101
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Schwenke PL, Park LK, Hauser L. Introgression among three rockfish species (Sebastes spp.) in the Salish Sea, northeast Pacific Ocean. PLoS One 2018; 13:e0194068. [PMID: 29566070 PMCID: PMC5864001 DOI: 10.1371/journal.pone.0194068] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 02/25/2018] [Indexed: 11/18/2022] Open
Abstract
Interspecific hybridization is often seen as a major conservation issue, potentially threatening endangered species and decreasing biodiversity. In natural populations, the conservation implications of hybridization depends on both on anthropogenic factors and the evolutionary processes maintaining the hybrid zone. However, the timeline and patterns of hybridization in the hybrid zone are often not known. Therefore, species conservation becomes a concern when recent anthropogenic changes influence hybridization and not if hybridization is part of a long-term process. Here, we use sequence data from one mitochondrial gene, three nuclear introns and one nuclear exon to estimate the direction, geographic extent, frequency and possible timeline of hybridization between three rockfish species (Sebastes auriculatus, S. caurinus, S. maliger) in the Salish Sea, Washington, USA. We show that (i) introgression occurred much more frequently in the Salish Sea than on the outer coast, (ii) introgression was highly asymmetrical from S. maliger into the other two species, (iii) almost 40% of individuals in the Salish Sea were hybrids, with frequency of hybrids increasing with isolation from the coast, and (iv) all hybrids were later generation backcrosses rather than F1 hybrids. Our results suggest long-standing low-level hybridization rather than recent onset of interbreeding because of human induced environmental change, possibly facilitated by specific environmental conditions in the sub-basins of the Salish Sea, and by differences in population sizes during recolonization of the area after the last glaciation. This rockfish hybrid system, with asymmetrical introgression and the maintenance of parental species, may prove useful to study both mechanisms that maintain species boundaries and that facilitate speciation in the presence of rapid environmental change.
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Affiliation(s)
- Piper L. Schwenke
- Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, Seattle, Washington, United States of America
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, Washington, United States of America
- * E-mail:
| | - Linda K. Park
- Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, Seattle, Washington, United States of America
| | - Lorenz Hauser
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, Washington, United States of America
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102
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Morales AE, Jackson ND, Dewey TA, O'Meara BC, Carstens BC. Speciation with Gene Flow in North American Myotis Bats. Syst Biol 2018; 66:440-452. [PMID: 27821704 DOI: 10.1093/sysbio/syw100] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 10/20/2016] [Indexed: 02/05/2023] Open
Abstract
Growing evidence supports the idea that species can diverge in the presence of gene flow. However, most methods of phylogeny estimation do not consider this process, despite the fact that ignoring gene flow is known to bias phylogenetic inference. Furthermore, studies that do consider divergence-with-gene-flow typically do so by estimating rates of gene flow using a isolation-with-migration model (IM), rather than evaluating scenarios of gene flow (such as divergence-with-gene flow or secondary contact) that represent very different types of diversification. In this investigation, we aim to infer the recent phylogenetic history of a clade of western long-eared bats while evaluating a number of different models that parameterize gene flow in a variety of ways. We utilize PHRAPL, a new tool for phylogeographic model selection, to compare the fit of a broad set of demographic models that include divergence, migration, or both among Myotis evotis, $M$. thysanodes and M. keenii. A genomic data set consisting of 808 loci of ultraconserved elements was used to explore such models in three steps using an incremental design where each successive set was informed by, and thus more focused than, the previous set of models. Specifically, the three steps were to (i) assess whether gene flow should be modeled and identify the best topologies, (ii) infer directionality of migration using the best topologies, and (iii) estimate the timing of gene flow. The best model (AIC model weight ${\sim}0.98$) included two divergence events (($M$. evotis, $M$. thysanodes), M. keenii) accompanied by gene flow at the initial stages of divergence. These results provide a striking example of speciation-with-gene-flow in an evolutionary lineage. [Myotis bats; PHRAPL; P2C2M; phylogeographic model selection; speciation with gene flow.].
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Affiliation(s)
- Ariadna E Morales
- Department of Evolution, Ecology and Organismal Biology, Ohio State University, 318 W. 12th Avenue, Columbus, OH 43210, USA
| | - Nathan D Jackson
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, 442 Hesler Biology Building, Knoxville, TN 37996, USA
| | - Tanya A Dewey
- Department of Biology, Colorado State University, 1878 Campus Delivery, Fort Collins, CO 80523, USA
| | - Brian C O'Meara
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, 442 Hesler Biology Building, Knoxville, TN 37996, USA
| | - Bryan C Carstens
- Department of Evolution, Ecology and Organismal Biology, Ohio State University, 318 W. 12th Avenue, Columbus, OH 43210, USA
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103
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Gélin P, Fauvelot C, Bigot L, Baly J, Magalon H. From population connectivity to the art of striping Russian dolls: the lessons from Pocillopora corals. Ecol Evol 2018; 8:1411-1426. [PMID: 29375807 PMCID: PMC5773318 DOI: 10.1002/ece3.3747] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 10/25/2017] [Accepted: 10/27/2017] [Indexed: 01/01/2023] Open
Abstract
Here, we examined the genetic variability in the coral genus Pocillopora, in particular within the Primary Species Hypothesis PSH09, identified by Gélin, Postaire, Fauvelot and Magalon (2017) using species delimitation methods [also named Pocillopora eydouxi/meandrina complex sensu, Schmidt-Roach, Miller, Lundgren, & Andreakis (2014)] and which was found to split into three secondary species hypotheses (SSH09a, SSH09b, and SSH09c) according to assignment tests using multi-locus genotypes (13 microsatellites). From a large sampling (2,507 colonies) achieved in three marine provinces [Western Indian Ocean (WIO), Tropical Southwestern Pacific (TSP), and Southeast Polynesia (SEP)], genetic structuring analysis conducted with two clustering analyses (structure and DAPC) using 13 microsatellites revealed that SSH09a was restricted to the WIO while SSH09b and SSH09c were almost exclusively in the TSP and SEP. More surprisingly, each SSH split into two to three genetically differentiated clusters, found in sympatry at the reef scale, leading to a pattern of nested hierarchical levels (PSH > SSH > cluster), each level hiding highly differentiated genetic groups. Thus, rather than structured populations within a single species, these three SSHs, and even the eight clusters, likely represent distinct genetic lineages engaged in a speciation process or real species. The issue is now to understand which hierarchical level (SSH, cluster, or even below) corresponds to the species one. Several hypotheses are discussed on the processes leading to this pattern of mixed clusters in sympatry, evoking formation of reproductive barriers, either by allopatric speciation or habitat selection.
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Affiliation(s)
- Pauline Gélin
- UMR ENTROPIE (Université de La Réunion, IRD, CNRS)Université de La RéunionSt DenisLa Réunion
- Laboratoire d'excellence‐CORAILPerpignanFrance
| | - Cécile Fauvelot
- Laboratoire d'excellence‐CORAILPerpignanFrance
- UMR ENTROPIE (IRD, Université de La Réunion, CNRS)Centre IRD de NouméaNoumeaNew Caledonia
- Present address:
Université Côte d'AzurCNRSNiceFrance
| | - Lionel Bigot
- UMR ENTROPIE (Université de La Réunion, IRD, CNRS)Université de La RéunionSt DenisLa Réunion
- Laboratoire d'excellence‐CORAILPerpignanFrance
| | - Joseph Baly
- Laboratoire d'excellence‐CORAILPerpignanFrance
- UMR ENTROPIE (IRD, Université de La Réunion, CNRS)Centre IRD de NouméaNoumeaNew Caledonia
| | - Hélène Magalon
- UMR ENTROPIE (Université de La Réunion, IRD, CNRS)Université de La RéunionSt DenisLa Réunion
- Laboratoire d'excellence‐CORAILPerpignanFrance
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104
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Blom MPK, Horner P, Moritz C. Convergence across a continent: adaptive diversification in a recent radiation of Australian lizards. Proc Biol Sci 2017; 283:rspb.2016.0181. [PMID: 27306048 DOI: 10.1098/rspb.2016.0181] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 05/19/2016] [Indexed: 12/11/2022] Open
Abstract
Recent radiations are important to evolutionary biologists, because they provide an opportunity to study the mechanisms that link micro- and macroevolution. The role of ecological speciation during adaptive radiation has been intensively studied, but radiations can arise from a diversity of evolutionary processes; in particular, on large continental landmasses where allopatric speciation might frequently precede ecological differentiation. It is therefore important to establish a phylogenetic and ecological framework for recent continental-scale radiations that are species-rich and ecologically diverse. Here, we use a genomic (approx. 1 200 loci, exon capture) approach to fit branch lengths on a summary-coalescent species tree and generate a time-calibrated phylogeny for a recent and ecologically diverse radiation of Australian scincid lizards; the genus Cryptoblepharus We then combine the phylogeny with a comprehensive phenotypic dataset for over 800 individuals across the 26 species, and use comparative methods to test whether habitat specialization can explain current patterns of phenotypic variation in ecologically relevant traits. We find significant differences in morphology between species that occur in distinct environments and convergence in ecomorphology with repeated habitat shifts across the continent. These results suggest that isolated analogous habitats have provided parallel ecological opportunity and have repeatedly promoted adaptive diversification. By contrast, speciation processes within the same habitat have resulted in distinct lineages with relatively limited morphological variation. Overall, our study illustrates how alternative diversification processes might have jointly stimulated species proliferation across the continent and generated a remarkably diverse group of Australian lizards.
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Affiliation(s)
- Mozes P K Blom
- Research School of Biology, The Australian National University, Canberra ACT 0200, Australia
| | - Paul Horner
- Museum and Art Gallery of the Northern Territory, GPO Box 4646, Darwin NT 0801, Australia
| | - Craig Moritz
- Research School of Biology, The Australian National University, Canberra ACT 0200, Australia
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105
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de Magalhães RF, Lemes P, Camargo A, Oliveira U, Brandão RA, Thomassen H, Garcia PCDA, Leite FSF, Santos FR. Evolutionarily significant units of the critically endangered leaf frog Pithecopus ayeaye (Anura, Phyllomedusidae) are not effectively preserved by the Brazilian protected areas network. Ecol Evol 2017; 7:8812-8828. [PMID: 29177033 PMCID: PMC5689491 DOI: 10.1002/ece3.3261] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Revised: 05/29/2017] [Accepted: 06/28/2017] [Indexed: 12/25/2022] Open
Abstract
Protected areas (PAs) are essential for biodiversity conservation, but their coverage is considered inefficient for the preservation of all species. Many species are subdivided into evolutionarily significant units (ESUs) and the effectiveness of PAs in protecting them needs to be investigated. We evaluated the usefulness of the Brazilian PAs network in protecting ESUs of the critically endangered Pithecopus ayeaye through ongoing climate change. This species occurs in a threatened mountaintop ecosystem known as campos rupestres. We used multilocus DNA sequences to delimit geographic clusters, which were further validated as ESUs with a coalescent approach. Ecological niche modeling was used to estimate spatial changes in ESUs' potential distributions, and a gap analysis was carried out to evaluate the effectiveness of the Brazilian PAs network to protect P. ayeaye in the face of climate changes. We tested the niche overlap between ESUs to gain insights for potential management alternatives for the species. Pithecopus ayeaye contains at least three ESUs isolated in distinct mountain regions, and one of them is not protected by any PA. There are no climatic niche differences between the units, and only 4% of the suitable potential area of the species is protected in present and future projections. The current PAs are not effective in preserving the intraspecific diversity of P. ayeaye in its present and future range distributions. The genetic structure of P. ayeaye could represent a typical pattern in campos rupestres endemics, which should be considered for evaluating its conservation status.
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Affiliation(s)
- Rafael Félix de Magalhães
- Programa de Pós‐Graduação em ZoologiaInstituto de Ciências BiológicasUniversidade Federal de Minas Gerais – UFMGBelo HorizonteMinas GeraisBrasil
- Programa de Desarrollo UniversitarioCentro Universitario de RiveraUniversidad de la República – UdelaRRiveraUruguay
| | - Priscila Lemes
- Laboratório de HerpetologiaDepartamento de ZoologiaInstituto de Biociências de Rio ClaroUniversidade Estadual “Júlio Mesquita Filho” – UNESPRio ClaroSão PauloBrasil
| | - Arley Camargo
- Programa de Desarrollo UniversitarioCentro Universitario de RiveraUniversidad de la República – UdelaRRiveraUruguay
| | - Ubirajara Oliveira
- Centro de Sensoriamento RemotoInstituto de GeociênciasUniversidade Federal de Minas Gerais – UFMGBelo HorizonteMinas GeraisBrasil
| | - Reuber Albuquerque Brandão
- Laboratório de Fauna e Unidades de ConservaçãoDepartamento de Engenharia FlorestalFaculdade de TecnologiaUniversidade de Brasília – UnBBrasíliaDistrito FederalBrasil
| | - Hans Thomassen
- Graduação em Ciências BiológicasInstituto de Ciências BiológicasUniversidade Federal de Minas Gerais – UFMGBelo HorizonteMinas GeraisBrasil
| | - Paulo Christiano de Anchietta Garcia
- Programa de Pós‐Graduação em ZoologiaInstituto de Ciências BiológicasUniversidade Federal de Minas Gerais – UFMGBelo HorizonteMinas GeraisBrasil
| | - Felipe Sá Fortes Leite
- Laboratório SagaranaInstituto de Ciências Biológicas e da SaúdeUniversidade Federal de Viçosa – UFVFlorestalMinas GeraisBrasil
| | - Fabrício Rodrigues Santos
- Programa de Pós‐Graduação em ZoologiaInstituto de Ciências BiológicasUniversidade Federal de Minas Gerais – UFMGBelo HorizonteMinas GeraisBrasil
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106
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Chung Y, Hey J. Bayesian Analysis of Evolutionary Divergence with Genomic Data under Diverse Demographic Models. Mol Biol Evol 2017; 34:1517-1528. [PMID: 28333230 DOI: 10.1093/molbev/msx070] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We present a new Bayesian method for estimating demographic and phylogenetic history using population genomic data. Several key innovations are introduced that allow the study of diverse models within an Isolation-with-Migration framework. The new method implements a 2-step analysis, with an initial Markov chain Monte Carlo (MCMC) phase that samples simple coalescent trees, followed by the calculation of the joint posterior density for the parameters of a demographic model. In step 1, the MCMC sampling phase, the method uses a reduced state space, consisting of coalescent trees without migration paths, and a simple importance sampling distribution without the demography of interest. Once obtained, a single sample of trees can be used in step 2 to calculate the joint posterior density for model parameters under multiple diverse demographic models, without having to repeat MCMC runs. Because migration paths are not included in the state space of the MCMC phase, but rather are handled by analytic integration in step 2 of the analysis, the method is scalable to a large number of loci with excellent MCMC mixing properties. With an implementation of the new method in the computer program MIST, we demonstrate the method's accuracy, scalability, and other advantages using simulated data and DNA sequences of two common chimpanzee subspecies: Pan troglodytes (P. t.) troglodytes and P. t. verus.
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Affiliation(s)
- Yujin Chung
- Center for Computational Genetics and Genomics, Temple University, Philadelphia, PA.,Department of Biology, Temple University, Philadelphia, PA
| | - Jody Hey
- Center for Computational Genetics and Genomics, Temple University, Philadelphia, PA.,Department of Biology, Temple University, Philadelphia, PA
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107
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Ottenburghs J, Megens HJ, Kraus RHS, van Hooft P, van Wieren SE, Crooijmans RPMA, Ydenberg RC, Groenen MAM, Prins HHT. A history of hybrids? Genomic patterns of introgression in the True Geese. BMC Evol Biol 2017; 17:201. [PMID: 28830337 PMCID: PMC5568201 DOI: 10.1186/s12862-017-1048-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 08/11/2017] [Indexed: 12/19/2022] Open
Abstract
Background The impacts of hybridization on the process of speciation are manifold, leading to distinct patterns across the genome. Genetic differentiation accumulates in certain genomic regions, while divergence is hampered in other regions by homogenizing gene flow, resulting in a heterogeneous genomic landscape. A consequence of this heterogeneity is that genomes are mosaics of different gene histories that can be compared to unravel complex speciation and hybridization events. However, incomplete lineage sorting (often the outcome of rapid speciation) can result in similar patterns. New statistical techniques, such as the D-statistic and hybridization networks, can be applied to disentangle the contributions of hybridization and incomplete lineage sorting. We unravel patterns of hybridization and incomplete lineage sorting during and after the diversification of the True Geese (family Anatidae, tribe Anserini, genera Anser and Branta) using an exon-based hybridization network approach and taking advantage of discordant gene tree histories by re-sequencing all taxa of this clade. In addition, we determine the timing of introgression and reconstruct historical effective population sizes for all goose species to infer which demographic or biogeographic factors might explain the observed patterns of introgression. Results We find indications for ancient interspecific gene flow during the diversification of the True Geese and were able to pinpoint several putative hybridization events. Specifically, in the genus Branta, both the ancestor of the White-cheeked Geese (Hawaiian Goose, Canada Goose, Cackling Goose and Barnacle Goose) and the ancestor of the Brent Goose hybridized with Red-breasted Goose. One hybridization network suggests a hybrid origin for the Red-breasted Goose, but this scenario seems unlikely and it not supported by the D-statistic analysis. The complex, highly reticulated evolutionary history of the genus Anser hampered the estimation of ancient hybridization events by means of hybridization networks. The reconstruction of historical effective population sizes shows that most species showed a steady increase during the Pliocene and Pleistocene. These large effective population sizes might have facilitated contact between diverging goose species, resulting in the establishment of hybrid zones and consequent gene flow. Conclusions Our analyses suggest that the evolutionary history of the True Geese is influenced by introgressive hybridization. The approach that we have used, based on genome-wide phylogenetic incongruence and network analyses, will be a useful procedure to reconstruct the complex evolutionary histories of many naturally hybridizing species groups. Electronic supplementary material The online version of this article (doi:10.1186/s12862-017-1048-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jente Ottenburghs
- Resource Ecology Group, Wageningen University & Research, Droevendaalsesteeg 3a, 6708 PB, Wageningen, the Netherlands.
| | - Hendrik-Jan Megens
- Animal Breeding and Genomics, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
| | - Robert H S Kraus
- Department of Migration and Immuno-Ecology, Max Planck Institute for Ornithology, Am Obstberg, 1D-78315, Radolfzell, Germany.,Department of Biology, University of Konstanz, D-78457, Constance, Germany
| | - Pim van Hooft
- Resource Ecology Group, Wageningen University & Research, Droevendaalsesteeg 3a, 6708 PB, Wageningen, the Netherlands
| | - Sipke E van Wieren
- Resource Ecology Group, Wageningen University & Research, Droevendaalsesteeg 3a, 6708 PB, Wageningen, the Netherlands
| | - Richard P M A Crooijmans
- Animal Breeding and Genomics, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
| | - Ronald C Ydenberg
- Resource Ecology Group, Wageningen University & Research, Droevendaalsesteeg 3a, 6708 PB, Wageningen, the Netherlands.,Centre for Wildlife Ecology, Simon Fraser University, V5A 1S6, Burnaby, BC, Canada
| | - Martien A M Groenen
- Animal Breeding and Genomics, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
| | - Herbert H T Prins
- Resource Ecology Group, Wageningen University & Research, Droevendaalsesteeg 3a, 6708 PB, Wageningen, the Netherlands
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108
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Peiman KS, Robinson BW. Comparative Analyses of Phenotypic Trait Covariation within and among Populations. Am Nat 2017; 190:451-468. [PMID: 28937814 DOI: 10.1086/693482] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Many morphological, behavioral, physiological, and life-history traits covary across the biological scales of individuals, populations, and species. However, the processes that cause traits to covary also change over these scales, challenging our ability to use patterns of trait covariance to infer process. Trait relationships are also widely assumed to have generic functional relationships with similar evolutionary potentials, and even though many different trait relationships are now identified, there is little appreciation that these may influence trait covariation and evolution in unique ways. We use a trait-performance-fitness framework to classify and organize trait relationships into three general classes, address which ones more likely generate trait covariation among individuals in a population, and review how selection shapes phenotypic covariation. We generate predictions about how trait covariance changes within and among populations as a result of trait relationships and in response to selection and consider how these can be tested with comparative data. Careful comparisons of covariation patterns can narrow the set of hypothesized processes that cause trait covariation when the form of the trait relationship and how it responds to selection yield clear predictions about patterns of trait covariation. We discuss the opportunities and limitations of comparative approaches to evaluate hypotheses about the evolutionary causes and consequences of trait covariation and highlight the importance of evaluating patterns within populations replicated in the same and in different selective environments. Explicit hypotheses about trait relationships are key to generating effective predictions about phenotype and its evolution using covariance data.
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109
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Raeymaekers JAM, Chaturvedi A, Hablützel PI, Verdonck I, Hellemans B, Maes GE, De Meester L, Volckaert FAM. Adaptive and non-adaptive divergence in a common landscape. Nat Commun 2017; 8:267. [PMID: 28814718 PMCID: PMC5559485 DOI: 10.1038/s41467-017-00256-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 06/15/2017] [Indexed: 01/08/2023] Open
Abstract
Species in a common landscape often face similar selective environments. The capacity of organisms to adapt to these environments may be largely species specific. Quantifying shared and unique adaptive responses across species within landscapes may thus improve our understanding of landscape-moderated biodiversity patterns. Here we test to what extent populations of two coexisting and phylogenetically related fishes—three-spined and nine-spined stickleback—differ in the strength and nature of neutral and adaptive divergence along a salinity gradient. Phenotypic differentiation, neutral genetic differentiation and genomic signatures of adaptation are stronger in the three-spined stickleback. Yet, both species show substantial phenotypic parallelism. In contrast, genomic signatures of adaptation involve different genomic regions, and are thus non-parallel. The relative contribution of spatial and environmental drivers of population divergence in each species reflects different strategies for persistence in the same landscape. These results provide insight in the mechanisms underlying variation in evolutionary versatility and ecological success among species within landscapes. The three-spined stickleback is a model species for the study of adaptive divergence. Here, Raeymaekers et al. compare how the three-spined stickleback and its relative the nine-spined stickleback vary at the phenotypic and genomic levels in response to the same spatial and environmental drivers.
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Affiliation(s)
- Joost A M Raeymaekers
- Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, B-3000, Leuven, Belgium. .,Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology, N-7491, Trondheim, Norway. .,Faculty of Biosciences and Aquaculture, Nord University, N-8049, Bodø, Norway.
| | - Anurag Chaturvedi
- Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, B-3000, Leuven, Belgium.,Laboratory of Aquatic Ecology, Evolution and Conservation, KU Leuven, B-3000, Leuven, Belgium
| | - Pascal I Hablützel
- Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, B-3000, Leuven, Belgium.,Flanders Marine Institute, B-8400, Oostende, Belgium
| | - Io Verdonck
- Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, B-3000, Leuven, Belgium
| | - Bart Hellemans
- Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, B-3000, Leuven, Belgium
| | - Gregory E Maes
- Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, B-3000, Leuven, Belgium.,Genomics Core, Center for Human Genetics, UZ Leuven, B-3000, Leuven, Belgium.,Centre for Sustainable Tropical Fisheries and Aquaculture, Comparative Genomics Centre, College of Science and Engineering, James Cook University, Townsville, QLD, 4811, Australia
| | - Luc De Meester
- Laboratory of Aquatic Ecology, Evolution and Conservation, KU Leuven, B-3000, Leuven, Belgium
| | - Filip A M Volckaert
- Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, B-3000, Leuven, Belgium
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110
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Richards EJ, Martin CH. Adaptive introgression from distant Caribbean islands contributed to the diversification of a microendemic adaptive radiation of trophic specialist pupfishes. PLoS Genet 2017; 13:e1006919. [PMID: 28796803 PMCID: PMC5552031 DOI: 10.1371/journal.pgen.1006919] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 07/12/2017] [Indexed: 12/19/2022] Open
Abstract
Rapid diversification often involves complex histories of gene flow that leave variable and conflicting signatures of evolutionary relatedness across the genome. Identifying the extent and source of variation in these evolutionary relationships can provide insight into the evolutionary mechanisms involved in rapid radiations. Here we compare the discordant evolutionary relationships associated with species phenotypes across 42 whole genomes from a sympatric adaptive radiation of Cyprinodon pupfishes endemic to San Salvador Island, Bahamas and several outgroup pupfish species in order to understand the rarity of these trophic specialists within the larger radiation of Cyprinodon. 82% of the genome depicts close evolutionary relationships among the San Salvador Island species reflecting their geographic proximity, but the vast majority of variants fixed between specialist species lie in regions with discordant topologies. Top candidate adaptive introgression regions include signatures of selective sweeps and adaptive introgression of genetic variation from a single population in the northwestern Bahamas into each of the specialist species. Hard selective sweeps of genetic variation on San Salvador Island contributed 5 times more to speciation of trophic specialists than adaptive introgression of Caribbean genetic variation; however, four of the 11 introgressed regions came from a single distant island and were associated with the primary axis of oral jaw divergence within the radiation. For example, standing variation in a proto-oncogene (ski) known to have effects on jaw size introgressed into one San Salvador Island specialist from an island 300 km away approximately 10 kya. The complex emerging picture of the origins of adaptive radiation on San Salvador Island indicates that multiple sources of genetic variation contributed to the adaptive phenotypes of novel trophic specialists on the island. Our findings suggest that a suite of factors, including rare adaptive introgression, may be necessary for adaptive radiation in addition to ecological opportunity.
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Affiliation(s)
- Emilie J. Richards
- Biology Department, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Christopher H. Martin
- Biology Department, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
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111
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Beltrán DM, Schizas NV, Appeldoorn RS, Prada C. Effective Dispersal of Caribbean Reef Fish is Smaller than Current Spacing Among Marine Protected Areas. Sci Rep 2017; 7:4689. [PMID: 28680075 PMCID: PMC5498645 DOI: 10.1038/s41598-017-04849-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 05/18/2017] [Indexed: 11/09/2022] Open
Abstract
The oceans are deteriorating at a fast pace. Conservation measures, such as Marine Protected Areas, are being implemented to relieve areas from local stressors and allow populations to restore to natural levels. Successful networks of MPAs operate if the space among MPAs is smaller than the dispersal capacity of the species under protection. We studied connectivity patterns across populations in a series of MPAs in the common yellowhead Jawfish, Opistognathus aurifrons. Using the power of genome-wide variation, we estimated that the maximum effective dispersal is 8.3 km. We found that MPAs exchange migrants likely via intermediate unprotected habitats through stepping stone dispersal. At scales >50 km such connectivity is decreased, particularly across the Mona Passage. The MPA network studied would be unable to maintain connectivity of these small benthic fishes if habitat in between them is extirpated. Our study highlights the power of SNPs to derive effective dispersal distance and the ability of SNPs to make inferences from single individuals. Given that overall reef fish diversity is driven by species with life histories similar to that of the yellowhead jawfish, managers face a challenge to develop strategies that allow connectivity and avoid isolation of populations and their possible extinction.
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Affiliation(s)
- Diana M Beltrán
- Department of Marine Sciences, University of Puerto Rico, Mayagüez, Call Box 9000, Mayagüez, 00681, Puerto Rico, USA
| | - Nikolaos V Schizas
- Department of Marine Sciences, University of Puerto Rico, Mayagüez, Call Box 9000, Mayagüez, 00681, Puerto Rico, USA
| | - Richard S Appeldoorn
- Department of Marine Sciences, University of Puerto Rico, Mayagüez, Call Box 9000, Mayagüez, 00681, Puerto Rico, USA
| | - Carlos Prada
- Smithsonian Tropical Research Institute, Box 2072, Balboa, Panama.
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112
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Winger BM. Consequences of divergence and introgression for speciation in Andean cloud forest birds. Evolution 2017; 71:1815-1831. [DOI: 10.1111/evo.13251] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 03/31/2017] [Indexed: 12/16/2022]
Affiliation(s)
- Benjamin M. Winger
- Committee on Evolutionary Biology The University of Chicago Chicago Illinois 60637
- Life Sciences Section, Integrative Research Center The Field Museum of Natural History Chicago Illinois 60605
- Current Addresses: Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan 1109 Geddes Avenue Ann Arbor Michigan 48109
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113
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Escoda L, González-Esteban J, Gómez A, Castresana J. Using relatedness networks to infer contemporary dispersal: Application to the endangered mammal Galemys pyrenaicus. Mol Ecol 2017; 26:3343-3357. [DOI: 10.1111/mec.14133] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 03/21/2017] [Indexed: 01/06/2023]
Affiliation(s)
- Lídia Escoda
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra); Barcelona Spain
| | | | | | - Jose Castresana
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra); Barcelona Spain
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114
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Matsubayashi KW, Kohyama TI, Kobayashi N, Yamasaki S, Kuwajima M, Katakura H. Genetic divergence with ongoing gene flow is maintained by the use of different hosts in phytophagous ladybird beetles genus Henosepilachna. J Evol Biol 2017; 30:1110-1123. [PMID: 28306172 DOI: 10.1111/jeb.13071] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 03/12/2017] [Indexed: 12/12/2022]
Abstract
Adaptation to different environments can promote population divergence via natural selection even in the presence of gene flow - a phenomenon that typically occurs during ecological speciation. To elucidate how natural selection promotes and maintains population divergence during speciation, we investigated the population genetic structure, degree of gene flow and heterogeneous genomic divergence in three closely related Japanese phytophagous ladybird beetles: Henosepilachna pustulosa, H. niponica and H. yasutomii. These species act as a generalist, a wild thistle (Cirsium spp.) specialist and a blue cohosh (Caulophyllum robustum) specialist, respectively, and their ranges differ accordingly. The two specialist species widely co-occur but are reproductively isolated solely due to their high specialization to a particular host plant. Genomewide amplified fragment-length polymorphism (AFLP) markers and mitochondrial cytochrome c oxidase subunit I (COI) gene sequences demonstrated obvious genomewide divergence associated with both geographic distance and ecological divergence. However, a hybridization assessment for both AFLP loci and the mitochondrial sequences revealed a certain degree of unidirectional gene flow between the two sympatric specialist species. Principal coordinates analysis (PCoA) based on all of the variable AFLP loci demonstrated that there are genetic similarities between populations from adjacent localities irrespective of the species (i.e. host range). However, a further comparative genome scan identified a few fractions of loci representing approximately 1% of all loci as different host-associated outliers. These results suggest that these three species had a complex origin, which could be obscured by current gene flow, and that ecological divergence can be maintained with only a small fraction of the genome is related to different host use even when there is a certain degree of gene flow between sympatric species pairs.
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Affiliation(s)
- K W Matsubayashi
- The Faculty of Arts and Science, Kyushu University, Fukuoka, Fukuoka, Japan
| | - T I Kohyama
- Faculty of Earth and Environmental Sciences, Hokkaido University, Sapporo, Hokkaido, Japan
| | - N Kobayashi
- Saitama Prefecture University, Koshigaya, Saitama, Japan
| | - S Yamasaki
- Department of Natural History Sciences, Faculty of Science, Hokkaido University, Sapporo, Hokkaido, Japan
| | - M Kuwajima
- Department of Natural History Sciences, Faculty of Science, Hokkaido University, Sapporo, Hokkaido, Japan
| | - H Katakura
- Department of Natural History Sciences, Faculty of Science, Hokkaido University, Sapporo, Hokkaido, Japan
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115
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Yang M, He Z, Shi S, Wu CI. Can genomic data alone tell us whether speciation happened with gene flow? Mol Ecol 2017; 26:2845-2849. [PMID: 28345182 DOI: 10.1111/mec.14117] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Revised: 03/08/2017] [Accepted: 03/20/2017] [Indexed: 01/02/2023]
Abstract
The allopatric model, which requires a period of geographical isolation for speciation to complete, has been the standard model in the modern era. Recently, "speciation with gene flow" has been widely discussed in relation to the model of "strict allopatry" and the level of DNA divergence across genomic regions. We wish to caution that genomic data by themselves may only permit the rejection of the simplest form of allopatry. Even a slightly more complex and realistic model that starts with subdivided populations would be impossible to reject by the genomic data alone. To resolve this central issue of speciation, other forms of observations such as the sequencing of reproductive isolation genes or the identification of geographical barrier(s) will be necessary.
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Affiliation(s)
- Ming Yang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Ziwen He
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Suhua Shi
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Chung-I Wu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.,Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
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116
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Costa RJ, Wilkinson-Herbots H. Inference of Gene Flow in the Process of Speciation: An Efficient Maximum-Likelihood Method for the Isolation-with-Initial-Migration Model. Genetics 2017; 205:1597-1618. [PMID: 28193727 PMCID: PMC5378116 DOI: 10.1534/genetics.116.188060] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 01/25/2017] [Indexed: 12/03/2022] Open
Abstract
The isolation-with-migration (IM) model is commonly used to make inferences about gene flow during speciation, using polymorphism data. However, it has been reported that the parameter estimates obtained by fitting the IM model are very sensitive to the model's assumptions-including the assumption of constant gene flow until the present. This article is concerned with the isolation-with-initial-migration (IIM) model, which drops precisely this assumption. In the IIM model, one ancestral population divides into two descendant subpopulations, between which there is an initial period of gene flow and a subsequent period of isolation. We derive a very fast method of fitting an extended version of the IIM model, which also allows for asymmetric gene flow and unequal population sizes. This is a maximum-likelihood method, applicable to data on the number of segregating sites between pairs of DNA sequences from a large number of independent loci. In addition to obtaining parameter estimates, our method can also be used, by means of likelihood-ratio tests, to distinguish between alternative models representing the following divergence scenarios: (a) divergence with potentially asymmetric gene flow until the present, (b) divergence with potentially asymmetric gene flow until some point in the past and in isolation since then, and (c) divergence in complete isolation. We illustrate the procedure on pairs of Drosophila sequences from ∼30,000 loci. The computing time needed to fit the most complex version of the model to this data set is only a couple of minutes. The R code to fit the IIM model can be found in the supplementary files of this article.
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Affiliation(s)
- Rui J Costa
- Department of Statistical Science, University College London, WC1E 6BT, United Kingdom
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117
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McLean AJ, Toon A, Schmidt DJ, Hughes JM, Joseph L. Phylogeography and geno-phenotypic discordance in a widespread Australian bird, the Variegated Fairy-wren, Malurus lamberti (Aves: Maluridae). Biol J Linn Soc Lond 2017. [DOI: 10.1093/biolinnean/blx004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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118
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119
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Hsiung HY, Huang BH, Chang JT, Huang YM, Huang CW, Liao PC. Local Climate Heterogeneity Shapes Population Genetic Structure of Two Undifferentiated Insular Scutellaria Species. FRONTIERS IN PLANT SCIENCE 2017; 8:159. [PMID: 28239386 PMCID: PMC5301026 DOI: 10.3389/fpls.2017.00159] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 01/25/2017] [Indexed: 06/06/2023]
Abstract
Spatial climate heterogeneity may not only affect adaptive gene frequencies but could also indirectly shape the genetic structure of neutral loci by impacting demographic dynamics. In this study, the effect of local climate on population genetic variation was tested in two phylogenetically close Scutellaria species in Taiwan. Scutellaria taipeiensis, which was originally assumed to be an endemic species of Taiwan Island, is shown to be part of the widespread species S. barbata based on the overlapping ranges of genetic variation and climatic niches as well as their morphological similarity. Rejection of the scenario of "early divergence with secondary contact" and the support for multiple origins of populations of S. taipeiensis from S. barbata provide strong evolutionary evidence for a taxonomic revision of the species combination. Further tests of a climatic effect on genetic variation were conducted. Regression analyses show nonlinear correlations among any pair of geographic, climatic, and genetic distances. However, significantly, the bioclimatic variables that represent the precipitation from late summer to early autumn explain roughly 13% of the genetic variation of our sampled populations. These results indicate that spatial differences of precipitation in the typhoon season may influence the regeneration rate and colonization rate of local populations. The periodic typhoon episodes explain the significant but nonlinear influence of climatic variables on population genetic differentiation. Although, the climatic difference does not lead to species divergence, the local climate variability indeed impacts the spatial genetic distribution at the population level.
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Affiliation(s)
- Huan-Yi Hsiung
- Department of Life Science, National Taiwan Normal UniversityTaipei, Taiwan
| | - Bing-Hong Huang
- Department of Life Science, National Taiwan Normal UniversityTaipei, Taiwan
| | - Jui-Tse Chang
- Department of Entomology, National Taiwan UniversityTaipei, Taiwan
| | - Yao-Moan Huang
- Division of Silviculture, Taiwan Forestry Research InstituteTaipei, Taiwan
| | - Chih-Wei Huang
- Department of Life Science, National Taiwan Normal UniversityTaipei, Taiwan
| | - Pei-Chun Liao
- Department of Life Science, National Taiwan Normal UniversityTaipei, Taiwan
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120
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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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121
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Oswald JA, Overcast I, Mauck WM, Andersen MJ, Smith BT. Isolation with asymmetric gene flow during the nonsynchronous divergence of dry forest birds. Mol Ecol 2017; 26:1386-1400. [PMID: 28100029 DOI: 10.1111/mec.14013] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Revised: 11/30/2016] [Accepted: 12/29/2016] [Indexed: 01/17/2023]
Abstract
Dry forest bird communities in South America are often fragmented by intervening mountains and rainforests, generating high local endemism. The historical assembly of dry forest communities likely results from dynamic processes linked to numerous population histories among codistributed species. Nevertheless, species may diversify in the same way through time if landscape and environmental features, or species ecologies, similarly structure populations. Here we tested whether six co-distributed taxon pairs that occur in the dry forests of the Tumbes and Marañón Valley of northwestern South America show concordant patterns and modes of diversification. We employed a genome reduction technique, double-digest restriction site-associated DNA sequencing, and obtained 4407-7186 genomewide SNPs. We estimated demographic history in each taxon pair and inferred that all pairs had the same best-fit demographic model: isolation with asymmetric gene flow from the Tumbes into the Marañón Valley, suggesting a common diversification mode. Overall, we also observed congruence in effective population size (Ne ) patterns where ancestral Ne were 2.9-11.0× larger than present-day Marañón Valley populations and 0.3-2.0× larger than Tumbesian populations. Present-day Marañón Valley Ne was smaller than Tumbes. In contrast, we found simultaneous population isolation due to a single event to be unlikely as taxon pairs diverged over an extended period of time (0.1-2.9 Ma) with multiple nonoverlapping divergence periods. Our results show that even when populations of codistributed species asynchronously diverge, the mode of their differentiation can remain conserved over millions of years. Divergence by allopatric isolation due to barrier formation does not explain the mode of differentiation between these two bird assemblages; rather, migration of individuals occurred before and after geographic isolation.
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Affiliation(s)
- Jessica A Oswald
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611-7800, USA.,Museum of Natural Science, Louisiana State University, 119 Foster Hall, Baton Rouge, LA, 70803, USA
| | - Isaac Overcast
- Subprogram in Ecology, Evolution and Behavior, The Graduate Center of the City University of New York, New York, NY, 10016, USA
| | - William M Mauck
- Department of Ornithology, American Museum of Natural History, Central Park West at 79th Street, New York, NY, 10024, USA
| | - Michael J Andersen
- Department of Ornithology, American Museum of Natural History, Central Park West at 79th Street, New York, NY, 10024, USA.,Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Brian Tilston Smith
- Department of Ornithology, American Museum of Natural History, Central Park West at 79th Street, New York, NY, 10024, USA
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122
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Levin DA, Scarpino SV. On the young age of intraspecific herbaceous taxa. THE NEW PHYTOLOGIST 2017; 213:1513-1520. [PMID: 27726173 DOI: 10.1111/nph.14224] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 08/30/2016] [Indexed: 06/06/2023]
Abstract
Dated phylogenies rarely include the divergence times of sister intraspecific taxa, and when they do little is said about this subject. We show that over 90% of the intraspecific plant taxa found in a literature search are estimated to be 5 million yr old or younger, with only 4% of taxa estimated to be over 10 million yr old or older. A Bayesian analysis of intraspecific taxon ages indicates that indeed these taxa are expected to be < 10 million yr old. This result for the young age of intraspecific taxa is consistent with the earlier observation that post-pollination reproductive barriers develop between 5 and 10 million yr after lineage splitting, thus leading to species formation. If lineages have not graduated to the species level of divergence by 10 million yr or so, they are likely to have gone extinct by that time as a result of narrow geographical distributions, narrow niche breadths, and relatively small numbers across populations.
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Affiliation(s)
- Donald A Levin
- Department of Integrative Biology, University of Texas, Austin, TX 78713, USA
| | - Samuel V Scarpino
- Department of Mathematics & Statistics, University of Vermont, Burlington, VT 05401, USA
- Complex Systems Center, University of Vermont, Burlington, VT 05401, USA
- Santa Fe Institute, Santa Fe, NM 87501, USA
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123
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Tipping points in the dynamics of speciation. Nat Ecol Evol 2017; 1:1. [DOI: 10.1038/s41559-016-0001] [Citation(s) in RCA: 131] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 10/11/2016] [Indexed: 01/06/2023]
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124
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Rysiewska A, Prevorčnik S, Osikowski A, Hofman S, Beran L, Falniowski A. Phylogenetic relationships inKerkiaand introgression betweenHauffeniaandKerkia(Caenogastropoda: Hydrobiidae). J ZOOL SYST EVOL RES 2016. [DOI: 10.1111/jzs.12159] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Aleksandra Rysiewska
- Department of Malacology; Institute of Zoology; Jagiellonian University; Kraków Poland
| | - Simona Prevorčnik
- Department of Biology; Biotechnical Faculty; University of Ljubljana; Ljubljana Slovenia
| | - Artur Osikowski
- Department of Animal Anatomy; Institute of Veterinary Science; University of Agriculture in Krakow; Kraków Poland
| | - Sebastian Hofman
- Department of Comparative Anatomy; Institute of Zoology; Jagiellonian University; Kraków Poland
| | - Luboš Beran
- Nature Conservation Agency of the Czech Republic; Regional Office Kokořínsko - Máchův kraj Protected Landscape Area Administration; Mělník Czech Republic
| | - Andrzej Falniowski
- Department of Malacology; Institute of Zoology; Jagiellonian University; Kraków Poland
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125
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Hertach T, Puissant S, Gogala M, Trilar T, Hagmann R, Baur H, Kunz G, Wade EJ, Loader SP, Simon C, Nagel P. Complex within a Complex: Integrative Taxonomy Reveals Hidden Diversity in Cicadetta brevipennis (Hemiptera: Cicadidae) and Unexpected Relationships with a Song Divergent Relative. PLoS One 2016; 11:e0165562. [PMID: 27851754 PMCID: PMC5112989 DOI: 10.1371/journal.pone.0165562] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 10/12/2016] [Indexed: 11/23/2022] Open
Abstract
Multiple sources of data in combination are essential for species delimitation and classification of difficult taxonomic groups. Here we investigate a cicada taxon with unusual cryptic diversity and we attempt to resolve seemingly contradictory data sets. Cicada songs act as species-specific premating barriers and have been used extensively to reveal hidden taxonomic diversity in morphologically similar species. The Palaearctic Cicadetta montana species complex is an excellent example where distinct song patterns have disclosed multiple recently described species. Indeed, two taxa turned out to be especially diverse in that they form a “complex within the complex”: the Cicadetta cerdaniensis song group (four species studied previously) and Cicadetta brevipennis (examined in details here). Based on acoustic, morphological, molecular, ecological and spatial data sampled throughout their broad European distribution, we find that Cicadetta brevipennis s. l. comprises five lineages. The most distinct lineage is identified as Cicadetta petryi Schumacher, 1924, which we re-assign to the species level. Cicadetta brevipennis litoralis Puissant & Hertach ssp. n. and Cicadetta brevipennis hippolaidica Hertach ssp. n. are new to science. The latter hybridizes with Cicadetta brevipennis brevipennis Fieber, 1876 at a zone inferred from intermediate song patterns. The fifth lineage requires additional investigation. The C. cerdaniensis and the C. brevipennis song groups exhibit characteristic, clearly distinct basic song patterns that act as reproductive barriers. However, they remain completely intermixed in the Bayesian and maximum likelihood COI and COII mitochondrial DNA phylogenies. The closest relative of each of the four cerdaniensis group species is a brevipennis group taxon. In our favoured scenario the phylogenetic pairs originated in common Pleistocene glacial refuges where the taxa speciated and experienced sporadic inter-group hybridization leading to extensive introgression and mitochondrial capture.
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Affiliation(s)
- Thomas Hertach
- Department of Environmental Sciences, Biogeography, University of Basel, Basel, Switzerland
- Naturhistorisches Museum der Burgergemeinde Bern, Department of Invertebrates, Bern, Switzerland
- * E-mail:
| | - Stéphane Puissant
- Muséum–Jardin des Sciences, Mairie de Dijon, Dijon, France
- Institut de Systématique, Évolution, Biodiversité, Muséum national d'Histoire naturelle, Sorbonne Universités, Paris, France
| | - Matija Gogala
- Slovenian Academy of Sciences and Arts, Ljubljana, Slovenia
| | - Tomi Trilar
- Slovenian Museum of Natural History, Ljubljana, Slovenia
| | - Reto Hagmann
- Department of Environmental Sciences, Biogeography, University of Basel, Basel, Switzerland
- Naturhistorisches Museum der Burgergemeinde Bern, Department of Invertebrates, Bern, Switzerland
| | - Hannes Baur
- Naturhistorisches Museum der Burgergemeinde Bern, Department of Invertebrates, Bern, Switzerland
- University of Bern, Institute of Ecology and Evolution, Bern, Switzerland
| | - Gernot Kunz
- Department of Zoology, Karl Franzens University of Graz, Graz, Austria
| | - Elizabeth J. Wade
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, Connecticut, United States of America
- United States Department of Agriculture, Center for Medical, Agricultural and Veterinary Entomology, Gainesville, Florida, United States of America
| | - Simon P. Loader
- Department of Environmental Sciences, Biogeography, University of Basel, Basel, Switzerland
- Life Sciences Department, University of Roehampton, London, United Kingdom
| | - Chris Simon
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, Connecticut, United States of America
| | - Peter Nagel
- Department of Environmental Sciences, Biogeography, University of Basel, Basel, Switzerland
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126
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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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127
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Christe C, Stölting KN, Paris M, Fraїsse C, Bierne N, Lexer C. Adaptive evolution and segregating load contribute to the genomic landscape of divergence in two tree species connected by episodic gene flow. Mol Ecol 2016; 26:59-76. [PMID: 27447453 DOI: 10.1111/mec.13765] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Revised: 06/09/2016] [Accepted: 07/14/2016] [Indexed: 12/18/2022]
Abstract
Speciation often involves repeated episodes of genetic contact between divergent populations before reproductive isolation (RI) is complete. Whole-genome sequencing (WGS) holds great promise for unravelling the genomic bases of speciation. We have studied two ecologically divergent, hybridizing species of the 'model tree' genus Populus (poplars, aspens, cottonwoods), Populus alba and P. tremula, using >8.6 million single nucleotide polymorphisms (SNPs) from WGS of population pools. We used the genomic data to (i) scan these species' genomes for regions of elevated and reduced divergence, (ii) assess key aspects of their joint demographic history based on genomewide site frequency spectra (SFS) and (iii) infer the potential roles of adaptive and deleterious coding mutations in shaping the genomic landscape of divergence. We identified numerous small, unevenly distributed genome regions without fixed polymorphisms despite high overall genomic differentiation. The joint SFS was best explained by ancient and repeated gene flow and allowed pinpointing candidate interspecific migrant tracts. The direction of selection (DoS) differed between genes in putative migrant tracts and the remainder of the genome, thus indicating the potential roles of adaptive divergence and segregating deleterious mutations on the evolution and breakdown of RI. Genes affected by positive selection during divergence were enriched for several functionally interesting groups, including well-known candidate 'speciation genes' involved in plant innate immunity. Our results suggest that adaptive divergence affects RI in these hybridizing species mainly through intrinsic and demographic processes. Integrating genomic with molecular data holds great promise for revealing the effects of particular genetic pathways on speciation.
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Affiliation(s)
- Camille Christe
- Department of Biology, University of Fribourg, Chemin du Musée 10, CH-1700, Fribourg, Switzerland
| | - Kai N Stölting
- Department of Biology, University of Fribourg, Chemin du Musée 10, CH-1700, Fribourg, Switzerland
| | - Margot Paris
- Department of Biology, University of Fribourg, Chemin du Musée 10, CH-1700, Fribourg, Switzerland
| | - Christelle Fraїsse
- Institut des Sciences de l'Evolution (UMR 5554), CNRS-UM2-IRD, Place Eugene Bataillon, F-34095, Montpellier, France.,Station Méditerranéenne de l'Environnement Littoral, Université Montpellier 2, 2 Rue des Chantiers, F-34200, Séte, France
| | - Nicolas Bierne
- Institut des Sciences de l'Evolution (UMR 5554), CNRS-UM2-IRD, Place Eugene Bataillon, F-34095, Montpellier, France.,Station Méditerranéenne de l'Environnement Littoral, Université Montpellier 2, 2 Rue des Chantiers, F-34200, Séte, France
| | - Christian Lexer
- Department of Biology, University of Fribourg, Chemin du Musée 10, CH-1700, Fribourg, Switzerland.,Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, A-1030, Vienna, Austria
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128
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Zieliński P, Nadachowska-Brzyska K, Dudek K, Babik W. Divergence history of the Carpathian and smooth newts modelled in space and time. Mol Ecol 2016; 25:3912-28. [PMID: 27288862 DOI: 10.1111/mec.13724] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Revised: 06/01/2016] [Accepted: 06/01/2016] [Indexed: 12/24/2022]
Abstract
Information about demographic history is essential for the understanding of the processes of divergence and speciation. Patterns of genetic variation within and between closely related species provide insights into the history of their interactions. Here, we investigated historical demography and genetic exchange between the Carpathian (Lissotriton montandoni, Lm) and smooth (L. vulgaris, Lv) newts. We combine an extensive geographical sampling and multilocus nuclear sequence data with the approximate Bayesian computation framework to test alternative scenarios of divergence and reconstruct the temporal and spatial pattern of gene flow between species. A model of recent (last glacial period) interspecific gene flow was favoured over alternative models. Thus, despite the relatively old divergence (4-6 mya) and presumably long periods of isolation, the species have retained the ability to exchange genes. Nevertheless, the low migration rates (ca. 10(-6) per gene copy per generation) are consistent with strong reproductive isolation between the species. Models allowing demographic changes were favoured, suggesting that the effective population sizes of both species at least doubled as divergence reaching the current ca. 0.2 million in Lm and 1 million in Lv. We found asymmetry in rates of interspecific gene flow between Lm and one evolutionary lineage of Lv. We suggest that intraspecific polymorphism for hybrid incompatibilities segregating within Lv could explain this pattern and propose further tests to distinguish between alternative explanations. Our study highlights the importance of incorporating intraspecific genetic structure into the models investigating the history of divergence.
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Affiliation(s)
- P Zieliński
- Institute of Environmental Sciences, Jagiellonian University, Gronostajowa 7, 30-387, Kraków, Poland
| | - K Nadachowska-Brzyska
- Department of Evolutionary Biology, Uppsala University, Norbyvägen 18D, 75236, Uppsala, Sweden
| | - K Dudek
- Institute of Environmental Sciences, Jagiellonian University, Gronostajowa 7, 30-387, Kraków, Poland
| | - W Babik
- Institute of Environmental Sciences, Jagiellonian University, Gronostajowa 7, 30-387, Kraków, Poland
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129
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Stuglik MT, Babik W. Genomic heterogeneity of historical gene flow between two species of newts inferred from transcriptome data. Ecol Evol 2016; 6:4513-25. [PMID: 27386093 PMCID: PMC4930998 DOI: 10.1002/ece3.2152] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Revised: 04/02/2016] [Accepted: 04/04/2016] [Indexed: 01/31/2023] Open
Abstract
The role of gene flow in species formation is a major unresolved issue in speciation biology. Progress in this area requires information on the long-term patterns of gene flow between diverging species. Here, we used thousands of single-nucleotide polymorphisms derived from transcriptome resequencing and a method modeling the joint frequency spectrum of these polymorphisms to reconstruct patterns of historical gene flow between two Lissotriton newts: L. vulgaris (Lv) and L. montandoni (Lm). We tested several models of divergence including complete isolation and various scenarios of historical gene flow. The model of secondary contact received the highest support. According to this model, the species split from their common ancestor ca. 5.5 million years (MY) ago, evolved in isolation for ca. 2 MY, and have been exchanging genes for the last 3.5 MY Demographic changes have been inferred in both species, with the current effective population size of ca. 0.7 million in Lv and 0.2 million in Lm. The postdivergence gene flow resulted in two-directional introgression which affected the genomes of both species, but was more pronounced from Lv to Lm. Interestingly, we found evidence for genomic heterogeneity of interspecific gene flow. This study demonstrates the complexity of long-term gene flow between distinct but incompletely reproductively isolated taxa which divergence was initiated millions of years ago.
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Affiliation(s)
- Michał T. Stuglik
- Institute of Environmental SciencesJagiellonian UniversityGronostajowa 730387KrakowPoland
| | - Wiesław Babik
- Institute of Environmental SciencesJagiellonian UniversityGronostajowa 730387KrakowPoland
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130
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Kautt AF, Machado-Schiaffino G, Meyer A. Multispecies Outcomes of Sympatric Speciation after Admixture with the Source Population in Two Radiations of Nicaraguan Crater Lake Cichlids. PLoS Genet 2016; 12:e1006157. [PMID: 27362536 PMCID: PMC4928843 DOI: 10.1371/journal.pgen.1006157] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 06/09/2016] [Indexed: 12/19/2022] Open
Abstract
The formation of species in the absence of geographic barriers (i.e. sympatric speciation) remains one of the most controversial topics in evolutionary biology. While theoretical models have shown that this most extreme case of primary divergence-with-gene-flow is possible, only a handful of accepted empirical examples exist. And even for the most convincing examples uncertainties remain; complex histories of isolation and secondary contact can make species falsely appear to have originated by sympatric speciation. This alternative scenario is notoriously difficult to rule out. Midas cichlids inhabiting small and remote crater lakes in Nicaragua are traditionally considered to be one of the best examples of sympatric speciation and lend themselves to test the different evolutionary scenarios that could lead to apparent sympatric speciation since the system is relatively small and the source populations known. Here we reconstruct the evolutionary history of two small-scale radiations of Midas cichlids inhabiting crater lakes Apoyo and Xiloá through a comprehensive genomic data set. We find no signs of differential admixture of any of the sympatric species in the respective radiations. Together with coalescent simulations of different demographic models our results support a scenario of speciation that was initiated in sympatry and does not result from secondary contact of already partly diverged populations. Furthermore, several species seem to have diverged simultaneously, making Midas cichlids an empirical example of multispecies outcomes of sympatric speciation. Importantly, however, the demographic models strongly support an admixture event from the source population into both crater lakes shortly before the onset of the radiations within the lakes. This opens the possibility that the formation of reproductive barriers involved in sympatric speciation was facilitated by genetic variants that evolved in a period of isolation between the initial founding population and the secondary migrants that came from the same source population. Thus, the exact mechanisms by which these species arose might be different from what had been thought before.
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Affiliation(s)
- Andreas F. Kautt
- Department of Biology, University of Konstanz, Konstanz, Baden-Württemberg, Germany
| | | | - Axel Meyer
- Department of Biology, University of Konstanz, Konstanz, Baden-Württemberg, Germany
- * E-mail:
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131
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Reifová R, Majerová V, Reif J, Ahola M, Lindholm A, Procházka P. Patterns of gene flow and selection across multiple species of Acrocephalus warblers: footprints of parallel selection on the Z chromosome. BMC Evol Biol 2016; 16:130. [PMID: 27311647 PMCID: PMC4910229 DOI: 10.1186/s12862-016-0692-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 05/25/2016] [Indexed: 01/11/2023] Open
Abstract
Background Understanding the mechanisms and selective forces leading to adaptive radiations and origin of biodiversity is a major goal of evolutionary biology. Acrocephalus warblers are small passerines that underwent an adaptive radiation in the last approximately 10 million years that gave rise to 37 extant species, many of which still hybridize in nature. Acrocephalus warblers have served as model organisms for a wide variety of ecological and behavioral studies, yet our knowledge of mechanisms and selective forces driving their radiation is limited. Here we studied patterns of interspecific gene flow and selection across three European Acrocephalus warblers to get a first insight into mechanisms of radiation of this avian group. Results We analyzed nucleotide variation at eight nuclear loci in three hybridizing Acrocephalus species with overlapping breeding ranges in Europe. Using an isolation-with-migration model for multiple populations, we found evidence for unidirectional gene flow from A. scirpaceus to A. palustris and from A. palustris to A. dumetorum. Gene flow was higher between genetically more closely related A. scirpaceus and A. palustris than between ecologically more similar A. palustris and A. dumetorum, suggesting that gradual accumulation of intrinsic barriers rather than divergent ecological selection are more efficient in restricting interspecific gene flow in Acrocephalus warblers. Although levels of genetic differentiation between different species pairs were in general not correlated, we found signatures of apparently independent instances of positive selection at the same two Z-linked loci in multiple species. Conclusions Our study brings the first evidence that gene flow occurred during Acrocephalus radiation and not only between sister species. Interspecific gene flow could thus be an important source of genetic variation in individual Acrocephalus species and could have accelerated adaptive evolution and speciation rate in this avian group by creating novel genetic combinations and new phenotypes. Independent instances of positive selection at the same loci in multiple species indicate an interesting possibility that the same loci might have contributed to reproductive isolation in several speciation events. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0692-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Radka Reifová
- Department of Zoology, Faculty of Science, Charles University in Prague, Prague, Czech Republic.
| | - Veronika Majerová
- Department of Zoology, Faculty of Science, Charles University in Prague, Prague, Czech Republic
| | - Jiří Reif
- Institute for Environmental Studies, Faculty of Science, Charles University in Prague, Prague, Czech Republic.,Department of Zoology and Laboratory of Ornithology, Faculty of Science, Palacký University in Olomouc, Olomouc, Czech Republic
| | - Markus Ahola
- Department of Biology, Section of Ecology, FI-20014 University of Turku, Turku, Finland.,Natural Resources Institute Finland, Itäinen Pitkäkatu 3, FI-20240, Turku, Finland
| | | | - Petr Procházka
- Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Brno, Czech Republic
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132
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Kornilios P, Thanou E, Kapli P, Parmakelis A, Chatzaki M. Peeking through the trapdoor: Historical biogeography of the Aegean endemic spider Cyrtocarenum Ausserer, 1871 with an estimation of mtDNA substitution rates for Mygalomorphae. Mol Phylogenet Evol 2016; 98:300-13. [DOI: 10.1016/j.ympev.2016.01.021] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Revised: 11/23/2015] [Accepted: 01/31/2016] [Indexed: 10/22/2022]
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133
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Osborne OG, Chapman MA, Nevado B, Filatov DA. Maintenance of Species Boundaries Despite Ongoing Gene Flow in Ragworts. Genome Biol Evol 2016; 8:1038-47. [PMID: 26979797 PMCID: PMC4860686 DOI: 10.1093/gbe/evw053] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/07/2016] [Indexed: 12/22/2022] Open
Abstract
The role of hybridization between diversifying species has been the focus of a huge amount of recent evolutionary research. While gene flow can prevent speciation or initiate species collapse, it can also generate new hybrid species. Similarly, while adaptive divergence can be wiped out by gene flow, new adaptive variation can be introduced via introgression. The relative frequency of these outcomes, and indeed the frequency of hybridization and introgression in general are largely unknown. One group of closely-related species with several documented cases of hybridization is the Mediterranean ragwort (genus: Senecio) species-complex. Examples of both polyploid and homoploid hybrid speciation are known in the clade, although their evolutionary relationships and the general frequency of introgressive hybridization among them remain unknown. Using a whole genome gene-space dataset comprising eight Senecio species we fully resolve the phylogeny of these species for the first time despite phylogenetic incongruence across the genome. Using a D-statistic approach, we demonstrate previously unknown cases of introgressive hybridization between multiple pairs of taxa across the species tree. This is an important step in establishing these species as a study system for diversification with gene flow, and suggests that introgressive hybridization may be a widespread and important process in plant evolution.
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Affiliation(s)
- Owen G Osborne
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom Department of Life Sciences, Imperial College London - Silwood Park Campus, Berkshire, United Kingdom
| | - Mark A Chapman
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom Department of Life Sciences, Imperial College London - Silwood Park Campus, Berkshire, United Kingdom Centre for Biological Sciences, Faculty of Natural & Environmental Sciences, University of Southampton, Southampton, United Kingdom
| | - Bruno Nevado
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | - Dmitry A Filatov
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
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134
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Rougemont Q, Roux C, Neuenschwander S, Goudet J, Launey S, Evanno G. Reconstructing the demographic history of divergence between European river and brook lampreys using approximate Bayesian computations. PeerJ 2016; 4:e1910. [PMID: 27077007 PMCID: PMC4830234 DOI: 10.7717/peerj.1910] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Accepted: 03/17/2016] [Indexed: 12/19/2022] Open
Abstract
Inferring the history of isolation and gene flow during species divergence is a central question in evolutionary biology. The European river lamprey (Lampetra fluviatilis) and brook lamprey (L. planeri) show a low reproductive isolation but have highly distinct life histories, the former being parasitic-anadromous and the latter non-parasitic and freshwater resident. Here we used microsatellite data from six replicated population pairs to reconstruct their history of divergence using an approximate Bayesian computation framework combined with a random forest model. In most population pairs, scenarios of divergence with recent isolation were outcompeted by scenarios proposing ongoing gene flow, namely the Secondary Contact (SC) and Isolation with Migration (IM) models. The estimation of demographic parameters under the SC model indicated a time of secondary contact close to the time of speciation, explaining why SC and IM models could not be discriminated. In case of an ancient secondary contact, the historical signal of divergence is lost and neutral markers converge to the same equilibrium as under the less parameterized model allowing ongoing gene flow. Our results imply that models of secondary contacts should be systematically compared to models of divergence with gene flow; given the difficulty to discriminate among these models, we suggest that genome-wide data are needed to adequately reconstruct divergence history.
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Affiliation(s)
- Quentin Rougemont
- UMR 985 Ecologie et Santé des Ecosystèmes, Institut National de la Recherche Agronomique, Rennes, France
- UMR 985 Ecologie et Santé des Ecosystèmes, Agrocampus Ouest, Rennes, France
| | - Camille Roux
- Department of Ecology and Evolution, Université de Lausanne, Lausanne, Switzerland
| | - Samuel Neuenschwander
- Department of Ecology and Evolution, Université de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Vital-IT, Lausanne, Switzerland
| | - Jérôme Goudet
- Department of Ecology and Evolution, Université de Lausanne, Lausanne, Switzerland
| | - Sophie Launey
- UMR 985 Ecologie et Santé des Ecosystèmes, Institut National de la Recherche Agronomique, Rennes, France
- UMR 985 Ecologie et Santé des Ecosystèmes, Agrocampus Ouest, Rennes, France
| | - Guillaume Evanno
- UMR 985 Ecologie et Santé des Ecosystèmes, Institut National de la Recherche Agronomique, Rennes, France
- UMR 985 Ecologie et Santé des Ecosystèmes, Agrocampus Ouest, Rennes, France
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135
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Pereira RJ, Martínez-Solano I, Buckley D. Hybridization during altitudinal range shifts: nuclear introgression leads to extensive cyto-nuclear discordance in the fire salamander. Mol Ecol 2016; 25:1551-65. [DOI: 10.1111/mec.13575] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Revised: 01/11/2016] [Accepted: 02/01/2016] [Indexed: 12/30/2022]
Affiliation(s)
- Ricardo J. Pereira
- Centre for GeoGenetics; Natural History Museum of Denmark; University of Copenhagen; Øster Voldgade 5-7 1350 Copenhagen Denmark
| | - Iñigo Martínez-Solano
- Instituto de Investigación en Recursos Cinegéticos (IREC-UCLM-CSIC-JCCM); Ronda de Toledo, s/n 13005 Ciudad Real Spain
- Ecology, Evolution and Development Group; Department of Wetland Ecology; Estación Biológica de Doñana (EBD-CSIC); Avenida Américo Vespucio, s/n 41092 Sevilla Spain
| | - David Buckley
- Departamento de Biodiversidad y Biología Evolutiva; Museo Nacional de Ciencias Naturales MNCN-CSIC; c/José Gutiérrez Abascal 2 28006 Madrid Spain
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136
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Harrison RG, Larson EL. Heterogeneous genome divergence, differential introgression, and the origin and structure of hybrid zones. Mol Ecol 2016; 25:2454-66. [PMID: 26857437 DOI: 10.1111/mec.13582] [Citation(s) in RCA: 125] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 01/19/2016] [Accepted: 01/25/2016] [Indexed: 12/16/2022]
Abstract
Hybrid zones have been promoted as windows on the evolutionary process and as laboratories for studying divergence and speciation. Patterns of divergence between hybridizing species can now be characterized on a genomewide scale, and recent genome scans have focused on the presence of 'islands' of divergence. Patterns of heterogeneous genomic divergence may reflect differential introgression following secondary contact and provide insights into which genome regions contribute to local adaptation, hybrid unfitness and positive assortative mating. However, heterogeneous genome divergence can also arise in the absence of any gene flow, as a result of variation in selection and recombination across the genome. We suggest that to understand hybrid zone origins and dynamics, it is essential to distinguish between genome regions that are divergent between pure parental populations and regions that show restricted introgression where these populations interact in hybrid zones. The latter, more so than the former, reveal the likely genetic architecture of reproductive isolation. Mosaic hybrid zones, because of their complex structure and multiple contacts, are particularly good subjects for distinguishing primary intergradation from secondary contact. Comparisons among independent hybrid zones or transects that involve the 'same' species pair can also help to distinguish between divergence with gene flow and secondary contact. However, data from replicate hybrid zones or replicate transects do not reveal consistent patterns; in a few cases, patterns of introgression are similar across independent transects, but for many taxa, there is distinct lack of concordance, presumably due to variation in environmental context and/or variation in the genetics of the interacting populations.
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Affiliation(s)
- Richard G Harrison
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Erica L Larson
- Division of Biological Sciences, University of Montana, Missoula, MT, 59812, USA
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137
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Edwards T, Tollis M, Hsieh P, Gutenkunst RN, Liu Z, Kusumi K, Culver M, Murphy RW. Assessing models of speciation under different biogeographic scenarios; an empirical study using multi-locus and RNA-seq analyses. Ecol Evol 2016; 6:379-96. [PMID: 26843925 PMCID: PMC4729248 DOI: 10.1002/ece3.1865] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2015] [Revised: 11/01/2015] [Accepted: 11/02/2015] [Indexed: 12/30/2022] Open
Abstract
Evolutionary biology often seeks to decipher the drivers of speciation, and much debate persists over the relative importance of isolation and gene flow in the formation of new species. Genetic studies of closely related species can assess if gene flow was present during speciation, because signatures of past introgression often persist in the genome. We test hypotheses on which mechanisms of speciation drove diversity among three distinct lineages of desert tortoise in the genus Gopherus. These lineages offer a powerful system to study speciation, because different biogeographic patterns (physical vs. ecological segregation) are observed at opposing ends of their distributions. We use 82 samples collected from 38 sites, representing the entire species' distribution and generate sequence data for mtDNA and four nuclear loci. A multilocus phylogenetic analysis in *BEAST estimates the species tree. RNA‐seq data yield 20,126 synonymous variants from 7665 contigs from two individuals of each of the three lineages. Analyses of these data using the demographic inference package ∂a∂i serve to test the null hypothesis of no gene flow during divergence. The best‐fit demographic model for the three taxa is concordant with the *BEAST species tree, and the ∂a∂i analysis does not indicate gene flow among any of the three lineages during their divergence. These analyses suggest that divergence among the lineages occurred in the absence of gene flow and in this scenario the genetic signature of ecological isolation (parapatric model) cannot be differentiated from geographic isolation (allopatric model).
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Affiliation(s)
- Taylor Edwards
- School of Natural Resources and the Environment The University of Arizona Tucson Arizona 85721; University of Arizona Genetics Core University of Arizona Tucson Arizona 85721
| | - Marc Tollis
- School of Life Sciences Arizona State University Tempe Arizona 85287
| | - PingHsun Hsieh
- Department of Ecology and Evolutionary Biology The University of Arizona Tucson Arizona 85721
| | - Ryan N Gutenkunst
- Department of Ecology and Evolutionary Biology The University of Arizona Tucson Arizona 85721; Department of Molecular and Cellular Biology The University of Arizona Tucson Arizona 85721
| | - Zhen Liu
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences Kunming 650223 China
| | - Kenro Kusumi
- School of Life Sciences Arizona State University Tempe Arizona 85287
| | - Melanie Culver
- School of Natural Resources and the Environment The University of Arizona Tucson Arizona 85721; Arizona Cooperative Fish & Wildlife Research Unit USGS University of Arizona Tucson Arizona 85721
| | - Robert W Murphy
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences Kunming 650223 China; Centre for Biodiversity and Conservation Biology Royal Ontario Museum Toronto ON Canada
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138
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Muirhead CA, Presgraves DC. Hybrid Incompatibilities, Local Adaptation, and the Genomic Distribution of Natural Introgression between Species. Am Nat 2016; 187:249-61. [DOI: 10.1086/684583] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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139
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Schneider DM, Baptestini EM, de Aguiar MAM. Diploid versus haploid models of neutral speciation. J Biol Phys 2016; 42:235-45. [PMID: 26755353 DOI: 10.1007/s10867-015-9404-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 11/15/2015] [Indexed: 11/28/2022] Open
Abstract
Neutral models of speciation based on isolation by distance and assortative mating, termed topopatric, have shown to be successful in describing abundance distributions and species-area relationships. Previous works have considered this type of process in the context of haploid genomes. Here we discuss the implementation of two schemes of dominance to analyze the effects of diploidy: a complete dominance model in which one allele dominates over the other and a perfect codominant model in which heterozygous genotypes give rise to a third phenotype. In the case of complete dominance, we observe that speciation requires stronger spatial inbreeding in comparison to the haploid model. For perfect codominance, instead, speciation demands stronger genetic assortativeness. Nevertheless, once speciation is established, the three models predict the same abundance distributions even at the quantitative level, revealing the robustness of the original mechanism to describe biodiversity features.
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Affiliation(s)
- David M Schneider
- Instituto de Física 'Gleb Wataghin', Universidade Estadual de Campinas, Unicamp, 13083-859, Campinas, SP, Brazil.
| | - Elizabeth M Baptestini
- Instituto de Física 'Gleb Wataghin', Universidade Estadual de Campinas, Unicamp, 13083-859, Campinas, SP, Brazil
| | - Marcus A M de Aguiar
- Instituto de Física 'Gleb Wataghin', Universidade Estadual de Campinas, Unicamp, 13083-859, Campinas, SP, Brazil
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140
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Stankowski S, Sobel JM, Streisfeld MA. The geography of divergence with gene flow facilitates multitrait adaptation and the evolution of pollinator isolation inMimulus aurantiacus. Evolution 2015; 69:3054-68. [DOI: 10.1111/evo.12807] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Revised: 09/16/2015] [Accepted: 10/18/2015] [Indexed: 01/07/2023]
Affiliation(s)
- Sean Stankowski
- Institute of Ecology and Evolution; University of Oregon; Eugene Oregon 97401
| | - James M. Sobel
- Department of Biological Sciences; Binghamton University; Binghamton New York 13902
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141
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The role of East Asian monsoon system in shaping population divergence and dynamics of a constructive desert shrub Reaumuria soongarica. Sci Rep 2015; 5:15823. [PMID: 26510579 PMCID: PMC4625182 DOI: 10.1038/srep15823] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 09/30/2015] [Indexed: 11/08/2022] Open
Abstract
Both of the uplift of Qinghai-Tibet Plateau (QTP) and the development of East Asian monsoon system (EAMS) could have comprehensively impacted the formation and evolution of Arid Central Asia (ACA). To understand how desert plants endemic to ACA responded to these two factors, we profiled the historical population dynamics and distribution range shift of a constructive desert shrub Reaumuria soongarica (Tamaricaceae) based on species wide investigation of sequence variation of chloroplast DNA and nuclear ribosomal ITS. Phylogenetic analysis uncovered a deep divergence occurring at ca. 2.96 Mya between the western and eastern lineages of R. soongarica, and ecological niche modeling analysis strongly supported that the monsoonal climate could have fragmented its habitats in both glacial and interglacial periods and impelled its intraspecific divergence. Additionally, the population from the east monsoonal zone expanded rapidly, suggesting that the local monsoonal climate significantly impacted its population dynamics. The isolation by distance tests supported strong maternal gene flow along the direction of the East Asian winter monsoon, whose intensification induced the genetic admixture along the latitudinal populations of R. soongarica. Our results presented a new case that the development of EAMS had prominently impacted the intraspecific divergence and population dynamics of this desert plant.
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142
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Sequential divergence and the multiplicative origin of community diversity. Proc Natl Acad Sci U S A 2015; 112:E5980-9. [PMID: 26499247 DOI: 10.1073/pnas.1424717112] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Phenotypic and genetic variation in one species can influence the composition of interacting organisms within communities and across ecosystems. As a result, the divergence of one species may not be an isolated process, as the origin of one taxon could create new niche opportunities for other species to exploit, leading to the genesis of many new taxa in a process termed "sequential divergence." Here, we test for such a multiplicative effect of sequential divergence in a community of host-specific parasitoid wasps, Diachasma alloeum, Utetes canaliculatus, and Diachasmimorpha mellea (Hymenoptera: Braconidae), that attack Rhagoletis pomonella fruit flies (Diptera: Tephritidae). Flies in the R. pomonella species complex radiated by sympatrically shifting and ecologically adapting to new host plants, the most recent example being the apple-infesting host race of R. pomonella formed via a host plant shift from hawthorn-infesting flies within the last 160 y. Using population genetics, field-based behavioral observations, host fruit odor discrimination assays, and analyses of life history timing, we show that the same host-related ecological selection pressures that differentially adapt and reproductively isolate Rhagoletis to their respective host plants (host-associated differences in the timing of adult eclosion, host fruit odor preference and avoidance behaviors, and mating site fidelity) cascade through the ecosystem and induce host-associated genetic divergence for each of the three members of the parasitoid community. Thus, divergent selection at lower trophic levels can potentially multiplicatively and rapidly amplify biodiversity at higher levels on an ecological time scale, which may sequentially contribute to the rich diversity of life.
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143
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Hey J, Chung Y, Sethuraman A. On the occurrence of false positives in tests of migration under an isolation-with-migration model. Mol Ecol 2015; 24:5078-83. [PMID: 26456794 DOI: 10.1111/mec.13381] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Revised: 07/02/2015] [Accepted: 07/15/2015] [Indexed: 12/24/2022]
Abstract
The population genetic study of divergence is often carried out using a Bayesian genealogy sampler, like those implemented in ima2 and related programs, and these analyses frequently include a likelihood ratio test of the null hypothesis of no migration between populations. Cruickshank and Hahn (2014, Molecular Ecology, 23, 3133-3157) recently reported a high rate of false-positive test results with ima2 for data simulated with small numbers of loci under models with no migration and recent splitting times. We confirm these findings and discover that they are caused by a failure of the assumptions underlying likelihood ratio tests that arises when using marginal likelihoods for a subset of model parameters. We also show that for small data sets, with little divergence between samples from two populations, an excellent fit can often be found by a model with a low migration rate and recent splitting time and a model with a high migration rate and a deep splitting time.
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Affiliation(s)
- Jody Hey
- Center for Computational Genetics and Genomics, Temple University, 1900 N. 12th Street, Philadelphia, PA, 19122, USA
| | - Yujin Chung
- Center for Computational Genetics and Genomics, Temple University, 1900 N. 12th Street, Philadelphia, PA, 19122, USA
| | - Arun Sethuraman
- Center for Computational Genetics and Genomics, Temple University, 1900 N. 12th Street, Philadelphia, PA, 19122, USA
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144
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Konijnendijk N, Shikano T, Daneels D, Volckaert FAM, Raeymaekers JAM. Signatures of selection in the three-spined stickleback along a small-scale brackish water - freshwater transition zone. Ecol Evol 2015; 5:4174-86. [PMID: 26445666 PMCID: PMC4588664 DOI: 10.1002/ece3.1671] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Revised: 07/13/2015] [Accepted: 07/22/2015] [Indexed: 01/31/2023] Open
Abstract
Local adaptation is often obvious when gene flow is impeded, such as observed at large spatial scales and across strong ecological contrasts. However, it becomes less certain at small scales such as between adjacent populations or across weak ecological contrasts, when gene flow is strong. While studies on genomic adaptation tend to focus on the former, less is known about the genomic targets of natural selection in the latter situation. In this study, we investigate genomic adaptation in populations of the three-spined stickleback Gasterosteus aculeatus L. across a small-scale ecological transition with salinities ranging from brackish to fresh. Adaptation to salinity has been repeatedly demonstrated in this species. A genome scan based on 87 microsatellite markers revealed only few signatures of selection, likely owing to the constraints that homogenizing gene flow puts on adaptive divergence. However, the detected loci appear repeatedly as targets of selection in similar studies of genomic adaptation in the three-spined stickleback. We conclude that the signature of genomic selection in the face of strong gene flow is weak, yet detectable. We argue that the range of studies of genomic divergence should be extended to include more systems characterized by limited geographical and ecological isolation, which is often a realistic setting in nature.
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Affiliation(s)
- Nellie Konijnendijk
- Laboratory of Biodiversity and Evolutionary Genomics University of Leuven Ch. Deberiotstraat 32, B-3000 Leuven Belgium
| | - Takahito Shikano
- Ecological Genetics Research Unit Department of Biosciences University of Helsinki P.O. Box 65 FI-000 14 Helsinki Finland
| | - Dorien Daneels
- Laboratory of Biodiversity and Evolutionary Genomics University of Leuven Ch. Deberiotstraat 32, B-3000 Leuven Belgium
| | - Filip A M Volckaert
- Laboratory of Biodiversity and Evolutionary Genomics University of Leuven Ch. Deberiotstraat 32, B-3000 Leuven Belgium
| | - Joost A M Raeymaekers
- Laboratory of Biodiversity and Evolutionary Genomics University of Leuven Ch. Deberiotstraat 32, B-3000 Leuven Belgium
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145
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Zakas C, Rockman MV. Gene-based polymorphisms reveal limited genomic divergence in a species with a heritable life-history dimorphism. Evol Dev 2015; 17:240-7. [DOI: 10.1111/ede.12128] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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146
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Gruenstaeudl M, Reid NM, Wheeler GL, Carstens BC. Posterior predictive checks of coalescent models: P2C2M, an R package. Mol Ecol Resour 2015; 16:193-205. [DOI: 10.1111/1755-0998.12435] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Revised: 05/22/2015] [Accepted: 05/26/2015] [Indexed: 02/04/2023]
Affiliation(s)
- Michael Gruenstaeudl
- Department of Evolution, Ecology & Organismal Biology; Ohio State University; Columbus OH 43210 USA
| | - Noah M. Reid
- Department of Environmental Toxicology; University of California; Davis CA 95616 USA
| | - Gregory L. Wheeler
- Department of Evolution, Ecology & Organismal Biology; Ohio State University; Columbus OH 43210 USA
| | - Bryan C. Carstens
- Department of Evolution, Ecology & Organismal Biology; Ohio State University; Columbus OH 43210 USA
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147
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Gante HF, Doadrio I, Alves MJ, Dowling TE. Semi-permeable species boundaries in Iberian barbels (Barbus and Luciobarbus, Cyprinidae). BMC Evol Biol 2015; 15:111. [PMID: 26066794 PMCID: PMC4465174 DOI: 10.1186/s12862-015-0392-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2015] [Accepted: 05/28/2015] [Indexed: 12/04/2022] Open
Abstract
BACKGROUND The evolution of species boundaries and the relative impact of selection and gene flow on genomic divergence are best studied in populations and species pairs exhibiting various levels of divergence along the speciation continuum. We studied species boundaries in Iberian barbels, Barbus and Luciobarbus, a system of populations and species spanning a wide degree of genetic relatedness, as well as geographic distribution and range overlap. We jointly analyze multiple types of molecular markers and morphological traits to gain a comprehensive perspective on the nature of species boundaries in these cyprinid fishes. RESULTS Intraspecific molecular and morphological differentiation is visible among many populations. Genomes of all sympatric species studied are porous to gene flow, even if they are not sister species. Compared to their allopatric counterparts, sympatric representatives of different species share alleles and show an increase in all measures of nucleotide polymorphism (S, Hd, K, π and θ). High molecular diversity is particularly striking in L. steindachneri from the Tejo and Guadiana rivers, which co-varies with other sympatric species. Interestingly, different nuclear markers introgress across species boundaries at various levels, with distinct impacts on population trees. As such, some loci exhibit limited introgression and population trees resemble the presumed species tree, while alleles at other loci introgress more freely and population trees reflect geographic affinities and interspecific gene flow. Additionally, extent of introgression decreases with increasing genetic divergence in hybridizing species pairs. CONCLUSIONS We show that reproductive isolation in Iberian Barbus and Luciobarbus is not complete and species boundaries are semi-permeable to (some) gene flow, as different species (including non-sister) are exchanging genes in areas of sympatry. Our results support a speciation-with-gene-flow scenario with heterogeneous barriers to gene flow across the genome, strengthening with genetic divergence. This is consistent with observations coming from other systems and supports the notion that speciation is not instantaneous but a gradual process, during which different species are still able to exchange some genes, while selection prevents gene flow at other loci. We also provide evidence for a hybrid origin of a barbel ecotype, L. steindachneri, suggesting that ecology plays a key role in species coexistence and hybridization in Iberian barbels. This ecotype with intermediate, yet variable, molecular, morphological, trophic and ecological characteristics is the local product of introgressive hybridization of L. comizo with up to three different species (with L. bocagei in the Tejo, with L. microcephalus and L. sclateri in the Guadiana). In spite of the homogenizing effects of ongoing gene flow, species can still be discriminated using a combination of morphological and molecular markers. Iberian barbels are thus an ideal system for the study of species boundaries, since they span a wide range of genetic divergences, with diverse ecologies and degrees of sympatry.
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Affiliation(s)
- Hugo F Gante
- School of Life Sciences, Arizona State University, 85287-4601, Tempe, AZ, USA.
- Museu Nacional de História Natural e da Ciência, Centre for Ecology, Evolution and Environmental Changes (Ce3C), Universidade de Lisboa, Rua da Escola Politécnica 58, 1250-102, Lisbon, Portugal.
- Current address: Zoological Institute, University of Basel, 4051, Basel, Switzerland.
| | - Ignacio Doadrio
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales, CSIC, c/José Gutiérrez Abascal 2, 28006, Madrid, Spain.
| | - Maria Judite Alves
- Museu Nacional de História Natural e da Ciência, Centre for Ecology, Evolution and Environmental Changes (Ce3C), Universidade de Lisboa, Rua da Escola Politécnica 58, 1250-102, Lisbon, Portugal.
| | - Thomas E Dowling
- School of Life Sciences, Arizona State University, 85287-4601, Tempe, AZ, USA.
- Current address: Department of Biological Sciences, Wayne State University, 5047 Gullen Mall, 48202, Detroit, MI, USA.
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148
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Silva MC, Matias R, Wanless RM, Ryan PG, Stephenson BM, Bolton M, Ferrand N, Coelho MM. Understanding the mechanisms of antitropical divergence in the seabird White-faced Storm-petrel (Procellariiformes: Pelagodroma marina) using a multilocus approach. Mol Ecol 2015; 24:3122-37. [PMID: 25903359 DOI: 10.1111/mec.13212] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Revised: 04/16/2015] [Accepted: 04/21/2015] [Indexed: 11/27/2022]
Abstract
Analytical methods that apply coalescent theory to multilocus data have improved inferences of demographic parameters that are critical to understanding population divergence and speciation. In particular, at the early stages of speciation, it is important to implement models that accommodate conflicting gene trees, and benefit from the presence of shared polymorphisms. Here, we employ eleven nuclear loci and the mitochondrial control region to investigate the phylogeography and historical demography of the pelagic seabird White-faced Storm-petrel (Pelagodroma marina) by sampling subspecies across its antitropical distribution. Groups are all highly differentiated: global mitochondrial ΦST = 0.89 (P < 0.01) and global nuclear ΦST varies between 0.22 and 0.83 (all P < 0.01). The complete lineage sorting of the mitochondrial locus between hemispheres is corroborated by approximately half of the nuclear genealogies, suggesting a long-term antitropical divergence in isolation. Coalescent-based estimates of demographic parameters suggest that hemispheric divergence of P. marina occurred approximately 840 000 ya (95% HPD 582 000-1 170 000), in the absence of gene flow, and divergence within the Southern Hemisphere occurred 190 000 ya (95% HPD 96 000-600 000), both probably associated with the profound palaeo-oceanographic changes of the Pleistocene. A fledgling sampled in St Helena (tropical South Atlantic) suggests recent colonization from the Northern Hemisphere. Despite the great potential for long-distance dispersal, P. marina antitropical groups have been evolving as independent, allopatric lineages, and divergence is probably maintained by philopatry coupled with asynchronous reproductive phenology and local adaptation.
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Affiliation(s)
- Mónica C Silva
- Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, 1749-016, Lisboa, Portugal
| | - Rafael Matias
- Centre for Ecology and Conservation, School of Biosciences, University of Exeter, Penryn, TR10 9EZ, UK.,Marine and Environmental Sciences Centre, ISPA-Instituto Universitário, 1149-041, Lisboa, Portugal
| | - Ross M Wanless
- Percy FitzPatrick Institute of African Ornithology, DST-NRF Centre of Excellence, University of Cape Town, Rondebosch, 7701, South Africa.,Seabird Conservation Program, BirdLife South Africa, PO Box 7119, Roggebaai, 8012, South Africa
| | - Peter G Ryan
- Percy FitzPatrick Institute of African Ornithology, DST-NRF Centre of Excellence, University of Cape Town, Rondebosch, 7701, South Africa
| | - Brent M Stephenson
- Eco-Vista: Photography & Research Ltd, PO Box 157, Bay View, Napier, 4149, New Zealand
| | - Mark Bolton
- RSPB Centre for Conservation Science, Royal Society for the Protection of Birds, The Lodge, Sandy, Beds, SG19 2DL, UK
| | - Nuno Ferrand
- CIBIO, Universidade do Porto, Campus Agrário Vairão, 4485-661, Vairão, Portugal
| | - M Manuela Coelho
- Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, 1749-016, Lisboa, Portugal
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149
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Papke RT, Corral P, Ram-Mohan N, de la Haba RR, Sánchez-Porro C, Makkay A, Ventosa A. Horizontal gene transfer, dispersal and haloarchaeal speciation. Life (Basel) 2015; 5:1405-26. [PMID: 25997110 PMCID: PMC4500145 DOI: 10.3390/life5021405] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Revised: 05/08/2015] [Accepted: 05/11/2015] [Indexed: 11/28/2022] Open
Abstract
The Halobacteria are a well-studied archaeal class and numerous investigations are showing how their diversity is distributed amongst genomes and geographic locations. Evidence indicates that recombination between species continuously facilitates the arrival of new genes, and within species, it is frequent enough to spread acquired genes amongst all individuals in the population. To create permanent independent diversity and generate new species, barriers to recombination are probably required. The data support an interpretation that rates of evolution (e.g., horizontal gene transfer and mutation) are faster at creating geographically localized variation than dispersal and invasion are at homogenizing genetic differences between locations. Therefore, we suggest that recurrent episodes of dispersal followed by variable periods of endemism break the homogenizing forces of intrapopulation recombination and that this process might be the principal stimulus leading to divergence and speciation in Halobacteria.
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Affiliation(s)
- R. Thane Papke
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA; E-Mails: (N.R.-M.); (A.M.)
- Author to whom correspondence should be addressed; E-Mail:
| | - Paulina Corral
- Department of Microbiology and Parasitology, University of Seville, 41004 Seville, Spain; E-Mails: (P.C.); (R.R.H.); (C.S.-P.); (A.V.)
| | - Nikhil Ram-Mohan
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA; E-Mails: (N.R.-M.); (A.M.)
| | - Rafael R. de la Haba
- Department of Microbiology and Parasitology, University of Seville, 41004 Seville, Spain; E-Mails: (P.C.); (R.R.H.); (C.S.-P.); (A.V.)
| | - Cristina Sánchez-Porro
- Department of Microbiology and Parasitology, University of Seville, 41004 Seville, Spain; E-Mails: (P.C.); (R.R.H.); (C.S.-P.); (A.V.)
| | - Andrea Makkay
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA; E-Mails: (N.R.-M.); (A.M.)
| | - Antonio Ventosa
- Department of Microbiology and Parasitology, University of Seville, 41004 Seville, Spain; E-Mails: (P.C.); (R.R.H.); (C.S.-P.); (A.V.)
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150
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Woodard SH, Lozier JD, Goulson D, Williams PH, Strange JP, Jha S. Molecular tools and bumble bees: revealing hidden details of ecology and evolution in a model system. Mol Ecol 2015; 24:2916-36. [PMID: 25865395 DOI: 10.1111/mec.13198] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 04/07/2015] [Accepted: 04/08/2015] [Indexed: 01/15/2023]
Abstract
Bumble bees are a longstanding model system for studies on behaviour, ecology and evolution, due to their well-studied social lifestyle, invaluable role as wild and managed pollinators, and ubiquity and diversity across temperate ecosystems. Yet despite their importance, many aspects of bumble bee biology have remained enigmatic until the rise of the genetic and, more recently, genomic eras. Here, we review and synthesize new insights into the ecology, evolution and behaviour of bumble bees that have been gained using modern genetic and genomic techniques. Special emphasis is placed on four areas of bumble bee biology: the evolution of eusociality in this group, population-level processes, large-scale evolutionary relationships and patterns, and immunity and resistance to pesticides. We close with a prospective on the future of bumble bee genomics research, as this rapidly advancing field has the potential to further revolutionize our understanding of bumble bees, particularly in regard to adaptation and resilience. Worldwide, many bumble bee populations are in decline. As such, throughout the review, connections are drawn between new molecular insights into bumble bees and our understanding of the causal factors involved in their decline. Ongoing and potential applications to bumble bee management and conservation are also included to demonstrate how genetics- and genomics-enabled research aids in the preservation of this threatened group.
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Affiliation(s)
- S Hollis Woodard
- Department of Integrative Biology, University of Texas, Austin, TX, 78712, USA.,Department of Entomology, University of California, Riverside, CA, 92521, USA
| | - Jeffrey D Lozier
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL, 35401, USA
| | - David Goulson
- Evolution, Behaviour & Environment, School of Life Sciences, University of Sussex, Falmer, East Sussex, BN1 9QG, UK
| | - Paul H Williams
- Department of Life Sciences, Natural History Museum, London, SW7 5BD, UK
| | - James P Strange
- USDA-ARS, Pollinating Insect Research Unit, Utah State University, Logan, UT, 84322, USA
| | - Shalene Jha
- Department of Integrative Biology, University of Texas, Austin, TX, 78712, USA
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