151
|
Dolman G, Joseph L. Multi-locus sequence data illuminate demographic drivers of Pleistocene speciation in semi-arid southern Australian birds (Cinclosoma spp.). BMC Evol Biol 2016; 16:226. [PMID: 27770777 PMCID: PMC5075194 DOI: 10.1186/s12862-016-0798-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 10/12/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND During the Pleistocene, shifts of species distributions and their isolation in disjunct refugia led to varied outcomes in how taxa diversified. Some species diverged, others did not. Here, we begin to address another facet of the role of the Pleistocene in generating today's diversity. We ask which processes contributed to divergence in semi-arid southern Australian birds. We isolated 11 autosomal nuclear loci and one mitochondrial locus from a total of 29 specimens of the sister species pair, Chestnut Quail-thrush Cinclosoma castanotum and Copperback Quail-thrush C. clarum. RESULTS A population clustering analysis confirmed the location of the current species boundary as a well-known biogeographical barrier in southern Australia, the Eyrean Barrier. Coalescent-based analyses placed the time of species divergence to the Middle Pleistocene. Gene flow between the species since divergence has been low. The analyses suggest the effective population size of the ancestor was 54 to 178 times smaller than populations since divergence. This contrasts with recent multi-locus studies in some other Australian birds (butcherbirds, ducks) where a lack of phenotypic divergence was accompanied by larger historical population sizes. Post-divergence population size histories of C. clarum and C. castanotum were inferred using the extended Bayesian skyline model. The population size of C. clarum increased substantially during the late Pleistocene and continued to increase through the Last Glacial Maximum and Holocene. The timing of this expansion across its vast range is broadly concordant with that documented in several other Australian birds. In contrast, effective population size of C. castanotum was much more constrained and may reflect its smaller range and more restricted habitat east of the Eyrean Barrier compared with that available to C. clarum to the west. CONCLUSIONS Our results contribute to awareness of increased population sizes, following significant contractions, as having been important in shaping diversity in Australian arid and semi-arid zones. Further, we improve knowledge of the role of Pleistocene climatic shifts in areas of the planet that were not glaciated at that time but which still experienced that period's cyclical climatic fluctuations.
Collapse
Affiliation(s)
- Gaynor Dolman
- Molecular Systematics Unit, Western Australian Museum, Locked Bag 49, Welshpool DC, WA, 6986, Australia. .,Australian National Wildlife Collection, CSIRO National Research Collections Australia, GPO Box 1700, Canberra, ACT, 2601, Australia. .,Australian Centre for Evolutionary Biology and Biodiversity, School of Biological Sciences, University of Adelaide, Adelaide, SA, 5005, Australia.
| | - Leo Joseph
- Australian National Wildlife Collection, CSIRO National Research Collections Australia, GPO Box 1700, Canberra, ACT, 2601, Australia
| |
Collapse
|
152
|
Fourdrilis S, Mardulyn P, Hardy OJ, Jordaens K, de Frias Martins AM, Backeljau T. Mitochondrial DNA hyperdiversity and its potential causes in the marine periwinkle Melarhaphe neritoides (Mollusca: Gastropoda). PeerJ 2016; 4:e2549. [PMID: 27761337 PMCID: PMC5068447 DOI: 10.7717/peerj.2549] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 09/12/2016] [Indexed: 12/18/2022] Open
Abstract
We report the presence of mitochondrial DNA (mtDNA) hyperdiversity in the marine periwinkle Melarhaphe neritoides (Linnaeus, 1758), the first such case among marine gastropods. Our dataset consisted of concatenated 16S-COI-Cytb gene fragments. We used Bayesian analyses to investigate three putative causes underlying genetic variation, and estimated the mtDNA mutation rate, possible signatures of selection and the effective population size of the species in the Azores archipelago. The mtDNA hyperdiversity in M. neritoides is characterized by extremely high haplotype diversity (Hd = 0.999 ± 0.001), high nucleotide diversity (π = 0.013 ± 0.001), and neutral nucleotide diversity above the threshold of 5% (πsyn = 0.0677). Haplotype richness is very high even at spatial scales as small as 100m2. Yet, mtDNA hyperdiversity does not affect the ability of DNA barcoding to identify M. neritoides. The mtDNA hyperdiversity in M. neritoides is best explained by the remarkably high mutation rate at the COI locus (μ = 5.82 × 10−5 per site per year or μ = 1.99 × 10−4 mutations per nucleotide site per generation), whereas the effective population size of this planktonic-dispersing species is surprisingly small (Ne = 5, 256; CI = 1,312–3,7495) probably due to the putative influence of selection. Comparison with COI nucleotide diversity values in other organisms suggests that mtDNA hyperdiversity may be more frequently linked to high μ values and that mtDNA hyperdiversity may be more common across other phyla than currently appreciated.
Collapse
Affiliation(s)
- Séverine Fourdrilis
- Directorate Taxonomy and Phylogeny & JEMU, Royal Belgian Institute of Natural Sciences , Brussels , Belgium
| | - Patrick Mardulyn
- Evolutionary Biology and Ecology, Université Libre de Bruxelles , Brussels , Belgium
| | - Olivier J Hardy
- Evolutionary Biology and Ecology, Université Libre de Bruxelles , Brussels , Belgium
| | - Kurt Jordaens
- Department of Biology, Invertebrate Section, Royal Museum for Central Africa , Tervuren , Belgium
| | - António Manuel de Frias Martins
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Pólo dos Açores, Departamento de Biologia da Universidade dos Açores, University of the Azores , Ponta Delgada , Portugal
| | - Thierry Backeljau
- Directorate Taxonomy and Phylogeny & JEMU, Royal Belgian Institute of Natural Sciences, Brussels, Belgium; Evolutionary Ecology Group, University of Antwerp, Antwerp, Belgium
| |
Collapse
|
153
|
Maisano Delser P, Corrigan S, Hale M, Li C, Veuille M, Planes S, Naylor G, Mona S. Population genomics of C. melanopterus using target gene capture data: demographic inferences and conservation perspectives. Sci Rep 2016; 6:33753. [PMID: 27651217 PMCID: PMC5030670 DOI: 10.1038/srep33753] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Accepted: 08/19/2016] [Indexed: 01/23/2023] Open
Abstract
Population genetics studies on non-model organisms typically involve sampling few markers from multiple individuals. Next-generation sequencing approaches open up the possibility of sampling many more markers from fewer individuals to address the same questions. Here, we applied a target gene capture method to deep sequence ~1000 independent autosomal regions of a non-model organism, the blacktip reef shark (Carcharhinus melanopterus). We devised a sampling scheme based on the predictions of theoretical studies of metapopulations to show that sampling few individuals, but many loci, can be extremely informative to reconstruct the evolutionary history of species. We collected data from a single deme (SID) from Northern Australia and from a scattered sampling representing various locations throughout the Indian Ocean (SCD). We explored the genealogical signature of population dynamics detected from both sampling schemes using an ABC algorithm. We then contrasted these results with those obtained by fitting the data to a non-equilibrium finite island model. Both approaches supported an Nm value ~40, consistent with philopatry in this species. Finally, we demonstrate through simulation that metapopulations exhibit greater resilience to recent changes in effective size compared to unstructured populations. We propose an empirical approach to detect recent bottlenecks based on our sampling scheme.
Collapse
Affiliation(s)
- Pierpaolo Maisano Delser
- Institut de Systématique, Évolution, Biodiversité, ISYEB-UMR 7205-CNRS, MNHN, UPMC, EPHE, Ecole Pratique des Hautes Etudes, 16 rue Buffon, CP39, 75005, Paris, France
- EPHE, PSL Research University, Paris, France
| | - Shannon Corrigan
- Department of Biology, College of Charleston, Charleston 29412, SC, USA
| | - Matthew Hale
- Medical University of South Carolina, College of Graduate Studies, Charleston 29403, SC, USA
| | - Chenhong Li
- Department of Biology, College of Charleston, Charleston 29412, SC, USA
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai 201306, China
| | - Michel Veuille
- Institut de Systématique, Évolution, Biodiversité, ISYEB-UMR 7205-CNRS, MNHN, UPMC, EPHE, Ecole Pratique des Hautes Etudes, 16 rue Buffon, CP39, 75005, Paris, France
- EPHE, PSL Research University, Paris, France
| | - Serge Planes
- CRIOBE-USR 3278, CNRS-EPHE-UPVD, Laboratoire d’Excellence ‘CORAIL’, 58 Avenue Paul Alduy, 66860 Perpignan, France
| | - Gavin Naylor
- Department of Biology, College of Charleston, Charleston 29412, SC, USA
| | - Stefano Mona
- Institut de Systématique, Évolution, Biodiversité, ISYEB-UMR 7205-CNRS, MNHN, UPMC, EPHE, Ecole Pratique des Hautes Etudes, 16 rue Buffon, CP39, 75005, Paris, France
- EPHE, PSL Research University, Paris, France
| |
Collapse
|
154
|
Derkarabetian S, Burns M, Starrett J, Hedin M. Population genomic evidence for multiple Pliocene refugia in a montane‐restricted harvestman (Arachnida, Opiliones,
Sclerobunus robustus
) from the southwestern United States. Mol Ecol 2016; 25:4611-31. [DOI: 10.1111/mec.13789] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Revised: 07/11/2016] [Accepted: 07/19/2016] [Indexed: 01/07/2023]
Affiliation(s)
- Shahan Derkarabetian
- Department of Biology San Diego State University 5500 Campanile Dr. San Diego CA 92182‐4614 USA
- Department of Biology University of California Riverside Riverside CA 92521 USA
| | - Mercedes Burns
- Department of Biology San Diego State University 5500 Campanile Dr. San Diego CA 92182‐4614 USA
| | - James Starrett
- Department of Biology San Diego State University 5500 Campanile Dr. San Diego CA 92182‐4614 USA
| | - Marshal Hedin
- Department of Biology San Diego State University 5500 Campanile Dr. San Diego CA 92182‐4614 USA
| |
Collapse
|
155
|
Mende MB, Bartel M, Hundsdoerfer AK. A comprehensive phylogeography of the Hyles euphorbiae complex (Lepidoptera: Sphingidae) indicates a 'glacial refuge belt'. Sci Rep 2016; 6:29527. [PMID: 27439775 PMCID: PMC4954964 DOI: 10.1038/srep29527] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 06/08/2016] [Indexed: 12/20/2022] Open
Abstract
We test the morphology based hypothesis that the Western Palaearctic spurge hawkmoths represent two species, the Eurasian H. euphorbiae and Afro-Macaronesian H. tithymali. It has been suggested that these species merged into several hybrid swarm populations, although a mitochondrial phylogeography revealed substructure with local differentiation. We analysed a three-gene mt-dataset (889 individuals) and 12 microsatellite loci (892 individuals). Microsatellite analyses revealed an overall weak differentiation and corroborated the superordinate division into two clusters. The data indicate that the populations studied belong to only one species according to the biological species concept, refuting the opening hypothesis. A future taxonomic revision appears necessary to reflect the division into two subgroups. Ancestral mitochondrial polymorphisms are retained in H. euphorbiae, indicating gene flow within a broad 'glacial refuge belt' and ongoing postglacial gene flow. Diverse patterns of extensive mito-nuclear discordance in the Mediterranean and the Middle East presumably evolved by more recent processes. This discordance indicates introgression of H. tithymali-related mitochondrial haplogroups, accompanied (to a lesser degree) by nuclear alleles, into Italian and Aegean H. euphorbiae populations as recently as the late Holocene. The complex mosaic of divergence and reintegration is assumed to have been influenced by locally differing environmental barriers to gene flow.
Collapse
Affiliation(s)
- Michael B Mende
- Senckenberg Naturhistorische Sammlungen Dresden, Museum für Tierkunde, Königsbrücker Landstraße 159, D-01109 Dresden, Germany.,Georg-August-Universität Göttingen, Johann-Friedrich-Blumenbach-Institut für Zoologie und Anthropologie, Abteilung für Morphologie, Systematik und Evolutionsbiologie, Berliner Str. 28, D-37073 Göttingen, Germany.,Biodiversität und Klima Forschungszentrum (BiK-F), Senckenberganlage 25, D-60325 Frankfurt am Main, Germany
| | - Manuela Bartel
- Senckenberg Naturhistorische Sammlungen Dresden, Museum für Tierkunde, Königsbrücker Landstraße 159, D-01109 Dresden, Germany
| | - Anna K Hundsdoerfer
- Senckenberg Naturhistorische Sammlungen Dresden, Museum für Tierkunde, Königsbrücker Landstraße 159, D-01109 Dresden, Germany.,Biodiversität und Klima Forschungszentrum (BiK-F), Senckenberganlage 25, D-60325 Frankfurt am Main, Germany
| |
Collapse
|
156
|
Zhou W, Song N, Wang J, Gao T. Effects of geological changes and climatic fluctuations on the demographic histories and low genetic diversity of Squaliobarbus curriculus in Yellow River. Gene 2016; 590:149-58. [PMID: 27317893 DOI: 10.1016/j.gene.2016.06.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Revised: 05/20/2016] [Accepted: 06/03/2016] [Indexed: 11/16/2022]
Abstract
The 104 samples of Squaliobarbus curriculus were collected from four localities in Yellow River and one region in Yangtze River. Analyses of the first hypervariable region of mitochondrial DNA control region of 555bp revealed only 15 polymorphism sites and defined 19 haplotypes. Low-to-moderate levels of haplotype diversity and low nucleotide diversity were observed in Yellow River populations (h=0.2529-0.7510, π=0.0712%-0.2197%). In contrast, Poyang Lake population showed high haplotype diversity and lower-middle nucleotide diversity (h=0.9636, π=0.5317%). Low genetic differentiation was estimated among Yellow River populations and significant level of genetic structure was detected between two rivers. Population genetic structure between two rivers was believed to be connected with geographical barriers and paleoclimatic events. The demographic history of S. curriculus in Yellow River examined by neutrality tests, mismatch distribution analysis, and Bayesian skyline analysis suggested a sudden and spatial population expansion dating to the Holocene. Climatic warming and changes of Yellow River course may have important effects on demographic facet of S. curriculus history. The same signal was also obtained on Poyang Lake population in late Pleistocene during the last interglacial period. During the period, the pronounced climatic change and the water system variation of PYL may have an important influence on the population.
Collapse
Affiliation(s)
- Wei Zhou
- Fisheries College, Ocean University of China, Qingdao 266003, China
| | - Na Song
- Fisheries College, Ocean University of China, Qingdao 266003, China
| | - Jun Wang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
| | - Tianxiang Gao
- Fisheries College, Zhejaing Ocean University, Zhoushan 316022, China.
| |
Collapse
|
157
|
Mirazo S, Mir D, Bello G, Ramos N, Musto H, Arbiza J. New insights into the hepatitis E virus genotype 3 phylodynamics and evolutionary history. INFECTION GENETICS AND EVOLUTION 2016; 43:267-73. [PMID: 27264728 DOI: 10.1016/j.meegid.2016.06.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Revised: 05/19/2016] [Accepted: 06/01/2016] [Indexed: 12/27/2022]
Abstract
Hepatitis E virus (HEV) is an emergent hepatotropic virus endemic mainly in Asia and other developing areas. However, in the last decade it has been increasingly reported in high-income countries. Human infecting HEV strains are currently classified into four genotypes (1-4). Genotype 3 (HEV-3) is the prevalent virus genotype and the mostly associated with autochthonous and sporadic cases of HEV in developed areas. The evolutionary history of HEV worldwide remains largely unknown. In this study we reconstructed the spatiotemporal and population dynamics of HEV-3 at global scale, but with particular emphasis in South America, where case reports have increased dramatically in the last years. To achieve this, we applied a Bayesian coalescent-based approach to a comprehensive data set comprising 97 GenBank HEV-3 sequences for which the location and sampling date was documented. Our phylogenetic analyses suggest that the worldwide genetic diversity of HEV-3 can be grouped into two main Clades (I and II) with a Ƭmrca dated in approximately 320years ago (95% HPD: 420-236years) and that a unique independent introduction of HEV-3 seems to have occurred in Uruguay, where most of the human HEV cases in South America have been described. The phylodynamic inference indicates that the population size of this virus suffered substantial temporal variations after the second half of the 20th century. In this sense and conversely to what is postulated to date, we suggest that the worldwide effective population size of HEV-3 is not decreasing and that frequently sources of error in its estimates stem from assumptions that the analyzed sequences are derived from a single panmictic population. Novel insights on the global population dynamics of HEV are given. Additionally, this work constitutes an attempt to further describe in a Bayesian coalescent framework, the phylodynamics and evolutionary history of HEV-3 in the South American region.
Collapse
Affiliation(s)
- Santiago Mirazo
- Sección Virología, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay
| | - Daiana Mir
- Laboratorio de AIDS & Imunologia Molecular, Instituto Oswaldo Cruz. Av. Brasil 4365, 21045900 Rio de Janeiro, Brazil
| | - Gonzalo Bello
- Laboratorio de AIDS & Imunologia Molecular, Instituto Oswaldo Cruz. Av. Brasil 4365, 21045900 Rio de Janeiro, Brazil
| | - Natalia Ramos
- Sección Virología, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay
| | - Héctor Musto
- Laboratorio de Organización y Evolución del Genoma, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400. Montevideo, Uruguay
| | - Juan Arbiza
- Sección Virología, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay.
| |
Collapse
|
158
|
Qian C, Yin H, Shi Y, Zhao J, Yin C, Luo W, Dong Z, Chen G, Yan X, Wang XR, Ma XF. Population dynamics of Agriophyllum squarrosum, a pioneer annual plant endemic to mobile sand dunes, in response to global climate change. Sci Rep 2016; 6:26613. [PMID: 27210568 PMCID: PMC4876407 DOI: 10.1038/srep26613] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 05/04/2016] [Indexed: 12/02/2022] Open
Abstract
Climate change plays an important role in the transition of ecosystems. Stratigraphic investigations have suggested that the Asian interior experienced frequent transitions between grassland and desert ecosystems as a consequence of global climate change. Using maternally and bi-parentally inherited markers, we investigated the population dynamics of Agriophyllum squarrosum (Chenopodiaceae), an annual pioneer plant endemic to mobile sand dunes. Phylogeographic analysis revealed that A. squarrosum could originate from Gurbantunggut desert since ~1.6 Ma, and subsequently underwent three waves of colonisation into other deserts and sandy lands corresponding to several glaciations. The rapid population expansion and distribution range shifts of A. squarrosum from monsoonal climate zones suggested that the development of the monsoonal climate significantly enhanced the population growth and gene flow of A. squarrosum. These data also suggested that desertification of the fragile grassland ecosystems in the Qinghai-Tibetan Plateau was more ancient than previously suggested and will be aggravated under global warming in the future. This study provides new molecular phylogeographic insights into how pioneer annual plant species in desert ecosystems respond to global climate change, and facilitates evaluation of the ecological potential and genetic resources of future crops for non-arable dry lands to mitigate climate change.
Collapse
Affiliation(s)
- Chaoju Qian
- Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions, Gansu Province, Department of Ecology and Agriculture Research, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou 730000, Gansu, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hengxia Yin
- Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions, Gansu Province, Department of Ecology and Agriculture Research, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou 730000, Gansu, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yong Shi
- Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions, Gansu Province, Department of Ecology and Agriculture Research, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou 730000, Gansu, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiecai Zhao
- Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions, Gansu Province, Department of Ecology and Agriculture Research, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou 730000, Gansu, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chengliang Yin
- Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions, Gansu Province, Department of Ecology and Agriculture Research, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou 730000, Gansu, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wanyin Luo
- Key Laboratory of Desert and Desertification, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou 730000, Gansu, China
| | - Zhibao Dong
- Key Laboratory of Desert and Desertification, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou 730000, Gansu, China
| | - Guoxiong Chen
- Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions, Gansu Province, Department of Ecology and Agriculture Research, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou 730000, Gansu, China
| | - Xia Yan
- Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions, Gansu Province, Department of Ecology and Agriculture Research, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou 730000, Gansu, China
- Key Laboratory of Eco-hydrology and of Inland River Basin, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou 730000, Gansu, China
| | - Xiao-Ru Wang
- Department of Ecology and Environmental Science, Umeå University, Umeå 90187, Sweden
| | - Xiao-Fei Ma
- Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions, Gansu Province, Department of Ecology and Agriculture Research, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou 730000, Gansu, China
| |
Collapse
|
159
|
Horreo JL, Jiménez-Valverde A, Fitze PS. Ecological change predicts population dynamics and genetic diversity over 120 000 years. GLOBAL CHANGE BIOLOGY 2016; 22:1737-1745. [PMID: 26666533 DOI: 10.1111/gcb.13196] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 12/08/2015] [Indexed: 06/05/2023]
Abstract
While ecological effects on short-term population dynamics are well understood, their effects over millennia are difficult to demonstrate and convincing evidence is scant. Using coalescent methods, we analysed past population dynamics of three lizard species (Psammodromus hispanicus, P. edwardsianus, P. occidentalis) and linked the results with climate change data covering the same temporal horizon (120 000 years). An increase in population size over time was observed in two species, and in P. occidentalis, no change was observed. Temporal changes in temperature seasonality and the maximum temperature of the warmest month were congruent with changes in population dynamics observed for the three species and both variables affected population density, either directly or indirectly (via a life-history trait). These results constitute the first solid link between ecological change and long-term population dynamics. The results moreover suggest that ecological change leaves genetic signatures that can be retrospectively traced, providing evidence that ecological change is a crucial driver of genetic diversity and speciation.
Collapse
Affiliation(s)
- Jose Luis Horreo
- Department of Ecology and Evolution, University of Lausanne, Biophore, 1015, Lausanne, Switzerland
| | - Alberto Jiménez-Valverde
- Department of Biogeography and Global Change, Museo Nacional de Ciencias Naturales (MNCN-CSIC), José Gutiérrez Abascal 2, 28006, Madrid, Spain
- Grupo de Investigación de Biología del Suelo y de los Ecosistemas Subterráneos, Departamento de Ciencias de la Vida, Universidad de Alcalá, A.P. 20 Campus Universitario E-28805, Alcalá de Henares, Madrid, Spain
| | - Patrick S Fitze
- Department of Ecology and Evolution, University of Lausanne, Biophore, 1015, Lausanne, Switzerland
- Instituto Pirenaico de Ecología (IPE-CSIC), Avda. Nuestra Señora de la Victoria 16, 22700, Jaca, Spain
- Fundación Araid, Edificio CEEI Aragón María de Luna 11, 50018, Zaragoza, Spain
| |
Collapse
|
160
|
Rieux A, Balloux F. Inferences from tip-calibrated phylogenies: a review and a practical guide. Mol Ecol 2016; 25:1911-24. [PMID: 26880113 PMCID: PMC4949988 DOI: 10.1111/mec.13586] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Revised: 02/01/2016] [Accepted: 02/04/2016] [Indexed: 12/25/2022]
Abstract
Molecular dating of phylogenetic trees is a growing discipline using sequence data to co‐estimate the timing of evolutionary events and rates of molecular evolution. All molecular‐dating methods require converting genetic divergence between sequences into absolute time. Historically, this could only be achieved by associating externally derived dates obtained from fossil or biogeographical evidence to internal nodes of the tree. In some cases, notably for fast‐evolving genomes such as viruses and some bacteria, the time span over which samples were collected may cover a significant proportion of the time since they last shared a common ancestor. This situation allows phylogenetic trees to be calibrated by associating sampling dates directly to the sequences representing the tips (terminal nodes) of the tree. The increasing availability of genomic data from ancient DNA extends the applicability of such tip‐based calibration to a variety of taxa including humans, extinct megafauna and various microorganisms which typically have a scarce fossil record. The development of statistical models accounting for heterogeneity in different aspects of the evolutionary process while accommodating very large data sets (e.g. whole genomes) has allowed using tip‐dating methods to reach inferences on divergence times, substitution rates, past demography or the age of specific mutations on a variety of spatiotemporal scales. In this review, we summarize the current state of the art of tip dating, discuss some recent applications, highlight common pitfalls and provide a ‘how to’ guide to thoroughly perform such analyses.
Collapse
Affiliation(s)
- Adrien Rieux
- Department of Genetics, Evolution and Environment, UCL Genetics Institute, University College London, Gower Street, London, WC1E 6BT, UK
| | - François Balloux
- Department of Genetics, Evolution and Environment, UCL Genetics Institute, University College London, Gower Street, London, WC1E 6BT, UK
| |
Collapse
|
161
|
Yuan ZY, Suwannapoom C, Yan F, Poyarkov NA, Nguyen SN, Chen HM, Chomdej S, Murphy RW, Che J. Red River barrier and Pleistocene climatic fluctuations shaped the genetic structure of Microhyla fissipes complex (Anura: Microhylidae) in southern China and Indochina. Curr Zool 2016; 62:531-543. [PMID: 29491943 PMCID: PMC5804247 DOI: 10.1093/cz/zow042] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 03/14/2016] [Indexed: 11/13/2022] Open
Abstract
South China and Indochina host striking species diversity and endemism. Complex tectonic and climatic evolutions appear to be the main drivers of the biogeographic patterns. In this study, based on the geologic history of this region, we test 2 hypotheses using the evolutionary history of Microhyla fissipes species complex. Using DNA sequence data from both mitochondrial and nuclear genes, we first test the hypothesis that the Red River is a barrier to gene flow and dispersal. Second, we test the hypothesis that Pleistocene climatic cycling affected the genetic structure and population history of these frogs. We detect 2 major genetic splits that associate with the Red River. Time estimation suggests that late Miocene tectonic movement associated with the Red River drove their diversification. Species distribution modeling (SDM) resolves significant ecological differences between sides of the Red River. Thus, ecological divergence also probably promoted and maintained the diversification. Genogeography, historical demography, and SDM associate patterns in southern China with climate changes of the last glacial maximum (LGM), but not Indochina. Differences in geography and climate between the 2 areas best explain the discovery. Responses to the Pleistocene glacial–interglacial cycling vary among species and regions.
Collapse
Affiliation(s)
- Zhi-Yong Yuan
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.,Kunming College of Life Science, University of the Chinese Academy of Sciences, Kunming 650204, China.,Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Menglun, Mengla, Yunnan 666303, China
| | - Chatmongkon Suwannapoom
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.,School of Agriculture and Natural Resources, University of Phayao, Phayao 56000, Thailand
| | - Fang Yan
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.,Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Menglun, Mengla, Yunnan 666303, China
| | - Nikolay A Poyarkov
- Department of Vertebrate Zoology, Biological faculty, Lomonosov Moscow State University, Leninskiye Gory, Moscow 119234, Russia.,Joint Russian-Vietnamese Tropical Research and Technological Center, A.N. Severtsov Institute of Ecology and Evolution RAS, South Branch, District 10, Ho Chi Minh 700000, Vietnam
| | - Sang Ngoc Nguyen
- Institute of Tropical Biology, Vietnam Academy of Science and Technology, 85 Tran Quoc Toan St., District 3, Ho Chi Minh 700000, Vietnam
| | - Hong-Man Chen
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.,Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Menglun, Mengla, Yunnan 666303, China
| | - Siriwadee Chomdej
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand, and
| | - Robert W Murphy
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.,Centre for Biodiversity and Conservation Biology, Royal Ontario Museum, 100 Queen's Park, Toronto, Ontario M5S2C6, Canada
| | - Jing Che
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.,Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Menglun, Mengla, Yunnan 666303, China
| |
Collapse
|
162
|
Younger JL, van den Hoff J, Wienecke B, Hindell M, Miller KJ. Contrasting responses to a climate regime change by sympatric, ice-dependent predators. BMC Evol Biol 2016; 16:61. [PMID: 26975876 PMCID: PMC5477764 DOI: 10.1186/s12862-016-0630-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 03/01/2016] [Indexed: 02/02/2023] Open
Abstract
Background Models that predict changes in the abundance and distribution of fauna under future climate change scenarios often assume that ecological niche and habitat availability are the major determinants of species’ responses to climate change. However, individual species may have very different capacities to adapt to environmental change, as determined by intrinsic factors such as their dispersal ability, genetic diversity, generation time and rate of evolution. These intrinsic factors are usually excluded from forecasts of species’ abundance and distribution changes. We aimed to determine the importance of these factors by comparing the impact of the most recent climate regime change, the late Pleistocene glacial-interglacial transition, on two sympatric, ice-dependent meso-predators, the emperor penguin (Aptenodytes forsteri) and Weddell seal (Leptonychotes weddellii). Methods We reconstructed the population trend of emperor penguins and Weddell seals in East Antarctica over the past 75,000 years using mitochondrial DNA sequences and an extended Bayesian skyline plot method. We also assessed patterns of contemporary population structure and genetic diversity. Results Despite their overlapping distributions and shared dependence on sea ice, our genetic data revealed very different responses to climate warming between these species. The emperor penguin population grew rapidly following the glacial-interglacial transition, but the size of the Weddell seal population did not change. The expansion of emperor penguin numbers during the warm Holocene may have been facilitated by their higher dispersal ability and gene flow among colonies, and fine-scale differences in preferred foraging locations. Conclusions The vastly different climate change responses of two sympatric ice-dependent predators suggests that differing adaptive capacities and/or fine-scale niche differences can play a major role in species’ climate change responses, and that adaptive capacity should be considered alongside niche and distribution in future species forecasts. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0630-3) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Jane L Younger
- Institute for Marine and Antarctic Studies, University of Tasmania, Private Bag 129, Hobart, 7001, Tasmania, Australia.
| | - John van den Hoff
- Australian Antarctic Division, 203 Channel Highway, Kingston, 7050, Tasmania, Australia
| | - Barbara Wienecke
- Australian Antarctic Division, 203 Channel Highway, Kingston, 7050, Tasmania, Australia
| | - Mark Hindell
- Institute for Marine and Antarctic Studies, University of Tasmania, Private Bag 129, Hobart, 7001, Tasmania, Australia
| | - Karen J Miller
- Australian Institute of Marine Science, The UWA Oceans Institute, 35 Stirling Highway, Crawley, WA, 6009, Australia.,School of Biological Sciences, Private Bag 5, University of Tasmania, Hobart, 7001, Tasmania, Australia
| |
Collapse
|
163
|
Boitard S, Rodríguez W, Jay F, Mona S, Austerlitz F. Inferring Population Size History from Large Samples of Genome-Wide Molecular Data - An Approximate Bayesian Computation Approach. PLoS Genet 2016; 12:e1005877. [PMID: 26943927 PMCID: PMC4778914 DOI: 10.1371/journal.pgen.1005877] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 01/27/2016] [Indexed: 12/02/2022] Open
Abstract
Inferring the ancestral dynamics of effective population size is a long-standing question in population genetics, which can now be tackled much more accurately thanks to the massive genomic data available in many species. Several promising methods that take advantage of whole-genome sequences have been recently developed in this context. However, they can only be applied to rather small samples, which limits their ability to estimate recent population size history. Besides, they can be very sensitive to sequencing or phasing errors. Here we introduce a new approximate Bayesian computation approach named PopSizeABC that allows estimating the evolution of the effective population size through time, using a large sample of complete genomes. This sample is summarized using the folded allele frequency spectrum and the average zygotic linkage disequilibrium at different bins of physical distance, two classes of statistics that are widely used in population genetics and can be easily computed from unphased and unpolarized SNP data. Our approach provides accurate estimations of past population sizes, from the very first generations before present back to the expected time to the most recent common ancestor of the sample, as shown by simulations under a wide range of demographic scenarios. When applied to samples of 15 or 25 complete genomes in four cattle breeds (Angus, Fleckvieh, Holstein and Jersey), PopSizeABC revealed a series of population declines, related to historical events such as domestication or modern breed creation. We further highlight that our approach is robust to sequencing errors, provided summary statistics are computed from SNPs with common alleles. Molecular data sampled from extant individuals contains considerable information about their demographic history. In particular, one classical question in population genetics is to reconstruct past population size changes from such data. Relating these changes to various climatic, geological or anthropogenic events allows characterizing the main factors driving genetic diversity and can have major outcomes for conservation. Until recently, mostly very simple histories, including one or two population size changes, could be estimated from genetic data. This has changed with the sequencing of entire genomes in many species, and several methods allow now inferring complex histories consisting of several tens of population size changes. However, analyzing entire genomes, while accounting for recombination, remains a statistical and numerical challenge. These methods, therefore, can only be applied to small samples with a few diploid genomes. We overcome this limitation by using an approximate estimation approach, where observed genomes are summarized using a small number of statistics related to allele frequencies and linkage disequilibrium. In contrast to previous approaches, we show that our method allows us to reconstruct also the most recent part (the last 100 generations) of the population size history. As an illustration, we apply it to large samples of whole-genome sequences in four cattle breeds.
Collapse
Affiliation(s)
- Simon Boitard
- Institut de Systématique, Évolution, Biodiversité ISYEB - UMR 7205 - CNRS & MNHN & UPMC & EPHE, Ecole Pratique des Hautes Etudes, Sorbonne Universités, Paris, France
- GABI, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
- * E-mail:
| | - Willy Rodríguez
- UMR CNRS 5219, Institut de Mathématiques de Toulouse, Université de Toulouse, Toulouse, France
| | - Flora Jay
- UMR 7206 Eco-anthropologie et Ethnobiologie, Muséum National d’Histoire Naturelle, CNRS, Université Paris Diderot, Paris, France
- LRI, Paris-Sud University, CNRS UMR 8623, Orsay, France
| | - Stefano Mona
- Institut de Systématique, Évolution, Biodiversité ISYEB - UMR 7205 - CNRS & MNHN & UPMC & EPHE, Ecole Pratique des Hautes Etudes, Sorbonne Universités, Paris, France
| | - Frédéric Austerlitz
- UMR 7206 Eco-anthropologie et Ethnobiologie, Muséum National d’Histoire Naturelle, CNRS, Université Paris Diderot, Paris, France
| |
Collapse
|
164
|
Hall MD, Woolhouse MEJ, Rambaut A. The effects of sampling strategy on the quality of reconstruction of viral population dynamics using Bayesian skyline family coalescent methods: A simulation study. Virus Evol 2016; 2:vew003. [PMID: 27774296 PMCID: PMC4989886 DOI: 10.1093/ve/vew003] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The ongoing large-scale increase in the total amount of genetic data for viruses and other pathogens has led to a situation in which it is often not possible to include every available sequence in a phylogenetic analysis and expect the procedure to complete in reasonable computational time. This raises questions about how a set of sequences should be selected for analysis, particularly if the data are used to infer more than just the phylogenetic tree itself. The design of sampling strategies for molecular epidemiology has been a neglected field of research. This article describes a large-scale simulation exercise that was undertaken to select an appropriate strategy when using the GMRF skygrid, one of the Bayesian skyline family of coalescent methods, in order to reconstruct past population dynamics. The simulated scenarios were intended to represent sampling for the population of an endemic virus across multiple geographical locations. Large phylogenies were simulated under a coalescent or structured coalescent model and sequences simulated from these trees; the resulting datasets were then downsampled for analyses according to a variety of schemes. Variation in results between different replicates of the same scheme was not insignificant, and as a result, we recommend that where possible analyses are repeated with different datasets in order to establish that elements of a reconstruction are not simply the result of the particular set of samples selected. We show that an individual stochastic choice of sequences can introduce spurious behaviour in the median line of the skygrid plot and that even marginal likelihood estimation can suggest complicated dynamics that were not in fact present. We recommend that the median line should not be used to infer historical events on its own. Sampling sequences with uniform probability with respect to both time and spatial location (deme) never performed worse than sampling with probability proportional to the effective population size at that time and in that location and frequently was superior. As a result, we recommend this approach in the design of future studies. We also confirm that the inclusion of many recent sequences from a single geographical location in an analysis tends to result in a spurious bottleneck effect in the reconstruction and caution against interpreting this as genuine.
Collapse
Affiliation(s)
- Matthew D Hall
- Institute of Evolutionary Biology, University of Edinburgh EH9 3FL, Edinburgh, UK,; Centre for Immunity, Infection and Evolution, University of Edinburgh EH9 3FL, Edinburgh, UK and
| | - Mark E J Woolhouse
- Institute of Evolutionary Biology, University of Edinburgh EH9 3FL, Edinburgh, UK,; Centre for Immunity, Infection and Evolution, University of Edinburgh EH9 3FL, Edinburgh, UK and
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh EH9 3FL, Edinburgh, UK,; Centre for Immunity, Infection and Evolution, University of Edinburgh EH9 3FL, Edinburgh, UK and; Fogarty International Center, National Institutes of Health, Bethesda, MD 20892-2220, USA
| |
Collapse
|
165
|
Barros T, Gaubert P, Rocha RG, Bandeira V, Souto L, Mira A, Fonseca C. Mitochondrial demographic history of the Egyptian mongoose (Herpestes ichneumon), an expanding carnivore in the Iberian Peninsula. Mamm Biol 2016. [DOI: 10.1016/j.mambio.2015.09.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
166
|
Lapierre M, Blin C, Lambert A, Achaz G, Rocha EPC. The Impact of Selection, Gene Conversion, and Biased Sampling on the Assessment of Microbial Demography. Mol Biol Evol 2016; 33:1711-25. [PMID: 26931140 PMCID: PMC4915353 DOI: 10.1093/molbev/msw048] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Recent studies have linked demographic changes and epidemiological patterns in bacterial populations using coalescent-based approaches. We identified 26 studies using skyline plots and found that 21 inferred overall population expansion. This surprising result led us to analyze the impact of natural selection, recombination (gene conversion), and sampling biases on demographic inference using skyline plots and site frequency spectra (SFS). Forward simulations based on biologically relevant parameters from Escherichia coli populations showed that theoretical arguments on the detrimental impact of recombination and especially natural selection on the reconstructed genealogies cannot be ignored in practice. In fact, both processes systematically lead to spurious interpretations of population expansion in skyline plots (and in SFS for selection). Weak purifying selection, and especially positive selection, had important effects on skyline plots, showing patterns akin to those of population expansions. State-of-the-art techniques to remove recombination further amplified these biases. We simulated three common sampling biases in microbiological research: uniform, clustered, and mixed sampling. Alone, or together with recombination and selection, they further mislead demographic inferences producing almost any possible skyline shape or SFS. Interestingly, sampling sub-populations also affected skyline plots and SFS, because the coalescent rates of populations and their sub-populations had different distributions. This study suggests that extreme caution is needed to infer demographic changes solely based on reconstructed genealogies. We suggest that the development of novel sampling strategies and the joint analyzes of diverse population genetic methods are strictly necessary to estimate demographic changes in populations where selection, recombination, and biased sampling are present.
Collapse
Affiliation(s)
- Marguerite Lapierre
- Atelier de Bioinformatique, UMR7205 ISYEB, MNHN-UPMC-CNRS-EPHE, Muséum National d'Histoire Naturelle, Paris, France Collège de France, Center for Interdisciplinary Research in Biology (CIRB), CNRS UMR 7241, Paris, France
| | - Camille Blin
- Sorbonne Universités, UPMC Univ Paris06, IFD, 4 Place Jussieu, Paris Cedex05, France Institut Pasteur, Microbial Evolutionary Genomics, Paris, France CNRS, UMR3525, Paris, France
| | - Amaury Lambert
- Collège de France, Center for Interdisciplinary Research in Biology (CIRB), CNRS UMR 7241, Paris, France UPMC Univ Paris 06, Laboratoire de Probabilités et Modèles Aléatoires (LPMA), CNRS UMR 7599, Paris, France
| | - Guillaume Achaz
- Atelier de Bioinformatique, UMR7205 ISYEB, MNHN-UPMC-CNRS-EPHE, Muséum National d'Histoire Naturelle, Paris, France Collège de France, Center for Interdisciplinary Research in Biology (CIRB), CNRS UMR 7241, Paris, France
| | - Eduardo P C Rocha
- Institut Pasteur, Microbial Evolutionary Genomics, Paris, France CNRS, UMR3525, Paris, France
| |
Collapse
|
167
|
Orozco-terWengel P. The devil is in the details: the effect of population structure on demographic inference. Heredity (Edinb) 2016; 116:349-50. [PMID: 26883182 DOI: 10.1038/hdy.2016.9] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
|
168
|
Ancient, but not recent, population declines have had a genetic impact on alpine yellow-bellied toad populations, suggesting potential for complete recovery. CONSERV GENET 2016. [DOI: 10.1007/s10592-016-0818-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
|
169
|
Wilfert L, Long G, Leggett HC, Schmid-Hempel P, Butlin R, Martin SJM, Boots M. Deformed wing virus is a recent global epidemic in honeybees driven by Varroa mites. Science 2016; 351:594-7. [DOI: 10.1126/science.aac9976] [Citation(s) in RCA: 297] [Impact Index Per Article: 37.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
|
170
|
Ornelas JF, González C, Hernández-Baños BE, García-Moreno J. Molecular and iridescent feather reflectance data reveal recent genetic diversification and phenotypic differentiation in a cloud forest hummingbird. Ecol Evol 2016; 6:1104-27. [PMID: 26811749 PMCID: PMC4722824 DOI: 10.1002/ece3.1950] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Revised: 12/14/2015] [Accepted: 12/15/2015] [Indexed: 01/31/2023] Open
Abstract
The present day distribution and spatial genetic diversity of Mesoamerican biota reflects a long history of responses to habitat change. The hummingbird Lampornis amethystinus is distributed in northern Mesoamerica, with geographically disjunct populations. Based on sampling across the species range using mitochondrial DNA (mtDNA) sequences and nuclear microsatellites jointly analysed with phenotypic and climatic data, we (1) test whether the fragmented distribution is correlated with main evolutionary lineages, (2) assess body size and plumage color differentiation of populations in geographic isolation, and (3) evaluate a set of divergence scenarios and demographic patterns of the hummingbird populations. Analysis of genetic variation revealed four main groups: blue‐throated populations (Sierra Madre del Sur); two groups of amethyst‐throated populations (Trans‐Mexican Volcanic Belt and Sierra Madre Oriental); and populations east of the Isthmus of Tehuantepec (IT) with males showing an amethyst throat. The most basal split is estimated to have originated in the Pleistocene, 2.39–0.57 million years ago (MYA), and corresponded to groups of populations separated by the IT. However, the estimated recent divergence time between blue‐ and amethyst‐throated populations does not correspond to the 2‐MY needed to be in isolation for substantial plumage divergence, likely because structurally iridescent colors are more malleable than others. Results of species distribution modeling and Approximate Bayesian Computation analysis fit a model of lineage divergence west of the Isthmus after the Last Glacial Maximum (LGM), and that the species’ suitable habitat was disjunct during past and current conditions. These results challenge the generality of the contraction/expansion glacial model to cloud forest‐interior species and urges management of cloud forest, a highly vulnerable ecosystem to climate change and currently facing destruction, to prevent further loss of genetic diversity or extinction.
Collapse
Affiliation(s)
- Juan Francisco Ornelas
- Departamento de Biología Evolutiva Instituto de Ecología AC (INECOL) Xalapa Veracruz 91070 Mexico
| | - Clementina González
- Departamento de Biología Evolutiva Instituto de Ecología AC (INECOL) Xalapa Veracruz 91070 Mexico; Instituto de Investigaciones sobre los Recursos Naturales Universidad Michoacana de San Nicolás de Hidalgo Morelia Michoacán Mexico
| | - Blanca E Hernández-Baños
- Museo de Zoología Departamento de Biología Evolutiva Facultad de Ciencias Universidad Nacional Autónoma de México México DF 04510 Mexico
| | | |
Collapse
|
171
|
Ellingson RA, Krug PJ. Reduced genetic diversity and increased reproductive isolation follow population-level loss of larval dispersal in a marine gastropod. Evolution 2015; 70:18-37. [PMID: 26635309 DOI: 10.1111/evo.12830] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 11/17/2015] [Indexed: 01/01/2023]
Abstract
Population-level consequences of dispersal ability remain poorly understood, especially for marine animals in which dispersal is typically considered a species-level trait governed by oceanographic transport of microscopic larvae. Transitions from dispersive (planktotrophic) to nondispersive, aplanktonic larvae are predicted to reduce connectivity, genetic diversity within populations, and the spatial scale at which reproductive isolation evolves. However, larval dimorphism within a species is rare, precluding population-level tests. We show the sea slug Costasiella ocellifera expresses both larval morphs in Florida and the Caribbean, regions with divergent mitochondrial lineages. Planktotrophy predominated at 11 sites, 10 of which formed a highly connected and genetically diverse Caribbean metapopulation. Four populations expressed mainly aplanktonic development and had markedly reduced connectivity, and lower genetic diversity at one mitochondrial and six nuclear loci. Aplanktonic dams showed partial postzygotic isolation in most interpopulation crosses, regardless of genetic or geographic distance to the sire's source, suggesting that outbreeding depression affects fragmented populations. Dams from genetically isolated and neighboring populations also exhibited premating isolation, consistent with reinforcement contingent on historical interaction. By increasing self-recruitment and genetic drift, the loss of dispersal may thus initiate a feedback loop resulting in the evolution of reproductive isolation over small spatial scales in the sea.
Collapse
Affiliation(s)
- Ryan A Ellingson
- Department of Biological Sciences, California State University, 5151 State University Dr., Los Angeles, California, 90032-8201
| | - Patrick J Krug
- Department of Biological Sciences, California State University, 5151 State University Dr., Los Angeles, California, 90032-8201.
| |
Collapse
|
172
|
Hoareau TB. Late Glacial Demographic Expansion Motivates a Clock Overhaul for Population Genetics. Syst Biol 2015; 65:449-64. [PMID: 26683588 DOI: 10.1093/sysbio/syv120] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2014] [Accepted: 12/10/2015] [Indexed: 12/18/2022] Open
Abstract
The molecular clock hypothesis is fundamental in evolutionary biology as by assuming constancy of the molecular rate it provides a timeframe for evolution. However, increasing evidence shows time dependence of inferred molecular rates with inflated values obtained using recent calibrations. As recent demographic calibrations are virtually non-existent in most species, older phylogenetic calibration points (>1 Ma) are commonly used, which overestimate demographic parameters. To obtain more reliable rates of molecular evolution for population studies, I propose the calibration of demographic transition (CDT) method, which uses the timing of climatic changes over the late glacial warming period to calibrate expansions in various species. Simulation approaches and empirical data sets from a diversity of species (from mollusk to humans) confirm that, when compared with other genealogy-based calibration methods, the CDT provides a robust and broadly applicable clock for population genetics. The resulting CDT rates of molecular evolution also confirm rate heterogeneity over time and among taxa. Comparisons of expansion dates with ecological evidence confirm the inaccuracy of phylogenetically derived divergence rates when dating population-level events. The CDT method opens opportunities for addressing issues such as demographic responses to past climate change and the origin of rate heterogeneity related to taxa, genes, time, and genetic information content.
Collapse
Affiliation(s)
- Thierry B Hoareau
- Molecular Ecology and Evolution Programme, Department of Genetics, University of Pretoria, Private bag X20, Hatfield, Pretoria 0028, South Africa
| |
Collapse
|
173
|
Genetic Diversity, Population Size, and Conservation of the Critically Endangered Perrier’s Sifaka (Propithecus perrieri). INT J PRIMATOL 2015. [DOI: 10.1007/s10764-015-9881-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
174
|
On the importance of being structured: instantaneous coalescence rates and human evolution--lessons for ancestral population size inference? Heredity (Edinb) 2015; 116:362-71. [PMID: 26647653 DOI: 10.1038/hdy.2015.104] [Citation(s) in RCA: 165] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Revised: 10/07/2015] [Accepted: 10/28/2015] [Indexed: 11/09/2022] Open
Abstract
Most species are structured and influenced by processes that either increased or reduced gene flow between populations. However, most population genetic inference methods assume panmixia and reconstruct a history characterized by population size changes. This is potentially problematic as population structure can generate spurious signals of population size change through time. Moreover, when the model assumed for demographic inference is misspecified, genomic data will likely increase the precision of misleading if not meaningless parameters. For instance, if data were generated under an n-island model (characterized by the number of islands and migrants exchanged) inference based on a model of population size change would produce precise estimates of a bottleneck that would be meaningless. In addition, archaeological or climatic events around the bottleneck's timing might provide a reasonable but potentially misleading scenario. In a context of model uncertainty (panmixia versus structure) genomic data may thus not necessarily lead to improved statistical inference. We consider two haploid genomes and develop a theory that explains why any demographic model with structure will necessarily be interpreted as a series of changes in population size by inference methods ignoring structure. We formalize a parameter, the inverse instantaneous coalescence rate, and show that it is equivalent to a population size only in panmictic models, and is mostly misleading for structured models. We argue that this issue affects all population genetics methods ignoring population structure which may thus infer population size changes that never took place. We apply our approach to human genomic data.
Collapse
|
175
|
Pedersen CET, Frandsen P, Wekesa SN, Heller R, Sangula AK, Wadsworth J, Knowles NJ, Muwanika VB, Siegismund HR. Time Clustered Sampling Can Inflate the Inferred Substitution Rate in Foot-And-Mouth Disease Virus Analyses. PLoS One 2015; 10:e0143605. [PMID: 26630483 PMCID: PMC4667911 DOI: 10.1371/journal.pone.0143605] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 11/06/2015] [Indexed: 11/24/2022] Open
Abstract
With the emergence of analytical software for the inference of viral evolution, a number of studies have focused on estimating important parameters such as the substitution rate and the time to the most recent common ancestor (tMRCA) for rapidly evolving viruses. Coupled with an increasing abundance of sequence data sampled under widely different schemes, an effort to keep results consistent and comparable is needed. This study emphasizes commonly disregarded problems in the inference of evolutionary rates in viral sequence data when sampling is unevenly distributed on a temporal scale through a study of the foot-and-mouth (FMD) disease virus serotypes SAT 1 and SAT 2. Our study shows that clustered temporal sampling in phylogenetic analyses of FMD viruses will strongly bias the inferences of substitution rates and tMRCA because the inferred rates in such data sets reflect a rate closer to the mutation rate rather than the substitution rate. Estimating evolutionary parameters from viral sequences should be performed with due consideration of the differences in short-term and longer-term evolutionary processes occurring within sets of temporally sampled viruses, and studies should carefully consider how samples are combined.
Collapse
Affiliation(s)
| | - Peter Frandsen
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | - Rasmus Heller
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | - Jemma Wadsworth
- The Pirbright Institute, Ash Road, Pirbright, United Kingdom
| | - Nick J. Knowles
- The Pirbright Institute, Ash Road, Pirbright, United Kingdom
| | - Vincent B. Muwanika
- Department of Environmental Management, College of Agricultural and Environmental Sciences, Makerere University, Kampala, Uganda
| | | |
Collapse
|
176
|
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
| |
Collapse
|
177
|
Alvarado‐Serrano DF, Hickerson MJ. Spatially explicit summary statistics for historical population genetic inference. Methods Ecol Evol 2015. [DOI: 10.1111/2041-210x.12489] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
| | - Michael J. Hickerson
- Biology Department The City College of New York City University of New York New York NY 10031 USA
- Program in Ecology, Evolutionary Biology & Behavior The Graduate Center City University of New York (CUNY) New York NY 10016 USA
- Division of Invertebrate Zoology American Museum of Natural History New York NY 10024 USA
| |
Collapse
|
178
|
Lv FH, Peng WF, Yang J, Zhao YX, Li WR, Liu MJ, Ma YH, Zhao QJ, Yang GL, Wang F, Li JQ, Liu YG, Shen ZQ, Zhao SG, Hehua E, Gorkhali NA, Farhad Vahidi SM, Muladno M, Naqvi AN, Tabell J, Iso-Touru T, Bruford MW, Kantanen J, Han JL, Li MH. Mitogenomic Meta-Analysis Identifies Two Phases of Migration in the History of Eastern Eurasian Sheep. Mol Biol Evol 2015; 32:2515-33. [PMID: 26085518 PMCID: PMC4576706 DOI: 10.1093/molbev/msv139] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Despite much attention, history of sheep (Ovis aries) evolution, including its dating, demographic trajectory and geographic spread, remains controversial. To address these questions, we generated 45 complete and 875 partial mitogenomic sequences, and performed a meta-analysis of these and published ovine mitochondrial DNA sequences (n = 3,229) across Eurasia. We inferred that O. orientalis and O. musimon share the most recent female ancestor with O. aries at approximately 0.790 Ma (95% CI: 0.637-0.934 Ma) during the Middle Pleistocene, substantially predating the domestication event (∼8-11 ka). By reconstructing historical variations in effective population size, we found evidence of a rapid population increase approximately 20-60 ka, immediately before the Last Glacial Maximum. Analyses of lineage expansions showed two sheep migratory waves at approximately 4.5-6.8 ka (lineages A and B: ∼6.4-6.8 ka; C: ∼4.5 ka) across eastern Eurasia, which could have been influenced by prehistoric West-East commercial trade and deliberate mating of domestic and wild sheep, respectively. A continent-scale examination of lineage diversity and approximate Bayesian computation analyses indicated that the Mongolian Plateau region was a secondary center of dispersal, acting as a "transportation hub" in eastern Eurasia: Sheep from the Middle Eastern domestication center were inferred to have migrated through the Caucasus and Central Asia, and arrived in North and Southwest China (lineages A, B, and C) and the Indian subcontinent (lineages B and C) through this region. Our results provide new insights into sheep domestication, particularly with respect to origins and migrations to and from eastern Eurasia.
Collapse
Affiliation(s)
- Feng-Hua Lv
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China
| | - Wei-Feng Peng
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China University of Chinese Academy of Sciences (UCAS), Beijing, China
| | - Ji Yang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China
| | - Yong-Xin Zhao
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China University of Chinese Academy of Sciences (UCAS), Beijing, China
| | - Wen-Rong Li
- Animal Biotechnology Research Institute, Xinjiang Academy of Animal Science, Urumqi, China
| | - Ming-Jun Liu
- Animal Biotechnology Research Institute, Xinjiang Academy of Animal Science, Urumqi, China
| | - Yue-Hui Ma
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Qian-Jun Zhao
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Guang-Li Yang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China College of Life Sciences, Shangqiu Normal University, Shangqiu, China
| | - Feng Wang
- Institute of Sheep and Goat Science, Nanjing Agricultural University, Nanjing, China
| | - Jin-Quan Li
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Yong-Gang Liu
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Zhi-Qiang Shen
- Shandong Binzhou Academy of Animal Science and Veterinary Medicine, Binzhou, China
| | - Sheng-Guo Zhao
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Eer Hehua
- Grass-Feeding Livestock Engineering Technology Research Center, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, China
| | - Neena A Gorkhali
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China Animal Breeding Division, National Animal Science Institute, Nepal Agriculture Research Council, Kathmandu, Nepal
| | - S M Farhad Vahidi
- Agricultural Biotechnology Research Institute of Iran-North Branch (ABRII), Rasht, Iran
| | - Muhammad Muladno
- Department of Animal Technology and Production Science, Bogor Agricultural University, Darmaga Campus, Bogor, Indonesia
| | - Arifa N Naqvi
- Faculty of Life Sciences, Karakoram International University, Gilgit, Baltistan, Pakistan
| | - Jonna Tabell
- Green Technology, Natural Resources Institute Finland (LUKE), Jokioinen, Finland
| | - Terhi Iso-Touru
- Green Technology, Natural Resources Institute Finland (LUKE), Jokioinen, Finland
| | - Michael W Bruford
- School of Biosciences and Sustainable Places Research Institute, Cardiff University, Cardiff, United Kingdom
| | - Juha Kantanen
- Green Technology, Natural Resources Institute Finland (LUKE), Jokioinen, Finland Department of Biology, University of Eastern Finland, Kuopio, Finland
| | - Jian-Lin Han
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Meng-Hua Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China
| |
Collapse
|
179
|
Demographic History of Indigenous Populations in Mesoamerica Based on mtDNA Sequence Data. PLoS One 2015; 10:e0131791. [PMID: 26292226 PMCID: PMC4546282 DOI: 10.1371/journal.pone.0131791] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 06/08/2015] [Indexed: 11/19/2022] Open
Abstract
The genetic characterization of Native American groups provides insights into their history and demographic events. We sequenced the mitochondrial D-loop region (control region) of 520 samples from eight Mexican indigenous groups. In addition to an analysis of the genetic diversity, structure and genetic relationship between 28 Native American populations, we applied Bayesian skyline methodology for a deeper insight into the history of Mesoamerica. AMOVA tests applying cultural, linguistic and geographic criteria were performed. MDS plots showed a central cluster of Oaxaca and Maya populations, whereas those from the North and West were located on the periphery. Demographic reconstruction indicates higher values of the effective number of breeding females (Nef) in Central Mesoamerica during the Preclassic period, whereas this pattern moves toward the Classic period for groups in the North and West. Conversely, Nef minimum values are distributed either in the Lithic period (i.e. founder effects) or in recent periods (i.e. population declines). The Mesomerican regions showed differences in population fluctuation as indicated by the maximum Inter-Generational Rate (IGRmax): i) Center-South from the lithic period until the Preclassic; ii) West from the beginning of the Preclassic period until early Classic; iii) North characterized by a wide range of temporal variation from the Lithic to the Preclassic. Our findings are consistent with the genetic variations observed between central, South and Southeast Mesoamerica and the North-West region that are related to differences in genetic drift, structure, and temporal survival strategies (agriculture versus hunter-gathering, respectively). Interestingly, although the European contact had a major negative demographic impact, we detect a previous decline in Mesoamerica that had begun a few hundred years before.
Collapse
|
180
|
Brunes TO, Thomé MTC, Alexandrino J, Haddad CFB, Sequeira F. Ancient divergence and recent population expansion in a leaf frog endemic to the southern Brazilian Atlantic forest. ORG DIVERS EVOL 2015. [DOI: 10.1007/s13127-015-0228-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
|
181
|
Moseley MA, Cox CL, Streicher JW, Roelke CE, Chippindale PT. Phylogeography and lineage-specific patterns of genetic diversity and molecular evolution in a group of North American skinks. Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12626] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Matthew A. Moseley
- Department of Biology; The University of Texas at Arlington; Arlington TX 76010 USA
| | - Christian L. Cox
- Department of Biology; The University of Texas at Arlington; Arlington TX 76010 USA
- Department of Biology; The University of Virginia; Charlottesville VA 22903 USA
- Department of Biology; Georgia Southern University; Statesboro GA USA
| | - Jeffrey W. Streicher
- Department of Biology; The University of Texas at Arlington; Arlington TX 76010 USA
- Department of Life Sciences; The Natural History Museum; London SW7 5BD UK
| | - Corey E. Roelke
- Department of Biology; The University of Texas at Arlington; Arlington TX 76010 USA
| | - Paul T. Chippindale
- Department of Biology; The University of Texas at Arlington; Arlington TX 76010 USA
| |
Collapse
|
182
|
Parreira BR, Chikhi L. On some genetic consequences of social structure, mating systems, dispersal, and sampling. Proc Natl Acad Sci U S A 2015; 112:E3318-26. [PMID: 26080393 PMCID: PMC4491764 DOI: 10.1073/pnas.1414463112] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Many species are spatially and socially organized, with complex social organizations and dispersal patterns that are increasingly documented. Social species typically consist of small age-structured units, where a limited number of individuals monopolize reproduction and exhibit complex mating strategies. Here, we model social groups as age-structured units and investigate the genetic consequences of social structure under distinct mating strategies commonly found in mammals. Our results show that sociality maximizes genotypic diversity, which contradicts the belief that social groups are necessarily subject to strong genetic drift and at high risk of inbreeding depression. Social structure generates an excess of genotypic diversity. This is commonly observed in ecological studies but rarely reported in population genetic studies that ignore social structure. This heterozygosity excess, when detected, is often interpreted as a consequence of inbreeding avoidance mechanisms, but we show that it can occur even in the absence of such mechanisms. Many seemly contradictory results from ecology and population genetics can be reconciled by genetic models that include the complexities of social species. We find that such discrepancies can be explained by the intrinsic properties of social groups and by the sampling strategies of real populations. In particular, the number of social groups and the nature of the individuals that compose samples (e.g., nonreproductive and reproductive individuals) are key factors in generating outbreeding signatures. Sociality is an important component of population structure that needs to be revisited by ecologists and population geneticists alike.
Collapse
Affiliation(s)
- Bárbara R Parreira
- Instituto Gulbenkian de Ciência, 2780-156 Oeiras, Portugal; Departamento de Biologia Vegetal, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisbon, Portugal;
| | - Lounès Chikhi
- Instituto Gulbenkian de Ciência, 2780-156 Oeiras, Portugal; CNRS, Université Paul Sabatier, Ecole Nationale de Formation Agronomique, UMR5174 EDB (Laboratoire Évolution & Diversité Biologique), F-31062 Toulouse, France
| |
Collapse
|
183
|
Mazet O, Rodríguez W, Chikhi L. Demographic inference using genetic data from a single individual: Separating population size variation from population structure. Theor Popul Biol 2015; 104:46-58. [PMID: 26120083 DOI: 10.1016/j.tpb.2015.06.003] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Revised: 06/11/2015] [Accepted: 06/16/2015] [Indexed: 10/23/2022]
Abstract
The rapid development of sequencing technologies represents new opportunities for population genetics research. It is expected that genomic data will increase our ability to reconstruct the history of populations. While this increase in genetic information will likely help biologists and anthropologists to reconstruct the demographic history of populations, it also represents new challenges. Recent work has shown that structured populations generate signals of population size change. As a consequence it is often difficult to determine whether demographic events such as expansions or contractions (bottlenecks) inferred from genetic data are real or due to the fact that populations are structured in nature. Given that few inferential methods allow us to account for that structure, and that genomic data will necessarily increase the precision of parameter estimates, it is important to develop new approaches. In the present study we analyze two demographic models. The first is a model of instantaneous population size change whereas the second is the classical symmetric island model. We (i) re-derive the distribution of coalescence times under the two models for a sample of size two, (ii) use a maximum likelihood approach to estimate the parameters of these models (iii) validate this estimation procedure under a wide array of parameter combinations, (iv) implement and validate a model rejection procedure by using a Kolmogorov-Smirnov test, and a model choice procedure based on the AIC, and (v) derive the explicit distribution for the number of differences between two non-recombining sequences. Altogether we show that it is possible to estimate parameters under several models and perform efficient model choice using genetic data from a single diploid individual.
Collapse
Affiliation(s)
- Olivier Mazet
- UMR 5219, Institut de Mathématiques de Toulouse, Université de Toulouse & CNRS, France
| | - Willy Rodríguez
- UMR 5219, Institut de Mathématiques de Toulouse, Université de Toulouse & CNRS, France
| | - Lounès Chikhi
- CNRS, Université Paul Sabatier, ENFA, UMR 5174 EDB (Laboratoire Évolution & Diversité Biologique), F-31062 Toulouse, France; Université de Toulouse, UPS, EDB, F-31062 Toulouse, France; Instituto Gulbenkian de Ciência, P-2780-156 Oeiras, Portugal.
| |
Collapse
|
184
|
Ruane S, Torres-Carvajal O, Burbrink FT. Independent Demographic Responses to Climate Change among Temperate and Tropical Milksnakes (Colubridae: Genus Lampropeltis). PLoS One 2015; 10:e0128543. [PMID: 26083467 PMCID: PMC4470684 DOI: 10.1371/journal.pone.0128543] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Accepted: 04/28/2015] [Indexed: 01/02/2023] Open
Abstract
The effects of Late Quaternary climate change have been examined for many temperate New World taxa, but the impact of Pleistocene glacial cycles on Neotropical taxa is less well understood, specifically with respect to changes in population demography. Here, we examine historical demographic trends for six species of milksnake with representatives in both the temperate and tropical Americas to determine if species share responses to climate change as a taxon or by area (i.e., temperate versus tropical environments). Using a multilocus dataset, we test for the demographic signature of population expansion and decline using non-genealogical summary statistics, as well as coalescent-based methods. In addition, we determine whether range sizes are correlated with effective population sizes for milksnakes. Results indicate that there are no identifiable trends with respect to demographic response based on location, and that species responded to changing climates independently, with tropical taxa showing greater instability. There is also no correlation between range size and effective population size, with the largest population size belonging to the species with the smallest geographic distribution. Our study highlights the importance of not generalizing the demographic histories of taxa by region and further illustrates that the New World tropics may not have been a stable refuge during the Pleistocene.
Collapse
Affiliation(s)
- Sara Ruane
- Department of Biology, College of Staten Island, 2800 Victory Blvd., Staten Island, NY, 10314, United States of America
- The Graduate Center, City University of New York, 365 5 Avenue, New York, NY, 10016, United States of America
- * E-mail:
| | - Omar Torres-Carvajal
- Museo de Zoología, Escuela de Biología, Pontificia Universidad Católica del Ecuador, Avenida 12 de Octubre y Roca, Apartado 17-01-2184, Quito, Ecuador
| | - Frank T. Burbrink
- Department of Biology, College of Staten Island, 2800 Victory Blvd., Staten Island, NY, 10314, United States of America
- The Graduate Center, City University of New York, 365 5 Avenue, New York, NY, 10016, United States of America
| |
Collapse
|
185
|
Grant WS. Problems and Cautions With Sequence Mismatch Analysis and Bayesian Skyline Plots to Infer Historical Demography. J Hered 2015; 106:333-46. [DOI: 10.1093/jhered/esv020] [Citation(s) in RCA: 164] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Accepted: 03/24/2015] [Indexed: 12/11/2022] Open
|
186
|
Stoffel C, Dufresnes C, Okello JBA, Noirard C, Joly P, Nyakaana S, Muwanika VB, Alcala N, Vuilleumier S, Siegismund HR, Fumagalli L. Genetic consequences of population expansions and contractions in the common hippopotamus (Hippopotamus amphibius) since the Late Pleistocene. Mol Ecol 2015; 24:2507-20. [PMID: 25827243 DOI: 10.1111/mec.13179] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Revised: 03/11/2015] [Accepted: 03/18/2015] [Indexed: 11/30/2022]
Abstract
Over the past two decades, an increasing amount of phylogeographic work has substantially improved our understanding of African biogeography, in particular the role played by Pleistocene pluvial-drought cycles on terrestrial vertebrates. However, still little is known on the evolutionary history of semi-aquatic animals, which faced tremendous challenges imposed by unpredictable availability of water resources. In this study, we investigate the Late Pleistocene history of the common hippopotamus (Hippopotamus amphibius), using mitochondrial and nuclear DNA sequence variation and range-wide sampling. We documented a global demographic and spatial expansion approximately 0.1-0.3 Myr ago, most likely associated with an episode of massive drainage overflow. These events presumably enabled a historical continent-wide gene flow among hippopotamus populations, and hence, no clear continental-scale genetic structuring remains. Nevertheless, present-day hippopotamus populations are genetically disconnected, probably as a result of the mid-Holocene aridification and contemporary anthropogenic pressures. This unique pattern contrasts with the biogeographic paradigms established for savannah-adapted ungulate mammals and should be further investigated in other water-associated taxa. Our study has important consequences for the conservation of the hippo, an emblematic but threatened species that requires specific protection to curtail its long-term decline.
Collapse
Affiliation(s)
- Céline Stoffel
- Department of Ecology and Evolution, Laboratory for Conservation Biology, University of Lausanne, Biophore Building, 1015, Lausanne, Switzerland
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
187
|
Stojak J, McDevitt AD, Herman JS, Searle JB, Wójcik JM. Post-glacial colonization of eastern Europe from the Carpathian refugium: evidence from mitochondrial DNA of the common voleMicrotus arvalis. Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12535] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Joanna Stojak
- Mammal Research Institute; Polish Academy of Sciences; 17-230 Białowieża Poland
| | - Allan D. McDevitt
- Mammal Research Institute; Polish Academy of Sciences; 17-230 Białowieża Poland
- Laboratory of Biodiversity and Evolutionary Genomics; University of Leuven; 3000 Leuven Belgium
| | - Jeremy S. Herman
- Department of Natural Sciences; National Museums Scotland; Edinburgh EH1 1JF UK
| | - Jeremy B. Searle
- Department of Ecology and Evolutionary Biology; Cornell University; Ithaca NY 14853-2701 USA
| | - Jan M. Wójcik
- Mammal Research Institute; Polish Academy of Sciences; 17-230 Białowieża Poland
| |
Collapse
|
188
|
McTavish EJ, Hillis DM. How do SNP ascertainment schemes and population demographics affect inferences about population history? BMC Genomics 2015; 16:266. [PMID: 25887858 PMCID: PMC4428227 DOI: 10.1186/s12864-015-1469-5] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 03/17/2015] [Indexed: 12/15/2022] Open
Abstract
Background The selection of variable sites for inclusion in genomic analyses can influence results, especially when exemplar populations are used to determine polymorphic sites. We tested the impact of ascertainment bias on the inference of population genetic parameters using empirical and simulated data representing the three major continental groups of cattle: European, African, and Indian. We simulated data under three demographic models. Each simulated data set was subjected to three ascertainment schemes: (I) random selection; (II) geographically biased selection; and (III) selection biased toward loci polymorphic in multiple groups. Empirical data comprised samples of 25 individuals representing each continental group. These cattle were genotyped for 47,506 loci from the bovine 50 K SNP panel. We compared the inference of population histories for the empirical and simulated data sets across different ascertainment conditions using FST and principal components analysis (PCA). Results Bias toward shared polymorphism across continental groups is apparent in the empirical SNP data. Bias toward uneven levels of within-group polymorphism decreases estimates of FST between groups. Subpopulation-biased selection of SNPs changes the weighting of principal component axes and can affect inferences about proportions of admixture and population histories using PCA. PCA-based inferences of population relationships are largely congruent across types of ascertainment bias, even when ascertainment bias is strong. Conclusions Analyses of ascertainment bias in genomic data have largely been conducted on human data. As genomic analyses are being applied to non-model organisms, and across taxa with deeper divergences, care must be taken to consider the potential for bias in ascertainment of variation to affect inferences. Estimates of FST, time of separation, and population divergence as estimated by principal components analysis can be misleading if this bias is not taken into account. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1469-5) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Emily Jane McTavish
- Department of Ecology and Evolutionary Biology, University of Kansas, 1200 Sunnyside Avenue, Lawrence, KS, 66045, USA. .,Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, Heidelberg, D-69118, Germany.
| | - David M Hillis
- Department of Integrative Biology, University of Texas, One University Station C0990, Austin, TX, 78712, USA.
| |
Collapse
|
189
|
Epidemic history of major genotypes of hepatitis C virus in Uruguay. INFECTION GENETICS AND EVOLUTION 2015; 32:231-8. [PMID: 25801607 DOI: 10.1016/j.meegid.2015.03.021] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Revised: 03/10/2015] [Accepted: 03/13/2015] [Indexed: 12/23/2022]
Abstract
Worldwide, more than 170 million people are chronically infected with the hepatitis C virus (HCV) and every year die more than 350,000 people from HCV-related liver diseases. Recently, HCV was reclassified into seven major genotypes and 67 subtypes. Some subtypes as 1a, 1b and 3a, have become epidemic as a result of the new parenteral transmission routes and are responsible for most HCV infections in Western countries. HCV 1a subtype have been sub-categorized into two separate sub clades. Recent studies based on the analysis of NS5B genome region, reveal that HCV epidemics in Argentina and Brazil are characterized by multiple introductions events of subtypes 1a, 1b and 3a, followed by subsequent local dispersion. There is no data about HCV genotypes circulating in Uruguay and their evolutionary and demographic history. To this end, a total of 153 HCV NS5B gene sequences were obtained from Uruguayan patients between 2005 and 2011. 86 (56%) sequences grouped with subtype 1a, 40 (26%) with subtype 3a and 27 (18%) with subtype 1b. Furthermore, subtype 1a sequences were distributed among both clades, 1 (n=62, 72%) and 2 (n=24, 28%). Four local HCV clades were found: UY-1a(I), UY-1a(II), UY-1a(III) and UY-3a; comprising a 39% of all HCV viruses analyzed in this study. HCV epidemic in Uruguay has been driving by multiple introductions of subtypes 1a, 1b and 3a and by local dissemination of a few country-specific strains. The evolutionary and demographic history of the major Uruguayan HCV clade UY-1a(I) was reconstructed under two different molecular clock rate models and displayed an epidemic history characterized by an initial phase of rapid expansion followed by a more recent reduction of growth rate since 2000-2005. This is the first comprehensive study about the molecular epidemiology and epidemic history of HCV in Uruguay.
Collapse
|
190
|
Karmin M, Saag L, Vicente M, Wilson Sayres MA, Järve M, Talas UG, Rootsi S, Ilumäe AM, Mägi R, Mitt M, Pagani L, Puurand T, Faltyskova Z, Clemente F, Cardona A, Metspalu E, Sahakyan H, Yunusbayev B, Hudjashov G, DeGiorgio M, Loogväli EL, Eichstaedt C, Eelmets M, Chaubey G, Tambets K, Litvinov S, Mormina M, Xue Y, Ayub Q, Zoraqi G, Korneliussen TS, Akhatova F, Lachance J, Tishkoff S, Momynaliev K, Ricaut FX, Kusuma P, Razafindrazaka H, Pierron D, Cox MP, Sultana GNN, Willerslev R, Muller C, Westaway M, Lambert D, Skaro V, Kovačevic L, Turdikulova S, Dalimova D, Khusainova R, Trofimova N, Akhmetova V, Khidiyatova I, Lichman DV, Isakova J, Pocheshkhova E, Sabitov Z, Barashkov NA, Nymadawa P, Mihailov E, Seng JWT, Evseeva I, Migliano AB, Abdullah S, Andriadze G, Primorac D, Atramentova L, Utevska O, Yepiskoposyan L, Marjanovic D, Kushniarevich A, Behar DM, Gilissen C, Vissers L, Veltman JA, Balanovska E, Derenko M, Malyarchuk B, Metspalu A, Fedorova S, Eriksson A, Manica A, Mendez FL, Karafet TM, Veeramah KR, Bradman N, Hammer MF, Osipova LP, Balanovsky O, Khusnutdinova EK, Johnsen K, Remm M, Thomas MG, Tyler-Smith C, Underhill PA, Willerslev E, Nielsen R, Metspalu M, Villems R, Kivisild T. A recent bottleneck of Y chromosome diversity coincides with a global change in culture. Genome Res 2015; 25:459-66. [PMID: 25770088 PMCID: PMC4381518 DOI: 10.1101/gr.186684.114] [Citation(s) in RCA: 231] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Accepted: 02/13/2015] [Indexed: 11/25/2022]
Abstract
It is commonly thought that human genetic diversity in non-African populations was shaped primarily by an out-of-Africa dispersal 50–100 thousand yr ago (kya). Here, we present a study of 456 geographically diverse high-coverage Y chromosome sequences, including 299 newly reported samples. Applying ancient DNA calibration, we date the Y-chromosomal most recent common ancestor (MRCA) in Africa at 254 (95% CI 192–307) kya and detect a cluster of major non-African founder haplogroups in a narrow time interval at 47–52 kya, consistent with a rapid initial colonization model of Eurasia and Oceania after the out-of-Africa bottleneck. In contrast to demographic reconstructions based on mtDNA, we infer a second strong bottleneck in Y-chromosome lineages dating to the last 10 ky. We hypothesize that this bottleneck is caused by cultural changes affecting variance of reproductive success among males.
Collapse
Affiliation(s)
- Monika Karmin
- Estonian Biocentre, Tartu, 51010, Estonia; Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, 51010, Estonia;
| | - Lauri Saag
- Estonian Biocentre, Tartu, 51010, Estonia; Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, 51010, Estonia
| | - Mário Vicente
- Division of Biological Anthropology, University of Cambridge, Cambridge, CB2 1QH, United Kingdom
| | - Melissa A Wilson Sayres
- Department of Integrative Biology, University of California Berkeley, Berkeley, California 94720, USA; School of Life Sciences and The Biodesign Institute, Tempe, Arizona 85287-5001, USA
| | - Mari Järve
- Estonian Biocentre, Tartu, 51010, Estonia
| | - Ulvi Gerst Talas
- Department of Bioinformatics, Institute of Molecular and Cell Biology, University of Tartu, Tartu, 51010, Estonia
| | | | - Anne-Mai Ilumäe
- Estonian Biocentre, Tartu, 51010, Estonia; Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, 51010, Estonia
| | - Reedik Mägi
- Estonian Genome Center, University of Tartu, Tartu, 51010, Estonia
| | - Mario Mitt
- Estonian Genome Center, University of Tartu, Tartu, 51010, Estonia; Department of Biotechnology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, 51010, Estonia
| | - Luca Pagani
- Division of Biological Anthropology, University of Cambridge, Cambridge, CB2 1QH, United Kingdom
| | - Tarmo Puurand
- Department of Bioinformatics, Institute of Molecular and Cell Biology, University of Tartu, Tartu, 51010, Estonia
| | - Zuzana Faltyskova
- Division of Biological Anthropology, University of Cambridge, Cambridge, CB2 1QH, United Kingdom
| | - Florian Clemente
- Division of Biological Anthropology, University of Cambridge, Cambridge, CB2 1QH, United Kingdom
| | - Alexia Cardona
- Division of Biological Anthropology, University of Cambridge, Cambridge, CB2 1QH, United Kingdom
| | - Ene Metspalu
- Estonian Biocentre, Tartu, 51010, Estonia; Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, 51010, Estonia
| | - Hovhannes Sahakyan
- Estonian Biocentre, Tartu, 51010, Estonia; Laboratory of Ethnogenomics, Institute of Molecular Biology, National Academy of Sciences, Yerevan, 0014, Armenia
| | - Bayazit Yunusbayev
- Estonian Biocentre, Tartu, 51010, Estonia; Institute of Biochemistry and Genetics, Ufa Scientific Center of the Russian Academy of Sciences, Ufa, 450054, Russia
| | - Georgi Hudjashov
- Estonian Biocentre, Tartu, 51010, Estonia; Department of Psychology, University of Auckland, Auckland, 1142, New Zealand
| | - Michael DeGiorgio
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | | | - Christina Eichstaedt
- Division of Biological Anthropology, University of Cambridge, Cambridge, CB2 1QH, United Kingdom
| | - Mikk Eelmets
- Estonian Biocentre, Tartu, 51010, Estonia; Department of Bioinformatics, Institute of Molecular and Cell Biology, University of Tartu, Tartu, 51010, Estonia
| | | | | | - Sergei Litvinov
- Estonian Biocentre, Tartu, 51010, Estonia; Institute of Biochemistry and Genetics, Ufa Scientific Center of the Russian Academy of Sciences, Ufa, 450054, Russia
| | - Maru Mormina
- Department of Applied Social Sciences, University of Winchester, Winchester, SO22 4NR, United Kingdom
| | - Yali Xue
- The Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, United Kingdom
| | - Qasim Ayub
- The Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, United Kingdom
| | - Grigor Zoraqi
- Center of Molecular Diagnosis and Genetic Research, University Hospital of Obstetrics and Gynecology, Tirana, ALB1005, Albania
| | - Thorfinn Sand Korneliussen
- Department of Integrative Biology, University of California Berkeley, Berkeley, California 94720, USA; Center for GeoGenetics, University of Copenhagen, Copenhagen, DK-1350, Denmark
| | - Farida Akhatova
- Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa, 450074, Russia; Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, 420008, Russia
| | - Joseph Lachance
- Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6145, USA; School of Biology, Georgia Institute of Technology, Atlanta, 30332, Georgia, USA
| | - Sarah Tishkoff
- Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6145, USA; Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6313, USA
| | | | - François-Xavier Ricaut
- Evolutionary Medicine Group, Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse, Centre National de la Recherche Scientifique, Université de Toulouse 3, Toulouse, 31073, France
| | - Pradiptajati Kusuma
- Evolutionary Medicine Group, Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse, Centre National de la Recherche Scientifique, Université de Toulouse 3, Toulouse, 31073, France; Eijkman Institute for Molecular Biology, Jakarta, 10430, Indonesia
| | - Harilanto Razafindrazaka
- Evolutionary Medicine Group, Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse, Centre National de la Recherche Scientifique, Université de Toulouse 3, Toulouse, 31073, France
| | - Denis Pierron
- Evolutionary Medicine Group, Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse, Centre National de la Recherche Scientifique, Université de Toulouse 3, Toulouse, 31073, France
| | - Murray P Cox
- Statistics and Bioinformatics Group, Institute of Fundamental Sciences, Massey University, Palmerston North, 4442, New Zealand
| | - Gazi Nurun Nahar Sultana
- Centre for Advanced Research in Sciences (CARS), DNA Sequencing Research Laboratory, University of Dhaka, Dhaka, Dhaka-1000, Bangladesh
| | - Rane Willerslev
- Arctic Research Centre, Aarhus University, Aarhus, DK-8000, Denmark
| | - Craig Muller
- Center for GeoGenetics, University of Copenhagen, Copenhagen, DK-1350, Denmark
| | - Michael Westaway
- Environmental Futures Research Institute, Griffith University, Nathan, 4111, Australia
| | - David Lambert
- Environmental Futures Research Institute, Griffith University, Nathan, 4111, Australia
| | - Vedrana Skaro
- Genos, DNA Laboratory, Zagreb, 10000, Croatia; University of Osijek, Medical School, Osijek, 31000, Croatia
| | | | - Shahlo Turdikulova
- Institute of Bioorganic Chemistry, Academy of Science, Tashkent, 100143, Uzbekistan
| | - Dilbar Dalimova
- Institute of Bioorganic Chemistry, Academy of Science, Tashkent, 100143, Uzbekistan
| | - Rita Khusainova
- Institute of Biochemistry and Genetics, Ufa Scientific Center of the Russian Academy of Sciences, Ufa, 450054, Russia; Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa, 450074, Russia
| | - Natalya Trofimova
- Estonian Biocentre, Tartu, 51010, Estonia; Institute of Biochemistry and Genetics, Ufa Scientific Center of the Russian Academy of Sciences, Ufa, 450054, Russia
| | - Vita Akhmetova
- Institute of Biochemistry and Genetics, Ufa Scientific Center of the Russian Academy of Sciences, Ufa, 450054, Russia
| | - Irina Khidiyatova
- Institute of Biochemistry and Genetics, Ufa Scientific Center of the Russian Academy of Sciences, Ufa, 450054, Russia; Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa, 450074, Russia
| | - Daria V Lichman
- Institute of Cytology and Genetics, Novosibirsk, 630090, Russia
| | - Jainagul Isakova
- Institute of Molecular Biology and Medicine, Bishkek, 720040, Kyrgyzstan
| | | | - Zhaxylyk Sabitov
- L.N. Gumilyov Eurasian National University, Astana, 010008, Kazakhstan; Center for Life Sciences, Nazarbayev University, Astana, 010000, Kazakhstan
| | - Nikolay A Barashkov
- Department of Molecular Genetics, Yakut Scientific Centre of Complex Medical Problems, Yakutsk, 677010, Russia; Laboratory of Molecular Biology, Institute of Natural Sciences, M.K. Ammosov North-Eastern Federal University, Yakutsk, 677000, Russia
| | | | - Evelin Mihailov
- Estonian Genome Center, University of Tartu, Tartu, 51010, Estonia
| | | | - Irina Evseeva
- Northern State Medical University, Arkhangelsk, 163000, Russia; Anthony Nolan, London, NW3 2NU, United Kingdom
| | | | | | - George Andriadze
- Scientific-Research Center of the Caucasian Ethnic Groups, St. Andrews Georgian University, Tbilisi, 0162, Georgia
| | - Dragan Primorac
- University of Osijek, Medical School, Osijek, 31000, Croatia; St. Catherine Specialty Hospital, Zabok, 49210, Croatia; Eberly College of Science, Pennsylvania State University, University Park, Pennsylvania 16802, USA; University of Split, Medical School, Split, 21000, Croatia
| | | | - Olga Utevska
- V.N. Karazin Kharkiv National University, Kharkiv, 61022, Ukraine
| | - Levon Yepiskoposyan
- Laboratory of Ethnogenomics, Institute of Molecular Biology, National Academy of Sciences, Yerevan, 0014, Armenia
| | - Damir Marjanovic
- Genos, DNA Laboratory, Zagreb, 10000, Croatia; Department of Genetics and Bioengineering, Faculty of Engineering and Information Technologies, International Burch University, Sarajevo, 71000, Bosnia and Herzegovina
| | - Alena Kushniarevich
- Estonian Biocentre, Tartu, 51010, Estonia; Institute of Genetics and Cytology, National Academy of Sciences, Minsk, 220072, Belarus
| | | | - Christian Gilissen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, 106525 GA, The Netherlands
| | - Lisenka Vissers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, 106525 GA, The Netherlands
| | - Joris A Veltman
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, 106525 GA, The Netherlands
| | - Elena Balanovska
- Research Centre for Medical Genetics, Russian Academy of Sciences, Moscow, 115478, Russia
| | - Miroslava Derenko
- Genetics Laboratory, Institute of Biological Problems of the North, Russian Academy of Sciences, Magadan, 685000, Russia
| | - Boris Malyarchuk
- Genetics Laboratory, Institute of Biological Problems of the North, Russian Academy of Sciences, Magadan, 685000, Russia
| | - Andres Metspalu
- Estonian Genome Center, University of Tartu, Tartu, 51010, Estonia
| | - Sardana Fedorova
- Department of Molecular Genetics, Yakut Scientific Centre of Complex Medical Problems, Yakutsk, 677010, Russia; Laboratory of Molecular Biology, Institute of Natural Sciences, M.K. Ammosov North-Eastern Federal University, Yakutsk, 677000, Russia
| | - Anders Eriksson
- Department of Zoology, University of Cambridge, Cambridge, CB2 3EJ, United Kingdom; Integrative Systems Biology Lab, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Andrea Manica
- Department of Zoology, University of Cambridge, Cambridge, CB2 3EJ, United Kingdom
| | - Fernando L Mendez
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305-5120, USA
| | - Tatiana M Karafet
- ARL Division of Biotechnology, University of Arizona, Tucson, Arizona 85721, USA
| | - Krishna R Veeramah
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York 11794-5245, USA
| | - Neil Bradman
- The Henry Stewart Group, London, WC1A 2HN, United Kingdom
| | - Michael F Hammer
- ARL Division of Biotechnology, University of Arizona, Tucson, Arizona 85721, USA
| | | | - Oleg Balanovsky
- Research Centre for Medical Genetics, Russian Academy of Sciences, Moscow, 115478, Russia; Vavilov Institute for General Genetics, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Elza K Khusnutdinova
- Institute of Biochemistry and Genetics, Ufa Scientific Center of the Russian Academy of Sciences, Ufa, 450054, Russia; Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa, 450074, Russia
| | - Knut Johnsen
- University Hospital of North Norway, Tromsøe, N-9038, Norway
| | - Maido Remm
- Department of Bioinformatics, Institute of Molecular and Cell Biology, University of Tartu, Tartu, 51010, Estonia
| | - Mark G Thomas
- Research Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, United Kingdom
| | - Chris Tyler-Smith
- The Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, United Kingdom
| | - Peter A Underhill
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305-5120, USA
| | - Eske Willerslev
- Center for GeoGenetics, University of Copenhagen, Copenhagen, DK-1350, Denmark
| | - Rasmus Nielsen
- Department of Integrative Biology, University of California Berkeley, Berkeley, California 94720, USA
| | - Mait Metspalu
- Estonian Biocentre, Tartu, 51010, Estonia; Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, 51010, Estonia
| | - Richard Villems
- Estonian Biocentre, Tartu, 51010, Estonia; Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, 51010, Estonia; Estonian Academy of Sciences, Tallinn, 10130, Estonia
| | - Toomas Kivisild
- Estonian Biocentre, Tartu, 51010, Estonia; Division of Biological Anthropology, University of Cambridge, Cambridge, CB2 1QH, United Kingdom;
| |
Collapse
|
191
|
Felappi JF, Vieira RC, Fagundes NJR, Verrastro LV. So far away, yet so close: strong genetic structure in Homonota uruguayensis (Squamata, Phyllodactylidae), a species with restricted geographic distribution in the Brazilian and Uruguayan Pampas. PLoS One 2015; 10:e0118162. [PMID: 25692471 PMCID: PMC4334718 DOI: 10.1371/journal.pone.0118162] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Accepted: 01/08/2015] [Indexed: 11/19/2022] Open
Abstract
The Pampas is a biologically rich South American biome, but is poorly represented in phylogeographic studies. While the Pleistocene glacial cycles may have affected the evolutionary history of species distributed in forested biomes, little is known about their effects on the habitats that remained stable through glacial cycles. The South American Pampas have been covered by grasslands during both glacial and interglacial periods and therefore represent an interesting system to test whether the genetic structure in such environments is less pronounced. In this study, we sampled Pampean populations of Homonota uruguayensis from Southern Brazil and Uruguay to assess the tempo and mode of population divergence, using both morphological measurements and molecular markers. Our results indicate that, in spite of its narrow geographic distribution, populations of H. uruguayensis show high levels of genetic structure. We found four major well-supported mtDNA clades with strong geographic associations. Estimates of their divergence times fell between 3.16 and 1.82 million years before the present. Populations from the central portion of the species distribution, on the border between Uruguay and Brazil, have high genetic diversity and may have undergone a population expansion approximately 250,000 years before the present. The high degree of genetic structure is reflected in the analyses of morphological characters, and most individuals could be correctly assigned to their parental population based on morphology alone. Finally, we discuss the biogeographic and conservation implications of these findings.
Collapse
Affiliation(s)
- Jéssica F. Felappi
- Departamento de Zoologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Renata C. Vieira
- Departamento de Zoologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Nelson J. R. Fagundes
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Laura V. Verrastro
- Departamento de Zoologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| |
Collapse
|
192
|
Emerson BC, Hickerson MJ. Lack of support for the time-dependent molecular evolution hypothesis. Mol Ecol 2015; 24:702-9. [DOI: 10.1111/mec.13070] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Revised: 12/17/2014] [Accepted: 12/30/2014] [Indexed: 01/24/2023]
Affiliation(s)
- Brent C. Emerson
- Island Ecology and Evolution Research Group; Instituto de Productos Naturales y Agrobiología (IPNA-CSIC); C/Astrofísico Francisco Sánchez 3 La Laguna Tenerife, Canary Islands 38206 Spain
| | - Michael J. Hickerson
- Biology Department; City College of New York; New York NY 10031 USA
- The Graduate Center; City University of New York; New York NY 10016 USA
| |
Collapse
|
193
|
Garrick RC, Kajdacsi B, Russello MA, Benavides E, Hyseni C, Gibbs JP, Tapia W, Caccone A. Naturally rare versus newly rare: demographic inferences on two timescales inform conservation of Galápagos giant tortoises. Ecol Evol 2015; 5:676-94. [PMID: 25691990 PMCID: PMC4328771 DOI: 10.1002/ece3.1388] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Revised: 11/26/2014] [Accepted: 12/01/2014] [Indexed: 02/05/2023] Open
Abstract
Long-term population history can influence the genetic effects of recent bottlenecks. Therefore, for threatened or endangered species, an understanding of the past is relevant when formulating conservation strategies. Levels of variation at neutral markers have been useful for estimating local effective population sizes (N e ) and inferring whether population sizes increased or decreased over time. Furthermore, analyses of genotypic, allelic frequency, and phylogenetic information can potentially be used to separate historical from recent demographic changes. For 15 populations of Galápagos giant tortoises (Chelonoidis sp.), we used 12 microsatellite loci and DNA sequences from the mitochondrial control region and a nuclear intron, to reconstruct demographic history on shallow (past ∽100 generations, ∽2500 years) and deep (pre-Holocene, >10 thousand years ago) timescales. At the deep timescale, three populations showed strong signals of growth, but with different magnitudes and timing, indicating different underlying causes. Furthermore, estimated historical N e of populations across the archipelago showed no correlation with island age or size, underscoring the complexity of predicting demographic history a priori. At the shallow timescale, all populations carried some signature of a genetic bottleneck, and for 12 populations, point estimates of contemporary N e were very small (i.e., < 50). On the basis of the comparison of these genetic estimates with published census size data, N e generally represented ∽0.16 of the census size. However, the variance in this ratio across populations was considerable. Overall, our data suggest that idiosyncratic and geographically localized forces shaped the demographic history of tortoise populations. Furthermore, from a conservation perspective, the separation of demographic events occurring on shallow versus deep timescales permits the identification of naturally rare versus newly rare populations; this distinction should facilitate prioritization of management action.
Collapse
Affiliation(s)
- Ryan C Garrick
- Department of Biology, University of MississippiOxford, Mississippi, 38677
| | - Brittney Kajdacsi
- Department of Ecology and Evolutionary Biology, Yale UniversityNew Haven, Connecticut, 06520
| | - Michael A Russello
- Department of Biology, University of British ColumbiaOkanagan Campus, Kelowna, British Columbia, V1V 1V7, Canada
| | - Edgar Benavides
- Department of Ecology and Evolutionary Biology, Yale UniversityNew Haven, Connecticut, 06520
| | - Chaz Hyseni
- Department of Biology, University of MississippiOxford, Mississippi, 38677
| | - James P Gibbs
- College of Environmental Science and Forestry, State University of New YorkSyracuse, New York, 13210
| | - Washington Tapia
- Department of Applied Research, Galápagos National Park ServicePuerto Ayora, Galápagos, Ecuador
- Biodiver S.A. ConsultoresKm 5 Vía a Baltra, Isla Santa Cruz, Galápagos, Ecuador
| | - Adalgisa Caccone
- Department of Ecology and Evolutionary Biology, Yale UniversityNew Haven, Connecticut, 06520
| |
Collapse
|
194
|
Orlando L, Cooper A. Using Ancient DNA to Understand Evolutionary and Ecological Processes. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2014. [DOI: 10.1146/annurev-ecolsys-120213-091712] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Ancient DNA provides a unique means to record genetic change through time and directly observe evolutionary and ecological processes. Although mostly based on mitochondrial DNA, the increasing availability of genomic sequences is leading to unprecedented levels of resolution. Temporal studies of population genetics have revealed dynamic patterns of change in many large vertebrates, featuring localized extinctions, migrations, and population bottlenecks. The pronounced climate cycles of the Late Pleistocene have played a key role, reducing the taxonomic and genetic diversity of many taxa and shaping modern populations. Importantly, the complex series of events revealed by ancient DNA data is seldom reflected in current biogeographic patterns. DNA preserved in ancient sediments and coprolites has been used to characterize a range of paleoenvironments and reconstruct functional relationships in paleoecological systems. In the near future, genome-level surveys of ancient populations will play an increasingly important role in revealing, calibrating, and testing evolutionary processes.
Collapse
Affiliation(s)
- Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350K Copenhagen, Denmark;,
| | - Alan Cooper
- Australian Center for Ancient DNA, University of Adelaide, Adelaide, South Australia
| |
Collapse
|
195
|
Vignaud TM, Mourier J, Maynard JA, Leblois R, Spaet J, Clua E, Neglia V, Planes S. Blacktip reef sharks, Carcharhinus melanopterus, have high genetic structure and varying demographic histories in their Indo-Pacific range. Mol Ecol 2014; 23:5193-207. [PMID: 25251515 DOI: 10.1111/mec.12936] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2014] [Accepted: 09/19/2014] [Indexed: 12/20/2022]
Abstract
For free-swimming marine species like sharks, only population genetics and demographic history analyses can be used to assess population health/status as baseline population numbers are usually unknown. We investigated the population genetics of blacktip reef sharks, Carcharhinus melanopterus; one of the most abundant reef-associated sharks and the apex predator of many shallow water reefs of the Indian and Pacific Oceans. Our sampling includes 4 widely separated locations in the Indo-Pacific and 11 islands in French Polynesia with different levels of coastal development. Four-teen microsatellite loci were analysed for samples from all locations and two mitochondrial DNA fragments, the control region and cytochrome b, were examined for 10 locations. For microsatellites, genetic diversity is higher for the locations in the large open systems of the Red Sea and Australia than for the fragmented habitat of the smaller islands of French Polynesia. Strong significant structure was found for distant locations with FST values as high as ~0.3, and a smaller but still significant structure is found within French Polynesia. Both mitochondrial genes show only a few mutations across the sequences with a dominant shared haplotype in French Polynesia and New Caledonia suggesting a common lineage different to that of East Australia. Demographic history analyses indicate population expansions in the Red Sea and Australia that may coincide with sea level changes after climatic events. Expansions and flat signals are indicated for French Polynesia as well as a significant recent bottleneck for Moorea, the most human-impacted lagoon of the locations in French Polynesia.
Collapse
Affiliation(s)
- Thomas M Vignaud
- Laboratoire d'Excellence "CORAIL", USR 3278 CNRS - EPHE, CRIOBE, BP 1013 - 98 729 Papetoai, Moorea, Polynésie, Française
| | | | | | | | | | | | | | | |
Collapse
|
196
|
Chan YL, Schanzenbach D, Hickerson MJ. Detecting concerted demographic response across community assemblages using hierarchical approximate Bayesian computation. Mol Biol Evol 2014; 31:2501-15. [PMID: 24925925 PMCID: PMC4137712 DOI: 10.1093/molbev/msu187] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Methods that integrate population-level sampling from multiple taxa into a single community-level analysis are an essential addition to the comparative phylogeographic toolkit. Detecting how species within communities have demographically tracked each other in space and time is important for understanding the effects of future climate and landscape changes and the resulting acceleration of extinctions, biological invasions, and potential surges in adaptive evolution. Here, we present a statistical framework for such an analysis based on hierarchical approximate Bayesian computation (hABC) with the goal of detecting concerted demographic histories across an ecological assemblage. Our method combines population genetic data sets from multiple taxa into a single analysis to estimate: 1) the proportion of a community sample that demographically expanded in a temporally clustered pulse and 2) when the pulse occurred. To validate the accuracy and utility of this new approach, we use simulation cross-validation experiments and subsequently analyze an empirical data set of 32 avian populations from Australia that are hypothesized to have expanded from smaller refugia populations in the late Pleistocene. The method can accommodate data set heterogeneity such as variability in effective population size, mutation rates, and sample sizes across species and exploits the statistical strength from the simultaneous analysis of multiple species. This hABC framework used in a multitaxa demographic context can increase our understanding of the impact of historical climate change by determining what proportion of the community responded in concert or independently and can be used with a wide variety of comparative phylogeographic data sets as biota-wide DNA barcoding data sets accumulate.
Collapse
Affiliation(s)
- Yvonne L Chan
- Hawai'i Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawai'i at Manoa
| | | | - Michael J Hickerson
- Biology Department, City College of New YorkThe Graduate Center, City University of New York
| |
Collapse
|
197
|
Hope AG, Ho SYW, Malaney JL, Cook JA, Talbot SL. ACCOUNTING FOR RATE VARIATION AMONG LINEAGES IN COMPARATIVE DEMOGRAPHIC ANALYSES. Evolution 2014; 68:2689-700. [DOI: 10.1111/evo.12469] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2013] [Accepted: 05/22/2014] [Indexed: 01/16/2023]
Affiliation(s)
- Andrew G. Hope
- U.S. Geological Survey; Alaska Science Center; 4210 University Drive Anchorage Alaska 99508
| | - Simon Y. W. Ho
- School of Biological Sciences; Edgeworth David Building A11; The University of Sydney; Sydney New South Wales 2006 Australia
| | - Jason L. Malaney
- Department of Natural Resources and Environmental Science; University of Nevada-Reno; Reno Nevada 89557
| | - Joseph A. Cook
- Department of Biology; University of New Mexico; Museum of Southwestern Biology MSC03 2020; Albuquerque New Mexico 87131
| | - Sandra L. Talbot
- U.S. Geological Survey; Alaska Science Center; 4210 University Drive Anchorage Alaska 99508
| |
Collapse
|
198
|
Leblois R, Pudlo P, Néron J, Bertaux F, Reddy Beeravolu C, Vitalis R, Rousset F. Maximum-likelihood inference of population size contractions from microsatellite data. Mol Biol Evol 2014; 31:2805-23. [PMID: 25016583 DOI: 10.1093/molbev/msu212] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Understanding the demographic history of populations and species is a central issue in evolutionary biology and molecular ecology. In this work, we develop a maximum-likelihood method for the inference of past changes in population size from microsatellite allelic data. Our method is based on importance sampling of gene genealogies, extended for new mutation models, notably the generalized stepwise mutation model (GSM). Using simulations, we test its performance to detect and characterize past reductions in population size. First, we test the estimation precision and confidence intervals coverage properties under ideal conditions, then we compare the accuracy of the estimation with another available method (MSVAR) and we finally test its robustness to misspecification of the mutational model and population structure. We show that our method is very competitive compared with alternative ones. Moreover, our implementation of a GSM allows more accurate analysis of microsatellite data, as we show that the violations of a single step mutation assumption induce very high bias toward false contraction detection rates. However, our simulation tests also showed some limits, which most importantly are large computation times for strong disequilibrium scenarios and a strong influence of some form of unaccounted population structure. This inference method is available in the latest implementation of the MIGRAINE software package.
Collapse
Affiliation(s)
- Raphaël Leblois
- INRA, UMR 1062 CBGP (INRA-IRD-CIRAD-Montpellier Supagro), Montpellier, France Muséum National d'Histoire Naturelle, CNRS, UMR OSEB, Paris, France Institut de Biologie Computationnelle, Montpellier, France
| | - Pierre Pudlo
- INRA, UMR 1062 CBGP (INRA-IRD-CIRAD-Montpellier Supagro), Montpellier, France Institut de Biologie Computationnelle, Montpellier, France Université Montpellier 2, CNRS, UMR I3M, Montpellier, France
| | - Joseph Néron
- Muséum National d'Histoire Naturelle, CNRS, UMR OSEB, Paris, France
| | - François Bertaux
- Muséum National d'Histoire Naturelle, CNRS, UMR OSEB, Paris, France INRIA Paris-Rocquencourt, BANG Team, Le Chesnay, France
| | | | - Renaud Vitalis
- INRA, UMR 1062 CBGP (INRA-IRD-CIRAD-Montpellier Supagro), Montpellier, France Institut de Biologie Computationnelle, Montpellier, France
| | - François Rousset
- Institut de Biologie Computationnelle, Montpellier, France Université Montpellier 2, CNRS, UMR ISEM, Montpellier, France
| |
Collapse
|
199
|
Teske PR, Sandoval-Castillo J, Waters JM, Beheregaray LB. Can novel genetic analyses help to identify low-dispersal marine invasive species? Ecol Evol 2014; 4:2848-66. [PMID: 25165524 PMCID: PMC4130444 DOI: 10.1002/ece3.1129] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2014] [Revised: 05/04/2014] [Accepted: 05/06/2014] [Indexed: 01/18/2023] Open
Abstract
Genetic methods can be a powerful tool to resolve the native versus introduced status of populations whose taxonomy and biogeography are poorly understood. The genetic study of introduced species is presently dominated by analyses that identify signatures of recent colonization by means of summary statistics. Unfortunately, such approaches cannot be used in low-dispersal species, in which recently established populations originating from elsewhere in the species' native range also experience periods of low population size because they are founded by few individuals. We tested whether coalescent-based molecular analyses that provide detailed information about demographic history supported the hypothesis that a sea squirt whose distribution is centered on Tasmania was recently introduced to mainland Australia and New Zealand through human activities. Methods comparing trends in population size (Bayesian Skyline Plots and Approximate Bayesian Computation) were no more informative than summary statistics, likely because of recent intra-Tasmanian dispersal. However, IMa2 estimates of divergence between putatively native and introduced populations provided information at a temporal scale suitable to differentiate between recent (potentially anthropogenic) introductions and ancient divergence, and indicated that all three non-Tasmanian populations were founded during the period of European settlement. While this approach can be affected by inaccurate molecular dating, it has considerable (albeit largely unexplored) potential to corroborate nongenetic information in species with limited dispersal capabilities.
Collapse
Affiliation(s)
- Peter R Teske
- Molecular Ecology Laboratory, School of Biological Sciences, Flinders University Adelaide, South Australia, 5001, Australia ; Department of Zoology, University of Johannesburg Auckland Park, 2006, Johannesburg, South Africa
| | - Jonathan Sandoval-Castillo
- Molecular Ecology Laboratory, School of Biological Sciences, Flinders University Adelaide, South Australia, 5001, Australia
| | - Jonathan M Waters
- Department of Zoology, University of Otago PO Box 56, Dunedin, New Zealand
| | - Luciano B Beheregaray
- Molecular Ecology Laboratory, School of Biological Sciences, Flinders University Adelaide, South Australia, 5001, Australia
| |
Collapse
|
200
|
Bonatelli IAS, Perez MF, Peterson AT, Taylor NP, Zappi DC, Machado MC, Koch I, Pires AHC, Moraes EM. Interglacial microrefugia and diversification of a cactus species complex: phylogeography and palaeodistributional reconstructions forPilosocereus aurisetusand allies. Mol Ecol 2014; 23:3044-63. [DOI: 10.1111/mec.12780] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2013] [Revised: 04/21/2014] [Accepted: 04/23/2014] [Indexed: 02/04/2023]
Affiliation(s)
- Isabel A. S. Bonatelli
- Departamento de Biologia; Universidade Federal de São Carlos; Rodovia João Leme dos Santos km 110 18052780 Sorocaba São Paulo Brazil
| | - Manolo F. Perez
- Departamento de Biologia; Universidade Federal de São Carlos; Rodovia João Leme dos Santos km 110 18052780 Sorocaba São Paulo Brazil
| | | | - Nigel P. Taylor
- National Parks Board; Singapore Botanic Gardens; 1 Cluny Road Singapore 259569 Singapore
- Royal Botanic Gardens; Kew Richmond Surrey TW9 3AB UK
| | - Daniela C. Zappi
- Royal Botanic Gardens; Kew Richmond Surrey TW9 3AB UK
- Gardens by the Bay; 18 Marina Gardens Drive Singapore Singapore
| | - Marlon C. Machado
- Departamento de Ciências Biológicas; Universidade Estadual de Feira de Santana; Rodovia BR 116 km 03 44031-460 Feira de Santana Bahia Brazil
| | - Ingrid Koch
- Departamento de Biologia; Universidade Federal de São Carlos; Rodovia João Leme dos Santos km 110 18052780 Sorocaba São Paulo Brazil
| | - Adriana H. C. Pires
- Departamento de Biologia; Universidade Federal de São Carlos; Rodovia João Leme dos Santos km 110 18052780 Sorocaba São Paulo Brazil
| | - Evandro M. Moraes
- Departamento de Biologia; Universidade Federal de São Carlos; Rodovia João Leme dos Santos km 110 18052780 Sorocaba São Paulo Brazil
| |
Collapse
|