251
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Wiegmann BM, Richards S. Genomes of Diptera. CURRENT OPINION IN INSECT SCIENCE 2018; 25:116-124. [PMID: 29602357 DOI: 10.1016/j.cois.2018.01.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 01/23/2018] [Indexed: 06/08/2023]
Abstract
Diptera (true flies) are among the most diverse holometabolan insect orders and were the first eukaryotic order to have a representative genome fully sequenced. 110 fly species have publically available genome assemblies and many hundreds of population-level genomes have been generated in the model organisms Drosophila melanogaster and the malaria mosquito Anopheles gambiae. Comparative genomics carried out in a phylogenetic context is illuminating many aspects of fly biology, providing unprecedented insight into variability in genome structure, gene content, genetic mechanisms, and rates and patterns of evolution in genes, populations, and species. Despite the rich availability of genomic resources in flies, there remain many fly lineages to which new genome sequencing efforts should be directed. Such efforts would be most valuable in fly families or clades that exhibit multiple origins of key fly behaviors such as blood feeding, phytophagy, parasitism, pollination, and mycophagy.
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Affiliation(s)
- Brian M Wiegmann
- Department of Entomology & Plant Pathology, North Carolina State University, Raleigh, NC 27695, United States.
| | - Stephen Richards
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77006, United States
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252
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Dalquen DA, Zhu T, Yang Z. Maximum Likelihood Implementation of an Isolation-with-Migration Model for Three Species. Syst Biol 2018; 66:379-398. [PMID: 27486180 DOI: 10.1093/sysbio/syw063] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Accepted: 07/08/2016] [Indexed: 01/03/2023] Open
Abstract
We develop a maximum likelihood (ML) method for estimating migration rates between species using genomic sequence data. A species tree is used to accommodate the phylogenetic relationships among three species, allowing for migration between the two sister species, while the third species is used as an out-group. A Markov chain characterization of the genealogical process of coalescence and migration is used to integrate out the migration histories at each locus analytically, whereas Gaussian quadrature is used to integrate over the coalescent times on each genealogical tree numerically. This is an extension of our early implementation of the symmetrical isolation-with-migration model for three species to accommodate arbitrary loci with two or three sequences per locus and to allow asymmetrical migration rates. Our implementation can accommodate tens of thousands of loci, making it feasible to analyze genome-scale data sets to test for gene flow. We calculate the posterior probabilities of gene trees at individual loci to identify genomic regions that are likely to have been transferred between species due to gene flow. We conduct a simulation study to examine the statistical properties of the likelihood ratio test for gene flow between the two in-group species and of the ML estimates of model parameters such as the migration rate. Inclusion of data from a third out-group species is found to increase dramatically the power of the test and the precision of parameter estimation. We compiled and analyzed several genomic data sets from the Drosophila fruit flies. Our analyses suggest no migration from D. melanogaster to D. simulans, and a significant amount of gene flow from D. simulans to D. melanogaster, at the rate of ~0.02 migrant individuals per generation. We discuss the utility of the multispecies coalescent model for species tree estimation, accounting for incomplete lineage sorting and migration.
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Affiliation(s)
- Daniel A Dalquen
- Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK
| | - Tianqi Zhu
- Center for Computational Genomics, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Ziheng Yang
- Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK.,Center for Computational Genomics, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
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253
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Thom G, Amaral FRD, Hickerson MJ, Aleixo A, Araujo-Silva LE, Ribas CC, Choueri E, Miyaki CY. Phenotypic and Genetic Structure Support Gene Flow Generating Gene Tree Discordances in an Amazonian Floodplain Endemic Species. Syst Biol 2018; 67:700-718. [DOI: 10.1093/sysbio/syy004] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 01/23/2018] [Indexed: 01/25/2023] Open
Affiliation(s)
- Gregory Thom
- Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo, Rua do Matão, 277, Cidade Universitária, São Paulo, SP 05508-090, Brazil
| | - Fabio Raposo Do Amaral
- Instituto de Ciências Ambientais, Químicas e Farmacêuticas, Laboratório de Genética Evolutiva, Universidade Federal de São Paulo, Rua Professor Artur Riedel, 275, Diadema, SP 09972–270, Brazil
| | - Michael J Hickerson
- Department of Biology, Marshak Science Building, City College of New York, 160, Convent Avenue, 10031 New York, NY, USA
| | - Alexandre Aleixo
- Departamento de Ornitologia, Museu Paraense Emílio Goeldi (MPEG), Caixa Postal 399, Belém, PA 66040-170, Brazil
| | - Lucas E Araujo-Silva
- Departamento de Ornitologia, Museu Paraense Emílio Goeldi (MPEG), Caixa Postal 399, Belém, PA 66040-170, Brazil
| | - Camila C Ribas
- Coordenação de biodiversidade, Instituto Nacional de Pesquisas da Amazônia (INPA), Av. André Araújo 2936, Manaus, AM 69060-001, Brazil
| | - Erik Choueri
- Coordenação de biodiversidade, Instituto Nacional de Pesquisas da Amazônia (INPA), Av. André Araújo 2936, Manaus, AM 69060-001, 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
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254
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Levänen R, Thulin CG, Spong G, Pohjoismäki JLO. Widespread introgression of mountain hare genes into Fennoscandian brown hare populations. PLoS One 2018; 13:e0191790. [PMID: 29370301 PMCID: PMC5784980 DOI: 10.1371/journal.pone.0191790] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 01/11/2018] [Indexed: 11/29/2022] Open
Abstract
In Fennoscandia, mountain hare (Lepus timidus) and brown hare (Lepus europaeus) hybridize and produce fertile offspring, resulting in gene flow across the species barrier. Analyses of maternally inherited mitochondrial DNA (mtDNA) show that introgression occur frequently, but unavailability of appropriate nuclear DNA markers has made it difficult to evaluate the scale- and significance for the species. The extent of introgression has become important as the brown hare is continuously expanding its range northward, at the apparent expense of the mountain hare, raising concerns about possible competition. We report here, based on analysis of 6833 SNP markers, that the introgression is highly asymmetrical in the direction of gene flow from mountain hare to brown hare, and that the levels of nuclear gene introgression are independent of mtDNA introgression. While it is possible that brown hares obtain locally adapted alleles from the resident mountain hares, the low levels of mountain hare alleles among allopatric brown hares suggest that hybridization is driven by stochastic processes. Interspecific geneflow with the brown hare is unlikely to have major impacts on mountain hare in Fennoscandia, but direct competition may.
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Affiliation(s)
- Riikka Levänen
- Department of Environmental and Biological Sciences, University of Eastern Finland, Joensuu, Finland
| | - Carl-Gustaf Thulin
- Molecular Ecology Group, Department of Wildlife, Fish, and Environmental Studies, Swedish University of Agricultural Sciences, Umeå, Sweden
- Department of Anatomy, Physiology and Biochemistry, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Göran Spong
- Molecular Ecology Group, Department of Wildlife, Fish, and Environmental Studies, Swedish University of Agricultural Sciences, Umeå, Sweden
- Forestry and Environmental Resources, College of Natural Resources, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Jaakko L. O. Pohjoismäki
- Department of Environmental and Biological Sciences, University of Eastern Finland, Joensuu, Finland
- * E-mail:
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255
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Zhu J, Wen D, Yu Y, Meudt HM, Nakhleh L. Bayesian inference of phylogenetic networks from bi-allelic genetic markers. PLoS Comput Biol 2018; 14:e1005932. [PMID: 29320496 PMCID: PMC5779709 DOI: 10.1371/journal.pcbi.1005932] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 01/23/2018] [Accepted: 12/14/2017] [Indexed: 12/04/2022] Open
Abstract
Phylogenetic networks are rooted, directed, acyclic graphs that model reticulate evolutionary histories. Recently, statistical methods were devised for inferring such networks from either gene tree estimates or the sequence alignments of multiple unlinked loci. Bi-allelic markers, most notably single nucleotide polymorphisms (SNPs) and amplified fragment length polymorphisms (AFLPs), provide a powerful source of genome-wide data. In a recent paper, a method called SNAPP was introduced for statistical inference of species trees from unlinked bi-allelic markers. The generative process assumed by the method combined both a model of evolution for the bi-allelic markers, as well as the multispecies coalescent. A novel component of the method was a polynomial-time algorithm for exact computation of the likelihood of a fixed species tree via integration over all possible gene trees for a given marker. Here we report on a method for Bayesian inference of phylogenetic networks from bi-allelic markers. Our method significantly extends the algorithm for exact computation of phylogenetic network likelihood via integration over all possible gene trees. Unlike the case of species trees, the algorithm is no longer polynomial-time on all instances of phylogenetic networks. Furthermore, the method utilizes a reversible-jump MCMC technique to sample the posterior of phylogenetic networks given bi-allelic marker data. Our method has a very good performance in terms of accuracy and robustness as we demonstrate on simulated data, as well as a data set of multiple New Zealand species of the plant genus Ourisia (Plantaginaceae). We implemented the method in the publicly available, open-source PhyloNet software package. The availability of genomic data has revolutionized the study of evolutionary histories and phylogeny inference. Inferring evolutionary histories from genomic data requires, in most cases, accounting for the fact that different genomic regions could have evolutionary histories that differ from each other as well as from that of the species from which the genomes were sampled. In this paper, we introduce a method for inferring evolutionary histories while accounting for two processes that could give rise to such differences across the genomes, namely incomplete lineage sorting and hybridization. We introduce a novel algorithm for computing the likelihood of phylogenetic networks from bi-allelic genetic markers and use it in a Bayesian inference method. Analyses of synthetic and empirical data sets show a very good performance of the method in terms of the estimates it obtains.
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Affiliation(s)
- Jiafan Zhu
- Computer Science, Rice University, Houston, Texas, United States of America
| | - Dingqiao Wen
- Computer Science, Rice University, Houston, Texas, United States of America
| | - Yun Yu
- Computer Science, Rice University, Houston, Texas, United States of America
| | - Heidi M. Meudt
- Museum of New Zealand Te Papa Tongarewa, Wellington, New Zealand
| | - Luay Nakhleh
- Computer Science, Rice University, Houston, Texas, United States of America
- BioSciences, Rice University, Houston, Texas, United States of America
- * E-mail:
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256
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What Microbial Population Genomics Has Taught Us About Speciation. POPULATION GENOMICS: MICROORGANISMS 2018. [DOI: 10.1007/13836_2018_10] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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257
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258
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Obertegger U, Cieplinski A, Fontaneto D, Papakostas S. Mitonuclear discordance as a confounding factor in the DNA taxonomy of monogonont rotifers. ZOOL SCR 2017. [DOI: 10.1111/zsc.12264] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Ulrike Obertegger
- Research and Innovation Centre; Fondazione Edmund Mach (FEM); San Michele all'Adige Italy
| | - Adam Cieplinski
- Research and Innovation Centre; Fondazione Edmund Mach (FEM); San Michele all'Adige Italy
- Research Institute for Limnology; Mondsee University of Innsbruck; Mondsee Austria
| | - Diego Fontaneto
- Consiglio Nazionale delle Ricerche; Istituto per lo Studio degli Ecosistemi; Verbania Pallanza Italy
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259
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Hybrid speciation leads to novel male secondary sexual ornamentation of an Amazonian bird. Proc Natl Acad Sci U S A 2017; 115:E218-E225. [PMID: 29279398 DOI: 10.1073/pnas.1717319115] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Hybrid speciation is rare in vertebrates, and reproductive isolation arising from hybridization is infrequently demonstrated. Here, we present evidence supporting a hybrid-speciation event involving the genetic admixture of the snow-capped (Lepidothrix nattereri) and opal-crowned (Lepidothrix iris) manakins of the Amazon basin, leading to the formation of the hybrid species, the golden-crowned manakin (Lepidothrix vilasboasi). We used a genome-wide SNP dataset together with analysis of admixture, population structure, and coalescent modeling to demonstrate that the golden-crowned manakin is genetically an admixture of these species and does not represent a hybrid zone but instead formed through ancient genetic admixture. We used spectrophotometry to quantify the coloration of the species-specific male crown patches. Crown patches are highly reflective white (snow-capped manakin) or iridescent whitish-blue to pink (opal-crowned manakin) in parental species but are a much less reflective yellow in the hybrid species. The brilliant coloration of the parental species results from nanostructural organization of the keratin matrix feather barbs of the crown. However, using electron microscopy, we demonstrate that the structural organization of this matrix is different in the two parental species and that the hybrid species is intermediate. The intermediate nature of the crown barbs, resulting from past admixture appears to have rendered a duller structural coloration. To compensate for reduced brightness, selection apparently resulted in extensive thickening of the carotenoid-laden barb cortex, producing the yellow crown coloration. The evolution of this unique crown-color signal likely culminated in premating isolation of the hybrid species from both parental species.
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260
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Roos C, Liedigk R, Thinh VN, Nadler T, Zinner D. The Hybrid Origin of the Indochinese Gray Langur Trachypithecus crepusculus. INT J PRIMATOL 2017. [DOI: 10.1007/s10764-017-0008-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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261
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Svardal H, Jasinska AJ, Apetrei C, Coppola G, Huang Y, Schmitt CA, Jacquelin B, Ramensky V, Müller-Trutwin M, Antonio M, Weinstock G, Grobler JP, Dewar K, Wilson RK, Turner TR, Warren WC, Freimer NB, Nordborg M. Ancient hybridization and strong adaptation to viruses across African vervet monkey populations. Nat Genet 2017; 49:1705-1713. [PMID: 29083404 PMCID: PMC5709169 DOI: 10.1038/ng.3980] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 09/27/2017] [Indexed: 12/16/2022]
Abstract
Vervet monkeys are among the most widely distributed nonhuman primates, show considerable phenotypic diversity, and have long been an important biomedical model for a variety of human diseases and in vaccine research. Using whole-genome sequencing data from 163 vervets sampled from across Africa and the Caribbean, we find high diversity within and between taxa and clear evidence that taxonomic divergence was reticulate rather than following a simple branching pattern. A scan for diversifying selection across taxa identifies strong and highly polygenic selection signals affecting viral processes. Furthermore, selection scores are elevated in genes whose human orthologs interact with HIV and in genes that show a response to experimental simian immunodeficiency virus (SIV) infection in vervet monkeys but not in rhesus macaques, suggesting that part of the signal reflects taxon-specific adaptation to SIV.
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Affiliation(s)
- Hannes Svardal
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria
| | - Anna J Jasinska
- Center for Neurobehavioral Genetics, University of California Los Angeles, Los Angeles, USA
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Cristian Apetrei
- Center for Vaccine Research, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Giovanni Coppola
- Center for Neurobehavioral Genetics, University of California Los Angeles, Los Angeles, USA
- Department of Neurology, University of California Los Angeles, USA
| | - Yu Huang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, China
| | | | | | - Vasily Ramensky
- Center for Neurobehavioral Genetics, University of California Los Angeles, Los Angeles, USA
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | | | - Martin Antonio
- Medical Research Council (MRC), The Gambia Unit, The Gambia
| | - George Weinstock
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA
| | - J Paul Grobler
- Department of Genetics, University of the Free State, Bloemfontein, South Africa
| | - Ken Dewar
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Richard K Wilson
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, USA
- Department of Anthropology, University of Wisconsin-Milwaukee, Milwaukee, USA
| | - Trudy R Turner
- Department of Genetics, University of the Free State, Bloemfontein, South Africa
| | - Wesley C Warren
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, USA
| | - Nelson B Freimer
- Center for Neurobehavioral Genetics, University of California Los Angeles, Los Angeles, USA
| | - Magnus Nordborg
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria
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262
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Abstract
Phylogeography, and its extensions into comparative phylogeography, have their roots in the layering of gene trees across geography, a paradigm that was greatly facilitated by the nonrecombining, fast evolution provided by animal mtDNA. As phylogeography moves into the era of next-generation sequencing, the specter of reticulation at several levels-within loci and genomes in the form of recombination and across populations and species in the form of introgression-has raised its head with a prominence even greater than glimpsed during the nuclear gene PCR era. Here we explore the theme of reticulation in comparative phylogeography, speciation analysis, and phylogenomics, and ask how the centrality of gene trees has fared in the next-generation era. To frame these issues, we first provide a snapshot of multilocus phylogeographic studies across the Carpentarian Barrier, a prominent biogeographic barrier dividing faunas spanning the monsoon tropics in northern Australia. We find that divergence across this barrier is evident in most species, but is heterogeneous in time and demographic history, often reflecting the taxonomic distinctness of lineages spanning it. We then discuss a variety of forces generating reticulate patterns in phylogeography, including introgression, contact zones, and the potential selection-driven outliers on next-generation molecular markers. We emphasize the continued need for demographic models incorporating reticulation at the level of genomes and populations, and conclude that gene trees, whether explicit or implicit, should continue to play a role in the future of phylogeography.
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263
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Schmickl R, Marburger S, Bray S, Yant L. Hybrids and horizontal transfer: introgression allows adaptive allele discovery. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:5453-5470. [PMID: 29096001 DOI: 10.1093/jxb/erx297] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Evolution has devised countless remarkable solutions to diverse challenges. Understanding the mechanistic basis of these solutions provides insights into how biological systems can be subtly tweaked without maladaptive consequences. The knowledge gained from illuminating these mechanisms is equally important to our understanding of fundamental evolutionary mechanisms as it is to our hopes of developing truly rational plant breeding and synthetic biology. In particular, modern population genomic approaches are proving very powerful in the detection of candidate alleles for mediating consequential adaptations that can be tested functionally. Especially striking are signals gained from contexts involving genetic transfers between populations, closely related species, or indeed between kingdoms. Here we discuss two major classes of these scenarios, adaptive introgression and horizontal gene flow, illustrating discoveries made across kingdoms.
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Affiliation(s)
- Roswitha Schmickl
- Institute of Botany, The Czech Academy of Sciences, Zámek 1, 252 43 Průhonice, Czech Republic
- Department of Botany, Faculty of Science, Charles University in Prague, Benátská 2, 128 01 Prague, Czech Republic
| | - Sarah Marburger
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
| | - Sian Bray
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
| | - Levi Yant
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
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264
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Abstract
While mutational biases strongly influence neutral molecular evolution, the role of mutational biases in shaping the course of adaptation is less clear. Here we consider the frequency of transitions relative to transversions among adaptive substitutions. Because mutation rates for transitions are higher than those for transversions, if mutational biases influence the dynamics of adaptation, then transitions should be overrepresented among documented adaptive substitutions. To test this hypothesis, we assembled two sets of data on putatively adaptive amino acid replacements that have occurred in parallel during evolution, either in nature or in the laboratory. We find that the frequency of transitions in these data sets is much higher than would be predicted under a null model where mutation has no effect. Our results are qualitatively similar even if we restrict ourself to changes that have occurred, not merely twice, but three or more times. These results suggest that the course of adaptation is biased by mutation.
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Affiliation(s)
- Arlin Stoltzfus
- Genome-scale Measurements Group, Material Measurement Laboratory, NIST, and Institute for Bioscience and Biotechnology Research, Rockville, MD 20850, USA
| | - David M McCandlish
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
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265
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Gompert Z, Mandeville EG, Buerkle CA. Analysis of Population Genomic Data from Hybrid Zones. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2017. [DOI: 10.1146/annurev-ecolsys-110316-022652] [Citation(s) in RCA: 118] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Zachariah Gompert
- Department of Biology and Ecology Center, Utah State University, Logan, Utah 84322
| | - Elizabeth G. Mandeville
- Department of Botany and Wyoming Cooperative Fish and Wildlife Research Unit, University of Wyoming, Laramie, Wyoming 82071
| | - C. Alex Buerkle
- Department of Botany and Program in Ecology, University of Wyoming, Laramie, Wyoming 82071
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266
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Furcation and fusion: The phylogenetics of evolutionary novelty. Dev Biol 2017; 431:69-76. [DOI: 10.1016/j.ydbio.2017.09.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Revised: 09/11/2017] [Accepted: 09/11/2017] [Indexed: 01/02/2023]
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267
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Zou Z, Zhang J. Gene Tree Discordance Does Not Explain Away the Temporal Decline of Convergence in Mammalian Protein Sequence Evolution. Mol Biol Evol 2017; 34:1682-1688. [PMID: 28379570 DOI: 10.1093/molbev/msx109] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Several authors reported lower frequencies of protein sequence convergence between more distantly related evolutionary lineages and attributed this trend to epistasis, which renders the acceptable amino acids at a site more different and convergence less likely in more divergent lineages. A recent primate study, however, suggested that this trend is at least partially and potentially entirely an artifact of gene tree discordance (GTD). Here, we demonstrate in a genome-wide data set from 17 mammals that the temporal trend remains (1) upon the control of the GTD level, (2) in genes whose genealogies are concordant with the species tree, and (3) for convergent changes, which are extremely unlikely to be caused by GTD. Similar results are observed in a comparable data set of 12 fruit flies in some but not all of these tests. We conclude that, at least in some cases, the temporal decline of convergence is genuine, reflecting an impact of epistasis on protein evolution.
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Affiliation(s)
- Zhengting Zou
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI
| | - Jianzhi Zhang
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI
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268
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McTavish EJ, Drew BT, Redelings B, Cranston KA. How and Why to Build a Unified Tree of Life. Bioessays 2017; 39. [PMID: 28980328 DOI: 10.1002/bies.201700114] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 08/27/2017] [Indexed: 01/20/2023]
Abstract
Phylogenetic trees are a crucial backbone for a wide breadth of biological research spanning systematics, organismal biology, ecology, and medicine. In 2015, the Open Tree of Life project published a first draft of a comprehensive tree of life, summarizing digitally available taxonomic and phylogenetic knowledge. This paper reviews, investigates, and addresses the following questions as a follow-up to that paper, from the perspective of researchers involved in building this summary of the tree of life: Is there a tree of life and should we reconstruct it? Is available data sufficient to reconstruct the tree of life? Do we have access to phylogenetic inferences in usable form? Can we combine different phylogenetic estimates across the tree of life? And finally, what is the future of understanding the tree of life?
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Affiliation(s)
| | - Bryan T Drew
- University of Nebraska at Kearney, Kerney, NE, 68849, USA
| | - Ben Redelings
- University of Kansas, Lawrence, KS, 66045, USA Duke University, Durham NC 27705 USA; Ronin Institute, Durham, NC 27705 USA
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269
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Chase MA, Stankowski S, Streisfeld MA. Genomewide variation provides insight into evolutionary relationships in a monkeyflower species complex (Mimulus sect. Diplacus). AMERICAN JOURNAL OF BOTANY 2017; 104:1510-1521. [PMID: 29885225 DOI: 10.3732/ajb.1700234] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 09/11/2017] [Indexed: 06/08/2023]
Abstract
PREMISE OF THE STUDY Evolutionary radiations provide excellent opportunities to study the origins of biodiversity, but rapid divergence and ongoing gene flow make inferring evolutionary relationships among taxa difficult. Consequently, combining morphological and genomic analyses will be necessary to clarify the evolutionary history of radiations. We used an integrative approach to shed light on relationships within a diverse radiation of monkeyflowers (Mimulus section Diplacus) with a controversial taxonomic history. METHODS We used genomewide single nucleotide polymorphism data and a combination of phylogenetic and population genomic analyses to infer the evolutionary relationships within the group. Tests for hybridization were performed to reveal sources of shared variation, and multivariate analyses of floral trait data were conducted to examine the correspondence between phenotypic and phylogenetic data. KEY RESULTS We identified four primary clades with evidence for some shared variation among them. We also detected evidence for recent gene flow between closely related subclades and populations. Strong discordance between floral trait and molecular data provides evidence for divergent and convergent phenotypic evolution. CONCLUSIONS Mimulus section Diplacus has all the hallmarks of a rapid radiation, including diverse taxa that are at different stages of divergence, extensive shared variation among taxa, and complex patterns of phenotypic evolution. Our findings will direct future evolutionary research and have important taxonomic implications that highlight the need for a new revision of section Diplacus.
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Affiliation(s)
- Madeline A Chase
- Institute of Ecology and Evolution, 335 Pacific Hall 5289, University of Oregon, Eugene, Oregon 97405 USA
| | - Sean Stankowski
- Institute of Ecology and Evolution, 335 Pacific Hall 5289, University of Oregon, Eugene, Oregon 97405 USA
| | - Matthew A Streisfeld
- Institute of Ecology and Evolution, 335 Pacific Hall 5289, University of Oregon, Eugene, Oregon 97405 USA
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270
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Lammers F, Gallus S, Janke A, Nilsson MA. Phylogenetic Conflict in Bears Identified by Automated Discovery of Transposable Element Insertions in Low-Coverage Genomes. Genome Biol Evol 2017; 9:2862-2878. [PMID: 28985298 PMCID: PMC5737362 DOI: 10.1093/gbe/evx170] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/28/2017] [Indexed: 12/15/2022] Open
Abstract
Phylogenetic reconstruction from transposable elements (TEs) offers an additional perspective to study evolutionary processes. However, detecting phylogenetically informative TE insertions requires tedious experimental work, limiting the power of phylogenetic inference. Here, we analyzed the genomes of seven bear species using high-throughput sequencing data to detect thousands of TE insertions. The newly developed pipeline for TE detection called TeddyPi (TE detection and discovery for Phylogenetic Inference) identified 150,513 high-quality TE insertions in the genomes of ursine and tremarctine bears. By integrating different TE insertion callers and using a stringent filtering approach, the TeddyPi pipeline produced highly reliable TE insertion calls, which were confirmed by extensive in vitro validation experiments. Analysis of single nucleotide substitutions in the flanking regions of the TEs shows that these substitutions correlate with the phylogenetic signal from the TE insertions. Our phylogenomic analyses show that TEs are a major driver of genomic variation in bears and enabled phylogenetic reconstruction of a well-resolved species tree, despite strong signals for incomplete lineage sorting and introgression. The analyses show that the Asiatic black, sun, and sloth bear form a monophyletic clade, in which phylogenetic incongruence originates from incomplete lineage sorting. TeddyPi is open source and can be adapted to various TE and structural variation callers. The pipeline makes it possible to confidently extract thousands of TE insertions even from low-coverage genomes (∼10×) of nonmodel organisms. This opens new possibilities for biologists to study phylogenies and evolutionary processes as well as rates and patterns of (retro-)transposition and structural variation.
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Affiliation(s)
- Fritjof Lammers
- Senckenberg Biodiversity and Climate Research Centre, Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany
- Institute for Ecology, Evolution & Diversity, Biologicum, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Susanne Gallus
- Senckenberg Biodiversity and Climate Research Centre, Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany
| | - Axel Janke
- Senckenberg Biodiversity and Climate Research Centre, Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany
- Institute for Ecology, Evolution & Diversity, Biologicum, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Maria A. Nilsson
- Senckenberg Biodiversity and Climate Research Centre, Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany
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271
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Duckworth RA, Semenov GA. Hybridization Associated with Cycles of Ecological Succession in a Passerine Bird. Am Nat 2017; 190:E94-E105. [DOI: 10.1086/693160] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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272
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Martin SH, Jiggins CD. Interpreting the genomic landscape of introgression. Curr Opin Genet Dev 2017; 47:69-74. [PMID: 28923541 DOI: 10.1016/j.gde.2017.08.007] [Citation(s) in RCA: 106] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Revised: 08/28/2017] [Accepted: 08/31/2017] [Indexed: 11/17/2022]
Abstract
Introgression, the transfer of genetic material between species through hybridisation, occurs in many taxa and has important consequences. Genomic studies allow us to characterise the landscape of introgression across the genome, shedding light on both its adaptive benefits and the incompatibilities that help to maintain species barriers. Studies taking a genome-wide view suggest that adaptive introgression may be common, but that introgressed variation between many species is selected against throughout much of the genome. Confounding factors can complicate interpretations from these data, and computational simulations have proved vital to illustrate expected patterns under different scenarios. Future developments will move beyond correlative evidence to explicit models that account for how selection and genetic drift influence introgressed variation.
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Affiliation(s)
- Simon H Martin
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, United Kingdom.
| | - Chris D Jiggins
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, United Kingdom
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273
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Tung J, Barreiro LB. The contribution of admixture to primate evolution. Curr Opin Genet Dev 2017; 47:61-68. [PMID: 28923540 DOI: 10.1016/j.gde.2017.08.010] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 08/08/2017] [Accepted: 08/31/2017] [Indexed: 12/16/2022]
Abstract
Genome-wide data on genetic variation are now available for multiple primate species and populations, facilitating analyses of evolutionary history within and across taxa. One emerging theme from these studies involves the central role of admixture. Genomic data sets indicate that both ancient gene flow following initial taxonomic divergence and ongoing gene flow at current species boundaries are common. These findings are of particular interest given evidence for a complex history of admixture in our own lineage, including examples of ecologically driven adaptive introgression. Like other aspects of human biology, studies of nonhuman primates thus provide both comparative context and a living model for understanding admixture dynamics in hominins. We highlight several open questions that could be addressed in future work.
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Affiliation(s)
- Jenny Tung
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA; Department of Biology, Duke University, Durham, NC 27708, USA; Duke University Population Research Institute, Duke University, Durham, NC 27708, USA; Institute of Primate Research, National Museums of Kenya, Karen, Nairobi, Kenya.
| | - Luis B Barreiro
- Department of Pediatrics, Sainte-Justine Hospital Research Centre, University of Montreal, Montreal, Canada
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274
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Kerbs B, Ressler J, Kelly JK, Mort ME, Santos-Guerra A, Gibson MJS, Caujapé-Castells J, Crawford DJ. The potential role of hybridization in diversification and speciation in an insular plant lineage: insights from synthetic interspecific hybrids. AOB PLANTS 2017; 9:plx043. [PMID: 29225761 PMCID: PMC5714139 DOI: 10.1093/aobpla/plx043] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2016] [Accepted: 08/25/2017] [Indexed: 05/17/2023]
Abstract
Hybridization is recognized as an important process in plant evolution, and this may be particularly true for island plants where several biotic and abiotic factors facilitate interspecific hybridization. Although rarely done, experimental studies could provide insights into the potential of natural hybridization to generate diversity when species come into contact in the dynamic island setting. The potential of hybridization to generate morphological variation was analysed within and among 12 families (inbred lines) of an F4 hybrid generation between two species of Tolpis endemic to the Canary Islands. Combinations of characters not seen in the parents were present in hybrids. Several floral and vegetative characters were transgressive relative to their parents. Morphometric studies of floral, vegetative and fruit characters revealed that several F4 families were phenotypically distinct from other families, and from their parents. The study demonstrates that morphologically distinct pollen-fertile lines, potentially worthy of taxonomic recognition if occurring in nature, can be generated in four generations. The ability of the hybrid lines to set self-seed would reduce gene flow among the lines, and among the hybrids and their parental species. Selfing would also facilitate the fixation of characters within each of the lines. Overall, the results show the considerable potential of hybridization for generating diversity and distinct phenotypes in island lineages.
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Affiliation(s)
- Benjamin Kerbs
- Department of Biological Sciences, Emporia State University, Emporia, KS 66801, USA
| | - Jacob Ressler
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - John K Kelly
- Department of Ecology & Evolutionary Biology, University of Kansas, Lawrence, KS 66045-7534, USA
| | - Mark E Mort
- Department of Ecology & Evolutionary Biology, University of Kansas, Lawrence, KS 66045-7534, USA
| | - Arnoldo Santos-Guerra
- Calle Guaidil 16, Urbanización Tamarco, 38280 Tegueste, Tenerife, Canary Islands, Spain
| | | | - Juli Caujapé-Castells
- Jardín Botánico 13 Canario “Viera y Clavijo”-Unidad Asociada al CSIC (Cabildo de Gran Canaria), Camino del palmeral 14 15 (Tafira Alta), 35017 Las Palmas de Gran Canaria, Spain
| | - Daniel J Crawford
- Department of Ecology & Evolutionary Biology, and the Biodiversity Institute, University of Kansas, Lawrence, KS 66045-7534, USA
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275
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Abstract
Many of the most important evolutionary variations that generated phenotypic adaptations and originated novel taxa resulted from complex cellular activities affecting genome content and expression. These activities included (i) the symbiogenetic cell merger that produced the mitochondrion-bearing ancestor of all extant eukaryotes, (ii) symbiogenetic cell mergers that produced chloroplast-bearing ancestors of photosynthetic eukaryotes, and (iii) interspecific hybridizations and genome doublings that generated new species and adaptive radiations of higher plants and animals. Adaptive variations also involved horizontal DNA transfers and natural genetic engineering by mobile DNA elements to rewire regulatory networks, such as those essential to viviparous reproduction in mammals. In the most highly evolved multicellular organisms, biological complexity scales with 'non-coding' DNA content rather than with protein-coding capacity in the genome. Coincidentally, 'non-coding' RNAs rich in repetitive mobile DNA sequences function as key regulators of complex adaptive phenotypes, such as stem cell pluripotency. The intersections of cell fusion activities, horizontal DNA transfers and natural genetic engineering of Read-Write genomes provide a rich molecular and biological foundation for understanding how ecological disruptions can stimulate productive, often abrupt, evolutionary transformations.
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Affiliation(s)
- James A Shapiro
- Department of Biochemistry and Molecular Biology, University of Chicago, GCISW123B, 979 E. 57th Street, Chicago, IL 60637, USA
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276
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Ravinet M, Faria R, Butlin RK, Galindo J, Bierne N, Rafajlović M, Noor MAF, Mehlig B, Westram AM. Interpreting the genomic landscape of speciation: a road map for finding barriers to gene flow. J Evol Biol 2017; 30:1450-1477. [DOI: 10.1111/jeb.13047] [Citation(s) in RCA: 306] [Impact Index Per Article: 43.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 01/31/2017] [Accepted: 02/01/2017] [Indexed: 12/14/2022]
Affiliation(s)
- M. Ravinet
- Centre for Ecological and Evolutionary Synthesis; University of Oslo; Oslo Norway
- National Institute of Genetics; Mishima Shizuoka Japan
| | - R. Faria
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos; InBIO, Laboratório Associado; Universidade do Porto; Vairão Portugal
- Department of Experimental and Health Sciences; IBE, Institute of Evolutionary Biology (CSIC-UPF); Pompeu Fabra University; Barcelona Spain
- Department of Animal and Plant Sciences; University of Sheffield; Sheffield UK
| | - R. K. Butlin
- Department of Animal and Plant Sciences; University of Sheffield; Sheffield UK
- Department of Marine Sciences; Centre for Marine Evolutionary Biology; University of Gothenburg; Gothenburg Sweden
| | - J. Galindo
- Department of Biochemistry, Genetics and Immunology; University of Vigo; Vigo Spain
| | - N. Bierne
- CNRS; Université Montpellier; ISEM; Station Marine Sète France
| | - M. Rafajlović
- Department of Physics; University of Gothenburg; Gothenburg Sweden
| | | | - B. Mehlig
- Department of Physics; University of Gothenburg; Gothenburg Sweden
| | - A. M. Westram
- Department of Animal and Plant Sciences; University of Sheffield; Sheffield UK
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277
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Shen J, Cong Q, Borek D, Otwinowski Z, Grishin NV. Complete Genome of Achalarus lyciades, The First Representative of the Eudaminae Subfamily of Skippers. Curr Genomics 2017; 18:366-374. [PMID: 29081692 PMCID: PMC5635620 DOI: 10.2174/1389202918666170426113315] [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: 02/11/2016] [Revised: 02/19/2016] [Accepted: 03/03/2016] [Indexed: 11/22/2022] Open
Abstract
Background: The Hoary Edge Skipper (Achalarus lyciades) is an eastern North America endemic butterfly from the Eudaminae subfamily of skippers named for an underside whitish patch near the hindwing edge. Its caterpillars feed on legumes, in contrast to Grass skippers (subfamily Hesperiinae) which feed exclusively on monocots. Results: To better understand the evolution and phenotypic diversification of Skippers (family Hesperiidae), we sequenced, assembled and annotated a complete genome draft and transcriptome of a wild-caught specimen of A. lyciades and compared it with the available genome of the Clouded Skipper (Lerema accius) from the Grass skipper subfamily. The genome of A. lyciades is nearly twice the size of L. accius (567 Mbp vs. 298 Mbp), however it encodes a smaller number of proteins (15881 vs. 17411). Gene expansions we identified previously in L. accius apparently did not occur in the genome of A. lyciades. For instance, a family of hypothetical cellulases that diverged from an endochitinase (possibly associated with feeding of L. accius caterpillars on nutrient-poor grasses) is absent in A. lyciades. While L. accius underwent gene expansion in pheromone binding proteins, A. lyciades has more opsins. This difference may be related to the mate recognition mechanisms of the two species: visual cues might be more important for the Eudaminae skippers (which have more variable wing patterns), whereas odor might be more important for Grass skippers (that are hardly distinguishable by their wings). Phylogenetically, A. lyciades is a sister species of L. accius, the only other Hesperiidae with a complete genome. Conclusions: A new reference genome of a dicot-feeding skippers, the first from the Eudaminae subfamily, reveals its larger size and suggests hypotheses about phenotypic traits and differences from monocot-feeding skippers.
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Affiliation(s)
- Jinhui Shen
- Department of Biophysics and Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas75390-8816, USA
| | - Qian Cong
- Department of Biophysics and Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas75390-8816, USA
| | - Dominika Borek
- Department of Biophysics and Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas75390-8816, USA
| | - Zbyszek Otwinowski
- Department of Biophysics and Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas75390-8816, USA
| | - Nick V Grishin
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas75390-9050, USA.,Department of Biophysics and Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas75390-8816, USA
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278
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Liu Y, Li D, Zhang Q, Song C, Zhong C, Zhang X, Wang Y, Yao X, Wang Z, Zeng S, Wang Y, Guo Y, Wang S, Li X, Li L, Liu C, McCann HC, He W, Niu Y, Chen M, Du L, Gong J, Datson PM, Hilario E, Huang H. Rapid radiations of both kiwifruit hybrid lineages and their parents shed light on a two-layer mode of species diversification. THE NEW PHYTOLOGIST 2017; 215:877-890. [PMID: 28543189 DOI: 10.1111/nph.14607] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 04/04/2017] [Indexed: 05/20/2023]
Abstract
Reticulate speciation caused by interspecific hybridization is now recognized as an important mechanism in the creation of biological diversity. However, depicting the patterns of phylogenetic networks for lineages that have undergone interspecific gene flow is challenging. Here we sequenced 25 taxa representing natural diversity in the genus Actinidia with an average mapping depth of 26× on the reference genome to reconstruct their reticulate history. We found evidence, including significant gene tree discordance, cytonuclear conflicts, and changes in genome-wide heterozygosity across taxa, collectively supporting extensive reticulation in the genus. Furthermore, at least two separate parental species pairs were involved in the repeated origin of the hybrid lineages, in some of which a further phase of syngameon was triggered. On the basis of the elucidated hybridization relationships, we obtained a highly resolved backbone phylogeny consisting of taxa exhibiting no evidence of hybrid origin. The backbone taxa have distinct demographic histories and are the product of recent rounds of rapid radiations via sorting of ancestral variation under variable climatic and ecological conditions. Our results suggest a mode for consecutive plant diversification through two layers of radiations, consisting of the rapid evolution of backbone lineages and the formation of hybrid swarms derived from these lineages.
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Affiliation(s)
- Yifei Liu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization and Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, The Chinese Academy of Sciences, Guangzhou, Guangdong, 510650, China
| | - Dawei Li
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
| | - Qiong Zhang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
| | - Chi Song
- Wuhan Benagen Tech Solutions Company Limited, Wuhan, Hubei, 430070, China
| | - Caihong Zhong
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
| | - Xudong Zhang
- Wuhan Benagen Tech Solutions Company Limited, Wuhan, Hubei, 430070, China
| | - Ying Wang
- Wuhan Benagen Tech Solutions Company Limited, Wuhan, Hubei, 430070, China
| | - Xiaohong Yao
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
| | - Zupeng Wang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization and Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, The Chinese Academy of Sciences, Guangzhou, Guangdong, 510650, China
| | - Shaohua Zeng
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization and Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, The Chinese Academy of Sciences, Guangzhou, Guangdong, 510650, China
| | - Ying Wang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization and Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, The Chinese Academy of Sciences, Guangzhou, Guangdong, 510650, China
| | - Yangtao Guo
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization and Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, The Chinese Academy of Sciences, Guangzhou, Guangdong, 510650, China
| | - Shuaibin Wang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization and Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, The Chinese Academy of Sciences, Guangzhou, Guangdong, 510650, China
| | - Xinwei Li
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
| | - Li Li
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
| | - Chunyan Liu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
| | - Honour C McCann
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization and Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, The Chinese Academy of Sciences, Guangzhou, Guangdong, 510650, China
- New Zealand Institute for Advanced Study, Massey University, Auckland, 0745, New Zealand
| | - Weiming He
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization and Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, The Chinese Academy of Sciences, Guangzhou, Guangdong, 510650, China
| | - Yan Niu
- Wuhan Benagen Tech Solutions Company Limited, Wuhan, Hubei, 430070, China
| | - Min Chen
- Wuhan Benagen Tech Solutions Company Limited, Wuhan, Hubei, 430070, China
| | - Liuwen Du
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
| | - Junjie Gong
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
| | - Paul M Datson
- The New Zealand Institute for Plant and Food Research Limited, Mt Albert Research Centre, Auckland, 1142, New Zealand
| | - Elena Hilario
- The New Zealand Institute for Plant and Food Research Limited, Mt Albert Research Centre, Auckland, 1142, New Zealand
| | - Hongwen Huang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization and Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, The Chinese Academy of Sciences, Guangzhou, Guangdong, 510650, China
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
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279
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Dujon BA, Louis EJ. Genome Diversity and Evolution in the Budding Yeasts (Saccharomycotina). Genetics 2017; 206:717-750. [PMID: 28592505 PMCID: PMC5499181 DOI: 10.1534/genetics.116.199216] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 04/03/2017] [Indexed: 12/15/2022] Open
Abstract
Considerable progress in our understanding of yeast genomes and their evolution has been made over the last decade with the sequencing, analysis, and comparisons of numerous species, strains, or isolates of diverse origins. The role played by yeasts in natural environments as well as in artificial manufactures, combined with the importance of some species as model experimental systems sustained this effort. At the same time, their enormous evolutionary diversity (there are yeast species in every subphylum of Dikarya) sparked curiosity but necessitated further efforts to obtain appropriate reference genomes. Today, yeast genomes have been very informative about basic mechanisms of evolution, speciation, hybridization, domestication, as well as about the molecular machineries underlying them. They are also irreplaceable to investigate in detail the complex relationship between genotypes and phenotypes with both theoretical and practical implications. This review examines these questions at two distinct levels offered by the broad evolutionary range of yeasts: inside the best-studied Saccharomyces species complex, and across the entire and diversified subphylum of Saccharomycotina. While obviously revealing evolutionary histories at different scales, data converge to a remarkably coherent picture in which one can estimate the relative importance of intrinsic genome dynamics, including gene birth and loss, vs. horizontal genetic accidents in the making of populations. The facility with which novel yeast genomes can now be studied, combined with the already numerous available reference genomes, offer privileged perspectives to further examine these fundamental biological questions using yeasts both as eukaryotic models and as fungi of practical importance.
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Affiliation(s)
- Bernard A Dujon
- Department Genomes and Genetics, Institut Pasteur, Centre National de la Recherche Scientifique UMR3525, 75724-CEDEX15 Paris, France
- Université Pierre et Marie Curie UFR927, 75005 Paris, France
| | - Edward J Louis
- Centre for Genetic Architecture of Complex Traits, University of Leicester, LE1 7RH, United Kingdom
- Department of Genetics, University of Leicester, LE1 7RH, United Kingdom
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280
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Challenges in Species Tree Estimation Under the Multispecies Coalescent Model. Genetics 2017; 204:1353-1368. [PMID: 27927902 DOI: 10.1534/genetics.116.190173] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 09/25/2016] [Indexed: 11/18/2022] Open
Abstract
The multispecies coalescent (MSC) model has emerged as a powerful framework for inferring species phylogenies while accounting for ancestral polymorphism and gene tree-species tree conflict. A number of methods have been developed in the past few years to estimate the species tree under the MSC. The full likelihood methods (including maximum likelihood and Bayesian inference) average over the unknown gene trees and accommodate their uncertainties properly but involve intensive computation. The approximate or summary coalescent methods are computationally fast and are applicable to genomic datasets with thousands of loci, but do not make an efficient use of information in the multilocus data. Most of them take the two-step approach of reconstructing the gene trees for multiple loci by phylogenetic methods and then treating the estimated gene trees as observed data, without accounting for their uncertainties appropriately. In this article we review the statistical nature of the species tree estimation problem under the MSC, and explore the conceptual issues and challenges of species tree estimation by focusing mainly on simple cases of three or four closely related species. We use mathematical analysis and computer simulation to demonstrate that large differences in statistical performance may exist between the two classes of methods. We illustrate that several counterintuitive behaviors may occur with the summary methods but they are due to inefficient use of information in the data by summary methods and vanish when the data are analyzed using full-likelihood methods. These include (i) unidentifiability of parameters in the model, (ii) inconsistency in the so-called anomaly zone, (iii) singularity on the likelihood surface, and (iv) deterioration of performance upon addition of more data. We discuss the challenges and strategies of species tree inference for distantly related species when the molecular clock is violated, and highlight the need for improving the computational efficiency and model realism of the likelihood methods as well as the statistical efficiency of the summary methods.
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281
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Bryant C, Fischer M, Linz S, Semple C. On the quirks of maximum parsimony and likelihood on phylogenetic networks. J Theor Biol 2017; 417:100-108. [PMID: 28087420 DOI: 10.1016/j.jtbi.2017.01.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Revised: 10/28/2016] [Accepted: 01/06/2017] [Indexed: 11/16/2022]
Abstract
Maximum parsimony is one of the most frequently-discussed tree reconstruction methods in phylogenetic estimation. However, in recent years it has become more and more apparent that phylogenetic trees are often not sufficient to describe evolution accurately. For instance, processes like hybridization or lateral gene transfer that are commonplace in many groups of organisms and result in mosaic patterns of relationships cannot be represented by a single phylogenetic tree. This is why phylogenetic networks, which can display such events, are becoming of more and more interest in phylogenetic research. It is therefore necessary to extend concepts like maximum parsimony from phylogenetic trees to networks. Several suggestions for possible extensions can be found in recent literature, for instance the softwired and the hardwired parsimony concepts. In this paper, we analyze the so-called big parsimony problem under these two concepts, i.e. we investigate maximum parsimonious networks and analyze their properties. In particular, we show that finding a softwired maximum parsimony network is possible in polynomial time. We also show that the set of maximum parsimony networks for the hardwired definition always contains at least one phylogenetic tree. Lastly, we investigate some parallels of parsimony to different likelihood concepts on phylogenetic networks.
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Affiliation(s)
| | - Mareike Fischer
- Department for Mathematics and Computer Science, Ernst Moritz Arndt University, Greifswald, Germany.
| | - Simone Linz
- Department of Computer Science, University of Auckland, New Zealand.
| | - Charles Semple
- School of Mathematics and Statistics, University of Canterbury, Christchurch, New Zealand.
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282
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Roda F, Mendes FK, Hahn MW, Hopkins R. Genomic evidence of gene flow during reinforcement in Texas Phlox. Mol Ecol 2017; 26:2317-2330. [DOI: 10.1111/mec.14041] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Revised: 01/17/2017] [Accepted: 01/18/2017] [Indexed: 12/25/2022]
Affiliation(s)
- Federico Roda
- Department of Organismic and Evolutionary Biology; The Arnold Arboretum of Harvard University; 1300 Centre Street Boston MA 02131 USA
| | - Fábio K. Mendes
- Department of Biology; Indiana University; 1001 E. Third Street Bloomington IN 47405 USA
| | - Matthew W. Hahn
- Department of Biology; Indiana University; 1001 E. Third Street Bloomington IN 47405 USA
- School of Informatics and Computing; Indiana University; 1001 E. Third Street Bloomington IN 47405 USA
| | - Robin Hopkins
- Department of Organismic and Evolutionary Biology; The Arnold Arboretum of Harvard University; 1300 Centre Street Boston MA 02131 USA
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283
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Potter S, Bragg JG, Blom MPK, Deakin JE, Kirkpatrick M, Eldridge MDB, Moritz C. Chromosomal Speciation in the Genomics Era: Disentangling Phylogenetic Evolution of Rock-wallabies. Front Genet 2017; 8:10. [PMID: 28265284 PMCID: PMC5301020 DOI: 10.3389/fgene.2017.00010] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 01/18/2017] [Indexed: 12/24/2022] Open
Abstract
The association of chromosome rearrangements (CRs) with speciation is well established, and there is a long history of theory and evidence relating to "chromosomal speciation." Genomic sequencing has the potential to provide new insights into how reorganization of genome structure promotes divergence, and in model systems has demonstrated reduced gene flow in rearranged segments. However, there are limits to what we can understand from a small number of model systems, which each only tell us about one episode of chromosomal speciation. Progressing from patterns of association between chromosome (and genic) change, to understanding processes of speciation requires both comparative studies across diverse systems and integration of genome-scale sequence comparisons with other lines of evidence. Here, we showcase a promising example of chromosomal speciation in a non-model organism, the endemic Australian marsupial genus Petrogale. We present initial phylogenetic results from exon-capture that resolve a history of divergence associated with extensive and repeated CRs. Yet it remains challenging to disentangle gene tree heterogeneity caused by recent divergence and gene flow in this and other such recent radiations. We outline a way forward for better integration of comparative genomic sequence data with evidence from molecular cytogenetics, and analyses of shifts in the recombination landscape and potential disruption of meiotic segregation and epigenetic programming. In all likelihood, CRs impact multiple cellular processes and these effects need to be considered together, along with effects of genic divergence. Understanding the effects of CRs together with genic divergence will require development of more integrative theory and inference methods. Together, new data and analysis tools will combine to shed light on long standing questions of how chromosome and genic divergence promote speciation.
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Affiliation(s)
- Sally Potter
- Research School of Biology, Australian National University, ActonACT, Australia
- Australian Museum Research Institute, Australian Museum, SydneyNSW, Australia
| | - Jason G. Bragg
- National Herbarium of New South Wales, The Royal Botanic Gardens and Domain Trust, SydneyNSW, Australia
| | - Mozes P. K. Blom
- Department of Bioinformatics and Genetics, Swedish Museum of Natural HistoryStockholm, Sweden
| | - Janine E. Deakin
- Institute for Applied Ecology, University of Canberra, BruceACT, Australia
| | - Mark Kirkpatrick
- Department of Integrative Biology, University of Texas, AustinTX, USA
| | - Mark D. B. Eldridge
- Australian Museum Research Institute, Australian Museum, SydneyNSW, Australia
| | - Craig Moritz
- Research School of Biology, Australian National University, ActonACT, Australia
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284
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Scavariello C, Luchetti A, Martoni F, Bonandin L, Mantovani B. Hybridogenesis and a potential case of R2 non-LTR retrotransposon horizontal transmission in Bacillus stick insects (Insecta Phasmida). Sci Rep 2017; 7:41946. [PMID: 28165062 PMCID: PMC5292737 DOI: 10.1038/srep41946] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 01/04/2017] [Indexed: 01/16/2023] Open
Abstract
Horizontal transfer (HT) is an event in which the genetic material is transferred from one species to another, even if distantly related, and it has been demonstrated as a possible essential part of the lifecycle of transposable elements (TEs). However, previous studies on the non-LTR R2 retrotransposon, a metazoan-wide distributed element, indicated its vertical transmission since the Radiata-Bilateria split. Here we present the first possible instances of R2 HT in stick insects of the genus Bacillus (Phasmida). Six R2 elements were characterized in the strictly bisexual subspecies B. grandii grandii, B. grandii benazzii and B. grandii maretimi and in the obligatory parthenogenetic taxon B. atticus. These elements were compared with those previously retrieved in the facultative parthenogenetic species B. rossius. Phylogenetic inconsistencies between element and host taxa, and age versus divergence analyses agree and support at least two HT events. These HT events can be explained by taking into consideration the complex Bacillus reproductive biology, which includes also hybridogenesis, gynogenesis and androgenesis. Through these non-canonical reproductive modes, R2 elements may have been transferred between Bacillus genomes. Our data suggest, therefore, a possible role of hybridization for TEs survival and the consequent reshaping of involved genomes.
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Affiliation(s)
- Claudia Scavariello
- Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Università di Bologna, Bologna, Italy
| | - Andrea Luchetti
- Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Università di Bologna, Bologna, Italy
| | - Francesco Martoni
- Bio-Protection Research Centre, Lincoln University, Lincoln 7647, New Zealand
| | - Livia Bonandin
- Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Università di Bologna, Bologna, Italy
| | - Barbara Mantovani
- Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Università di Bologna, Bologna, Italy
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285
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Hong Y, Luo Y, Gao Q, Ren C, Yuan Q, Yang QE. Phylogeny and reclassification of Aconitum subgenus Lycoctonum (Ranunculaceae). PLoS One 2017; 12:e0171038. [PMID: 28141851 PMCID: PMC5334035 DOI: 10.1371/journal.pone.0171038] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 01/13/2017] [Indexed: 11/18/2022] Open
Abstract
Phylogenetic analyses were performed using multiple nuclear (ITS and ETS) and chloroplast regions (ndhF-trnL, psbA-trnH, psbD-trnT, and trnT-trnL) to test the monophyly of Aconitum subgen. Lycoctonum (Ranunculaceae) and reconstruct the phylogenetic relationships within the subgenus. The subgenus as currently circumscribed is revealed to be polyphyletic. To achieve its monophyly, sect. Galeata and sect. Fletcherum, both being unispecific and each having a unique array of characters (the latter even having the aberrant base chromosome number of x = 6), must be removed from the subgenus. The subgenus Lycoctonum should thus be redefined to include only two sections, the unispecific sect. Alatospermum and the relatively species-rich sect. Lycoctonum. The section Alatospermum, which is both morphologically and karyologically in the primitive condition, is resolved as the first diverging lineage of the subgenus Lycoctonum clade. The monophyly of sect. Lycoctonum is strongly supported, but all the ten series currently recognized within the section are revealed to be para- or poly-phyletic. Five major clades are recovered within the section. We propose to treat them as five series: ser. Crassiflora, ser. Scaposa, ser. Volubilia, ser. Longicassidata, and ser. Lycoctonia. Thus, a formal reclassification of subgen. Lycoctonum is presented, which involves segregating both sect. Galeata and sect. Fletcherum from the subgenus as two independent subgenera within the genus Aconitum, reinstating one series (ser. Crassiflora) and abolishing six series (ser. Laevia, ser. Longibracteolata, ser. Micrantha, ser. Ranunculoidea, ser. Reclinata, and ser. Umbrosa) within sect. Lycoctonum. The series affiliation of some species within the section is adjusted accordingly.
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Affiliation(s)
- Yu Hong
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Yan Luo
- Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, People’s Republic of China
| | - Qi Gao
- Guangxi Institute of Botany, Guangxi Zhuangzu Autonomous Region and Chinese Academy of Sciences, Guilin, People’s Republic of China
| | - Chen Ren
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, People’s Republic of China
| | - Qiong Yuan
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, People’s Republic of China
| | - Qin-Er Yang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, People’s Republic of China
- * E-mail:
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286
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Rosser NL, Thomas L, Stankowski S, Richards ZT, Kennington WJ, Johnson MS. Phylogenomics provides new insight into evolutionary relationships and genealogical discordance in the reef-building coral genus Acropora. Proc Biol Sci 2017; 284:20162182. [PMID: 28077772 PMCID: PMC5247495 DOI: 10.1098/rspb.2016.2182] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 12/12/2016] [Indexed: 01/08/2023] Open
Abstract
Understanding the genetic basis of reproductive isolation is a long-standing goal of speciation research. In recently diverged populations, genealogical discordance may reveal genes and genomic regions that contribute to the speciation process. Previous work has shown that conspecific colonies of Acropora that spawn in different seasons (spring and autumn) are associated with highly diverged lineages of the phylogenetic marker PaxC Here, we used 10 034 single-nucleotide polymorphisms to generate a genome-wide phylogeny and compared it with gene genealogies from the PaxC intron and the mtDNA Control Region in 20 species of Acropora, including three species with spring- and autumn-spawning cohorts. The PaxC phylogeny separated conspecific autumn and spring spawners into different genetic clusters in all three species; however, this pattern was not supported in two of the three species at the genome level, suggesting a selective connection between PaxC and reproductive timing in Acropora corals. This genome-wide phylogeny provides an improved foundation for resolving phylogenetic relationships in Acropora and, combined with PaxC, provides a fascinating platform for future research into regions of the genome that influence reproductive isolation and speciation in corals.
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Affiliation(s)
- Natalie L Rosser
- School of Animal Biology, University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Luke Thomas
- School of Plant Biology, University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Sean Stankowski
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA
| | - Zoe T Richards
- Department of Aquatic Zoology, Western Australian Museum, 49 Kew Street, Welshpool, Western Australia 6106, Australia
| | - W Jason Kennington
- School of Animal Biology, University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Michael S Johnson
- School of Animal Biology, University of Western Australia, Crawley, Western Australia 6009, Australia
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287
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Goulet BE, Roda F, Hopkins R. Hybridization in Plants: Old Ideas, New Techniques. PLANT PHYSIOLOGY 2017; 173:65-78. [PMID: 27895205 PMCID: PMC5210733 DOI: 10.1104/pp.16.01340] [Citation(s) in RCA: 126] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 11/24/2016] [Indexed: 05/18/2023]
Abstract
Hybridization has played an important role in the evolution of many lineages. With the growing availability of genomic tools and advancements in genomic analyses, it is becoming increasingly clear that gene flow between divergent taxa can generate new phenotypic diversity, allow for adaptation to novel environments, and contribute to speciation. Hybridization can have immediate phenotypic consequences through the expression of hybrid vigor. On longer evolutionary time scales, hybridization can lead to local adaption through the introgression of novel alleles and transgressive segregation and, in some cases, result in the formation of new hybrid species. Studying both the abundance and the evolutionary consequences of hybridization has deep historical roots in plant biology. Many of the hypotheses concerning how and why hybridization contributes to biological diversity currently being investigated were first proposed tens and even hundreds of years ago. In this Update, we discuss how new advancements in genomic and genetic tools are revolutionizing our ability to document the occurrence of and investigate the outcomes of hybridization in plants.
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Affiliation(s)
- Benjamin E Goulet
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138 (B.E.G., F.R., R.H.); and
- Arnold Arboretum of Harvard University, Boston, Massachusetts 02131 (R.H.)
| | - Federico Roda
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138 (B.E.G., F.R., R.H.); and
- Arnold Arboretum of Harvard University, Boston, Massachusetts 02131 (R.H.)
| | - Robin Hopkins
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138 (B.E.G., F.R., R.H.); and
- Arnold Arboretum of Harvard University, Boston, Massachusetts 02131 (R.H.)
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288
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Guiller G, Lourdais O, Ursenbacher S. Hybridization between a Euro‐Siberian (
Vipera berus
) and a Para‐Mediterranean viper (
V. aspis
) at their contact zone in western France. J Zool (1987) 2016. [DOI: 10.1111/jzo.12431] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - O. Lourdais
- Centre d'Etudes Biologiques de Chizé CNRS UMR 7372 Villiers en Bois France
| | - S. Ursenbacher
- Section of Conservation Biology Department of Environmental Sciences University of Basel Basel Switzerland
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289
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Mendes FK, Hahn Y, Hahn MW. Gene Tree Discordance Can Generate Patterns of Diminishing Convergence over Time. Mol Biol Evol 2016; 33:3299-3307. [PMID: 27634870 DOI: 10.1093/molbev/msw197] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Phenotypic convergence is an exciting outcome of adaptive evolution, occurring when different species find similar solutions to the same problem. Unraveling the molecular basis of convergence provides a way to link genotype to adaptive phenotypes, but can also shed light on the extent to which molecular evolution is repeatable and predictable. Many recent genome-wide studies have uncovered a striking pattern of diminishing convergence over time, ascribing this pattern to the presence of intramolecular epistatic interactions. Here, we consider gene tree discordance as an alternative cause of changes in convergence levels over time in a primate dataset. We demonstrate that gene tree discordance can produce patterns of diminishing convergence by itself, and that controlling for discordance as a cause of apparent convergence makes the pattern disappear. We also show that synonymous substitutions, where neither selection nor epistasis should be prevalent, have the same diminishing pattern of molecular convergence in primates. Finally, we demonstrate that even in situations where biological discordance is not possible, discordance due to errors in species tree inference can drive similar patterns. Though intramolecular epistasis could in principle create a pattern of declining convergence over time, our results suggest a possible alternative explanation for this widespread pattern. These results contribute to a growing appreciation not just of the presence of gene tree discordance, but of the unpredictable effects this discordance can have on analyses of molecular evolution.
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Affiliation(s)
- Fábio K Mendes
- Department of Biology, Indiana University, Bloomington, IN
| | - Yoonsoo Hahn
- Department of Life Science, Research Center for Biomolecules and Biosystems, Chung-Ang University, Seoul, Republic of Korea
| | - Matthew W Hahn
- Department of Biology, Indiana University, Bloomington, IN.,School of Informatics and Computing, Indiana University, Bloomington, IN
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290
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Zarza E, Faircloth BC, Tsai WL, Bryson RW, Klicka J, McCormack JE. Hidden histories of gene flow in highland birds revealed with genomic markers. Mol Ecol 2016; 25:5144-5157. [DOI: 10.1111/mec.13813] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Revised: 08/10/2016] [Accepted: 08/12/2016] [Indexed: 01/03/2023]
Affiliation(s)
- Eugenia Zarza
- Moore Laboratory of Zoology Occidental College Los Angeles CA 90041 USA
| | - Brant C. Faircloth
- Department of Biological Sciences and Museum of Natural Science Louisiana State University Baton Rouge LA 70803 USA
| | - Whitney L.E. Tsai
- Moore Laboratory of Zoology Occidental College Los Angeles CA 90041 USA
| | - Robert W. Bryson
- Moore Laboratory of Zoology Occidental College Los Angeles CA 90041 USA
- Burke Museum of Natural History and Culture and Department of Biology University of Washington Seattle WA 98195 USA
| | - John Klicka
- Burke Museum of Natural History and Culture and Department of Biology University of Washington Seattle WA 98195 USA
| | - John E. McCormack
- Moore Laboratory of Zoology Occidental College Los Angeles CA 90041 USA
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291
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Abstract
Anopheles melas is a member of the recently diverged An. gambiae species complex, a model for speciation studies, and is a locally important malaria vector along the West-African coast where it breeds in brackish water. A recent population genetic study of An. melas revealed species-level genetic differentiation between three population clusters. An. melas West extends from The Gambia to the village of Tiko, Cameroon. The other mainland cluster, An. melas South, extends from the southern Cameroonian village of Ipono to Angola. Bioko Island, Equatorial Guinea An. melas populations are genetically isolated from mainland populations. To examine how genetic differentiation between these An. melas forms is distributed across their genomes, we conducted a genome-wide analysis of genetic differentiation and selection using whole genome sequencing data of pooled individuals (Pool-seq) from a representative population of each cluster. The An. melas forms exhibit high levels of genetic differentiation throughout their genomes, including the presence of numerous fixed differences between clusters. Although the level of divergence between the clusters is on a par with that of other species within the An. gambiae complex, patterns of genome-wide divergence and diversity do not provide evidence for the presence of pre- and/or postmating isolating mechanisms in the form of speciation islands. These results are consistent with an allopatric divergence process with little or no introgression.
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292
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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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293
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Abstract
Serpentine barrens represent extreme hazards for plant colonists. These sites are characterized by high porosity leading to drought, lack of essential mineral nutrients, and phytotoxic levels of metals. Nevertheless, nature forged populations adapted to these challenges. Here, we use a population-based evolutionary genomic approach coupled with elemental profiling to assess how autotetraploid Arabidopsis arenosa adapted to a multichallenge serpentine habitat in the Austrian Alps. We first demonstrate that serpentine-adapted plants exhibit dramatically altered elemental accumulation levels in common conditions, and then resequence 24 autotetraploid individuals from three populations to perform a genome scan. We find evidence for highly localized selective sweeps that point to a polygenic, multitrait basis for serpentine adaptation. Comparing our results to a previous study of independent serpentine colonizations in the closely related diploid Arabidopsis lyrata in the United Kingdom and United States, we find the highest levels of differentiation in 11 of the same loci, providing candidate alleles for mediating convergent evolution. This overlap between independent colonizations in different species suggests that a limited number of evolutionary strategies are suited to overcome the multiple challenges of serpentine adaptation. Interestingly, we detect footprints of selection in A. arenosa in the context of substantial gene flow from nearby off-serpentine populations of A. arenosa, as well as from A. lyrata In several cases, quantitative tests of introgression indicate that some alleles exhibiting strong selective sweep signatures appear to have been introgressed from A. lyrata This finding suggests that migrant alleles may have facilitated adaptation of A. arenosa to this multihazard environment.
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294
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Bayesian Inference of Reticulate Phylogenies under the Multispecies Network Coalescent. PLoS Genet 2016; 12:e1006006. [PMID: 27144273 PMCID: PMC4856265 DOI: 10.1371/journal.pgen.1006006] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2015] [Accepted: 04/04/2016] [Indexed: 11/19/2022] Open
Abstract
The multispecies coalescent (MSC) is a statistical framework that models how gene genealogies grow within the branches of a species tree. The field of computational phylogenetics has witnessed an explosion in the development of methods for species tree inference under MSC, owing mainly to the accumulating evidence of incomplete lineage sorting in phylogenomic analyses. However, the evolutionary history of a set of genomes, or species, could be reticulate due to the occurrence of evolutionary processes such as hybridization or horizontal gene transfer. We report on a novel method for Bayesian inference of genome and species phylogenies under the multispecies network coalescent (MSNC). This framework models gene evolution within the branches of a phylogenetic network, thus incorporating reticulate evolutionary processes, such as hybridization, in addition to incomplete lineage sorting. As phylogenetic networks with different numbers of reticulation events correspond to points of different dimensions in the space of models, we devise a reversible-jump Markov chain Monte Carlo (RJMCMC) technique for sampling the posterior distribution of phylogenetic networks under MSNC. We implemented the methods in the publicly available, open-source software package PhyloNet and studied their performance on simulated and biological data. The work extends the reach of Bayesian inference to phylogenetic networks and enables new evolutionary analyses that account for reticulation. Trees have long formed in biology the basic structure with which to represent and understand evolutionary relationships. Mathematical models, computational methods, and software tools for inferring phylogenetic trees and studying their mathematical properties are currently the norm in biology. The availability of genomic data from closely related species, as well as from multiple individuals within species, have brought the two fields of phylogenetics and population genetics closer than ever. In particular, the last two decades have witnessed a great flourish in the development and implementation of phylogenetic methods based on the multispecies coalescent model to capture the intricate relationship between gene and genome evolution. However, when reticulation processes such as hybridization occur, the phylogenetic history is best represented by a network. In this work, we demonstrate how the multispecies coalescent model can be adapted to reticulate evolutionary histories and report on a Bayesian method for inference of such histories under this extended model. As networks subsume trees, the model and method provide a principled and unified statistical framework for inferring treelike and non-treelike evolutionary relationships.
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295
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Rosenzweig BK, Pease JB, Besansky NJ, Hahn MW. Powerful methods for detecting introgressed regions from population genomic data. Mol Ecol 2016; 25:2387-97. [PMID: 26945783 DOI: 10.1111/mec.13610] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 02/22/2016] [Indexed: 12/31/2022]
Abstract
Understanding the types and functions of genes that are able to cross species boundaries-and those that are not-is an important step in understanding the forces maintaining species as largely independent lineages across the remainder of the genome. With large next-generation sequencing data sets we are now able to ask whether introgression has occurred across the genome, and multiple methods have been proposed to detect the signature of such events. Here, we introduce a new summary statistic that can be used to test for introgression, RNDmin , that makes use of the minimum pairwise sequence distance between two population samples relative to divergence to an outgroup. We find that our method offers a modest increase in power over other, related tests, but that all such tests have high power to detect introgressed loci when migration is recent and strong. RNDmin is robust to variation in the mutation rate, and remains reliable even when estimates of the divergence time between sister species are inaccurate. We apply RNDmin to population genomic data from the African mosquitoes Anopheles quadriannulatus and A. arabiensis, identifying three novel candidate regions for introgression. Interestingly, one of the introgressed loci is on the X chromosome, but outside of an inversion separating these two species. Our results suggest that significant, but rare, sharing of alleles is occurring between species that diverged more than 1 million years ago, and that application of these methods to additional systems are likely to reveal similar results.
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Affiliation(s)
- Benjamin K Rosenzweig
- School of Informatics and Computing, Indiana University, Bloomington, IN, 47405, USA
| | - James B Pease
- School of Informatics and Computing, Indiana University, Bloomington, IN, 47405, USA.,Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Nora J Besansky
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, 46556, USA.,Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Matthew W Hahn
- School of Informatics and Computing, Indiana University, Bloomington, IN, 47405, USA.,Department of Biology, Indiana University, Bloomington, IN, 47405, USA
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296
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Abstract
Concepts and definitions of species have been debated by generations of biologists and remain controversial. Microbes pose a particular challenge because of their genetic diversity, asexual reproduction, and often promiscuous horizontal gene transfer (HGT). However, microbes also present an opportunity to study and understand speciation because of their rapid evolution, both in nature and in the lab, and small, easily sequenced genomes. Here, we review how microbial population genomics has enabled us to catch speciation "in the act" and how the results have challenged and enriched our concepts of species, with implications for all domains of life. We describe how recombination (including HGT and introgression) has shaped the genomes of nascent microbial, animal, and plant species and argue for a prominent role of natural selection in initiating and maintaining speciation. We ask how universal is the process of speciation across the tree of life, and what lessons can be drawn from microbes? Comparative genomics showing the extent of HGT in natural populations certainly jeopardizes the relevance of vertical descent (i.e., the species tree) in speciation. Nevertheless, we conclude that species do indeed exist as clusters of genetic and ecological similarity and that speciation is driven primarily by natural selection, regardless of the balance between horizontal and vertical descent.
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Affiliation(s)
- B. Jesse Shapiro
- Département de sciences biologiques, Université de Montréal, Montréal, Quebec, Canada
| | - Jean-Baptiste Leducq
- Département de sciences biologiques, Université de Montréal, Montréal, Quebec, Canada
| | - James Mallet
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
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Hu H, Hu Q, Al-Shehbaz IA, Luo X, Zeng T, Guo X, Liu J. Species Delimitation and Interspecific Relationships of the Genus Orychophragmus (Brassicaceae) Inferred from Whole Chloroplast Genomes. FRONTIERS IN PLANT SCIENCE 2016; 7:1826. [PMID: 27999584 PMCID: PMC5138468 DOI: 10.3389/fpls.2016.01826] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 11/21/2016] [Indexed: 05/20/2023]
Abstract
Genetic variations from few chloroplast DNA fragments show lower discriminatory power in the delimitation of closely related species and less resolution ability in discerning interspecific relationships than from nrITS. Here we use Orychophragmus (Brassicaceae) as a model system to test the hypothesis that the whole chloroplast genomes (plastomes), with accumulation of more variations despite the slow evolution, can overcome these weaknesses. We used Illumina sequencing technology via a reference-guided assembly to construct complete plastomes of 17 individuals from six putatively assumed species in the genus. All plastomes are highly conserved in genome structure, gene order, and orientation, and they are around 153 kb in length and contain 113 unique genes. However, nucleotide variations are quite substantial to support the delimitation of all sampled species and to resolve interspecific relationships with high statistical supports. As expected, the estimated divergences between major clades and species are lower than those estimated from nrITS probably due to the slow substitution rate of the plastomes. However, the plastome and nrITS phylogenies were contradictory in the placements of most species, thus suggesting that these species may have experienced complex non-bifurcating evolutions with incomplete lineage sorting and/or hybrid introgressions. Overall, our case study highlights the importance of using plastomes to examine species boundaries and establish an independent phylogeny to infer the speciation history of plants.
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Affiliation(s)
- Huan Hu
- MOE Key Laboratory for Bio-Resources and Eco-Environment, College of Life Science, Sichuan UniversityChengdu, China
| | - Quanjun Hu
- MOE Key Laboratory for Bio-Resources and Eco-Environment, College of Life Science, Sichuan UniversityChengdu, China
| | | | - Xin Luo
- MOE Key Laboratory for Bio-Resources and Eco-Environment, College of Life Science, Sichuan UniversityChengdu, China
| | - Tingting Zeng
- MOE Key Laboratory for Bio-Resources and Eco-Environment, College of Life Science, Sichuan UniversityChengdu, China
| | - Xinyi Guo
- MOE Key Laboratory for Bio-Resources and Eco-Environment, College of Life Science, Sichuan UniversityChengdu, China
| | - Jianquan Liu
- MOE Key Laboratory for Bio-Resources and Eco-Environment, College of Life Science, Sichuan UniversityChengdu, China
- *Correspondence: Jianquan Liu
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