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Musher LJ, Del-Rio G, Marcondes RS, Brumfield RT, Bravo GA, Thom G. Geogenomic Predictors of Genetree Heterogeneity Explain Phylogeographic and Introgression History: A Case Study in an Amazonian Bird (Thamnophilus aethiops). Syst Biol 2024; 73:36-52. [PMID: 37804132 DOI: 10.1093/sysbio/syad061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 09/14/2023] [Accepted: 10/04/2023] [Indexed: 10/08/2023] Open
Abstract
Can knowledge about genome architecture inform biogeographic and phylogenetic inference? Selection, drift, recombination, and gene flow interact to produce a genomic landscape of divergence wherein patterns of differentiation and genealogy vary nonrandomly across the genomes of diverging populations. For instance, genealogical patterns that arise due to gene flow should be more likely to occur on smaller chromosomes, which experience high recombination, whereas those tracking histories of geographic isolation (reduced gene flow caused by a barrier) and divergence should be more likely to occur on larger and sex chromosomes. In Amazonia, populations of many bird species diverge and introgress across rivers, resulting in reticulated genomic signals. Herein, we used reduced representation genomic data to disentangle the evolutionary history of 4 populations of an Amazonian antbird, Thamnophilus aethiops, whose biogeographic history was associated with the dynamic evolution of the Madeira River Basin. Specifically, we evaluate whether a large river capture event ca. 200 Ka, gave rise to reticulated genealogies in the genome by making spatially explicit predictions about isolation and gene flow based on knowledge about genomic processes. We first estimated chromosome-level phylogenies and recovered 2 primary topologies across the genome. The first topology (T1) was most consistent with predictions about population divergence and was recovered for the Z-chromosome. The second (T2), was consistent with predictions about gene flow upon secondary contact. To evaluate support for these topologies, we trained a convolutional neural network to classify our data into alternative diversification models and estimate demographic parameters. The best-fit model was concordant with T1 and included gene flow between non-sister taxa. Finally, we modeled levels of divergence and introgression as functions of chromosome length and found that smaller chromosomes experienced higher gene flow. Given that (1) genetrees supporting T2 were more likely to occur on smaller chromosomes and (2) we found lower levels of introgression on larger chromosomes (and especially the Z-chromosome), we argue that T1 represents the history of population divergence across rivers and T2 the history of secondary contact due to barrier loss. Our results suggest that a significant portion of genomic heterogeneity arises due to extrinsic biogeographic processes such as river capture interacting with intrinsic processes associated with genome architecture. Future phylogeographic studies would benefit from accounting for genomic processes, as different parts of the genome reveal contrasting, albeit complementary histories, all of which are relevant for disentangling the intricate geogenomic mechanisms of biotic diversification. [Amazonia; biogeography; demographic modeling; gene flow; gene tree; genome architecture; geogenomics; introgression; linked selection; neural network; phylogenomic; phylogeography; reproductive isolation; speciation; species tree.].
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Affiliation(s)
- Lukas J Musher
- Department of Ornithology, The Academy of Natural Sciences of Drexel University, Philadelphia, PA 19103, USA
- Department of Ornithology, American Museum of Natural History, New York, NY 10024, USA
| | - Glaucia Del-Rio
- Cornell Laboratory of Ornithology and Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14853, USA
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - Rafael S Marcondes
- Department of Biology and Museum of Natural Science, Louisiana State University, Baton Rouge, LA 70803, USA
- Department of BioSciences, Rice University, Houston, TX 77005, USA
| | - Robb T Brumfield
- Department of Biology and Museum of Natural Science, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Gustavo A Bravo
- Sección de Ornitología, Colecciones Biológicas, Instituto de Investigación de Recursos Biológicos Alexander von Humboldt, Claustro de San Agustín, Villa de Leyva, Boyacá 111311, Colombia
- Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Gregory Thom
- Department of Biology and Museum of Natural Science, Louisiana State University, Baton Rouge, LA 70803, USA
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2
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Bernstein JM, Voris HK, Stuart BL, Karns DR, McGuire JA, Iskandar DT, Riyanto A, Calderón-Acevedo CA, Brown RM, Gehara M, Soto-Centeno JA, Ruane S. Integrative methods reveal multiple drivers of diversification in rice paddy snakes. Sci Rep 2024; 14:4727. [PMID: 38472264 DOI: 10.1038/s41598-024-54744-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 02/15/2024] [Indexed: 03/14/2024] Open
Abstract
Divergence dating analyses in systematics provide a framework to develop and test biogeographic hypotheses regarding speciation. However, as molecular datasets grow from multilocus to genomic, sample sizes decrease due to computational burdens, and the testing of fine-scale biogeographic hypotheses becomes difficult. In this study, we use coalescent demographic models to investigate the diversification of poorly known rice paddy snakes from Southeast Asia (Homalopsidae: Hypsiscopus), which have conflicting dates of origin based on previous studies. We use coalescent modeling to test the hypothesis that Hypsiscopus diversified 2.5 mya during the Khorat Plateau uplift in Thailand. Additionally, we use ecological niche analyses to identify potential differences in the niche space of the two most widely distributed species in the past and present. Our results suggest Hypsiscopus diversified ~ 2.4 mya, supporting that the Khorat Plateau may have initiated the diversification of rice paddy snakes. We also find significant niche differentiation and shifts between species of Hypsiscopus, indicating that environmental differences may have sustained differentiation of this genus after the Khorat Plateau uplift. Our study expands on the diversification history of snakes in Southeast Asia, and highlights how results from smaller multilocus datasets can be useful in developing and testing biogeographic hypotheses alongside genomic datasets.
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Affiliation(s)
- Justin M Bernstein
- Center for Genomics, University of Kansas, Dyche Hall, 1345 Jayhawk Blvd, Lawrence, KS, 66045, USA.
| | - Harold K Voris
- Life Sciences Section, Negaunee Integrative Research Center, Field Museum, 1400 S. Lake Shore Drive, Chicago, IL, 60605, USA
| | - Bryan L Stuart
- Section of Research and Collections, North Carolina Museum of Natural Sciences, Raleigh, NC, 27601, USA
| | - Daryl R Karns
- Biology Department, Hanover College, Hanover, IN, 47243, USA
| | - Jimmy A McGuire
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA, 94720, USA
| | - Djoko T Iskandar
- School of Life Sciences and Technology, Institut Teknologi Bandung, Bandung, Indonesia
| | - Awal Riyanto
- Museum Zoologicum Bogoriense, Research Center for Biology, National Research and Innovation Agency of Indonesia (BRIN), Cibinong, 16911, Indonesia
| | - Camilo A Calderón-Acevedo
- State University of New York: College of Environmental Science and Forestry, Syracuse, NY, 13210, USA
| | - Rafe M Brown
- Department of Ecology and Evolutionary Biology and Biodiversity Institute, University of Kansas, Lawrence, KS, 66045, USA
| | - Marcelo Gehara
- Department of Earth and Environmental Science, Rutgers University-Newark, Newark, NJ, 07102, USA
| | - J Angel Soto-Centeno
- Department of Earth and Environmental Science, Rutgers University-Newark, Newark, NJ, 07102, USA
- Department of Mammalogy, American Museum of Natural History, New York, NY, 10024, USA
| | - Sara Ruane
- Life Sciences Section, Negaunee Integrative Research Center, Field Museum, 1400 S. Lake Shore Drive, Chicago, IL, 60605, USA
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3
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Thom G, Moreira LR, Batista R, Gehara M, Aleixo A, Smith BT. Genomic Architecture Predicts Tree Topology, Population Structuring, and Demographic History in Amazonian Birds. Genome Biol Evol 2024; 16:evae002. [PMID: 38236173 PMCID: PMC10823491 DOI: 10.1093/gbe/evae002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 10/26/2023] [Accepted: 12/12/2023] [Indexed: 01/19/2024] Open
Abstract
Geographic barriers are frequently invoked to explain genetic structuring across the landscape. However, inferences on the spatial and temporal origins of population variation have been largely limited to evolutionary neutral models, ignoring the potential role of natural selection and intrinsic genomic processes known as genomic architecture in producing heterogeneity in differentiation across the genome. To test how variation in genomic characteristics (e.g. recombination rate) impacts our ability to reconstruct general patterns of differentiation between species that cooccur across geographic barriers, we sequenced the whole genomes of multiple bird populations that are distributed across rivers in southeastern Amazonia. We found that phylogenetic relationships within species and demographic parameters varied across the genome in predictable ways. Genetic diversity was positively associated with recombination rate and negatively associated with species tree support. Gene flow was less pervasive in genomic regions of low recombination, making these windows more likely to retain patterns of population structuring that matched the species tree. We further found that approximately a third of the genome showed evidence of selective sweeps and linked selection, skewing genome-wide estimates of effective population sizes and gene flow between populations toward lower values. In sum, we showed that the effects of intrinsic genomic characteristics and selection can be disentangled from neutral processes to elucidate spatial patterns of population differentiation.
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Affiliation(s)
- Gregory Thom
- Department of Ornithology, American Museum of Natural History, New York, NY, USA
- Museum of Natural Science, Louisiana State University, Baton Rouge, LA, USA
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
| | - Lucas Rocha Moreira
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Department of Vertebrate Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Romina Batista
- Programa de Coleções Biológicas, Instituto Nacional de Pesquisas da Amazônia, Manaus, Brazil
- School of Science, Engineering and Environment, University of Salford, Manchester, UK
| | - Marcelo Gehara
- Department of Earth and Environmental Sciences, Rutgers University, Newark, NJ, USA
| | - Alexandre Aleixo
- Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
- Department of Environmental Genomics, Instituto Tecnológico Vale, Belém, Brazil
| | - Brian Tilston Smith
- Department of Ornithology, American Museum of Natural History, New York, NY, USA
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4
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Roux C, Vekemans X, Pannell J. Inferring the Demographic History and Inheritance Mode of Tetraploid Species Using ABC. Methods Mol Biol 2023; 2545:325-348. [PMID: 36720821 DOI: 10.1007/978-1-0716-2561-3_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Genomic patterns of diversity and divergence are impacted by certain life history traits, reproductive systems, and demographic history. The latter is characterized by fluctuations in population sizes over time, as well as by temporal patterns of introgression. For a given organism, identifying a demographic history that deviates from the standard neutral model allows a better understanding of its evolution but also helps to reduce the risk of false positives when screening for molecular targets of natural selection. Tetraploid organisms and beyond have demographic histories that are complicated by the mode of polyploidization, the mode of inheritance, and different scenarios of gene flow between sub-genomes and diploid parental species. Here we provide guidelines for experimenters wishing to address these issues through a flexible statistical framework: approximate Bayesian computation (ABC). The emphasis is on the general philosophy of the approach to encourage future users to exploit the enormous flexibility of ABC beyond the limitations imposed by generalist data analysis pipelines.
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Affiliation(s)
- Camille Roux
- Univ. Lille, CNRS, UMR 8198 - Evo-Eco-Paleo, Lille, France.
| | | | - John Pannell
- Department of Ecology and Evolution, Biophore Building, University of Lausanne, Lausanne, Switzerland
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5
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Luna LW, Naka LN, Thom G, Knowles LL, Sawakuchi AO, Aleixo A, Ribas CC. Late Pleistocene landscape changes and habitat specialization as promoters of population genomic divergence in Amazonian floodplain birds. Mol Ecol 2023; 32:214-228. [PMID: 36261866 DOI: 10.1111/mec.16741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 09/28/2022] [Accepted: 10/06/2022] [Indexed: 12/29/2022]
Abstract
Although vicariant processes are expected to leave similar genomic signatures among codistributed taxa, ecological traits such as habitat and stratum can influence genetic divergence within species. Here, we combined landscape history and habitat specialization to understand the historical and ecological factors responsible for current levels of genetic divergence in three species of birds specialized in seasonally flooded habitats in muddy rivers and which are widespread in the Amazon basin but have isolated populations in the Rio Branco. Populations of the white-bellied spinetail (Mazaria propinqua), lesser wagtail-tyrant (Stigmatura napensis) and bicolored conebill (Conirostrum bicolor) are currently isolated in the Rio Branco by the black-waters of the lower Rio Negro, offering a unique opportunity to test the effect of river colour as a barrier to gene flow. We used ultraconserved elements (UCEs) to test alternative hypotheses of population history in a comparative phylogeographical approach by modelling genetic structure, demographic history and testing for shared divergence time among codistributed taxa. Our analyses revealed that (i) all three populations from the Rio Branco floodplains are genetically distinct from other populations along the Amazon River floodplains; (ii) these divergences are the result of at least two distinct events, consistent with species habitat specialization; and (iii) the most likely model of population evolution includes lower population connectivity during the Late Pleistocene transition (~250,000 years ago), with gene flow being completely disrupted after the Last Glacial Maximum (~21,000 years ago). Our findings highlight how landscape evolution modulates population connectivity in habitat specialist species and how organisms can have different responses to the same historical processes of environmental change, depending on their habitat affinity.
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Affiliation(s)
- Leilton Willians Luna
- Department of Ecosystem Science and Management, Pennsylvania State University, University Park, Pennsylvania, USA.,Department of Zoology, Universidade Federal do Pará/Emílio Goeldi Museum, Belém, Brazil
| | - Luciano Nicolas Naka
- Laboratory of Avian Ecology and Evolution, Department of Zoology, Universidade Federal do Pernambuco, Recife, Brazil
| | - Gregory Thom
- Museum of Natural Science, Louisiana State University, Baton Rouge, Louisiana, USA
| | - Laura Lacey Knowles
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
| | | | - Alexandre Aleixo
- Department of Zoology, Universidade Federal do Pará/Emílio Goeldi Museum, Belém, Brazil.,Instituto Tecnológico Vale, Belém, Brazil.,Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
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6
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Coelho FEA, Guillory WX, Gehara M. Coalescent simulations indicate that the São Francisco River is a biogeographic barrier for six vertebrates in a seasonally dry South American forest. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.983134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The riverine barrier hypothesis has been extensively explored in Neotropical rainforests, while its importance in drier regions such as the Caatinga, a seasonally dry tropical forest in northeastern Brazil, has only recently received more attention. The Caatinga is bisected by the São Francisco River (SFR), which has long been suggested to be an important biogeographic feature in the region. However, recent studies have found mixed support for the role of the SFR as a hard barrier, most of them relying on the presence or absence of genetic breaks congruent with its course. Here, we used published multilocus and next-generation data from six vertebrate species to test the SFR’s strength as a barrier. Using model-based approaches (approximate Bayesian computation and supervised machine learning), we tested demographic models incorporating full, intermediate, and zero migration across the SFR, estimating divergence times and migration rates for each species. We found support for the SFR’s role as a barrier, allowing gene flow for some species. Estimated divergence times varied among species but are limited to the late Pleistocene, coherent with one of several proposed paleocourse changes in the river’s geological history. Contrary to the mixed results of previous studies, our study supports the SFR as an important phylogeographic barrier across different taxonomic groups, driving diversification in the Caatinga.
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7
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Tavares MM, Ferro M, Leal BSS, Palma‐Silva C. Speciation with gene flow between two Neotropical sympatric species (
Pitcairnia
spp.: Bromeliaceae). Ecol Evol 2022; 12:e8834. [PMID: 35509614 PMCID: PMC9055293 DOI: 10.1002/ece3.8834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 03/23/2022] [Accepted: 03/29/2022] [Indexed: 11/10/2022] Open
Affiliation(s)
- Marília Manuppella Tavares
- Departamento de Biologia Vegetal Instituto de Biologia Universidade Estadual de Campinas Campinas Brazil
| | - Milene Ferro
- Departamento de Biologia Geral e Aplicada Universidade Estadual Paulista Rio Claro Brazil
| | - Bárbara Simões Santos Leal
- Departamento de Biologia Vegetal Instituto de Biologia Universidade Estadual de Campinas Campinas Brazil
| | - Clarisse Palma‐Silva
- Departamento de Biologia Vegetal Instituto de Biologia Universidade Estadual de Campinas Campinas Brazil
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8
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Baumdicker F, Bisschop G, Goldstein D, Gower G, Ragsdale AP, Tsambos G, Zhu S, Eldon B, Ellerman EC, Galloway JG, Gladstein AL, Gorjanc G, Guo B, Jeffery B, Kretzschmar WW, Lohse K, Matschiner M, Nelson D, Pope NS, Quinto-Cortés CD, Rodrigues MF, Saunack K, Sellinger T, Thornton K, van Kemenade H, Wohns AW, Wong Y, Gravel S, Kern AD, Koskela J, Ralph PL, Kelleher J. Efficient ancestry and mutation simulation with msprime 1.0. Genetics 2021; 220:6460344. [PMID: 34897427 PMCID: PMC9176297 DOI: 10.1093/genetics/iyab229] [Citation(s) in RCA: 91] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 12/03/2021] [Indexed: 11/13/2022] Open
Abstract
Stochastic simulation is a key tool in population genetics, since the models involved are often analytically intractable and simulation is usually the only way of obtaining ground-truth data to evaluate inferences. Because of this, a large number of specialized simulation programs have been developed, each filling a particular niche, but with largely overlapping functionality and a substantial duplication of effort. Here, we introduce msprime version 1.0, which efficiently implements ancestry and mutation simulations based on the succinct tree sequence data structure and the tskit library. We summarize msprime’s many features, and show that its performance is excellent, often many times faster and more memory efficient than specialized alternatives. These high-performance features have been thoroughly tested and validated, and built using a collaborative, open source development model, which reduces duplication of effort and promotes software quality via community engagement.
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Affiliation(s)
- Franz Baumdicker
- Cluster of Excellence "Controlling Microbes to Fight Infections", Mathematical and Computational Population Genetics, University of Tübingen, 72076 Tübingen, Germany
| | - Gertjan Bisschop
- Institute of Evolutionary Biology,The University of Edinburgh, EH9 3FL, UK
| | - Daniel Goldstein
- Khoury College of Computer Sciences, Northeastern University, MA 02115, USA.,No affiliation
| | - Graham Gower
- Lundbeck GeoGenetics Centre, Globe Institute, University of Copenhagen, 1350 Copenhagen K, Denmark
| | - Aaron P Ragsdale
- Department of Integrative Biology, University of Wisconsin-Madison, WI 53706, USA
| | - Georgia Tsambos
- Melbourne Integrative Genomics, School of Mathematics and Statistics, University of Melbourne, Victoria, 3010, Australia
| | - Sha Zhu
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, OX3 7LF, UK
| | - Bjarki Eldon
- Leibniz Institute for Evolution and Biodiversity Science,Museum für Naturkunde Berlin, 10115, Germany
| | | | - Jared G Galloway
- Institute of Ecology and Evolution, Department of Biology, University of Oregon, OR 97403-5289, USA.,Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98102, USA
| | - Ariella L Gladstein
- Department of Genetics, University of North Carolina at Chapel Hill, NC 27599-7264, USA.,Embark Veterinary, Inc., Boston, MA 02111, USA
| | - Gregor Gorjanc
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, EH25 9RG, UK
| | - Bing Guo
- Institute for Genome Sciences,University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Ben Jeffery
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, OX3 7LF, UK
| | - Warren W Kretzschmar
- Center for Hematology and Regenerative Medicine, Karolinska Institute, 141 83 Huddinge, Sweden
| | - Konrad Lohse
- Institute of Evolutionary Biology,The University of Edinburgh, EH9 3FL, UK
| | | | - Dominic Nelson
- Department of Human Genetics, McGill University, Montréal, QC H3A 0C7, Canada
| | - Nathaniel S Pope
- Department of Entomology, Pennsylvania State University, PA 16802, USA
| | - Consuelo D Quinto-Cortés
- National Laboratory of Genomics for Biodiversity (LANGEBIO), Unit of Advanced Genomics, CINVESTAV, Irapuato, Mexico
| | - Murillo F Rodrigues
- Institute of Ecology and Evolution, Department of Biology, University of Oregon, OR 97403-5289, USA
| | - Kumar Saunack
- IIT Bombay, Powai, Mumbai 400 076, Maharashtra, India
| | - Thibaut Sellinger
- Professorship for Population Genetics, Department of Life Science Systems, Technical University of Munich, 85354 Freising, Germany
| | - Kevin Thornton
- Ecology and Evolutionary Biology, University of California, Irvine, CA 92697, USA
| | | | - Anthony W Wohns
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, OX3 7LF, UK.,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Yan Wong
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, OX3 7LF, UK
| | - Simon Gravel
- Department of Human Genetics, McGill University, Montréal, QC H3A 0C7, Canada
| | - Andrew D Kern
- Institute of Ecology and Evolution, Department of Biology, University of Oregon, OR 97403-5289, USA
| | - Jere Koskela
- Department of Statistics, University of Warwick, CV4 7AL, UK
| | - Peter L Ralph
- Institute of Ecology and Evolution, Department of Biology, University of Oregon, OR 97403-5289, USA.,Department of Mathematics, University of Oregon, OR 97403-5289 USA
| | - Jerome Kelleher
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, OX3 7LF, UK
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9
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Thom G, Gehara M, Smith BT, Miyaki CY, do Amaral FR. Microevolutionary dynamics show tropical valleys are deeper for montane birds of the Atlantic Forest. Nat Commun 2021; 12:6269. [PMID: 34725329 PMCID: PMC8560783 DOI: 10.1038/s41467-021-26537-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 10/08/2021] [Indexed: 11/18/2022] Open
Abstract
Tropical mountains hold more biodiversity than their temperate counterparts, and this disparity is often associated with the latitudinal climatic gradient. However, distinguishing the impact of latitude versus the background effects of species history and traits is challenging due to the evolutionary distance between tropical and temperate assemblages. Here, we test whether microevolutionary processes are linked to environmental variation across a sharp latitudinal transition in 21 montane birds of the southern Atlantic Forest in Brazil. We find that effective dispersal within populations in the tropical mountains is lower and genomic differentiation is better predicted by the current environmental complexity of the region than within the subtropical populations. The concordant response of multiple co-occurring populations is consistent with spatial climatic variability as a major process driving population differentiation. Our results provide evidence for how a narrow latitudinal gradient can shape microevolutionary processes and contribute to broader scale biodiversity patterns. There are many hypotheses for why the tropics are more biodiverse than higher latitudes. Phylogenomic analyses of 21 montane birds finds that tropical birds disperse less and have more genetically structured populations than their counterparts at higher latitudes, possibly due to a larger elevational climate gradient in the tropics
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Affiliation(s)
- Gregory Thom
- Department of Ornithology, American Museum of Natural History, Central Park West at 79th Street, New York, NY, 10024, USA. .,Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo, Rua do Matão, 277, Cidade Universitária, São Paulo, SP, 05508-090, Brazil.
| | - Marcelo Gehara
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY, 10024, USA.,Department of Earth and Environmental Sciences, Rutgers University Newark, 195 University Ave, Newark, NJ, 07102, USA
| | - Brian Tilston Smith
- Department of Ornithology, American Museum of Natural History, Central Park West at 79th Street, New York, NY, 10024, USA
| | - Cristina Y Miyaki
- Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo, Rua do Matão, 277, Cidade Universitária, São Paulo, SP, 05508-090, Brazil
| | - Fábio Raposo do Amaral
- Departamento de Ecologia e Biologia Evolutiva, Universidade Federal de São Paulo, Rua Prof. Artur Riedel, 275, Jardim Eldorado, Diadema, SP, CEP 09972-270, Brazil
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10
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Raposo do Amaral F, Thom G, Lima-Ribeiro MS, Alvarado-Serrano DF, Montesanti JAC, Pellegrino KCM, Miyaki CY, Hickerson MJ, Maldonado-Coelho M. Rugged relief and climate promote isolation and divergence between two neotropical cold-associated birds. Evolution 2021; 75:2371-2387. [PMID: 34375460 DOI: 10.1111/evo.14318] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Revised: 06/21/2021] [Accepted: 07/19/2021] [Indexed: 01/15/2023]
Abstract
The role of historical factors in establishing patterns of diversity in tropical mountains is of interest to understand the buildup of megadiverse biotas. In these regions, the historical processes of range fragmentation and contraction followed by dispersal are thought to be mediated by the interplay between rugged relief (complex topography) and climate fluctuations and likely explain most of the dynamics of diversification in plants and animals. Although empirical studies addressing the interaction between climate and topography have provided invaluable insights into population divergence and speciation patterns in tropical montane organisms, a more detailed and robust test of such processes in an explicit spatio-temporal framework is still lacking. Consequently, our ability to gain insights into historical range shifts over time and the genomic footprint left by them is limited. Here, we used niche modeling and subgenomic population-level datasets to explore the evolution of two species of warbling finches (genus Microspingus) disjunctly distributed across the Montane Atlantic Forest, a Neotropical region with complex geological and environmental histories. Population structure inferences suggest a scenario of three genetically differentiated populations, which are congruent with both geography and phenotypic variation. Demographic simulations support asynchronous isolation of these populations as recently as ∼40,000 years ago, relatively stable population sizes over recent time, and past gene flow subsequent to divergence. Throughout the last 800,000 years, niche models predicted extensive expansion into lowland areas with increasing overlap of species distributions during glacial periods, with prominent retractions and isolation into higher altitudes during interglacials, which are in line with signs of introgression of currently isolated populations. These results support a dual role of cyclical climatic changes: population divergence and persistence in mountain tops during warm periods followed by periods of expansion and admixture in lower elevations during cold periods. Our results underscore the role of the interplay between landscape and climate as an important mechanism in the evolution of the Neotropical montane biota.
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Affiliation(s)
- Fábio Raposo do Amaral
- Departamento de Ecologia e Biologia Evolutiva, Universidade Federal de São Paulo, Rua Professor Artur Riedel, 275, Diadema, SP, 09972-270, Brazil
| | - Gregory Thom
- Department of Ornithology, Division of Vertebrate Zoology, American Museum of Natural History, Central Park West at 79th Street, New York, NY, 10024-5192, USA
| | - Matheus S Lima-Ribeiro
- Departamento de Ciências Biológicas, Universidade Federal de Jataí, CP 03, Jataí, GO, 75804-020, Brazil
| | - Diego F Alvarado-Serrano
- Department of Biological Sciences, Ohio Center for Ecology and Evolutionary Studies, Ohio University, Life Sciences Building R219, Athens, OH, 45701, USA
| | - Julia A C Montesanti
- Departamento de Ecologia e Biologia Evolutiva, Universidade Federal de São Paulo, Rua Professor Artur Riedel, 275, Diadema, SP, 09972-270, Brazil
| | - Katia C M Pellegrino
- Departamento de Ecologia e Biologia Evolutiva, Universidade Federal de São Paulo, Rua Professor Artur Riedel, 275, Diadema, SP, 09972-270, Brazil
| | - Cristina Y Miyaki
- Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo, Rua do Matão, 277, Cidade Universitária, São Paulo, SP, 05508-090, Brazil
| | - Michael J Hickerson
- Department of Biology, City College of New York, 160, Convent Avenue, New York, NY, 10031, USA
| | - Marcos Maldonado-Coelho
- Departamento de Ecologia e Biologia Evolutiva, Universidade Federal de São Paulo, Rua Professor Artur Riedel, 275, Diadema, SP, 09972-270, Brazil.,Department of Biology, Lund University, Lund, SE-223 62, Sweden
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11
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Bauer DuMont VL, White SL, Zinshteyn D, Aquadro CF. Molecular population genetics of Sex-lethal ( Sxl) in the Drosophila melanogaster species group: a locus that genetically interacts with Wolbachia pipientis in Drosophila melanogaster. G3 GENES|GENOMES|GENETICS 2021; 11:6296609. [PMID: 34849818 PMCID: PMC8496275 DOI: 10.1093/g3journal/jkab197] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 06/01/2021] [Indexed: 11/13/2022]
Abstract
Abstract
Sex-lethal (Sxl) is the sex determination switch in Drosophila, and also plays a critical role in germ-line stem cell daughter differentiation in Drosophila melanogaster. Three female-sterile alleles at Sxl in D. melanogaster were previously shown to genetically interact to varying degrees with the maternally inherited endosymbiont Wolbachia pipientis. Given this genetic interaction and W. pipientis’ ability to manipulate reproduction in Drosophila, we carried out a careful study of both the population genetics (within four Drosophila species) and molecular evolutionary analysis (across 20 Drosophila species) of Sxl. Consistent with earlier studies, we find that selective constraint has played a prominent role in Sxl’s molecular evolution within Drosophila, but we also observe patterns that suggest both episodic bursts of protein evolution and recent positive selection at Sxl. The episodic nature of Sxl’s protein evolution is discussed in light of its genetic interaction with W. pipientis.
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Affiliation(s)
| | - Simone L White
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Daniel Zinshteyn
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Charles F Aquadro
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
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12
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Bourgeois YXC, Warren BH. An overview of current population genomics methods for the analysis of whole-genome resequencing data in eukaryotes. Mol Ecol 2021; 30:6036-6071. [PMID: 34009688 DOI: 10.1111/mec.15989] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 04/26/2021] [Accepted: 05/11/2021] [Indexed: 01/01/2023]
Abstract
Characterizing the population history of a species and identifying loci underlying local adaptation is crucial in functional ecology, evolutionary biology, conservation and agronomy. The constant improvement of high-throughput sequencing techniques has facilitated the production of whole genome data in a wide range of species. Population genomics now provides tools to better integrate selection into a historical framework, and take into account selection when reconstructing demographic history. However, this improvement has come with a profusion of analytical tools that can confuse and discourage users. Such confusion limits the amount of information effectively retrieved from complex genomic data sets, and impairs the diffusion of the most recent analytical tools into fields such as conservation biology. It may also lead to redundancy among methods. To address these isssues, we propose an overview of more than 100 state-of-the-art methods that can deal with whole genome data. We summarize the strategies they use to infer demographic history and selection, and discuss some of their limitations. A website listing these methods is available at www.methodspopgen.com.
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Affiliation(s)
| | - Ben H Warren
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, UA, CP 51, Paris, France
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13
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Fonseca EM, Colli GR, Werneck FP, Carstens BC. Phylogeographic model selection using convolutional neural networks. Mol Ecol Resour 2021; 21:2661-2675. [PMID: 33973350 DOI: 10.1111/1755-0998.13427] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 04/02/2021] [Accepted: 04/28/2021] [Indexed: 11/26/2022]
Abstract
The discipline of phylogeography has evolved rapidly in terms of the analytical toolkit used to analyse large genomic data sets. Despite substantial advances, analytical tools that could potentially address the challenges posed by increased model complexity have not been fully explored. For example, deep learning techniques are underutilized for phylogeographic model selection. In non-model organisms, the lack of information about their ecology and evolution can lead to uncertainty about which demographic models are appropriate. Here, we assess the utility of convolutional neural networks (CNNs) for assessing demographic models in South American lizards in the genus Norops. Three demographic scenarios (constant, expansion, and bottleneck) were considered for each of four inferred population-level lineages, and we found that the overall model accuracy was higher than 98% for all lineages. We then evaluated a set of 26 models that accounted for evolutionary relationships, gene flow, and changes in effective population size among the four lineages, identifying a single model with an estimated overall accuracy of 87% when using CNNs. The inferred demography of the lizard system suggests that gene flow between non-sister populations and changes in effective population sizes through time, probably in response to Pleistocene climatic oscillations, have shaped genetic diversity in this system. Approximate Bayesian computation (ABC) was applied to provide a comparison to the performance of CNNs. ABC was unable to identify a single model among the larger set of 26 models in the subsequent analysis. Our results demonstrate that CNNs can be easily and usefully incorporated into the phylogeographer's toolkit.
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Affiliation(s)
- Emanuel M Fonseca
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, USA
| | - Guarino R Colli
- Departamento de Zoologia, Universidade de Brasília, Brasília, Brazil
| | - Fernanda P Werneck
- Coordenação de Biodiversidade, Programa de Coleções Científicas Biológicas, Instituto Nacional de Pesquisas da Amazônia (INPA), Manaus, Brazil
| | - Bryan C Carstens
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, USA
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14
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Vasilarou M, Alachiotis N, Garefalaki J, Beloukas A, Pavlidis P. Population Genomics Insights into the First Wave of COVID-19. Life (Basel) 2021; 11:129. [PMID: 33562321 PMCID: PMC7914631 DOI: 10.3390/life11020129] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 01/30/2021] [Accepted: 02/04/2021] [Indexed: 01/09/2023] Open
Abstract
Full-genome-sequence computational analyses of the SARS-coronavirus (CoV)-2 genomes allow us to understand the evolutionary events and adaptability mechanisms. We used population genetics analyses on human SARS-CoV-2 genomes available on 2 April 2020 to infer the mutation rate and plausible recombination events between the Betacoronavirus genomes in nonhuman hosts that may have contributed to the evolution of SARS-CoV-2. Furthermore, we localized the targets of recent and strong, positive selection during the first pandemic wave. The genomic regions that appear to be under positive selection are largely co-localized with regions in which recombination from nonhuman hosts took place. Our results suggest that the pangolin coronavirus genome may have contributed to the SARS-CoV-2 genome by recombination with the bat coronavirus genome. However, we find evidence for additional recombination events that involve coronavirus genomes from other hosts, i.e., hedgehogs and sparrows. We further infer that recombination may have recently occurred within human hosts. Finally, we estimate the parameters of a demographic scenario involving an exponential growth of the size of the SARS-CoV-2 populations that have infected European, Asian, and Northern American cohorts, and we demonstrate that a rapid exponential growth in population size from the first wave can support the observed polymorphism patterns in SARS-CoV-2 genomes.
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Affiliation(s)
- Maria Vasilarou
- Foundation for Research and Technology Hellas (FORTH) and Department of Biology, Institute of Molecular Biology and Biotechnology (IMBB), University of Crete, 70013 Crete, Greece;
| | | | - Joanna Garefalaki
- Institute of Computer Science (ICS), Foundation for Research and Technology Hellas (FORTH), 70013 Heraklion, Greece;
| | - Apostolos Beloukas
- Department of Biomedical Sciences, University of West Attica, 12243 Athens, Greece
- Institute of Infection and Global Health, University of Liverpool, Liverpool L69 7BE, UK
| | - Pavlos Pavlidis
- Institute of Computer Science (ICS), Foundation for Research and Technology Hellas (FORTH), 70013 Heraklion, Greece;
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15
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Funk ER, Spellman GM, Winker K, Withrow JJ, Ruegg KC, Zavaleta E, Taylor SA. Phylogenomic Data Reveal Widespread Introgression Across the Range of an Alpine and Arctic Specialist. Syst Biol 2020; 70:527-541. [PMID: 32941630 DOI: 10.1093/sysbio/syaa071] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 08/28/2020] [Accepted: 08/31/2020] [Indexed: 01/10/2023] Open
Abstract
Understanding how gene flow affects population divergence and speciation remains challenging. Differentiating one evolutionary process from another can be difficult because multiple processes can produce similar patterns, and more than one process can occur simultaneously. Although simple population models produce predictable results, how these processes balance in taxa with patchy distributions and complicated natural histories is less certain. These types of populations might be highly connected through migration (gene flow), but can experience stronger effects of genetic drift and inbreeding, or localized selection. Although different signals can be difficult to separate, the application of high-throughput sequence data can provide the resolution necessary to distinguish many of these processes. We present whole-genome sequence data for an avian species group with an alpine and arctic tundra distribution to examine the role that different population genetic processes have played in their evolutionary history. Rosy-finches inhabit high elevation mountaintop sky islands and high-latitude island and continental tundra. They exhibit extensive plumage variation coupled with low levels of genetic variation. Additionally, the number of species within the complex is debated, making them excellent for studying the forces involved in the process of diversification, as well as an important species group in which to investigate species boundaries. Total genomic variation suggests a broadly continuous pattern of allele frequency changes across the mainland taxa of this group in North America. However, phylogenomic analyses recover multiple distinct, well supported, groups that coincide with previously described morphological variation and current species-level taxonomy. Tests of introgression using D-statistics and approximate Bayesian computation reveal significant levels of introgression between multiple North American taxa. These results provide insight into the balance between divergent and homogenizing population genetic processes and highlight remaining challenges in interpreting conflict between different types of analytical approaches with whole-genome sequence data. [ABBA-BABA; approximate Bayesian computation; gene flow; phylogenomics; speciation; whole-genome sequencing.].
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Affiliation(s)
- Erik R Funk
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, 1900 Pleasant St. 334 UCB, Boulder, CO 80309, USA
| | - Garth M Spellman
- Department of Zoology, Denver Museum of Nature and Science, 2001 Colorado Blvd., Denver, CO 80205, USA
| | - Kevin Winker
- University of Alaska Museum, University of Alaska Fairbanks, 1962 Yukon Dr., Fairbanks, AK 99775, USA
| | - Jack J Withrow
- University of Alaska Museum, University of Alaska Fairbanks, 1962 Yukon Dr., Fairbanks, AK 99775, USA
| | - Kristen C Ruegg
- Department of Biology, Colorado State University, 251 W Pitkin St., Fort Collins, CO 80521, USA
| | - Erika Zavaleta
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, 1156 High St., Santa Cruz CA, 95064, USA
| | - Scott A Taylor
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, 1900 Pleasant St. 334 UCB, Boulder, CO 80309, USA
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16
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Dong F, Li SH, Chiu CC, Dong L, Yao CT, Yang XJ. Strict allopatric speciation of sky island Pyrrhula erythaca species complex. Mol Phylogenet Evol 2020; 153:106941. [PMID: 32818596 DOI: 10.1016/j.ympev.2020.106941] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 07/01/2020] [Accepted: 08/13/2020] [Indexed: 10/23/2022]
Abstract
Increasing evidence of post-divergence gene flow between taxa is shifting our understanding on the mode of speciation. A fundamental question arises concerning the circumstances under which strict allopatric speciation still holds true. Sky island populations might undergo reduced gene flow by niche conservatism to highland habitats and follow divergence in an allopatric manner. In this study, we tested this hypothesis in the sky island Grey-headed Bullfinch (Pyrrhula erythaca) species complex via statistical analyses of both genetic and ecological data. Results of coalescent-based analysis of multiple nuclear loci suggested that P. e. owstoni likely colonized Taiwan island during the severe mid-Pleistocene glacial climate followed by strictly allopatric divergence from P. e. erythaca distributed in Himalayas-Hengduan mountains and central North China. Results of ecological niche modeling suggested that their speciation may be attributed to the niche conservatism of these birds and the lack of a suitable ecological corridor during subsequent milder glacial episodes. In addition, we delimited the traditionally defined P. erythaca into two full species, P. erythaca in the Asian mainland and P. owstoni on the island of Taiwan, based on both genetic and behavioural evidences. These results suggest that ecology can have a dynamic role in allowing highland populations to expand their ranges and isolated by habitat barriers to diversify in a strictly allopatric manner.
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Affiliation(s)
- Feng Dong
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Shou-Hsien Li
- Department of Life Science, National Taiwan Normal University, Taipei 116, Taiwan
| | - Chi-Cheng Chiu
- Department of Life Science, National Taiwan Normal University, Taipei 116, Taiwan
| | - Lu Dong
- Ministry of Education Key Laboratory for Biodiversity and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Cheng-Te Yao
- Endemic Species Research Institute, Minsheng East Road, Jiji Township, Nantou County 552, Taiwan.
| | - Xiao-Jun Yang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.
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17
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Zhu Z, Guan Z, Liu G, Wang Y, Zhang Z. SGID: a comprehensive and interactive database of the silkworm. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2020; 2019:5677404. [PMID: 31836898 PMCID: PMC6911161 DOI: 10.1093/database/baz134] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 10/27/2019] [Accepted: 11/01/2019] [Indexed: 11/12/2022]
Abstract
Although the domestic silkworm (Bombyx mori) is an important model and economic animal, there is a lack of comprehensive database for this organism. Here, we developed the silkworm genome informatics database (SGID). It aims to bring together all silkworm-related biological data and provide an interactive platform for gene inquiry and analysis. The function annotation in SGID is thorough and covers 98% of the silkworm genes. The annotation details include function description, Gene Ontology, Kyoto Encyclopedia of Genes and Genomes pathway, subcellular location, transmembrane topology, protein secondary/tertiary structure, homologous group and transcription factor. SGID provides genome-scale visualization of population genetics test results based on high-depth resequencing data of 158 silkworm samples. It also provides interactive analysis tools of transcriptomic and epigenomic data from 79 NCBI BioProjects. SGID will be extremely useful to silkworm research in the future.
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Affiliation(s)
- Zhenglin Zhu
- School of Life Sciences, Chongqing University, No.55 Daxuecheng South Rd., Shapingba, Chongqing, 401331, China
| | - Zhufen Guan
- School of Life Sciences, Chongqing University, No.55 Daxuecheng South Rd., Shapingba, Chongqing, 401331, China
| | - Gexin Liu
- School of Life Sciences, Chongqing University, No.55 Daxuecheng South Rd., Shapingba, Chongqing, 401331, China
| | - Yawang Wang
- School of Life Sciences, Chongqing University, No.55 Daxuecheng South Rd., Shapingba, Chongqing, 401331, China.,Khoury College of Computer Sciences, Northeastern University, 401 Terry Ave N, Seattle, WA, 98109, USA
| | - Ze Zhang
- School of Life Sciences, Chongqing University, No.55 Daxuecheng South Rd., Shapingba, Chongqing, 401331, China
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18
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Climatic dynamics and topography control genetic variation in Atlantic Forest montane birds. Mol Phylogenet Evol 2020; 148:106812. [PMID: 32259655 DOI: 10.1016/j.ympev.2020.106812] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 02/17/2020] [Accepted: 03/25/2020] [Indexed: 11/20/2022]
Abstract
Montane organisms responded to Quaternary climate change by tracking suitable habitat along elevational gradients. However, it is unclear whether these past climatic dynamics generated predictable patterns of genetic diversity in co-occurring montane taxa. To test if the genetic variation is associated with historical changes in the elevational distribution of montane habitats, we integrated paleoclimatic data and a model selection approach for testing the demographic history of five co-distributed bird species occurring in the southern Atlantic Forest sky islands. We found that changes in historical population sizes and current genetic diversity are attributable to habitat dynamics among time periods and the current elevational distribution of populations. Taxa with populations restricted to the more climatically dynamic southern mountain block (SMB) had, on average, a six-fold demographic expansion, whereas the populations from the northern mountain block (NMB) remained constant. In the current configuration of the southern Atlantic Forest montane habitats, populations in the SMB have more widespread elevational distributions, occur at lower elevations, and harbor higher levels of genetic diversity than NMB populations. Despite the apparent coupling of demographic and climatic oscillations, our data rejected simultaneous population structuring due to historical habitat fragmentation. Demographic modeling indicated that the species had different modes of differentiation, and varied in the timing of divergence and the degree of gene flow across mountain blocks. Our results suggest that the heterogeneous distribution of genetic variation in birds of the Atlantic Forest sky islands is associated with the interplay between topography and climate of distinct mountains, leading to predictable patterns of genetic diversity.
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19
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Dumas E, Feurtey A, Rodríguez de la Vega RC, Le Prieur S, Snirc A, Coton M, Thierry A, Coton E, Le Piver M, Roueyre D, Ropars J, Branca A, Giraud T. Independent domestication events in the blue-cheese fungus Penicillium roqueforti. Mol Ecol 2020; 29:2639-2660. [PMID: 31960565 PMCID: PMC7497015 DOI: 10.1111/mec.15359] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 01/02/2020] [Accepted: 01/04/2020] [Indexed: 12/13/2022]
Abstract
Domestication provides an excellent framework for studying adaptive divergence. Using population genomics and phenotypic assays, we reconstructed the domestication history of the blue cheese mould Penicillium roqueforti. We showed that this fungus was domesticated twice independently. The population used in Roquefort originated from an old domestication event associated with weak bottlenecks and exhibited traits beneficial for pre‐industrial cheese production (slower growth in cheese and greater spore production on bread, the traditional multiplication medium). The other cheese population originated more recently from the selection of a single clonal lineage, was associated with all types of blue cheese worldwide except Roquefort, and displayed phenotypes more suited for industrial cheese production (high lipolytic activity, efficient cheese cavity colonization ability and salt tolerance). We detected genomic regions affected by recent positive selection and putative horizontal gene transfers. This study sheds light on the processes of rapid adaptation and raises questions about genetic resource conservation. see also the Perspective by Brigida Gallone, Jan Steensels and Kevin J. Verstrepen.
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Affiliation(s)
- Emilie Dumas
- Ecologie Systématique et Evolution, CNRS, AgroParisTech, Ecologie Systématique Evolution, Université Paris-Saclay, Orsay, France.,Laboratory for Molecular Immunology and Inflammation, Department of Rheumatology, University Hospital Ghent, The Vlaams Instituut voor Biotechnologie (VIB) Center for Inflammation Research (IRC), Ghent, Belgium
| | - Alice Feurtey
- Ecologie Systématique et Evolution, CNRS, AgroParisTech, Ecologie Systématique Evolution, Université Paris-Saclay, Orsay, France.,Environmental Genomics, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Ricardo C Rodríguez de la Vega
- Ecologie Systématique et Evolution, CNRS, AgroParisTech, Ecologie Systématique Evolution, Université Paris-Saclay, Orsay, France
| | - Stéphanie Le Prieur
- Ecologie Systématique et Evolution, CNRS, AgroParisTech, Ecologie Systématique Evolution, Université Paris-Saclay, Orsay, France
| | - Alodie Snirc
- Ecologie Systématique et Evolution, CNRS, AgroParisTech, Ecologie Systématique Evolution, Université Paris-Saclay, Orsay, France
| | - Monika Coton
- Univ Brest, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, Plouzané, France
| | - Anne Thierry
- Science et Technologie du Lait et de l'Œuf (STLO), UMR1253, Agrocampus Ouest, INRAE, Rennes, France
| | - Emmanuel Coton
- Univ Brest, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, Plouzané, France
| | - Mélanie Le Piver
- Laboratoire Interprofessionnel de Production - SAS L.I.P, Aurillac, France
| | - Daniel Roueyre
- Laboratoire Interprofessionnel de Production - SAS L.I.P, Aurillac, France
| | - Jeanne Ropars
- Ecologie Systématique et Evolution, CNRS, AgroParisTech, Ecologie Systématique Evolution, Université Paris-Saclay, Orsay, France
| | - Antoine Branca
- Ecologie Systématique et Evolution, CNRS, AgroParisTech, Ecologie Systématique Evolution, Université Paris-Saclay, Orsay, France
| | - Tatiana Giraud
- Ecologie Systématique et Evolution, CNRS, AgroParisTech, Ecologie Systématique Evolution, Université Paris-Saclay, Orsay, France
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20
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Dong F, Hung CM, Yang XJ. Secondary contact after allopatric divergence explains avian speciation and high species diversity in the Himalayan-Hengduan Mountains. Mol Phylogenet Evol 2020; 143:106671. [DOI: 10.1016/j.ympev.2019.106671] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 11/05/2019] [Accepted: 11/05/2019] [Indexed: 11/25/2022]
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21
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Wang X, Maher KH, Zhang N, Que P, Zheng C, Liu S, Wang B, Huang Q, Chen D, Yang X, Zhang Z, Székely T, Urrutia AO, Liu Y. Demographic Histories and Genome-Wide Patterns of Divergence in Incipient Species of Shorebirds. Front Genet 2019; 10:919. [PMID: 31781152 PMCID: PMC6857203 DOI: 10.3389/fgene.2019.00919] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Accepted: 08/30/2019] [Indexed: 12/30/2022] Open
Abstract
Understanding how incipient species are maintained with gene flow is a fundamental question in evolutionary biology. Whole genome sequencing of multiple individuals holds great potential to illustrate patterns of genomic differentiation as well as the associated evolutionary histories. Kentish (Charadrius alexandrinus) and the white-faced (C. dealbatus) plovers, which differ in their phenotype, ecology and behavior, are two incipient species and parapatrically distributed in East Asia. Previous studies show evidence of genetic diversification with gene flow between the two plovers. Under this scenario, it is of great importance to explore the patterns of divergence at the genomic level and to determine whether specific regions are involved in reproductive isolation and local adaptation. Here we present the first population genomic analysis of the two incipient species based on the de novo Kentish plover reference genome and resequenced populations. We show that the two plover lineages are distinct in both nuclear and mitochondrial genomes. Using model-based coalescence analysis, we found that population sizes of Kentish plover increased whereas white-faced plovers declined during the Last Glaciation Period. Moreover, the two plovers diverged allopatrically, with gene flow occurring after secondary contact. This has resulted in low levels of genome-wide differentiation, although we found evidence of a few highly differentiated genomic regions in both the autosomes and the Z-chromosome. This study illustrates that incipient shorebird species with gene flow after secondary contact can exhibit discrete divergence at specific genomic regions and provides basis to further exploration on the genetic basis of relevant phenotypic traits.
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Affiliation(s)
- Xuejing Wang
- State Key Laboratory of Biocontrol, Department of Ecology, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Kathryn H Maher
- Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom.,Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | - Nan Zhang
- State Key Laboratory of Biocontrol, Department of Ecology, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Pinjia Que
- Ministry of Education Key Laboratory for Biodiversity and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Chenqing Zheng
- State Key Laboratory of Biocontrol, Department of Ecology, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.,Department of Bioinformatics, Shenzhen Realomics Biological Technology Ltd, Shenzhen, China
| | - Simin Liu
- State Key Laboratory of Biocontrol, Department of Ecology, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Biao Wang
- School of Biosciences, University of Melbourne, Parkville, VIC, Australia
| | - Qin Huang
- State Key Laboratory of Biocontrol, Department of Ecology, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - De Chen
- Ministry of Education Key Laboratory for Biodiversity and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Xu Yang
- Department of Bioinformatics, Shenzhen Realomics Biological Technology Ltd, Shenzhen, China
| | - Zhengwang Zhang
- Ministry of Education Key Laboratory for Biodiversity and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Tamás Székely
- State Key Laboratory of Biocontrol, Department of Ecology, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.,Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom.,Ministry of Education Key Laboratory for Biodiversity and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Araxi O Urrutia
- Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom.,Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Yang Liu
- State Key Laboratory of Biocontrol, Department of Ecology, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
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22
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Smith CCR, Flaxman SM. Leveraging whole genome sequencing data for demographic inference with approximate Bayesian computation. Mol Ecol Resour 2019; 20:125-139. [DOI: 10.1111/1755-0998.13092] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 08/30/2019] [Accepted: 09/06/2019] [Indexed: 01/16/2023]
Affiliation(s)
- Chris C. R. Smith
- Department of Ecology and Evolutionary Biology University of Colorado Boulder CO USA
| | - Samuel M. Flaxman
- Department of Ecology and Evolutionary Biology University of Colorado Boulder CO USA
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23
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Smith CCR, Flaxman SM, Scordato ESC, Kane NC, Hund AK, Sheta BM, Safran RJ. Demographic inference in barn swallows using whole-genome data shows signal for bottleneck and subspecies differentiation during the Holocene. Mol Ecol 2018; 27:4200-4212. [PMID: 30176075 DOI: 10.1111/mec.14854] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 08/27/2018] [Indexed: 12/20/2022]
Abstract
Accounting for historical demographic features is vital for many types of evolutionary inferences, including the estimation of divergence times between closely related populations. In barn swallow, Hirundo rustica, inferring historical population sizes and subspecies divergence times can shed light on the recent co-evolution of this species with humans. Pairwise sequentially Markovian coalescent uncovered population growth beginning on the order of one million years ago-which may reflect the radiation of the broader Hirundo genus-and a more recent population decline. Additionally, we used approximate Bayesian computation to evaluate hypotheses about recent timescale barn swallow demography, including population growth due to human commensalism, and a potential founder event associated with the onset of nesting on human structures. We found signal for a bottleneck event approximately 7,700 years ago, near the time that humans began building substantial structures, although there was considerable uncertainty associated with this estimate. Subspecies differentiation and subsequent growth occurred after the bottleneck in the best-supported model, an order of magnitude more recently than previous estimates in this system. We also compared results obtained from whole-genome sequencing versus reduced representation sequencing, finding many similar results despite substantial allelic dropout in the reduced representation data, which may have affected estimates of some parameters. This study presents the first genetic evidence of a potential barn swallow founder effect and subspecies divergence coinciding with the Holocene, which is an important step in analysing the biogeographical history of a well-known human commensal species.
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Affiliation(s)
- Chris C R Smith
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado
| | - Samuel M Flaxman
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado
| | - Elizabeth S C Scordato
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado.,Biological Sciences Department, California State Polytechnic University, Pomona, California
| | - Nolan C Kane
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado
| | - Amanda K Hund
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado
| | - Basma M Sheta
- Zoology Department, Faculty of Science, Damietta University, Damietta, Egypt
| | - Rebecca J Safran
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado
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24
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Ravinet M, Yoshida K, Shigenobu S, Toyoda A, Fujiyama A, Kitano J. The genomic landscape at a late stage of stickleback speciation: High genomic divergence interspersed by small localized regions of introgression. PLoS Genet 2018; 14:e1007358. [PMID: 29791436 PMCID: PMC5988309 DOI: 10.1371/journal.pgen.1007358] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 06/05/2018] [Accepted: 04/11/2018] [Indexed: 12/17/2022] Open
Abstract
Speciation is a continuous process and analysis of species pairs at different stages of divergence provides insight into how it unfolds. Previous genomic studies on young species pairs have revealed peaks of divergence and heterogeneous genomic differentiation. Yet less known is how localised peaks of differentiation progress to genome-wide divergence during the later stages of speciation in the presence of persistent gene flow. Spanning the speciation continuum, stickleback species pairs are ideal for investigating how genomic divergence builds up during speciation. However, attention has largely focused on young postglacial species pairs, with little knowledge of the genomic signatures of divergence and introgression in older stickleback systems. The Japanese stickleback species pair, composed of the Pacific Ocean three-spined stickleback (Gasterosteus aculeatus) and the Japan Sea stickleback (G. nipponicus), which co-occur in the Japanese islands, is at a late stage of speciation. Divergence likely started well before the end of the last glacial period and crosses between Japan Sea females and Pacific Ocean males result in hybrid male sterility. Here we use coalescent analyses and Approximate Bayesian Computation to show that the two species split approximately 0.68-1 million years ago but that they have continued to exchange genes at a low rate throughout divergence. Population genomic data revealed that, despite gene flow, a high level of genomic differentiation is maintained across the majority of the genome. However, we identified multiple, small regions of introgression, occurring mainly in areas of low recombination rate. Our results demonstrate that a high level of genome-wide divergence can establish in the face of persistent introgression and that gene flow can be localized to small genomic regions at the later stages of speciation with gene flow.
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Affiliation(s)
- Mark Ravinet
- Division of Ecological Genetics, Department of Population Genetics, National Institute of Genetics, Mishima, Shizuoka, Japan
- Centre for Ecological and Evolutionary Synthesis, University of Oslo, Oslo, Norway
| | - Kohta Yoshida
- Division of Ecological Genetics, Department of Population Genetics, National Institute of Genetics, Mishima, Shizuoka, Japan
- Integrative Evolutionary Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Shuji Shigenobu
- Functional Genomics Facility, National Institute for Basic Biology, Okazaki, Aichi, Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Asao Fujiyama
- Comparative Genomics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Jun Kitano
- Division of Ecological Genetics, Department of Population Genetics, National Institute of Genetics, Mishima, Shizuoka, Japan
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25
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Elleouet JS, Aitken SN. Exploring Approximate Bayesian Computation for inferring recent demographic history with genomic markers in nonmodel species. Mol Ecol Resour 2018; 18:525-540. [DOI: 10.1111/1755-0998.12758] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 01/16/2018] [Indexed: 01/11/2023]
Affiliation(s)
- Joane S. Elleouet
- Department of Forest and Conservation Sciences; Faculty of Forestry; University of British Columbia; Vancouver BC Canada
| | - Sally N. Aitken
- Department of Forest and Conservation Sciences; Faculty of Forestry; University of British Columbia; Vancouver BC Canada
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26
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Karabatsos G, Leisen F. An approximate likelihood perspective on ABC methods. STATISTICS SURVEYS 2018. [DOI: 10.1214/18-ss120] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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27
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Wang J, Ai B, Kong H, Kang M. Speciation history of a species complex of Primulina eburnea (Gesneriaceae) from limestone karsts of southern China, a biodiversity hot spot. Evol Appl 2017; 10:919-934. [PMID: 29151883 PMCID: PMC5680421 DOI: 10.1111/eva.12495] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 05/22/2017] [Indexed: 11/30/2022] Open
Abstract
Limestone karsts in southern China are characterized by high edaphic and topographic heterogeneity and host high levels of species richness and endemism. However, the evolutionary mechanisms for generating such biodiversity remain poorly understood. Here, we performed species delimitation, population genetic analyses, simulations of gene flow and analyses of floral morphological traits to infer the geographic history of speciation in a species complex of Primulina eburnea from limestone karsts of southern China. Using Bayesian species delimitation, we determined that there are seven distinct species that correspond well to the putative morphological species. Species tree reconstruction, Structure and Neighbor‐Net analyses all recovered four lineages in agreement with currently species geographic boundaries. High levels of genetic differentiation were observed both within and among species. Isolation–migration coalescent analysis provides evidence for significant but low gene flow among species. Approximate Bayesian computation (ABC) analysis supports a scenario of historical gene flow rather than recent contemporary gene flow for most species divergences. Finally, we found no evidence of divergent selection contributing to population differentiation of a suite of flower traits. These results support the prevalence of allopatric speciation and highlight the role of geographic isolation in the diversification process. At small geographic scales, limited hybridization occurred in the past between proximate populations but did not eliminate species boundaries. We conclude that limited gene flow might have been the predominant evolutionary force in promoting population differentiation and speciation.
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Affiliation(s)
- Jing Wang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization South China Botanical Garden Chinese Academy of Sciences Guangzhou China
| | - Bin Ai
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization South China Botanical Garden Chinese Academy of Sciences Guangzhou China
| | - Hanghui Kong
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization South China Botanical Garden Chinese Academy of Sciences Guangzhou China
| | - Ming Kang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization South China Botanical Garden Chinese Academy of Sciences Guangzhou China.,Southeast Asia Biodiversity Research Institute Chinese Academy of Sciences Nay Pyi Taw Myanmar
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28
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Yoichi W, Tamaki I, Sakaguchi S, Song JS, Yamamoto SI, Tomaru N. Population demographic history of a temperate shrub, Rhododendron weyrichii (Ericaceae), on continental islands of Japan and South Korea. Ecol Evol 2016; 6:8800-8810. [PMID: 28035270 PMCID: PMC5192946 DOI: 10.1002/ece3.2576] [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: 08/18/2016] [Revised: 11/04/2016] [Accepted: 10/06/2016] [Indexed: 01/18/2023] Open
Abstract
Continental islands provide opportunities for testing the effects of isolation and migration on genetic variation in plant populations. In characteristic of continental islands is that the geographic connections between these islands, which are currently distinguished by seaways, have experienced fluctuations caused by sea‐level changes due to climate oscillations during the Quaternary. Plant populations on the islands have migrated between these islands via the exposed seafloors or been isolated. Here, we examined the demographic history of a temperate shrub, Rhododendron weyrichii, which is distributed in the southwestern parts of the Japanese archipelago and on an island of South Korea, using statistical phylogeographic approaches based on the DNA sequences of two chloroplast and eight nuclear loci in samples analyzed from 18 populations on eight continental islands, and palaeodistribution modeling. Time estimates for four island populations indicate that the durations of vicariance history are different between these populations, and these events have continued since the last glacial or may have predated the last glacial. The constancy or expansion of population sizes on the Japanese islands, and in contrast a bottleneck in population size on the Korean island Jeju, suggests that these islands may have provided different conditions for sustaining populations. The result of palaeodistribution modeling indicates that the longitudinal range of the species as a whole has not changed greatly since the last glacial maximum. These results indicate that exposed seafloors during the glacial period formed both effective and ineffective migration corridors. These findings may shed light on the effects of seafloor exposure on the migration of plants distributed across continental islands.
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Affiliation(s)
- Watanabe Yoichi
- Graduate School of Bioagricultural Sciences Nagoya University Nagoya Japan; Present address: Graduate School of Horticulture Chiba University Matsudo 648 Matsudo Chiba 271-8510 Japan
| | - Ichiro Tamaki
- Gifu Academy of Forest Science and Culture Mino Gifu Japan
| | - Shota Sakaguchi
- Graduate School of Human and Environmental Studies Kyoto University Kyoto Japan
| | - Jong-Suk Song
- Department of Biological Science College of Natural Sciences Andong National University Andong Gyeongbuk Korea
| | | | - Nobuhiro Tomaru
- Graduate School of Bioagricultural Sciences Nagoya University Nagoya Japan
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29
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Faisal M, Futschik A, Hussain I, Abd-el.Moemen M. Choosing summary statistics by least angle regression for approximate Bayesian computation. J Appl Stat 2016. [DOI: 10.1080/02664763.2015.1134447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Muhammad Faisal
- Faculty of Health Studies, University of Bradford, Bradford, UK
- Bradford Institute for Health Research, Bradford Teaching Hospitals NHS Foundation Trust, Bradford, UK
- Department of Statistics and Operations Research, University of Vienna, Vienna, Austria
| | - Andreas Futschik
- Institute of Applied Statistics, JK University Linz, Linz, Austria
| | - Ijaz Hussain
- Department of Statistics, Quaid-i-Azam University, Islamabad, Pakistan
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30
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Novikova PY, Hohmann N, Nizhynska V, Tsuchimatsu T, Ali J, Muir G, Guggisberg A, Paape T, Schmid K, Fedorenko OM, Holm S, Säll T, Schlötterer C, Marhold K, Widmer A, Sese J, Shimizu KK, Weigel D, Krämer U, Koch MA, Nordborg M. Sequencing of the genus Arabidopsis identifies a complex history of nonbifurcating speciation and abundant trans-specific polymorphism. Nat Genet 2016; 48:1077-82. [PMID: 27428747 DOI: 10.1038/ng.3617] [Citation(s) in RCA: 126] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 06/14/2016] [Indexed: 12/17/2022]
Abstract
The notion of species as reproductively isolated units related through a bifurcating tree implies that gene trees should generally agree with the species tree and that sister taxa should not share polymorphisms unless they diverged recently and should be equally closely related to outgroups. It is now possible to evaluate this model systematically. We sequenced multiple individuals from 27 described taxa representing the entire Arabidopsis genus. Cluster analysis identified seven groups, corresponding to described species that capture the structure of the genus. However, at the level of gene trees, only the separation of Arabidopsis thaliana from the remaining species was universally supported, and, overall, the amount of shared polymorphism demonstrated that reproductive isolation was considerably more recent than the estimated divergence times. We uncovered multiple cases of past gene flow that contradict a bifurcating species tree. Finally, we showed that the pattern of divergence differs between gene ontologies, suggesting a role for selection.
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Affiliation(s)
- Polina Yu Novikova
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria.,Vienna Graduate School of Population Genetics, Institut für Populationsgenetik, Vetmeduni, Vienna, Austria
| | - Nora Hohmann
- Centre for Organismal Studies Heidelberg, University of Heidelberg, Heidelberg, Germany
| | - Viktoria Nizhynska
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria
| | - Takashi Tsuchimatsu
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria
| | - Jamshaid Ali
- Department of Plant Physiology, Ruhr-Universität Bochum, Bochum, Germany
| | - Graham Muir
- Vienna Graduate School of Population Genetics, Institut für Populationsgenetik, Vetmeduni, Vienna, Austria
| | | | - Tim Paape
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Karl Schmid
- Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, Stuttgart, Germany
| | - Olga M Fedorenko
- Institute of Biology, Karelian Research Center of the Russian Academy of Sciences, Petrozavodsk, Russia
| | - Svante Holm
- Faculty of Science, Technology and Media, Department of Natural Sciences, Mid Sweden University, Sundsvall, Sweden
| | - Torbjörn Säll
- Department of Biology, Lund University, Lund, Sweden
| | | | - Karol Marhold
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic.,Institute of Botany, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Alex Widmer
- Department of Plant Physiology, Ruhr-Universität Bochum, Bochum, Germany
| | - Jun Sese
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
| | - Kentaro K Shimizu
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Detlef Weigel
- Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Ute Krämer
- Department of Plant Physiology, Ruhr-Universität Bochum, Bochum, Germany
| | - Marcus A Koch
- Centre for Organismal Studies Heidelberg, University of Heidelberg, Heidelberg, Germany
| | - Magnus Nordborg
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria
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31
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Günther T, Lampei C, Barilar I, Schmid KJ. Genomic and phenotypic differentiation of Arabidopsis thaliana along altitudinal gradients in the North Italian Alps. Mol Ecol 2016; 25:3574-92. [PMID: 27220345 DOI: 10.1111/mec.13705] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Revised: 04/19/2016] [Accepted: 05/02/2016] [Indexed: 12/25/2022]
Abstract
Altitudinal gradients in mountain regions are short-range clines of different environmental parameters such as temperature or radiation. We investigated genomic and phenotypic signatures of adaptation to such gradients in five Arabidopsis thaliana populations from the North Italian Alps that originated from 580 to 2350 m altitude by resequencing pools of 19-29 individuals from each population. The sample includes two pairs of low- and high-altitude populations from two different valleys. High-altitude populations showed a lower nucleotide diversity and negative Tajima's D values and were more closely related to each other than to low-altitude populations from the same valley. Despite their close geographic proximity, demographic analysis revealed that low- and high-altitude populations split between 260 000 and 15 000 years before present. Single nucleotide polymorphisms whose allele frequencies were highly differentiated between low- and high-altitude populations identified genomic regions of up to 50 kb length where patterns of genetic diversity are consistent with signatures of local selective sweeps. These regions harbour multiple genes involved in stress response. Variation among populations in two putative adaptive phenotypic traits, frost tolerance and response to light/UV stress was not correlated with altitude. Taken together, the spatial distribution of genetic diversity reflects a potentially adaptive differentiation between low- and high-altitude populations, whereas the phenotypic differentiation in the two traits investigated does not. It may resemble an interaction between adaptation to the local microhabitat and demographic history influenced by historical glaciation cycles, recent seed dispersal and genetic drift in local populations.
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Affiliation(s)
- Torsten Günther
- Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, Stuttgart, Germany.,Department of Evolutionary Biology, EBC, Uppsala University, Uppsala, Sweden
| | - Christian Lampei
- Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, Stuttgart, Germany
| | - Ivan Barilar
- Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, Stuttgart, Germany
| | - Karl J Schmid
- Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, Stuttgart, Germany
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32
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Papadantonakis S, Poirazi P, Pavlidis P. CoMuS: simulating coalescent histories and polymorphic data from multiple species. Mol Ecol Resour 2016; 16:1435-1448. [PMID: 27238297 DOI: 10.1111/1755-0998.12544] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Revised: 04/30/2016] [Accepted: 05/06/2016] [Indexed: 01/25/2023]
Abstract
The simultaneous analysis of intra- and interspecies variation is challenging mainly because our knowledge about patterns of polymorphisms where both intra- and interspecies samples coexist is limited. In this study, we present CoMuS (Coalescent of Multiple Species), a multispecies coalescent software that can simulate intra- and interspecies polymorphisms. CoMuS supports a variety of speciation models and demographic scenarios related to the history of each species. In CoMuS, speciation can be accompanied by either instant or gradual isolation between sister species. Sampling may also occur in the past, and thus, we can study simultaneously extinct and extant species. Our software supports both the infinite- and the finite-site model, with substitution rate heterogeneity among sites and a user-defined proportion of invariable sites. We demonstrate the usage of CoMuS in various applications: species delimitation, software testing, model selection and parameter inference involving present-day and ancestral samples, comparison between gradual and instantaneous isolation models, estimation of speciation time between human and chimpanzee using both intra- and interspecies variation. We expect that CoMuS will be particularly useful for studies where species have been separated recently from their common ancestor and phenomena such as incomplete lineage sorting or introgression still occur.
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Affiliation(s)
- S Papadantonakis
- Department of Biology, University of Crete, PO Box 2208, 71409, Heraklio, Greece
| | - P Poirazi
- Institute of Molecular Biology and Biotechnology (IMBB), Foundation for Research and Technology-Hellas (FORTH), 70013, Heraklio, Greece
| | - P Pavlidis
- Institute of Molecular Biology and Biotechnology (IMBB), Foundation for Research and Technology-Hellas (FORTH), 70013, Heraklio, Greece.
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33
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Bao L, Kudureti A, Bai W, Chen R, Wang T, Wang H, Ge J. Contributions of multiple refugia during the last glacial period to current mainland populations of Korean pine (Pinus koraiensis). Sci Rep 2015; 5:18608. [PMID: 26691230 PMCID: PMC4686996 DOI: 10.1038/srep18608] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 11/09/2015] [Indexed: 12/30/2022] Open
Abstract
The northern microrefugia that existed during the Last Glacial Maximum (LGM) are a key factor in the demographic history of species. Pinus koraiensis has a unique distribution in northeast Asia. The Changbai Mountains and the Korean peninsula (CM/KP) are usually considered to be the LGM refugia for P. koraiensis. However, the Xiaoxingan Range (XR), at the northern part of this species' distribution, is another possible refugium. We used chloroplast sequencing and ten nuclear single-copy gene loci to calculate the genetic diversity pattern of P. koraiensis. The probabilities of a single LGM refugium and of multiple LGM refugia were calculated based on approximate Bayesian computation. The effect of the latitudinal gradient on genetic diversity was not significant. However, unique alleles occurred at low frequencies in CM/KP and XR. A conservative estimate of the coalescence time between CM/KP and XR is 0.4 million years ago, a time prior to the LGM. Gene flow between CM/KP and XR was estimated to be more than one in per generation, an amount that may be sufficient to limit genetic divergence between the regions. Our study strongly supports the hypothesis that XR was another LGM refugium in addition to CM/KP.
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Affiliation(s)
- Lei Bao
- State Key Laboratory of Earth Surface Processes and Resource Ecology, Ministry of Education Key Laboratory for Biodiversity Science and Engineering & College of Life Sciences, Beijing Normal University, Beijing, China
| | - Ayijiamali Kudureti
- State Key Laboratory of Earth Surface Processes and Resource Ecology, Ministry of Education Key Laboratory for Biodiversity Science and Engineering & College of Life Sciences, Beijing Normal University, Beijing, China
| | - Weining Bai
- State Key Laboratory of Earth Surface Processes and Resource Ecology, Ministry of Education Key Laboratory for Biodiversity Science and Engineering & College of Life Sciences, Beijing Normal University, Beijing, China
| | - Rongzhang Chen
- State Key Laboratory of Earth Surface Processes and Resource Ecology, Ministry of Education Key Laboratory for Biodiversity Science and Engineering & College of Life Sciences, Beijing Normal University, Beijing, China
| | - Tianming Wang
- State Key Laboratory of Earth Surface Processes and Resource Ecology, Ministry of Education Key Laboratory for Biodiversity Science and Engineering & College of Life Sciences, Beijing Normal University, Beijing, China
| | - Hongfang Wang
- State Key Laboratory of Earth Surface Processes and Resource Ecology, Ministry of Education Key Laboratory for Biodiversity Science and Engineering & College of Life Sciences, Beijing Normal University, Beijing, China
| | - Jianping Ge
- State Key Laboratory of Earth Surface Processes and Resource Ecology, Ministry of Education Key Laboratory for Biodiversity Science and Engineering & College of Life Sciences, Beijing Normal University, Beijing, China
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34
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Oliveira EF, Gehara M, São-Pedro VA, Chen X, Myers EA, Burbrink FT, Mesquita DO, Garda AA, Colli GR, Rodrigues MT, Arias FJ, Zaher H, Santos RML, Costa GC. Speciation with gene flow in whiptail lizards from a Neotropical xeric biome. Mol Ecol 2015; 24:5957-75. [PMID: 26502084 DOI: 10.1111/mec.13433] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Revised: 10/15/2015] [Accepted: 10/21/2015] [Indexed: 11/29/2022]
Abstract
Two main hypotheses have been proposed to explain the diversification of the Caatinga biota. The riverine barrier hypothesis (RBH) claims that the São Francisco River (SFR) is a major biogeographic barrier to gene flow. The Pleistocene climatic fluctuation hypothesis (PCH) states that gene flow, geographic genetic structure and demographic signatures on endemic Caatinga taxa were influenced by Quaternary climate fluctuation cycles. Herein, we analyse genetic diversity and structure, phylogeographic history, and diversification of a widespread Caatinga lizard (Cnemidophorus ocellifer) based on large geographical sampling for multiple loci to test the predictions derived from the RBH and PCH. We inferred two well-delimited lineages (Northeast and Southwest) that have diverged along the Cerrado-Caatinga border during the Mid-Late Miocene (6-14 Ma) despite the presence of gene flow. We reject both major hypotheses proposed to explain diversification in the Caatinga. Surprisingly, our results revealed a striking complex diversification pattern where the Northeast lineage originated as a founder effect from a few individuals located along the edge of the Southwest lineage that eventually expanded throughout the Caatinga. The Southwest lineage is more diverse, older and associated with the Cerrado-Caatinga boundaries. Finally, we suggest that C. ocellifer from the Caatinga is composed of two distinct species. Our data support speciation in the presence of gene flow and highlight the role of environmental gradients in the diversification process.
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Affiliation(s)
- Eliana F Oliveira
- Pós-Graduação em Ecologia, Universidade Federal do Rio Grande do Norte, Natal, RN, 59072-970, Brazil
| | - Marcelo Gehara
- Pós-Graduação em Sistemática e Evolução, Universidade Federal do Rio Grande do Norte, Natal, RN, 59072-970, Brazil
| | - Vinícius A São-Pedro
- Pós-Graduação em Ecologia, Universidade Federal do Rio Grande do Norte, Natal, RN, 59072-970, Brazil
| | - Xin Chen
- Department of Biology, 6S-143, College of Staten Island, The City University of New York, 2800 Victory Boulevard, Staten Island, NY, 10314, USA.,Department of Biology, The Graduate School, City University of New York, New York, NY, 10016, USA
| | - Edward A Myers
- Department of Biology, 6S-143, College of Staten Island, The City University of New York, 2800 Victory Boulevard, Staten Island, NY, 10314, USA.,Department of Biology, The Graduate School, City University of New York, New York, NY, 10016, USA
| | - Frank T Burbrink
- Department of Biology, 6S-143, College of Staten Island, The City University of New York, 2800 Victory Boulevard, Staten Island, NY, 10314, USA.,Department of Biology, The Graduate School, City University of New York, New York, NY, 10016, USA.,Department of Herpetology, American Museum of Natural History, Central Park West at 79th Street, New York, NY, 10024-5192, USA
| | - Daniel O Mesquita
- Departamento de Sistemática e Ecologia, Universidade Federal da Paraíba, João Pessoa, PB, 58000-00, Brazil
| | - Adrian A Garda
- Departamento de Botânica e Zoologia, Centro de Biociências, Universidade Federal do Rio Grande do Norte, Natal, RN, 59072-970, Brazil
| | - Guarino R Colli
- Departamento de Zoologia, Universidade de Brasília, Brasília, DF, 70910-900, Brazil
| | - Miguel T Rodrigues
- Departamento de Zoologia, Universidade de São Paulo, São Paulo, SP, 05422-970, Brazil
| | - Federico J Arias
- Departamento de Zoologia, Universidade de São Paulo, São Paulo, SP, 05422-970, Brazil
| | - Hussam Zaher
- Museu de Zoologia, Universidade de São Paulo, São Paulo, SP, 04263-000, Brazil
| | - Rodrigo M L Santos
- Departamento de Zoologia, Universidade de São Paulo, São Paulo, SP, 05422-970, Brazil
| | - Gabriel C Costa
- Departamento de Ecologia, Universidade Federal do Rio Grande do Norte, Natal, RN, 59072-970, Brazil
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35
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van de Crommenacker J, Bourgeois YXC, Warren BH, Jackson H, Fleischer-Dogley F, Groombridge J, Bunbury N. Using molecular tools to guide management of invasive alien species: assessing the genetic impact of a recently introduced island bird population. DIVERS DISTRIB 2015. [DOI: 10.1111/ddi.12364] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Affiliation(s)
- J. van de Crommenacker
- Seychelles Islands Foundation; La Ciotat Building, Mont Fleuri, Mahé Victoria Seychelles
- Durrell Institute of Conservation and Ecology (DICE); School of Anthropology and Conservation; University of Kent; Marlowe Building Canterbury Kent UK
| | - Y. X. C. Bourgeois
- Zoologisches Institut, Evolutionsbiologie; University of Basel; Vesalgasse 1 4051 Basel Switzerland
| | - B. H. Warren
- Institute of Systematic Botany; University of Zurich; Zollikerstrasse 107 8008 Zurich Switzerland
| | - H. Jackson
- Durrell Institute of Conservation and Ecology (DICE); School of Anthropology and Conservation; University of Kent; Marlowe Building Canterbury Kent UK
| | - F. Fleischer-Dogley
- Seychelles Islands Foundation; La Ciotat Building, Mont Fleuri, Mahé Victoria Seychelles
| | - J. Groombridge
- Durrell Institute of Conservation and Ecology (DICE); School of Anthropology and Conservation; University of Kent; Marlowe Building Canterbury Kent UK
| | - N. Bunbury
- Seychelles Islands Foundation; La Ciotat Building, Mont Fleuri, Mahé Victoria Seychelles
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36
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Shaner PJL, Tsao TH, Lin RC, Liang W, Yeh CF, Yang XJ, Lei FM, Zhou F, Yang CC, Hung LM, Hsu YC, Li SH. Climate niche differentiation between two passerines despite ongoing gene flow. J Anim Ecol 2015; 84:829-839. [PMID: 25582865 DOI: 10.1111/1365-2656.12331] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Accepted: 12/12/2014] [Indexed: 01/23/2023]
Abstract
Niche evolution underpins the generation and maintenance of biological diversity, but niche conservatism, in which niches remain little changed over time in closely related taxa, and the role of ecology in niche evolution are continually debated. To test whether climate niches are conserved in two closely related passerines in East Asia - the vinous-throated (Paradoxornis webbianus) and ashy-throated (P. alphonsianus) parrotbills - we established their potential allopatric and sympatric regions using ecological niche models and compared differences in their climate niches using niche overlap indices in background tests and multivariate statistical analyses. We also used polymorphism data on 44 nuclear genes to infer their divergence demography. We found that these two parrotbills occupy different climate niches, in both their allopatric and potential sympatric regions. Because the potential sympatric region is the area predicted to be suitable for both parrotbills based on the ecological niche models, it can serve as a natural common garden. Therefore, their observed niche differences in this potential sympatry were not simply rendered by phenotypic plasticity and probably had a genetic basis. Our genetic analyses revealed that the two parrotbills are not evolutionarily independent for the most recent part of their divergence history. The two parrotbills diverged c. 856,000 years ago and have had substantial gene flow since a presumed secondary contact c. 290,000 years ago. This study provides an empirical case demonstrating that climate niches may not be homogenized in nascent species in spite of substantial, ongoing gene flow, which in turn suggests a role for ecology in promoting and maintaining diversification among incipient species.
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Affiliation(s)
- Pei-Jen L Shaner
- Department of Life Science, National Taiwan Normal University, Taipei, 116, Taiwan
| | - Tzu-Hsuan Tsao
- Department of Life Science, National Taiwan Normal University, Taipei, 116, Taiwan
| | - Rong-Chien Lin
- Department of Life Science, National Taiwan Normal University, Taipei, 116, Taiwan
| | - Wei Liang
- Ministry of Education Key Laboratory for Tropical Plant and Animal Ecology, College of Life Sciences, Hainan Normal University, Haikou, 571158, China
| | - Chia-Fen Yeh
- Department of Life Science, National Taiwan Normal University, Taipei, 116, Taiwan
| | - Xiao-Jun Yang
- China State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Science, Kunming, 650223, China
| | - Fu-Min Lei
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100080, China
| | - Fang Zhou
- College of Animal Science and Technology, Guangxi University, Nanning, 530005, China
| | - Can-Chao Yang
- Ministry of Education Key Laboratory for Tropical Plant and Animal Ecology, College of Life Sciences, Hainan Normal University, Haikou, 571158, China
| | - Le Manh Hung
- Department of Zoological Museum, Institute of Ecology and Biological Resources, 18 Hoang Quoc Viet - Cau Giay, Hanoi, VietNam
| | - Yu-Cheng Hsu
- Department of Natural Resources and Environmental Studies, National Dong Hwa University, Hualien, 97401, Taiwan
| | - Shou-Hsien Li
- Department of Life Science, National Taiwan Normal University, Taipei, 116, Taiwan
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37
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Adaptive evolution of genes involved in the regulation of germline stem cells in Drosophila melanogaster and D. simulans. G3-GENES GENOMES GENETICS 2015; 5:583-92. [PMID: 25670770 PMCID: PMC4390574 DOI: 10.1534/g3.114.015875] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Population genetic and comparative analyses in diverse taxa have shown that numerous genes involved in reproduction are adaptively evolving. Two genes involved in germline stem cell regulation, bag of marbles (bam) and benign gonial cell neoplasm (bgcn), have been shown previously to experience recurrent, adaptive evolution in both Drosophila melanogaster and D. simulans. Here we report a population genetic survey on eight additional genes involved in germline stem cell regulation in D. melanogaster and D. simulans that reveals all eight of these genes reject a neutral model of evolution in at least one test and one species after correction for multiple testing using a false-discovery rate of 0.05. These genes play diverse roles in the regulation of germline stem cells, suggesting that positive selection in response to several evolutionary pressures may be acting to drive the adaptive evolution of these genes.
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38
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Shafer ABA, Gattepaille LM, Stewart REA, Wolf JBW. Demographic inferences using short-read genomic data in an approximate Bayesian computation framework: in silico evaluation of power, biases and proof of concept in Atlantic walrus. Mol Ecol 2015; 24:328-45. [DOI: 10.1111/mec.13034] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Revised: 11/29/2014] [Accepted: 12/03/2014] [Indexed: 01/01/2023]
Affiliation(s)
- Aaron B. A. Shafer
- Department of Evolutionary Biology; Evolutionary Biology Centre; Uppsala SE-75236 Sweden
| | - Lucie M. Gattepaille
- Department of Evolutionary Biology; Evolutionary Biology Centre; Uppsala SE-75236 Sweden
| | - Robert E. A. Stewart
- Fisheries and Oceans Canada; Freshwater Institute; 501 University Crescent Winnipeg Manitoba R3T 2N6 Canada
| | - Jochen B. W. Wolf
- Department of Evolutionary Biology; Evolutionary Biology Centre; Uppsala SE-75236 Sweden
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39
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Rittmeyer EN, Austin CC. Combined next-generation sequencing and morphology reveal fine-scale speciation in Crocodile Skinks (Squamata: Scincidae: Tribolonotus). Mol Ecol 2015; 24:466-83. [PMID: 25470077 DOI: 10.1111/mec.13030] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Revised: 11/17/2014] [Accepted: 11/28/2014] [Indexed: 02/03/2023]
Abstract
Next-generation sequencing has vast potential to revolutionize the fields of phylogenetics and population genetics through its ability to collect genomic scale data sets of thousands of orthologous loci. Despite this potential, other types of data (e.g. morphology, ecology) remain important, particularly for studies endeavouring to delimit species. Here, we integrate next-generation sequencing with morphology to examine divergence between populations of Tribolonotus pseudoponceleti on the islands of Buka and Bougainville in the Solomon Archipelago. We used the Ion Torrent PGM to collect over 648 Mbp of sequence data for 12 samples, representing 1526 loci recovered from all samples, and 3342 were recovered from at least six samples. Genetic structure analyses strongly support the distinctiveness of these two populations, and Bayes factor delimitations decisively select speciation between Buka and Bougainville. Principal components and discriminant function analyses reveal concordant morphological divergence. Finally, demographic analyses via diffusion approximation and approximate Bayesian computation prefer a complex model of mid-Pleistocene divergence with migration, and a later decrease or cessation of migration and population size shift, suggesting a scenario in which migration was enabled by Pleistocene merging of these two islands, and limited when isolated by higher sea levels. Further analysis of four Sanger sequenced loci in IMa2 had limited power to distinguish among models including and excluding migration, but resulted in similar population size and divergence time estimates, although with much broader confidence intervals. This study represents a framework for how next-generation sequencing and morphological data can be combined and leveraged towards validating putative species and testing demographic scenarios for speciation.
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Affiliation(s)
- Eric N Rittmeyer
- Department of Biological Sciences, Museum of Natural Science, Louisiana State University, 119 Foster Hall, Baton Rouge, LA, 70803, USA
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40
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Dong F, Zou FS, Lei FM, Liang W, Li SH, Yang XJ. Testing hypotheses of mitochondrial gene-tree paraphyly: unravelling mitochondrial capture of the Streak-breasted Scimitar Babbler (Pomatorhinus ruficollis) by the Taiwan Scimitar Babbler (Pomatorhinus musicus). Mol Ecol 2014; 23:5855-67. [DOI: 10.1111/mec.12981] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Revised: 10/02/2014] [Accepted: 10/14/2014] [Indexed: 01/08/2023]
Affiliation(s)
- Feng Dong
- State Key Laboratory of Genetic Resources and Evolution; Kunming Institute of Zoology; Chinese Academy of Sciences; Kunming 650223 China
| | - Fa-Sheng Zou
- South China Institute of Endangered Animals; Guangzhou 510260 China
| | - Fu-Min Lei
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Chinese Academy of Sciences; Beijing 100101 China
| | - Wei Liang
- Ministry of Education Key Laboratory for Tropical Plant and Animal Ecology; College of Life Sciences; Hainan Normal University; Haikou 571158 China
| | - Shou-Hsien Li
- Department of Life Science; National Taiwan Normal University; Taipei 116 Taiwan
| | - Xiao-Jun Yang
- State Key Laboratory of Genetic Resources and Evolution; Kunming Institute of Zoology; Chinese Academy of Sciences; Kunming 650223 China
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41
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Tseng SP, Li SH, Hsieh CH, Wang HY, Lin SM. Influence of gene flow on divergence dating - implications for the speciation history of Takydromus grass lizards. Mol Ecol 2014; 23:4770-84. [PMID: 25142551 DOI: 10.1111/mec.12889] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Revised: 08/07/2014] [Accepted: 08/08/2014] [Indexed: 11/28/2022]
Abstract
Dating the time of divergence and understanding speciation processes are central to the study of the evolutionary history of organisms but are notoriously difficult. The difficulty is largely rooted in variations in the ancestral population size or in the genealogy variation across loci. To depict the speciation processes and divergence histories of three monophyletic Takydromus species endemic to Taiwan, we sequenced 20 nuclear loci and combined with one mitochondrial locus published in GenBank. They were analysed by a multispecies coalescent approach within a Bayesian framework. Divergence dating based on the gene tree approach showed high variation among loci, and the divergence was estimated at an earlier date than when derived by the species-tree approach. To test whether variations in the ancestral population size accounted for the majority of this variation, we conducted computer inferences using isolation-with-migration (IM) and approximate Bayesian computation (ABC) frameworks. The results revealed that gene flow during the early stage of speciation was strongly favoured over the isolation model, and the initiation of the speciation process was far earlier than the dates estimated by gene- and species-based divergence dating. Due to their limited dispersal ability, it is suggested that geographical isolation may have played a major role in the divergence of these Takydromus species. Nevertheless, this study reveals a more complex situation and demonstrates that gene flow during the speciation process cannot be overlooked and may have a great impact on divergence dating. By using multilocus data and incorporating Bayesian coalescence approaches, we provide a more biologically realistic framework for delineating the divergence history of Takydromus.
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Affiliation(s)
- Shu-Ping Tseng
- Department of Life Science, National Taiwan Normal University, Taipei, 116, Taiwan; Department of Entomology, National Taiwan University, Taipei, 106, Taiwan; Graduate Institute of Clinical Medicine, National Taiwan University, Taipei, 100, Taiwan
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42
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An Adaptive Transposable Element Insertion in the Regulatory Region of the EO Gene in the Domesticated Silkworm, Bombyx mori. Mol Biol Evol 2014; 31:3302-13. [DOI: 10.1093/molbev/msu261] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
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43
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Robinson JD, Bunnefeld L, Hearn J, Stone GN, Hickerson MJ. ABC inference of multi-population divergence with admixture from unphased population genomic data. Mol Ecol 2014; 23:4458-71. [PMID: 25113024 PMCID: PMC4285295 DOI: 10.1111/mec.12881] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Revised: 08/04/2014] [Accepted: 08/06/2014] [Indexed: 01/13/2023]
Abstract
Rapidly developing sequencing technologies and declining costs have made it possible to collect genome-scale data from population-level samples in nonmodel systems. Inferential tools for historical demography given these data sets are, at present, underdeveloped. In particular, approximate Bayesian computation (ABC) has yet to be widely embraced by researchers generating these data. Here, we demonstrate the promise of ABC for analysis of the large data sets that are now attainable from nonmodel taxa through current genomic sequencing technologies. We develop and test an ABC framework for model selection and parameter estimation, given histories of three-population divergence with admixture. We then explore different sampling regimes to illustrate how sampling more loci, longer loci or more individuals affects the quality of model selection and parameter estimation in this ABC framework. Our results show that inferences improved substantially with increases in the number and/or length of sequenced loci, while less benefit was gained by sampling large numbers of individuals. Optimal sampling strategies given our inferential models included at least 2000 loci, each approximately 2 kb in length, sampled from five diploid individuals per population, although specific strategies are model and question dependent. We tested our ABC approach through simulation-based cross-validations and illustrate its application using previously analysed data from the oak gall wasp, Biorhiza pallida.
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Affiliation(s)
- John D Robinson
- Department of Biology, City College of New York, 160 Convent Ave., MR 526, New York, NY, 10031, USA
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44
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Carneiro M, Rubin CJ, Di Palma F, Albert FW, Alföldi J, Martinez Barrio A, Pielberg G, Rafati N, Sayyab S, Turner-Maier J, Younis S, Afonso S, Aken B, Alves JM, Barrell D, Bolet G, Boucher S, Burbano HA, Campos R, Chang JL, Duranthon V, Fontanesi L, Garreau H, Heiman D, Johnson J, Mage RG, Peng Z, Queney G, Rogel-Gaillard C, Ruffier M, Searle S, Villafuerte R, Xiong A, Young S, Forsberg-Nilsson K, Good JM, Lander ES, Ferrand N, Lindblad-Toh K, Andersson L. Rabbit genome analysis reveals a polygenic basis for phenotypic change during domestication. Science 2014; 345:1074-1079. [PMID: 25170157 PMCID: PMC5421586 DOI: 10.1126/science.1253714] [Citation(s) in RCA: 267] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The genetic changes underlying the initial steps of animal domestication are still poorly understood. We generated a high-quality reference genome for the rabbit and compared it to resequencing data from populations of wild and domestic rabbits. We identified more than 100 selective sweeps specific to domestic rabbits but only a relatively small number of fixed (or nearly fixed) single-nucleotide polymorphisms (SNPs) for derived alleles. SNPs with marked allele frequency differences between wild and domestic rabbits were enriched for conserved noncoding sites. Enrichment analyses suggest that genes affecting brain and neuronal development have often been targeted during domestication. We propose that because of a truly complex genetic background, tame behavior in rabbits and other domestic animals evolved by shifts in allele frequencies at many loci, rather than by critical changes at only a few domestication loci.
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MESH Headings
- Animals
- Animals, Domestic/anatomy & histology
- Animals, Domestic/genetics
- Animals, Domestic/psychology
- Animals, Wild/anatomy & histology
- Animals, Wild/genetics
- Animals, Wild/psychology
- Base Sequence
- Behavior, Animal
- Breeding
- Evolution, Molecular
- Gene Frequency
- Genetic Loci
- Genome/genetics
- Molecular Sequence Data
- Phenotype
- Polymorphism, Single Nucleotide
- Rabbits/anatomy & histology
- Rabbits/genetics
- Rabbits/psychology
- Selection, Genetic
- Sequence Analysis, DNA
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Affiliation(s)
- Miguel Carneiro
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Universidade do Porto, 4485-661, Vairão, Portugal
| | - Carl-Johan Rubin
- Science of Life Laboratory Uppsala, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Federica Di Palma
- Broad Institute of Harvard and MIT, 7 Cambridge Center, Cambridge, MA 02142, USA
- Vertebrate and Health Genomics, The Genome Analysis Center, Norwich, UK
| | - Frank W Albert
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Jessica Alföldi
- Broad Institute of Harvard and MIT, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Alvaro Martinez Barrio
- Science of Life Laboratory Uppsala, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Gerli Pielberg
- Science of Life Laboratory Uppsala, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Nima Rafati
- Science of Life Laboratory Uppsala, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Shumaila Sayyab
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Jason Turner-Maier
- Broad Institute of Harvard and MIT, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Shady Younis
- Science of Life Laboratory Uppsala, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Department of Animal Production, Ain Shams University, Shoubra El-Kheima, Cairo, Egypt
| | - Sandra Afonso
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Universidade do Porto, 4485-661, Vairão, Portugal
| | - Bronwen Aken
- Wellcome Trust Sanger Institute, Hinxton, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Joel M Alves
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Universidade do Porto, 4485-661, Vairão, Portugal
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, UK
| | - Daniel Barrell
- Wellcome Trust Sanger Institute, Hinxton, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Gerard Bolet
- INRA, UMR1388 Génétique, Physiologie et Systèmes d'Elevage, F-31326 Castanet-Tolosan, France
| | | | - Hernán A Burbano
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Rita Campos
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Universidade do Porto, 4485-661, Vairão, Portugal
| | - Jean L Chang
- Broad Institute of Harvard and MIT, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Veronique Duranthon
- INRA, UMR1198 Biologie du Développement et Reproduction, F-78350 Jouy-en-Josas, France
| | - Luca Fontanesi
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, 40127 Bologna Italy
| | - Hervé Garreau
- INRA, UMR1388 Génétique, Physiologie et Systèmes d'Elevage, F-31326 Castanet-Tolosan, France
| | - David Heiman
- Broad Institute of Harvard and MIT, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Jeremy Johnson
- Broad Institute of Harvard and MIT, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Rose G Mage
- Laboratory of Immunology, NIAID, NIH, Bethesda, MD, 20892, USA
| | - Ze Peng
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, 2800 Mitchell Drive, Walnut Creek, CA 94598
| | | | - Claire Rogel-Gaillard
- INRA, UMR1313 Génétique Animale et Biologie Intégrative, F- 78350, Jouy-en-Josas, France
| | - Magali Ruffier
- Wellcome Trust Sanger Institute, Hinxton, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | | | - Rafael Villafuerte
- Instituto de Estudios Sociales Avanzados, (IESA-CSIC) Campo Santo de los Mártires 7, Córdoba Spain
| | - Anqi Xiong
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Sarah Young
- Broad Institute of Harvard and MIT, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Karin Forsberg-Nilsson
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Jeffrey M Good
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Division of Biological Sciences, The University of Montana, Missoula, MT 59812, USA
| | - Eric S Lander
- Broad Institute of Harvard and MIT, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Nuno Ferrand
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Universidade do Porto, 4485-661, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n. 4169-007 Porto, Portugal
| | - Kerstin Lindblad-Toh
- Science of Life Laboratory Uppsala, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Broad Institute of Harvard and MIT, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Leif Andersson
- Science of Life Laboratory Uppsala, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, USA
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45
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Hsieh CH, Ko CC, Chung CH, Wang HY. Multilocus approach to clarify species status and the divergence history of the Bemisia tabaci (Hemiptera: Aleyrodidae) species complex. Mol Phylogenet Evol 2014; 76:172-80. [DOI: 10.1016/j.ympev.2014.03.021] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Revised: 01/24/2014] [Accepted: 03/21/2014] [Indexed: 10/25/2022]
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46
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Saïdou AA, Clotault J, Couderc M, Mariac C, Devos KM, Thuillet AC, Amoukou IA, Vigouroux Y. Association mapping, patterns of linkage disequilibrium and selection in the vicinity of the PHYTOCHROME C gene in pearl millet. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2014; 127:19-32. [PMID: 24114050 DOI: 10.1007/s00122-013-2197-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Accepted: 09/13/2013] [Indexed: 05/09/2023]
Abstract
Linkage analysis confirmed the association in the region of PHYC in pearl millet. The comparison of genes found in this region suggests that PHYC is the best candidate. Major efforts are currently underway to dissect the phenotype-genotype relationship in plants and animals using existing populations. This method exploits historical recombinations accumulated in these populations. However, linkage disequilibrium sometimes extends over a relatively long distance, particularly in genomic regions containing polymorphisms that have been targets for selection. In this case, many genes in the region could be statistically associated with the trait shaped by the selected polymorphism. Statistical analyses could help in identifying the best candidate genes into such a region where an association is found. In a previous study, we proposed that a fragment of the PHYTOCHROME C gene (PHYC) is associated with flowering time and morphological variations in pearl millet. In the present study, we first performed linkage analyses using three pearl millet F2 families to confirm the presence of a QTL in the vicinity of PHYC. We then analyzed a wider genomic region of ~100 kb around PHYC to pinpoint the gene that best explains the association with the trait in this region. A panel of 90 pearl millet inbred lines was used to assess the association. We used a Markov chain Monte Carlo approach to compare 75 markers distributed along this 100-kb region. We found the best candidate markers on the PHYC gene. Signatures of selection in this region were assessed in an independent data set and pointed to the same gene. These results foster confidence in the likely role of PHYC in phenotypic variation and encourage the development of functional studies.
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Affiliation(s)
- Abdoul-Aziz Saïdou
- Institut de Recherche pour le Développement, UMR DIADE, 911 avenue Agropolis, BP 64501, 34394, Montpellier, France
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47
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Nadachowska-Brzyska K, Burri R, Olason PI, Kawakami T, Smeds L, Ellegren H. Demographic divergence history of pied flycatcher and collared flycatcher inferred from whole-genome re-sequencing data. PLoS Genet 2013; 9:e1003942. [PMID: 24244198 PMCID: PMC3820794 DOI: 10.1371/journal.pgen.1003942] [Citation(s) in RCA: 94] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Accepted: 09/23/2013] [Indexed: 01/05/2023] Open
Abstract
Profound knowledge of demographic history is a prerequisite for the understanding and inference of processes involved in the evolution of population differentiation and speciation. Together with new coalescent-based methods, the recent availability of genome-wide data enables investigation of differentiation and divergence processes at unprecedented depth. We combined two powerful approaches, full Approximate Bayesian Computation analysis (ABC) and pairwise sequentially Markovian coalescent modeling (PSMC), to reconstruct the demographic history of the split between two avian speciation model species, the pied flycatcher and collared flycatcher. Using whole-genome re-sequencing data from 20 individuals, we investigated 15 demographic models including different levels and patterns of gene flow, and changes in effective population size over time. ABC provided high support for recent (mode 0.3 my, range <0.7 my) species divergence, declines in effective population size of both species since their initial divergence, and unidirectional recent gene flow from pied flycatcher into collared flycatcher. The estimated divergence time and population size changes, supported by PSMC results, suggest that the ancestral species persisted through one of the glacial periods of middle Pleistocene and then split into two large populations that first increased in size before going through severe bottlenecks and expanding into their current ranges. Secondary contact appears to have been established after the last glacial maximum. The severity of the bottlenecks at the last glacial maximum is indicated by the discrepancy between current effective population sizes (20,000-80,000) and census sizes (5-50 million birds) of the two species. The recent divergence time challenges the supposition that avian speciation is a relatively slow process with extended times for intrinsic postzygotic reproductive barriers to evolve. Our study emphasizes the importance of using genome-wide data to unravel tangled demographic histories. Moreover, it constitutes one of the first examples of the inference of divergence history from genome-wide data in non-model species.
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Affiliation(s)
| | - Reto Burri
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Pall I. Olason
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Takeshi Kawakami
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Linnéa Smeds
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Hans Ellegren
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
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48
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Purifying selection after episodes of recurrent adaptive diversification in fungal pathogens. INFECTION GENETICS AND EVOLUTION 2013; 17:123-31. [DOI: 10.1016/j.meegid.2013.03.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2012] [Revised: 02/26/2013] [Accepted: 03/07/2013] [Indexed: 11/20/2022]
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49
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Duchen P, Zivkovic D, Hutter S, Stephan W, Laurent S. Demographic inference reveals African and European admixture in the North American Drosophila melanogaster population. Genetics 2013; 193:291-301. [PMID: 23150605 PMCID: PMC3527251 DOI: 10.1534/genetics.112.145912] [Citation(s) in RCA: 117] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2012] [Accepted: 10/30/2012] [Indexed: 11/18/2022] Open
Abstract
Drosophila melanogaster spread from sub-Saharan Africa to the rest of the world colonizing new environments. Here, we modeled the joint demography of African (Zimbabwe), European (The Netherlands), and North American (North Carolina) populations using an approximate Bayesian computation (ABC) approach. By testing different models (including scenarios with continuous migration), we found that admixture between Africa and Europe most likely generated the North American population, with an estimated proportion of African ancestry of 15%. We also revisited the demography of the ancestral population (Africa) and found-in contrast to previous work-that a bottleneck fits the history of the population of Zimbabwe better than expansion. Finally, we compared the site-frequency spectrum of the ancestral population to analytical predictions under the estimated bottleneck model.
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Affiliation(s)
- Pablo Duchen
- Evolutionary Biology, University of Munich, 82152 Planegg-Martinsried, Germany.
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50
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Catalán A, Hutter S, Parsch J. Population and sex differences in Drosophila melanogaster brain gene expression. BMC Genomics 2012; 13:654. [PMID: 23170910 PMCID: PMC3527002 DOI: 10.1186/1471-2164-13-654] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Accepted: 11/16/2012] [Indexed: 01/07/2023] Open
Abstract
Background Changes in gene regulation are thought to be crucial for the adaptation of organisms to their environment. Transcriptome analyses can be used to identify candidate genes for ecological adaptation, but can be complicated by variation in gene expression between tissues, sexes, or individuals. Here we use high-throughput RNA sequencing of a single Drosophila melanogaster tissue to detect brain-specific differences in gene expression between the sexes and between two populations, one from the ancestral species range in sub-Saharan Africa and one from the recently colonized species range in Europe. Results Relatively few genes (<100) displayed sexually dimorphic expression in the brain, but there was an enrichment of sex-biased genes, especially male-biased genes, on the X chromosome. Over 340 genes differed in brain expression between flies from the African and European populations, with the inter-population divergence being highly correlated between males and females. The differentially expressed genes included those involved in stress response, olfaction, and detoxification. Expression differences were associated with transposable element insertions at two genes implicated in insecticide resistance (Cyp6g1 and CHKov1). Conclusions Analysis of the brain transcriptome revealed many genes differing in expression between populations that were not detected in previous studies using whole flies. There was little evidence for sex-specific regulatory adaptation in the brain, as most expression differences between populations were observed in both males and females. The enrichment of genes with sexually dimorphic expression on the X chromosome is consistent with dosage compensation mechanisms affecting sex-biased expression in somatic tissues.
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Affiliation(s)
- Ana Catalán
- Department of Biology II, University of Munich (LMU), Grosshaderner Str. 2, Planegg-Martinsried 82152, Germany
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