570 DOI: 10.1007/s10265-019-01152-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 11/07/2019] [Indexed: 06/10/2023]
Abstract
Protocols for DNA extraction from plants generally involve physical and chemical destruction of tissues. Use of these conventional methods precludes preservation of morphological information from herbarium specimens, especially for small plants with few leaves, and reduces the voucher value of specimens. Here, we developed a new, non-destructive DNA extraction protocol (Protocol 1) that only needs a small piece of leaf (< 25 mm2) to obtain DNA suitable for DNA sequencing from fragile herbarium specimens. The protocol was very simple and rapid; an extraction buffer was placed on the leaf surface of an intact specimen for 30 min at room temperature (20 °C). The quality of extracted DNA was checked by PCR amplification of two standard plant DNA barcode regions, the maturase K gene (matK, ca. 850 bp) and the ribulose-1,5-bisphosphatecarboxylase/oxygenase gene (rbcL, ca. 550 bp), for 14 vascular plant species encompassing various taxonomic groups. The protocol retrieved sequences from 80.0% of specimens for matK and 46.2% of specimens for rbcL. Placing of the extraction buffer onto specimens did not cause any tears or deformation, but caused discoloration in some plants. To improve DNA yield for specimens incompatible with Protocol 1, we developed an alternative protocol for DNA extraction with minimally invasive destruction of specimens (Protocol 2). In this protocol, a cut leaf was immersed in the extraction buffer for 30 min and stored subsequently in a fragment pocket on the specimen sheet. This alternative method retrieved matK sequences from 80.0% of specimens and rbcL sequences from 92.8% of specimens. The combination of Protocols 1 and 2 enabled us to obtain matK sequences from 90.0% of specimens and rbcL sequences form 92.8% of specimens. The new protocols facilitate the use of museum specimens for use of DNA of museum specimens while still preserving morphological information.
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Affiliation(s)
- Norimasa Sugita
- Department of Botany, National Museum of Nature and Science, Tsukuba, Ibaraki, 305-0005, Japan.
| | - Atsushi Ebihara
- Department of Botany, National Museum of Nature and Science, Tsukuba, Ibaraki, 305-0005, Japan
| | - Tsuyoshi Hosoya
- Department of Botany, National Museum of Nature and Science, Tsukuba, Ibaraki, 305-0005, Japan
| | - Utsugi Jinbo
- Department of Zoology, National Museum of Nature and Science, Tsukuba, Ibaraki, 305-0005, Japan
| | - Shingo Kaneko
- Faculty of Symbiotic Systems Science, Fukushima University, Fukushima, Fukushima, 960-1296, Japan
| | - Takahide Kurosawa
- Faculty of Symbiotic Systems Science, Fukushima University, Fukushima, Fukushima, 960-1296, Japan
| | - Masanori Nakae
- Department of Zoology, National Museum of Nature and Science, Tsukuba, Ibaraki, 305-0005, Japan
| | - Tomohisa Yukawa
- Department of Botany, National Museum of Nature and Science, Tsukuba, Ibaraki, 305-0005, Japan
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10
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Verry AJF, Scarsbrook L, Scofield RP, Tennyson AJD, Weston KA, Robertson BC, Rawlence NJ. Who, Where, What, Wren? Using Ancient DNA to Examine the Veracity of Museum Specimen Data: A Case Study of the New Zealand Rock Wren (Xenicus gilviventris). Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00496] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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11
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Fenderson LE, Kovach AI, Llamas B. Spatiotemporal landscape genetics: Investigating ecology and evolution through space and time. Mol Ecol 2019; 29:218-246. [DOI: 10.1111/mec.15315] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 09/22/2019] [Accepted: 11/13/2019] [Indexed: 12/22/2022]
Affiliation(s)
- Lindsey E. Fenderson
- Australian Centre for Ancient DNA School of Biological Sciences Environment Institute University of Adelaide Adelaide South Australia Australia
- Department of Natural Resources and the Environment University of New Hampshire Durham NH USA
| | - Adrienne I. Kovach
- Department of Natural Resources and the Environment University of New Hampshire Durham NH USA
| | - Bastien Llamas
- Australian Centre for Ancient DNA School of Biological Sciences Environment Institute University of Adelaide Adelaide South Australia Australia
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12
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Miller MP, Vilstrup JT, Mullins TD, McDearman W, Walters JR, Haig SM. Changes in genetic diversity and differentiation in Red-cockaded woodpeckers ( Dryobates borealis) over the past century. Ecol Evol 2019; 9:5420-5432. [PMID: 31110690 PMCID: PMC6509371 DOI: 10.1002/ece3.5135] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 01/31/2019] [Accepted: 02/08/2019] [Indexed: 11/11/2022] Open
Abstract
Red-cockaded woodpeckers (RCW; Dryobates borealis) declined after human activities reduced their fire-maintained pine ecosystem to <3% of its historical range in the southeastern United States and degraded remaining habitat. An estimated 1.6 million RCW cooperative breeding groups declined to about 3,500 groups with no more than 10,000 birds by 1978. Management has increased RCW population abundances since they were at their lowest in the 1990s. However, no range-wide study has been undertaken since then to investigate the impacts of this massive bottleneck or infer the effects of conservation management and recent demographic recoveries. We used mitochondrial DNA sequences (mtDNA) and nine nuclear microsatellite loci to determine if range-wide demographic declines resulted in changes to genetic structure and diversity in RCW by comparing samples collected before 1970 (mtDNA data only), between 1992 and 1995 (mtDNA and microsatellites), and between 2010 and 2014 (mtDNA and microsatellites). We show that genetic diversity has been lost as detected by a reduction in the number of mitochondrial haplotypes. This reduction was apparent in comparisons of pre-1970 mtDNA data with data from the 1992-1995 and 2010-2014 time points, with no change between the latter two time points in mtDNA and microsatellite analyses. The mtDNA data also revealed increases in range-wide genetic differentiation, with a genetically panmictic population present throughout the southeastern United States in the pre-1970s data and subsequent development of genetic structure that has remained unchanged since the 1990s. Genetic structure was also uncovered with the microsatellite data, which like the mtDNA data showed little change between the 1992-1995 and 2010-2014 data sets. Temporal haplotype networks revealed a consistent, star-like phylogeny, suggesting that despite the overall loss of haplotypes, no phylogenetically distinct mtDNA lineages were lost when the population declined. Our results may suggest that management during the last two decades has prevented additional losses of genetic diversity.
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Affiliation(s)
- Mark P. Miller
- U.S. Geological Survey, Forest and Rangeland Ecosystem Science CenterCorvallisOregon
| | - Julia T. Vilstrup
- U.S. Geological Survey, Forest and Rangeland Ecosystem Science CenterCorvallisOregon
- Department of Fisheries and WildlifeOregon State UniversityCorvallisOregon
- Present address:
PublonsWellingtonNew Zealand
| | - Thomas D. Mullins
- U.S. Geological Survey, Forest and Rangeland Ecosystem Science CenterCorvallisOregon
| | - Will McDearman
- Division of Restoration and RecoveryU.S. Fish and Wildlife ServiceJacksonMississippi
| | | | - Susan M. Haig
- U.S. Geological Survey, Forest and Rangeland Ecosystem Science CenterCorvallisOregon
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13
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The Promise of Paleogenomics Beyond Our Own Species. Trends Genet 2019; 35:319-329. [PMID: 30954285 DOI: 10.1016/j.tig.2019.02.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 02/18/2019] [Accepted: 02/25/2019] [Indexed: 02/06/2023]
Abstract
Paleogenomics, also known as genome-wide ancient DNA analysis, is transforming our understanding of the human past, but has been much less intensively used to understand the history of other species. However, paleogenomic studies of non-human animals and plants have the potential to address an equally rich range of evolutionary, paleoecological, paleoenvironmental, and archaeological research questions. Three recent case studies of cave bears, horses, and maize provide examples of the ways that paleogenomics can be used to examine potential causes of extinctions and dynamic processes of domestication. Much more research in these areas is needed, and we conclude by highlighting key future directions.
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14
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Dures SG, Carbone C, Loveridge AJ, Maude G, Midlane N, Aschenborn O, Gottelli D. A century of decline: Loss of genetic diversity in a southern African lion‐conservation stronghold. DIVERS DISTRIB 2019. [DOI: 10.1111/ddi.12905] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Affiliation(s)
- Simon G. Dures
- Institute of Zoology Zoological Society of London London UK
- Department of Life Sciences Imperial College London Ascot UK
| | - Chris Carbone
- Institute of Zoology Zoological Society of London London UK
| | - Andrew J. Loveridge
- Department of Zoology, Wildlife Conservation Research Unit, Recanati‐Kaplan Centre University of Oxford Tubney UK
| | - Glyn Maude
- Kalahari Research and Conservation Maun Botswana
| | | | | | - Dada Gottelli
- Institute of Zoology Zoological Society of London London UK
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15
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Dufresnes C, Miquel C, Remollino N, Biollaz F, Salamin N, Taberlet P, Fumagalli L. Howling from the past: historical phylogeography and diversity losses in European grey wolves. Proc Biol Sci 2018; 285:rspb.2018.1148. [PMID: 30068681 DOI: 10.1098/rspb.2018.1148] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 07/06/2018] [Indexed: 12/18/2022] Open
Abstract
Genetic bottlenecks resulting from human-induced population declines make alarming symbols for the irreversible loss of our natural legacy worldwide. The grey wolf (Canis lupus) is an iconic example of extreme declines driven by anthropogenic factors. Here, we assessed the genetic signatures of 150 years of wolf persecution throughout the Western Palaearctic by high-throughput mitochondrial DNA sequencing of historical specimens in an unprecedented spatio-temporal framework. Despite Late Pleistocene bottlenecks, we show that historical genetic variation had remained high throughout Europe until the last several hundred years. In Western Europe, where wolves nearly got fully exterminated, diversity dramatically collapsed at the turn of the twentieth century and recolonization from few homogeneous relict populations induced drastic shifts of genetic composition. By contrast, little genetic displacement and steady levels of diversity were maintained in Eastern European regions, where human persecution had lesser effects on wolf demography. By comparing prehistoric, historic and modern patterns of genetic diversity, our study hence traces the timeframe and the active human role in the decline of the grey wolf, an emblematic yet controversial animal which symbolizes the complex relationship between human societies and nature conservation.
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Affiliation(s)
- Christophe Dufresnes
- Laboratory for Conservation Biology, Department of Ecology and Evolution University of Lausanne, Biophore Building, CH-1015 Lausanne, Switzerland.,Department of Animal and Plant Sciences, University of Sheffield, Alfred Denny Building, Western Bank, Sheffield S10 2TN, UK
| | - Christian Miquel
- Laboratoire d'Écologie Alpine (LECA), UMR5553, BP53, 38041 Grenoble, Cedex 9, France
| | - Nadège Remollino
- Laboratory for Conservation Biology, Department of Ecology and Evolution University of Lausanne, Biophore Building, CH-1015 Lausanne, Switzerland
| | - François Biollaz
- Laboratory for Conservation Biology, Department of Ecology and Evolution University of Lausanne, Biophore Building, CH-1015 Lausanne, Switzerland.,Route Pra de Louetse 32, 1968 Mase, Switzerland
| | - Nicolas Salamin
- Department of Ecology and Evolution University of Lausanne, Biophore Building, CH-1015 Lausanne, Switzerland.,Department of Computational Biology University of Lausanne, Biophore Building, CH-1015 Lausanne, Switzerland
| | - Pierre Taberlet
- Laboratoire d'Écologie Alpine (LECA), UMR5553, BP53, 38041 Grenoble, Cedex 9, France
| | - Luca Fumagalli
- Laboratory for Conservation Biology, Department of Ecology and Evolution University of Lausanne, Biophore Building, CH-1015 Lausanne, Switzerland
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16
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Casas-Marce M, Marmesat E, Soriano L, Martínez-Cruz B, Lucena-Perez M, Nocete F, Rodríguez-Hidalgo A, Canals A, Nadal J, Detry C, Bernáldez-Sánchez E, Fernández-Rodríguez C, Pérez-Ripoll M, Stiller M, Hofreiter M, Rodríguez A, Revilla E, Delibes M, Godoy JA. Spatiotemporal Dynamics of Genetic Variation in the Iberian Lynx along Its Path to Extinction Reconstructed with Ancient DNA. Mol Biol Evol 2018; 34:2893-2907. [PMID: 28962023 PMCID: PMC5850336 DOI: 10.1093/molbev/msx222] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
There is the tendency to assume that endangered species have been both genetically and demographically healthier in the past, so that any genetic erosion observed today was caused by their recent decline. The Iberian lynx (Lynx pardinus) suffered a dramatic and continuous decline during the 20th century, and now shows extremely low genome- and species-wide genetic diversity among other signs of genomic erosion. We analyze ancient (N = 10), historical (N = 245), and contemporary (N = 172) samples with microsatellite and mitogenome data to reconstruct the species' demography and investigate patterns of genetic variation across space and time. Iberian lynx populations transitioned from low but significantly higher genetic diversity than today and shallow geographical differentiation millennia ago, through a structured metapopulation with varying levels of diversity during the last centuries, to two extremely genetically depauperate and differentiated remnant populations by 2002. The historical subpopulations show varying extents of genetic drift in relation to their recent size and time in isolation, but these do not predict whether the populations persisted or went finally extinct. In conclusion, current genetic patterns were mainly shaped by genetic drift, supporting the current admixture of the two genetic pools and calling for a comprehensive genetic management of the ongoing conservation program. This study illustrates how a retrospective analysis of demographic and genetic patterns of endangered species can shed light onto their evolutionary history and this, in turn, can inform conservation actions.
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Affiliation(s)
- Mireia Casas-Marce
- Department of Integrative Ecology, Doñana Biological Station (EBD) Spanish National Research Council (CSIC), Sevilla, Spain
| | - Elena Marmesat
- Department of Integrative Ecology, Doñana Biological Station (EBD) Spanish National Research Council (CSIC), Sevilla, Spain
| | - Laura Soriano
- Department of Integrative Ecology, Doñana Biological Station (EBD) Spanish National Research Council (CSIC), Sevilla, Spain
| | - Begoña Martínez-Cruz
- Department of Integrative Ecology, Doñana Biological Station (EBD) Spanish National Research Council (CSIC), Sevilla, Spain
| | - Maria Lucena-Perez
- Department of Integrative Ecology, Doñana Biological Station (EBD) Spanish National Research Council (CSIC), Sevilla, Spain
| | - Francisco Nocete
- Grupo de Investigación MIDAS, Departamento Historia I (Prehistoria), Universidad de Huelva, Huelva, Spain
| | - Antonio Rodríguez-Hidalgo
- Department of Prehistory, Complutense University, Madrid, Spain.,IDEA (Instituto de Evolución en África), Madrid, Spain.,Equipo de Investigación Primeros Pobladores de Extremadura, Casa de la Cultura Rodríguez Moñino, Cáceres, Spain
| | - Antoni Canals
- Equipo de Investigación Primeros Pobladores de Extremadura, Casa de la Cultura Rodríguez Moñino, Cáceres, Spain.,IPHES, Institut Català de Paleoecologia Humana i Evolució Social (Catalan Institute of Human Paleoecology and Social Evolution), Tarragona, Spain.,Area de Prehistoria (Department of Prehistory), Universitat Rovira i Virgili (URV), Tarragona, Spain
| | - Jordi Nadal
- SERP, Departament de Prehistòria, Història Antiga i Arqueologia, Universitat de Barcelona, Barcelona, Spain
| | - Cleia Detry
- UNIARQ - Centro de Arqueologia da Faculdade de Letras da Universidade de Lisboa, Alameda da Universidade, Lisboa, Portugal
| | - Eloísa Bernáldez-Sánchez
- Laboratorio de Paleobiología, Instituto Andaluz del Patrimonio Histórico, Consejería de Cultura de la Junta de Andalucía, Seville, Spain
| | | | - Manuel Pérez-Ripoll
- Prehistory and Archaeology Department, University of Valencia, Valencia, Spain
| | - Mathias Stiller
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA
| | - Michael Hofreiter
- Evolutionary Adaptive Genomics, Institute of Biochemistry and Biology, Faculty of Mathematics and Life Sciences, University of Potsdam, Potsdam, Germany
| | - Alejandro Rodríguez
- Department of Conservation Biology, Doñana Biological Station (EBD), Spanish National Research Council (CSIC), Sevilla, Spain
| | - Eloy Revilla
- Department of Conservation Biology, Doñana Biological Station (EBD), Spanish National Research Council (CSIC), Sevilla, Spain
| | - Miguel Delibes
- Department of Conservation Biology, Doñana Biological Station (EBD), Spanish National Research Council (CSIC), Sevilla, Spain
| | - José A Godoy
- Department of Integrative Ecology, Doñana Biological Station (EBD) Spanish National Research Council (CSIC), Sevilla, Spain
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17
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Marr MM, Brace S, Schreve DC, Barnes I. Identifying source populations for the reintroduction of the Eurasian beaver, Castor fiber L. 1758, into Britain: evidence from ancient DNA. Sci Rep 2018; 8:2708. [PMID: 29426903 PMCID: PMC5807398 DOI: 10.1038/s41598-018-21173-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 01/17/2018] [Indexed: 11/09/2022] Open
Abstract
Establishing true phylogenetic relationships between populations is a critical consideration when sourcing individuals for translocation. This presents huge difficulties with threatened and endangered species that have become extirpated from large areas of their former range. We utilise ancient DNA (aDNA) to reconstruct the phylogenetic relationships of a keystone species which has become extinct in Britain, the Eurasian beaver Castor fiber. We sequenced seventeen 492 bp partial tRNAPro and control region sequences from Late Pleistocene and Holocene age beavers and included these in network, demographic and genealogy analyses. The mode of postglacial population expansion from refugia was investigated by employing tests of neutrality and a pairwise mismatch distribution analysis. We found evidence of a pre-Late Glacial Maximum ancestor for the Western C. fiber clade which experienced a rapid demographic expansion during the terminal Pleistocene to early Holocene period. Ancient British beavers were found to originate from the Western phylogroup but showed no phylogenetic affinity to any one modern relict population over another. Instead, we find that they formed part of a large, continuous, pan-Western European clade that harbored little internal substructure. Our study highlights the utility of aDNA in reconstructing population histories of extirpated species which has real-world implications for conservation planning.
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Affiliation(s)
- Melissa M Marr
- Department of Geography, Royal Holloway University of London, Egham Hill, Egham, Surrey, TW20 0EX, UK.
- Department of Earth Sciences, Natural History Museum London, Cromwell Road, South Kensington, London, SW7 5BD, UK.
| | - Selina Brace
- Department of Earth Sciences, Natural History Museum London, Cromwell Road, South Kensington, London, SW7 5BD, UK
| | - Danielle C Schreve
- Department of Geography, Royal Holloway University of London, Egham Hill, Egham, Surrey, TW20 0EX, UK
| | - Ian Barnes
- Department of Earth Sciences, Natural History Museum London, Cromwell Road, South Kensington, London, SW7 5BD, UK
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18
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Spatiotemporal genetic structure of anadromous Arctic char (Salvelinus alpinus) populations in a region experiencing pronounced climate change. CONSERV GENET 2018. [DOI: 10.1007/s10592-018-1047-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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19
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Johnson BM, Kemp BM, Thorgaard GH. Increased mitochondrial DNA diversity in ancient Columbia River basin Chinook salmon Oncorhynchus tshawytscha. PLoS One 2018; 13:e0190059. [PMID: 29320518 PMCID: PMC5761847 DOI: 10.1371/journal.pone.0190059] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 12/07/2017] [Indexed: 01/20/2023] Open
Abstract
The Columbia River and its tributaries provide essential spawning and rearing habitat for many salmonid species, including Chinook salmon (Oncorhynchus tshawytscha). Chinook salmon were historically abundant throughout the basin and Native Americans in the region relied heavily on these fish for thousands of years. Following the arrival of Europeans in the 1800s, salmon in the basin experienced broad declines linked to overfishing, water diversion projects, habitat destruction, connectivity reduction, introgression with hatchery-origin fish, and hydropower development. Despite historical abundance, many native salmonids are now at risk of extinction. Research and management related to Chinook salmon is usually explored under what are termed "the four H's": habitat, harvest, hatcheries, and hydropower; here we explore a fifth H, history. Patterns of prehistoric and contemporary mitochondrial DNA variation from Chinook salmon were analyzed to characterize and compare population genetic diversity prior to recent alterations and, thus, elucidate a deeper history for this species. A total of 346 ancient and 366 contemporary samples were processed during this study. Species was determined for 130 of the ancient samples and control region haplotypes of 84 of these were sequenced. Diversity estimates from these 84 ancient Chinook salmon were compared to 379 contemporary samples. Our analysis provides the first direct measure of reduced genetic diversity for Chinook salmon from the ancient to the contemporary period, as measured both in direct loss of mitochondrial haplotypes and reductions in haplotype and nucleotide diversity. However, these losses do not appear equal across the basin, with higher losses of diversity in the mid-Columbia than in the Snake subbasin. The results are unexpected, as the two groups were predicted to share a common history as parts of the larger Columbia River Basin, and instead indicate that Chinook salmon in these subbasins may have divergent demographic histories.
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Affiliation(s)
- Bobbi M. Johnson
- School of Biological Sciences, Washington State University, Pullman, Washington, United States of America
- * E-mail:
| | - Brian M. Kemp
- School of Biological Sciences, Washington State University, Pullman, Washington, United States of America
- Department of Anthropology, Washington State University, Pullman, Washington, United States of America
| | - Gary H. Thorgaard
- School of Biological Sciences, Washington State University, Pullman, Washington, United States of America
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20
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Woods R, Marr MM, Brace S, Barnes I. The Small and the Dead: A Review of Ancient DNA Studies Analysing Micromammal Species. Genes (Basel) 2017; 8:E312. [PMID: 29117125 PMCID: PMC5704225 DOI: 10.3390/genes8110312] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 10/13/2017] [Accepted: 10/13/2017] [Indexed: 02/06/2023] Open
Abstract
The field of ancient DNA (aDNA) has recently been in a state of exponential growth, largely driven by the uptake of Next Generation Sequencing (NGS) techniques. Much of this work has focused on the mammalian megafauna and ancient humans, with comparatively less studies looking at micromammal fauna, despite the potential of these species in testing evolutionary, environmental and taxonomic theories. Several factors make micromammal fauna ideally suited for aDNA extraction and sequencing. Micromammal subfossil assemblages often include the large number of individuals appropriate for population level analyses, and, furthermore, the assemblages are frequently found in cave sites where the constant temperature and sheltered environment provide favourable conditions for DNA preservation. This review looks at studies that include the use of aDNA in molecular analysis of micromammal fauna, in order to examine the wide array of questions that can be answered in the study of small mammals using new palaeogenetic techniques. This study highlights the bias in current aDNA studies and assesses the future use of aDNA as a tool for the study of micromammal fauna.
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Affiliation(s)
- Roseina Woods
- Department of Earth Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK.
| | - Melissa M Marr
- Department of Earth Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK.
| | - Selina Brace
- Department of Earth Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK.
| | - Ian Barnes
- Department of Earth Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK.
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21
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Engelhardt A, Muniz L, Perwitasari-Farajallah D, Widdig A. Highly Polymorphic Microsatellite Markers for the Assessment of Male Reproductive Skew and Genetic Variation in Critically Endangered Crested Macaques ( Macaca nigra). INT J PRIMATOL 2017; 38:672-691. [PMID: 28845069 PMCID: PMC5550527 DOI: 10.1007/s10764-017-9973-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 05/11/2017] [Indexed: 11/24/2022]
Abstract
Genetic analyses based on noninvasively collected samples have become an important tool for evolutionary biology and conservation. Crested macaques (Macaca nigra), endemic to Sulawesi, Indonesia, are important for our understanding of primate evolution as Sulawesi macaques represent an exceptional example of primate adaptive radiation. Crested macaques are also Critically Endangered. However, to date we know very little about their genetics. The aim of our study was to find and validate microsatellite markers useful for evolutionary, conservation, and other genetic studies on wild crested macaques. Using fecal samples of 176 wild macaques living in the Tangkoko Reserve, Sulawesi, we identified 12 polymorphic microsatellite loci through cross-species polymerase chain reaction amplification with later modification of some of these primers. We tested their suitability by investigating and exploring patterns of paternity, observed heterozygosity, and evidence for inbreeding. We assigned paternity to 63 of 65 infants with high confidence. Among cases with solved paternity, we found no evidence of extragroup paternity and natal breeding. We found a relatively steep male reproductive skew B index of 0.330 ± 0.267; mean ± SD) and mean alpha paternity of 65% per year with large variation across groups and years (29–100%). Finally, we detected an excess in observed heterozygosity and no evidence of inbreeding across our three study groups, with an observed heterozygosity of 0.766 ± 0.059 and expected heterozygosity of 0.708 ± 0.059, and an inbreeding coefficient of −0.082 ± 0.035. Our results indicate that the selected markers are useful for genetic studies on wild crested macaques, and possibly also on other Sulawesi and closely related macaques. They further suggest that the Tangkoko population of crested macaques is still genetically variable despite its small size, isolation, and the species’ reproductive patterns. This gives us hope that other endangered primate species living in small, isolated populations may also retain a healthy gene pool, at least in the short term.
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Affiliation(s)
- Antje Engelhardt
- School of Natural Sciences and Psychology, Liverpool John Moores University, L3 3AF, Liverpool, UK.,Junior Research Group of Primate Sexual Selection, German Primate Center, 37077 Göttingen, Germany.,Courant Research Center Evolution of Social Behavior, Georg August University, 37077 Göttingen, Germany
| | - Laura Muniz
- Junior Research Group of Primate Kin Selection, Department of Primatology, Max-Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany.,Research Group of Behavioural Ecology, Institute of Biology, University of Leipzig, 04103 Leipzig, Germany
| | - Dyah Perwitasari-Farajallah
- Primate Research Centre, Bogor Agricultural University, Bogor, Indonesia.,Department of Biology, Faculty of Mathematics and Natural Sciences, Bogor Agricultural University, Bogor, Indonesia
| | - Anja Widdig
- Junior Research Group of Primate Kin Selection, Department of Primatology, Max-Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany.,Research Group of Behavioural Ecology, Institute of Biology, University of Leipzig, 04103 Leipzig, Germany.,German Center for Integrative Biodiversity Research, 04103 Leipzig, Germany
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22
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Time to Spread Your Wings: A Review of the Avian Ancient DNA Field. Genes (Basel) 2017; 8:genes8070184. [PMID: 28718817 PMCID: PMC5541317 DOI: 10.3390/genes8070184] [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: 05/31/2017] [Revised: 06/27/2017] [Accepted: 07/10/2017] [Indexed: 01/16/2023] Open
Abstract
Ancient DNA (aDNA) has the ability to inform the evolutionary history of both extant and extinct taxa; however, the use of aDNA in the study of avian evolution is lacking in comparison to other vertebrates, despite birds being one of the most species-rich vertebrate classes. Here, we review the field of “avian ancient DNA” by summarising the past three decades of literature on this topic. Most studies over this time have used avian aDNA to reconstruct phylogenetic relationships and clarify taxonomy based on the sequencing of a few mitochondrial loci, but recent studies are moving toward using a comparative genomics approach to address developmental and functional questions. Applying aDNA analysis with more practical outcomes in mind (such as managing conservation) is another increasingly popular trend among studies that utilise avian aDNA, but the majority of these have yet to influence management policy. We find that while there have been advances in extracting aDNA from a variety of avian substrates including eggshell, feathers, and coprolites, there is a bias in the temporal focus; the majority of the ca. 150 studies reviewed here obtained aDNA from late Holocene (100–1000 yBP) material, with few studies investigating Pleistocene-aged material. In addition, we identify and discuss several other issues within the field that require future attention. With more than one quarter of Holocene bird extinctions occurring in the last several hundred years, it is more important than ever to understand the mechanisms driving the evolution and extinction of bird species through the use of aDNA.
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23
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Phillips NM, Fearing A, Morgan DL. Genetic bottlenecks in Pristis sawfishes in northern Australian waters. ENDANGER SPECIES RES 2017. [DOI: 10.3354/esr00815] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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24
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Bennett EA, Champlot S, Peters J, Arbuckle BS, Guimaraes S, Pruvost M, Bar-David S, Davis SJM, Gautier M, Kaczensky P, Kuehn R, Mashkour M, Morales-Muñiz A, Pucher E, Tournepiche JF, Uerpmann HP, Bălăşescu A, Germonpré M, Gündem CY, Hemami MR, Moullé PE, Ötzan A, Uerpmann M, Walzer C, Grange T, Geigl EM. Taming the late Quaternary phylogeography of the Eurasiatic wild ass through ancient and modern DNA. PLoS One 2017; 12:e0174216. [PMID: 28422966 PMCID: PMC5396879 DOI: 10.1371/journal.pone.0174216] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 03/06/2017] [Indexed: 11/24/2022] Open
Abstract
Taxonomic over-splitting of extinct or endangered taxa, due to an incomplete knowledge of both skeletal morphological variability and the geographical ranges of past populations, continues to confuse the link between isolated extant populations and their ancestors. This is particularly problematic with the genus Equus. To more reliably determine the evolution and phylogeographic history of the endangered Asiatic wild ass, we studied the genetic diversity and inter-relationships of both extinct and extant populations over the last 100,000 years, including samples throughout its previous range from Western Europe to Southwest and East Asia. Using 229 bp of the mitochondrial hypervariable region, an approach which allowed the inclusion of information from extremely poorly preserved ancient samples, we classify all non-African wild asses into eleven clades that show a clear phylogeographic structure revealing their phylogenetic history. This study places the extinct European wild ass, E. hydruntinus, the phylogeny of which has been debated since the end of the 19th century, into its phylogenetic context within the Asiatic wild asses and reveals recent mitochondrial introgression between populations currently regarded as separate species. The phylogeographic organization of clades resulting from these efforts can be used not only to improve future taxonomic determination of a poorly characterized group of equids, but also to identify historic ranges, interbreeding events between various populations, and the impact of ancient climatic changes. In addition, appropriately placing extant relict populations into a broader phylogeographic and genetic context can better inform ongoing conservation strategies for this highly-endangered species.
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Affiliation(s)
- E. Andrew Bennett
- Institut Jacques Monod, UMR7592, CNRS-Université Paris Diderot, Paris, France
| | - Sophie Champlot
- Institut Jacques Monod, UMR7592, CNRS-Université Paris Diderot, Paris, France
| | - Joris Peters
- Institute of Palaeoanatomy, Domestication Research and the History of Veterinary Medicine, Ludwig-Maximilian University, Munich, Germany
- SNSB, Bavarian State Collection of Anthropology and Palaeoanatomy, München, Germany
| | - Benjamin S. Arbuckle
- Department of Anthropology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Silvia Guimaraes
- Institut Jacques Monod, UMR7592, CNRS-Université Paris Diderot, Paris, France
| | - Mélanie Pruvost
- Institute of Palaeoanatomy, Domestication Research and the History of Veterinary Medicine, Ludwig-Maximilian University, Munich, Germany
| | - Shirli Bar-David
- Mitrani Department of Desert Ecology, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, Midreshet Ben-Gurion, Israel
| | | | - Mathieu Gautier
- Centre de Biologie pour la Gestion des Populations CBGP, Montferrier-sur-Lez, France
| | - Petra Kaczensky
- Research Institute of Wildlife Ecology, University of Veterinary Medicine, Vienna, Austria
| | - Ralph Kuehn
- Technische Universität München, AG Molekulare Zoologie/Lehrstuhl für Zoologie, Freising, Germany
| | - Marjan Mashkour
- CNRS and Muséum national d'Histoire naturelle, UMR 7209, Archéozoologie, archéobotanique: sociétés, pratiques et environnements, Département Ecologie et Gestion de la Biodiversité, Paris, France
| | - Arturo Morales-Muñiz
- Laboratory of Archaeozoology, Dept. Biologia, Universidad Autonoma de Madrid, Madrid, Spain
| | | | | | - Hans-Peter Uerpmann
- Eberhard-Karls-Universität Tübingen, Institut für Ur- und Frühgeschichte und Archäologie des Mittelalters, Abteilung Ältere Urgeschichte und Quartärökologie, Zentrum für Naturwissenschaftliche Archäologie, Tübingen, Germany
| | - Adrian Bălăşescu
- National History Museum of Romania, National Centre of Pluridisciplinary Research, Bucureşti, Romania
| | - Mietje Germonpré
- Royal Belgian Institute of Natural Sciences, Earth and History of Life, Brussels, Belgium
| | - Can Y. Gündem
- Eberhard-Karls-Universität Tübingen, Institut für Ur- und Frühgeschichte und Archäologie des Mittelalters, Abteilung Ältere Urgeschichte und Quartärökologie, Zentrum für Naturwissenschaftliche Archäologie, Tübingen, Germany
| | - Mahmoud-Reza Hemami
- Department of Natural Resources, Isfahan University of Technology, Isfahan, Iran
| | | | - Aliye Ötzan
- Ankara Üniversitesi Dil ve Tarih-Coğrafya Fakültesi, Ankara, Turkey
| | - Margarete Uerpmann
- Eberhard-Karls-Universität Tübingen, Institut für Ur- und Frühgeschichte und Archäologie des Mittelalters, Abteilung Ältere Urgeschichte und Quartärökologie, Zentrum für Naturwissenschaftliche Archäologie, Tübingen, Germany
| | - Chris Walzer
- Research Institute of Wildlife Ecology, University of Veterinary Medicine, Vienna, Austria
| | - Thierry Grange
- Institut Jacques Monod, UMR7592, CNRS-Université Paris Diderot, Paris, France
- * E-mail: (EMG); (TG)
| | - Eva-Maria Geigl
- Institut Jacques Monod, UMR7592, CNRS-Université Paris Diderot, Paris, France
- * E-mail: (EMG); (TG)
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25
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Grosser S, Abdelkrim J, Wing J, Robertson BC, Gemmell NJ. Strong isolation by distance argues for separate population management of endangered blue duck (Hymenolaimus malacorhynchos). CONSERV GENET 2016. [DOI: 10.1007/s10592-016-0908-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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26
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Bergner LM, Dussex N, Jamieson IG, Robertson BC. European Colonization, Not Polynesian Arrival, Impacted Population Size and Genetic Diversity in the Critically Endangered New Zealand Kākāpō. J Hered 2016; 107:593-602. [DOI: 10.1093/jhered/esw065] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Accepted: 09/14/2016] [Indexed: 11/13/2022] Open
Abstract
Abstract
Island endemic species are often vulnerable to decline and extinction following human settlement, and the genetic study of historical museum specimens can be useful in understanding these processes. The kākāpō (Strigops habroptilus) is a critically endangered New Zealand parrot that was formerly widespread and abundant. It is well established that both Polynesian and European colonization of New Zealand impacted the native avifauna, but the timeframe and severity of impacts have differed depending on species. Here, we investigated the relative importance of the 2 waves of human settlement on kākāpō decline, using microsatellites and mitochondrial DNA (mtDNA) to characterize recent kākāpō genetic and demographic history. We analyzed samples from 49 contemporary individuals and 54 museum specimens dating from 1884 to 1985. Genetic diversity decreased significantly between historical and contemporary kākāpō, with a decline in mean number of microsatellite alleles from 6.15 to 3.08 and in number of mtDNA haplotypes from 17 to 3. Modeling of demographic history indicated a recent population bottleneck linked to the period of European colonization (approximately 5 generations ago) but did not support a major decline linked to Polynesian settlement. Effective population size estimates were also larger for historical than contemporary kākāpō. Our findings inform contemporary kākāpō management by indicating the timeframe and possible cause of the bottleneck, which has implications for the management of extant genetic diversity. We demonstrate the broader utility of a historical perspective in understanding causes of decline and managing extinction risk in contemporary endangered species.
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Affiliation(s)
- Laura M. Bergner
- From the Allan Wilson Centre for Molecular Ecology and Evolution, Department of Zoology, University of Otago, 340 Great King Street, Dunedin 9016, New Zealand (Bergner, Dussex, Jamieson, and Robertson) and Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow G12 8QQ, UK (Bergner)
| | - Nicolas Dussex
- From the Allan Wilson Centre for Molecular Ecology and Evolution, Department of Zoology, University of Otago, 340 Great King Street, Dunedin 9016, New Zealand (Bergner, Dussex, Jamieson, and Robertson) and Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow G12 8QQ, UK (Bergner)
| | - Ian G. Jamieson
- From the Allan Wilson Centre for Molecular Ecology and Evolution, Department of Zoology, University of Otago, 340 Great King Street, Dunedin 9016, New Zealand (Bergner, Dussex, Jamieson, and Robertson) and Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow G12 8QQ, UK (Bergner)
| | - Bruce C. Robertson
- From the Allan Wilson Centre for Molecular Ecology and Evolution, Department of Zoology, University of Otago, 340 Great King Street, Dunedin 9016, New Zealand (Bergner, Dussex, Jamieson, and Robertson) and Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow G12 8QQ, UK (Bergner)
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27
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Shultz AJ, Baker AJ, Hill GE, Nolan PM, Edwards SV. SNPs across time and space: population genomic signatures of founder events and epizootics in the House Finch ( Haemorhous mexicanus). Ecol Evol 2016; 6:7475-7489. [PMID: 28725414 PMCID: PMC5513257 DOI: 10.1002/ece3.2444] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 08/11/2016] [Indexed: 12/27/2022] Open
Abstract
Identifying genomic signatures of natural selection can be challenging against a background of demographic changes such as bottlenecks and population expansions. Here, we disentangle the effects of demography from selection in the House Finch (Haemorhous mexicanus) using samples collected before and after a pathogen‐induced selection event. Using ddRADseq, we genotyped over 18,000 SNPs across the genome in native pre‐epizootic western US birds, introduced birds from Hawaii and the eastern United States, post‐epizootic eastern birds, and western birds sampled across a similar time span. We found 14% and 7% reductions in nucleotide diversity, respectively, in Hawaiian and pre‐epizootic eastern birds relative to pre‐epizootic western birds, as well as elevated levels of linkage disequilibrium and other signatures of founder events. Despite finding numerous significant frequency shifts (outlier loci) between pre‐epizootic native and introduced populations, we found no signal of reduced genetic diversity, elevated linkage disequilibrium, or outlier loci as a result of the epizootic. Simulations demonstrate that the proportion of outliers associated with founder events could be explained by genetic drift. This rare view of genetic evolution across time in an invasive species provides direct evidence that demographic shifts like founder events have genetic consequences more widespread across the genome than natural selection.
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Affiliation(s)
- Allison J Shultz
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology Harvard University Cambridge MA USA
| | - Allan J Baker
- Department of Natural History, Royal Ontario Museum Department of Ecology and Evolutionary Biology University of Toronto Toronto ON Canada
| | - Geoffrey E Hill
- Department of Biological Sciences Auburn University Auburn AL USA
| | - Paul M Nolan
- Department of Biology The Citadel Charleston SC USA
| | - Scott V Edwards
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology Harvard University Cambridge MA USA
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Waters JM, Grosser S. Managing shifting species: Ancient DNA reveals conservation conundrums in a dynamic world. Bioessays 2016; 38:1177-1184. [PMID: 27586443 DOI: 10.1002/bies.201600044] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The spread of exotic species represents a major driver of biological change across the planet. While dispersal and colonization are natural biological processes, we suggest that the failure to recognize increasing rates of human-facilitated self-introductions may represent a threat to native lineages. Notably, recent biogeographic analyses have revealed numerous cases of biological range shifts in response to anthropogenic impacts and climate change. In particular, ancient DNA analyses have revealed several cases in which lineages traditionally thought to be long-established "natives" are in fact recent colonizers. Such range expansion events have apparently occurred in response to human-mediated native biodiversity declines and ecosystem change, particularly in recently colonized, isolated ecosystems such as New Zealand. While such events can potentially boost local biodiversity, the spread of exotic lineages may also hasten the decline of indigenous species, so it is essential that conservation managers recognize these rapid biotic shifts..
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Affiliation(s)
| | - Stefanie Grosser
- Department of Zoology, University of Otago, Dunedin, New Zealand.,Department of Animal Behaviour, Bielefeld University, Bielefeld, Germany
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Splendiani A, Fioravanti T, Giovannotti M, Negri A, Ruggeri P, Olivieri L, Nisi Cerioni P, Lorenzoni M, Caputo Barucchi V. The Effects of Paleoclimatic Events on Mediterranean Trout: Preliminary Evidences from Ancient DNA. PLoS One 2016; 11:e0157975. [PMID: 27331397 PMCID: PMC4917132 DOI: 10.1371/journal.pone.0157975] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 06/08/2016] [Indexed: 11/19/2022] Open
Abstract
In this pilot study for the first time, ancient DNA has been extracted from bone remains of Salmo trutta. These samples were from a stratigraphic succession located in a coastal cave of Calabria (southern Italy) inhabited by humans from upper Palaeolithic to historical times. Seven pairs of primers were used to PCR-amplify and sequence from 128 to 410 bp of the mtDNA control region of eleven samples. Three haplotypes were observed: two (ADcs-1 and MEcs-1) already described in rivers from the Italian peninsula; one (ATcs-33) belonging to the southern Atlantic clade of the AT Salmo trutta mtDNA lineage (sensu Bernatchez). The prehistoric occurrence of this latter haplotype in the water courses of the Italian peninsula has been detected for the first time in this study. Finally, we observed a correspondence between frequency of trout remains and variation in haplotype diversity that we related with ecological and demographic changes resulting from a period of rapid cooling known as the Younger Dryas.
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Affiliation(s)
- Andrea Splendiani
- Dipartimento di Scienze della Vita e dell'Ambiente (DiSVA), Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Tatiana Fioravanti
- Dipartimento di Scienze della Vita e dell'Ambiente (DiSVA), Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Massimo Giovannotti
- Dipartimento di Scienze della Vita e dell'Ambiente (DiSVA), Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Alessandra Negri
- Dipartimento di Scienze della Vita e dell'Ambiente (DiSVA), Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Paolo Ruggeri
- Dipartimento di Scienze della Vita e dell'Ambiente (DiSVA), Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Luigi Olivieri
- Dipartimento di Scienze della Vita e dell'Ambiente (DiSVA), Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Paola Nisi Cerioni
- Dipartimento di Scienze della Vita e dell'Ambiente (DiSVA), Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Massimo Lorenzoni
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, Via Elce di Sotto, 06123 Perugia, Italy
| | - Vincenzo Caputo Barucchi
- Dipartimento di Scienze della Vita e dell'Ambiente (DiSVA), Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona, Italy
- Istituto Italiano di Paleontologia Umana, Is.I.P.U., Convitto Nazionale Regina Margherita, Piazza Ruggero Bonghi 2. 03012 Anagni, Italy
- * E-mail:
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30
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Towards population-level conservation in the critically endangered Antarctic blue whale: the number and distribution of their populations. Sci Rep 2016; 6:22291. [PMID: 26951747 PMCID: PMC4782106 DOI: 10.1038/srep22291] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Accepted: 02/11/2016] [Indexed: 02/04/2023] Open
Abstract
Population-level conservation is required to prevent biodiversity loss within a species, but it first necessitates determining the number and distribution of populations. Many whale populations are still depleted due to 20th century whaling. Whales are one of the most logistically difficult and expensive animals to study because of their mobility, pelagic lifestyle and often remote habitat. We tackle the question of population structure in the Antarctic blue whale (Balaenoptera musculus intermedia) – a critically endangered subspecies and the largest extant animal – by capitalizing on the largest genetic dataset to date for Antarctic blue whales. We found evidence of three populations that are sympatric in the Antarctic feeding grounds and likely occupy separate breeding grounds. Our study adds to knowledge of population structure in the Antarctic blue whale. Future research should invest in locating the breeding grounds and migratory routes of Antarctic blue whales through satellite telemetry to confirm their population structure and allow population-level conservation.
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Banhos A, Hrbek T, Sanaiotti TM, Farias IP. Reduction of Genetic Diversity of the Harpy Eagle in Brazilian Tropical Forests. PLoS One 2016; 11:e0148902. [PMID: 26871719 PMCID: PMC4752245 DOI: 10.1371/journal.pone.0148902] [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: 08/12/2015] [Accepted: 01/24/2016] [Indexed: 01/30/2023] Open
Abstract
Habitat loss and fragmentation intensify the effects of genetic drift and endogamy, reducing genetic variability of populations with serious consequences for wildlife conservation. The Harpy Eagle (Harpia harpyja) is a forest dwelling species that is considered near threatened and suffers from habitat loss in the forests of the Neotropical region. In this study, 72 historical and current samples were assessed using eight autosomal microsatellite markers to investigate the distribution of genetic diversity of the Harpy Eagle of the Amazonian and Atlantic forests in Brazil. The results showed that the genetic diversity of Harpy Eagle decreased in the regions where deforestation is intense in the southern Amazon and Atlantic Forest.
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Affiliation(s)
- Aureo Banhos
- Departamento de Biologia, Centro de Ciências Exatas, Naturais e da Saúde, Universidade Federal do Espírito Santo, Alegre, Espírito Santo, Brazil
- Programa de Conservação do Gavião-real, Instituto Nacional de Pesquisas da Amazônia, Manaus, Amazonas, Brazil
- * E-mail:
| | - Tomas Hrbek
- Laboratório de Evolução e Genética Animal, Departamento de Genética, Instituto de Ciências Biológicas, Universidade Federal do Amazonas, Manaus, Amazonas, Brazil
| | - Tânia M. Sanaiotti
- Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus, Amazonas, Brazil
- Programa de Conservação do Gavião-real, Instituto Nacional de Pesquisas da Amazônia, Manaus, Amazonas, Brazil
| | - Izeni Pires Farias
- Laboratório de Evolução e Genética Animal, Departamento de Genética, Instituto de Ciências Biológicas, Universidade Federal do Amazonas, Manaus, Amazonas, Brazil
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32
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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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33
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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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Conservation archaeogenomics: ancient DNA and biodiversity in the Anthropocene. Trends Ecol Evol 2015; 30:540-9. [PMID: 26169594 DOI: 10.1016/j.tree.2015.06.008] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Revised: 06/11/2015] [Accepted: 06/15/2015] [Indexed: 11/22/2022]
Abstract
There is growing consensus that we have entered the Anthropocene, a geologic epoch characterized by human domination of the ecosystems of the Earth. With the future uncertain, we are faced with understanding how global biodiversity will respond to anthropogenic perturbations. The archaeological record provides perspective on human-environment relations through time and across space. Ancient DNA (aDNA) analyses of plant and animal remains from archaeological sites are particularly useful for understanding past human-environment interactions, which can help guide conservation decisions during the environmental changes of the Anthropocene. Here, we define the emerging field of conservation archaeogenomics, which integrates archaeological and genomic data to generate baselines or benchmarks for scientists, managers, and policy-makers by evaluating climatic and human impacts on past, present, and future biodiversity.
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35
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Maebe K, Meeus I, Ganne M, De Meulemeester T, Biesmeijer K, Smagghe G. Microsatellite Analysis of Museum Specimens Reveals Historical Differences in Genetic Diversity between Declining and More Stable Bombus Species. PLoS One 2015; 10:e0127870. [PMID: 26061732 PMCID: PMC4464549 DOI: 10.1371/journal.pone.0127870] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Accepted: 04/21/2015] [Indexed: 11/19/2022] Open
Abstract
Worldwide most pollinators, e.g. bumblebees, are undergoing global declines. Loss of genetic diversity can play an essential role in these observed declines. In this paper, we investigated the level of genetic diversity of seven declining Bombus species and four more stable species with the use of microsatellite loci. Hereto we genotyped a unique collection of museum specimens. Specimens were collected between 1918 and 1926, in 6 provinces of the Netherlands which allowed us to make interspecific comparisons of genetic diversity. For the stable species B. pascuorum, we also selected populations from two additional time periods: 1949-1955 and 1975-1990. The genetic diversity and population structure in B. pascuorum remained constant over the three time periods. However, populations of declining bumblebee species showed a significantly lower genetic diversity than co-occurring stable species before their major declines. This historical difference indicates that the repeatedly observed reduced genetic diversity in recent populations of declining bumblebee species is not caused solely by the decline itself. The historically low genetic diversity in the declined species may be due to the fact that these species were already rare, making them more vulnerable to the major drivers of bumblebee decline.
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Affiliation(s)
- Kevin Maebe
- Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, Coupure links 653, Ghent, Belgium
| | - Ivan Meeus
- Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, Coupure links 653, Ghent, Belgium
| | - Maarten Ganne
- Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, Coupure links 653, Ghent, Belgium
| | | | - Koos Biesmeijer
- Naturalis Biodiversity Center, Darwinweg 2, Leiden, the Netherlands
| | - Guy Smagghe
- Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, Coupure links 653, Ghent, Belgium
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36
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Harms V, Nowak C, Carl S, Muñoz-Fuentes V. Experimental evaluation of genetic predator identification from saliva traces on wildlife kills. J Mammal 2015. [DOI: 10.1093/jmammal/gyu014] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Meachen JA, O'Keefe FR, Sadleir RW. Evolution in the sabre-tooth cat, Smilodon fatalis, in response to Pleistocene climate change. J Evol Biol 2014; 27:714-23. [PMID: 24779050 DOI: 10.1111/jeb.12340] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The late Pleistocene was a time of environmental change, culminating in an extinction event. Few fossil localities record a temporal series of carnivore fossil populations from this interesting interval as well as Rancho La Brea (RLB). We analysed mandibles of Smilodon fatalis from RLB using 2-D geometric morphometrics to examine whether, and how, mandibular shape changes through time. Smilodon fatalis shows mandibular evolution with oscillations between a small, ancestral-type morph in pits 77 (≈37 Kybp) and 2051 (≈26 Kybp), a larger, more derived morph in pits 91 (≈28 Kybp) and 61-67 (≈13.6 Kybp), and an intermediate morph from pit 13 (≈17.7 Kybp). These oscillations end in pit 61-67, with greatest body size, and are estimated to have its widest gape and lowest bite force. Additionally, variation is lowest in pit 61-67, which was deposited concurrent with the Bølling–Allerød warming event, which may have important implications for the timing or conditions during the extinction event. Contra to a temporal Bergmann's rule, such rapid warming events appear to be correlated with larger, derived, morphologies whereas static, cooler, climates correlate with gracile, ancestral morphologies.
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Segelbacher G, Strand TM, Quintela M, Axelsson T, Jansman HAH, Koelewijn HP, Höglund J. Analyses of historical and current populations of black grouse in Central Europe reveal strong effects of genetic drift and loss of genetic diversity. CONSERV GENET 2014. [DOI: 10.1007/s10592-014-0610-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Jansson E, Harmoinen J, Ruokonen M, Aspi J. Living on the edge: reconstructing the genetic history of the Finnish wolf population. BMC Evol Biol 2014; 14:64. [PMID: 24678616 PMCID: PMC4033686 DOI: 10.1186/1471-2148-14-64] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Accepted: 03/05/2014] [Indexed: 11/19/2022] Open
Abstract
Background Many western European carnivore populations became almost or completely eradicated during the last ~200 years, but are now recovering. Extirpation of wolves started in Finland in the 19th century, and for more than 150 years the population size of wolves has remained small. To investigate historical patterns of genetic variation, we extracted DNA from 114 wolf samples collected in zoological museums over the last ~150 years. Fifteen microsatellite loci were used to look at genotypic variation in this historical sample. Additionally, we amplified a 430 bp sequence of mtDNA control region from the same samples. Contemporary wolf samples (N = 298) obtained after the population recovery in the mid-1990s, were used as a reference. Results Our analyses of mtDNA revealed reduced variation in the mtDNA control region through the loss of historical haplotypes observed prior to wolf declines. Heterozygosity at autosomal microsatellite loci did not decrease significantly. However, almost 20% of microsatellite alleles were unique to wolves collected before the 1960s. The genetic composition of the population changed gradually with the largest changes occurring prior to 1920. Half of the oldest historical samples formed a distinguishable genetic cluster not detected in the modern-day Finnish or Russian samples, and might therefore represent northern genetic variation lost from today’s gene pool. Point estimates of Ne were small (13.2 and 20.5) suggesting population fragmentation. Evidence of a genetic population bottleneck was also detected. Conclusions Our genetic analyses confirm changes in the genetic composition of the Finnish wolf population through time, despite the geographic interconnectivity to a much larger population in Russia. Our results emphasize the need for restoration of the historical connectivity between the present wolf populations to secure long-term viability. This might be challenging, however, because the management policies between Western and Eastern Europe often differ greatly. Additionally, wolf conservation is still a rather controversial issue, and anthropogenic pressure towards wolves remains strong.
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Affiliation(s)
| | | | | | - Jouni Aspi
- Department of Biology, University of Oulu, P,O, Box 3000, FIN-90014 Oulu, Finland.
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40
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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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Baker KH, Hoelzel AR. Influence of Holocene environmental change and anthropogenic impact on the diversity and distribution of roe deer. Heredity (Edinb) 2014; 112:607-15. [PMID: 24448563 DOI: 10.1038/hdy.2013.142] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Revised: 10/28/2013] [Accepted: 11/25/2013] [Indexed: 11/09/2022] Open
Abstract
Extant patterns of population structure and levels of diversity are a consequence of factors that vary in both space and time. Our objective in this study is to investigate a species that has responded to both natural and anthropogenic changes in ways that have shaped modern populations and provide insight into the key processes. The roe deer (Capreolus capreolus) is one of the two species of deer native to Britain. During the last glacial maximum (LGM), the British habitat was largely under ice and there was a land bridge to mainland Europe. As the Earth warmed during the early Holocene, the land bridge was lost. Subsequent hunting on the British mainland left the southern region extirpated of roe deer, whereas a refugial population remained in the north. Later reintroductions from Europe led to population expansion, especially in southern United Kingdom. Here, we combine data from ancient and modern DNA to track population dynamics and patterns of connectivity, and test hypotheses about the influence of natural and anthropogenic environmental change. We find that past expansion and divergence events coincided with a warming environment and the subsequent closure of the land bridge between Europe and the United Kingdom. We also find turnover in British roe deer haplotypes between the late-Holocene and modern day that have likely resulted from recent human disturbance activities such as habitat perturbation, overhunting and restocking.
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Affiliation(s)
- K H Baker
- School of Biological and Biomedical Sciences, Durham University, Durham, UK
| | - A R Hoelzel
- School of Biological and Biomedical Sciences, Durham University, Durham, UK
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42
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McDowell MC. Holocene vertebrate fossils aid the management and restoration of Australian ecosystems. ECOLOGICAL MANAGEMENT & RESTORATION 2014. [DOI: 10.1111/emr.12075] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Beatty GE, Reid N, Provan J. Retrospective genetic monitoring of the threatened Yellow marsh saxifrage (Saxifraga hirculus) reveals genetic erosion but provides valuable insights for conservation strategies. DIVERS DISTRIB 2013. [DOI: 10.1111/ddi.12158] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Affiliation(s)
- Gemma E. Beatty
- Quercus; School of Biological Sciences; Queen's University Belfast; 97 Lisburn Road Belfast BT9 7BL UK
- School of Biological Sciences; Queen's University Belfast; 97 Lisburn Road Belfast BT9 7BL UK
| | - Neil Reid
- Quercus; School of Biological Sciences; Queen's University Belfast; 97 Lisburn Road Belfast BT9 7BL UK
| | - Jim Provan
- School of Biological Sciences; Queen's University Belfast; 97 Lisburn Road Belfast BT9 7BL UK
- Institute for Global Food Security; Queen's University Belfast
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Ramírez O, Gómez-Díaz E, Olalde I, Illera JC, Rando JC, González-Solís J, Lalueza-Fox C. Population connectivity buffers genetic diversity loss in a seabird. Front Zool 2013; 10:28. [PMID: 23688345 PMCID: PMC3662614 DOI: 10.1186/1742-9994-10-28] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Accepted: 05/02/2013] [Indexed: 11/10/2022] Open
Abstract
Background Ancient DNA has revolutionized conservation genetic studies as it allows monitoring of the genetic variability of species through time and predicting the impact of ecosystems’ threats on future population dynamics and viability. Meanwhile, the consequences of anthropogenic activities and climate change to island faunas, particularly seabirds, remain largely unknown. In this study, we examined temporal changes in the genetic diversity of a threatened seabird, the Cory’s shearwater (Calonectris borealis). Findings We analysed the mitochondrial DNA control region of ancient bone samples from the late-Holocene retrieved from the Canary archipelago (NE Atlantic) together with modern DNA sequences representative of the entire breeding range of the species. Our results show high levels of ancient genetic diversity in the Canaries comparable to that of the extant population. The temporal haplotype network further revealed rare but recurrent long-distance dispersal between ocean basins. The Bayesian demographic analyses reveal both regional and local population size expansion events, and this is in spite of the demographic decline experienced by the species over the last millennia. Conclusions Our findings suggest that population connectivity of the species has acted as a buffer of genetic losses and illustrate the use of ancient DNA to uncover such cryptic genetic events.
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Affiliation(s)
- Oscar Ramírez
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Elena Gómez-Díaz
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Iñigo Olalde
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Juan Carlos Illera
- Research Unit of Biodiversity (UO-CSIC-PA), Oviedo University, Asturias, Spain
| | - Juan Carlos Rando
- Departamento de Biología Animal (UDI Zoología), Universidad de La Laguna, La Laguna, Tenerife, Spain
| | - Jacob González-Solís
- Institut de Recerca de la Biodiversitat and Departament de Biologia Animal, Universitat de Barcelona, Barcelona, Spain
| | - Carles Lalueza-Fox
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
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45
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Therkildsen NO, Hemmer-Hansen J, Als TD, Swain DP, Morgan MJ, Trippel EA, Palumbi SR, Meldrup D, Nielsen EE. Microevolution in time and space: SNP analysis of historical DNA reveals dynamic signatures of selection in Atlantic cod. Mol Ecol 2013; 22:2424-40. [PMID: 23551301 DOI: 10.1111/mec.12260] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Revised: 12/29/2012] [Accepted: 01/09/2013] [Indexed: 01/09/2023]
Abstract
Little is known about how quickly natural populations adapt to changes in their environment and how temporal and spatial variation in selection pressures interact to shape patterns of genetic diversity. We here address these issues with a series of genome scans in four overfished populations of Atlantic cod (Gadus morhua) studied over an 80-year period. Screening of >1000 gene-associated single-nucleotide polymorphisms (SNPs) identified 77 loci that showed highly elevated levels of differentiation, likely as an effect of directional selection, in either time, space or both. Exploratory analysis suggested that temporal allele frequency shifts at certain loci may correlate with local temperature variation and with life history changes suggested to be fisheries induced. Interestingly, however, largely nonoverlapping sets of loci were temporal outliers in the different populations and outliers from the 1928 to 1960 period showed almost complete stability during later decades. The contrasting microevolutionary trajectories among populations resulted in sequential shifts in spatial outliers, with no locus maintaining elevated spatial differentiation throughout the study period. Simulations of migration coupled with observations of temporally stable spatial structure at neutral loci suggest that population replacement or gene flow alone could not explain all the observed allele frequency variation. Thus, the genetic changes are likely to at least partly be driven by highly dynamic temporally and spatially varying selection. These findings have important implications for our understanding of local adaptation and evolutionary potential in high gene flow organisms and underscore the need to carefully consider all dimensions of biocomplexity for evolutionarily sustainable management.
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Affiliation(s)
- Nina O Therkildsen
- Section for Population Ecology and Genetics, National Institute of Aquatic Resources, Technical University of Denmark, Silkeborg, Denmark.
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46
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Hung CM, Lin RC, Chu JH, Yeh CF, Yao CJ, Li SH. The de novo assembly of mitochondrial genomes of the extinct passenger pigeon (Ectopistes migratorius) with next generation sequencing. PLoS One 2013; 8:e56301. [PMID: 23437111 PMCID: PMC3577829 DOI: 10.1371/journal.pone.0056301] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2012] [Accepted: 01/11/2013] [Indexed: 11/18/2022] Open
Abstract
The information from ancient DNA (aDNA) provides an unparalleled opportunity to infer phylogenetic relationships and population history of extinct species and to investigate genetic evolution directly. However, the degraded and fragmented nature of aDNA has posed technical challenges for studies based on conventional PCR amplification. In this study, we present an approach based on next generation sequencing to efficiently sequence the complete mitochondrial genome (mitogenome) of two extinct passenger pigeons (Ectopistes migratorius) using de novo assembly of massive short (90 bp), paired-end or single-end reads. Although varying levels of human contamination and low levels of postmortem nucleotide lesion were observed, they did not impact sequencing accuracy. Our results demonstrated that the de novo assembly of shotgun sequence reads could be a potent approach to sequence mitogenomes, and offered an efficient way to infer evolutionary history of extinct species.
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Affiliation(s)
- Chih-Ming Hung
- Bell Museum and Department of Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, Minnesota, United States of America
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Rong-Chien Lin
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Jui-Hua Chu
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Chia-Fen Yeh
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Chiou-Ju Yao
- Department of Biology, National Museum of Natural Science, Taichung, Taiwan
| | - Shou-Hsien Li
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
- * E-mail:
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47
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Conservation Genetics. Mol Ecol 2012. [DOI: 10.1002/9780470979365.ch8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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48
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Unraveling natural versus anthropogenic effects on genetic diversity within the southeastern beach mouse (Peromyscus polionotus niveiventris). CONSERV GENET 2012. [DOI: 10.1007/s10592-012-0417-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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49
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Ochoa A, Gasca J, Ceballos GJ, Eguiarte LE. Spatiotemporal population genetics of the endangered Perote ground squirrel (Xerospermophilus perotensis) in a fragmented landscape. J Mammal 2012. [DOI: 10.1644/11-mamm-a-371.1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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50
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Effective size and genetic composition of two exploited, migratory whitefish (Coregonus lavaretus lavaretus) populations. CONSERV GENET 2012. [DOI: 10.1007/s10592-012-0394-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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