51
|
Semenov GA, Scordato ESC, Khaydarov DR, Smith C, Kane NC, Safran RJ. Effects of assortative mate choice on the genomic and morphological structure of a hybrid zone between two bird subspecies. Mol Ecol 2017; 26:6430-6444. [DOI: 10.1111/mec.14376] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Revised: 08/15/2017] [Accepted: 09/27/2017] [Indexed: 12/20/2022]
Affiliation(s)
- Georgy A. Semenov
- Department of Ecology & Evolutionary Biology The University of Arizona Tucson AZ USA
- Institute of Systematics and Ecology of Animals Novosibirsk Russia
| | | | | | - Chris C. R. Smith
- Department of Ecology and Evolutionary Biology The University of Colorado Boulder CO USA
| | - Nolan C. Kane
- Department of Ecology and Evolutionary Biology The University of Colorado Boulder CO USA
| | - Rebecca J. Safran
- Department of Ecology and Evolutionary Biology The University of Colorado Boulder CO USA
| |
Collapse
|
52
|
Delahaie B, Cornuault J, Masson C, Bertrand JAM, Bourgeois YXC, Milá B, Thébaud C. Narrow hybrid zones in spite of very low population differentiation in neutral markers in an island bird species complex. J Evol Biol 2017; 30:2132-2145. [DOI: 10.1111/jeb.13177] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 07/26/2017] [Accepted: 09/07/2017] [Indexed: 02/06/2023]
Affiliation(s)
- B. Delahaie
- Laboratoire Évolution et Diversité Biologique (EDB); UMR 5174 Centre National de la Recherche Scientifique (CNRS) - Université Paul Sabatier - Ecole Nationale de Formation Agronomique (ENFA); Toulouse France
- Centre d'Ecologie Fonctionnelle et Evolutive; CNRS-UMR5175 CEFE; Montpellier France
| | - J. Cornuault
- Laboratoire Évolution et Diversité Biologique (EDB); UMR 5174 Centre National de la Recherche Scientifique (CNRS) - Université Paul Sabatier - Ecole Nationale de Formation Agronomique (ENFA); Toulouse France
| | - C. Masson
- Laboratoire Évolution et Diversité Biologique (EDB); UMR 5174 Centre National de la Recherche Scientifique (CNRS) - Université Paul Sabatier - Ecole Nationale de Formation Agronomique (ENFA); Toulouse France
| | - J. A. M. Bertrand
- Laboratoire Évolution et Diversité Biologique (EDB); UMR 5174 Centre National de la Recherche Scientifique (CNRS) - Université Paul Sabatier - Ecole Nationale de Formation Agronomique (ENFA); Toulouse France
| | - Y. X. C. Bourgeois
- Laboratoire Évolution et Diversité Biologique (EDB); UMR 5174 Centre National de la Recherche Scientifique (CNRS) - Université Paul Sabatier - Ecole Nationale de Formation Agronomique (ENFA); Toulouse France
| | - B. Milá
- National Museum of Natural Sciences; Spanish National Research Council (CSIC); Madrid Spain
| | - C. Thébaud
- Laboratoire Évolution et Diversité Biologique (EDB); UMR 5174 Centre National de la Recherche Scientifique (CNRS) - Université Paul Sabatier - Ecole Nationale de Formation Agronomique (ENFA); Toulouse France
| |
Collapse
|
53
|
Scordato ESC, Wilkins MR, Semenov G, Rubtsov AS, Kane NC, Safran RJ. Genomic variation across two barn swallow hybrid zones reveals traits associated with divergence in sympatry and allopatry. Mol Ecol 2017; 26:5676-5691. [DOI: 10.1111/mec.14276] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 07/19/2017] [Accepted: 07/24/2017] [Indexed: 12/31/2022]
Affiliation(s)
| | - Matthew R. Wilkins
- Department of Ecology and Evolutionary Biology The University of Colorado Boulder CO USA
- School of Biological Sciences University of Nebraska‐Lincoln Lincoln NE USA
| | - Georgy Semenov
- Department of Ecology & Evolutionary Biology University of Arizona Tucson AZ USA
- Institute of Systematics and Ecology of Animals Novosibirsk Russia
| | | | - Nolan C. Kane
- Department of Ecology and Evolutionary Biology The University of Colorado Boulder CO USA
| | - Rebecca J. Safran
- Department of Ecology and Evolutionary Biology The University of Colorado Boulder CO USA
| |
Collapse
|
54
|
|
55
|
Wielstra B, Burke T, Butlin RK, Avcı A, Üzüm N, Bozkurt E, Olgun K, Arntzen JW. A genomic footprint of hybrid zone movement in crested newts. Evol Lett 2017; 1:93-101. [PMID: 30283642 PMCID: PMC6121819 DOI: 10.1002/evl3.9] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 04/04/2017] [Indexed: 01/18/2023] Open
Abstract
Speciation typically involves a stage in which species can still exchange genetic material. Interspecific gene flow is facilitated by the hybrid zones that such species establish upon secondary contact. If one member of a hybridizing species pair displaces the other, their hybrid zone would move across the landscape. Although theory predicts that moving hybrid zones quickly stagnate, hybrid zones tracked over one or a few decades do not always follow such a limitation. This suggests that hybrid zones have the potential to traverse considerable distances over extended periods of time. When hybrid zones move, introgression is predicted to result in biased gene flow of selectively neutral alleles, from the receding species into the advancing species. We test for such a genomic footprint of hybrid zone movement in a pair of crested newt species (genus Triturus) for which we have a priori support for westward hybrid zone movement. We perform a multilocus phylogeographical survey and conduct Bayesian clustering analysis, estimation of ancestry and heterozygosity, and geographical cline analysis. In a 600 km wide area east of the present day hybrid zone a genomic footprint constitutes empirical evidence consistent with westward hybrid zone movement. The crested newt case suggests that hybrid zone movement can occur over an extensive span of time and space. Inferring hybrid zone movement provides fundamental insight into historical biogeography and the speciation process, and we anticipate that hybrid zones will prove to be far more mobile than currently appreciated.
Collapse
Affiliation(s)
- Ben Wielstra
- Department of Animal and Plant Sciences University of Sheffield S10 2TN Sheffield United Kingdom.,Naturalis Biodiversity Center 2300 RA Leiden The Netherlands.,Department of Ecology and Evolutionary Biology University of California Los Angeles California 90095
| | - Terry Burke
- Department of Animal and Plant Sciences University of Sheffield S10 2TN Sheffield United Kingdom
| | - Roger K Butlin
- Department of Animal and Plant Sciences University of Sheffield S10 2TN Sheffield United Kingdom.,Department of Marine Sciences University of Gothenburg S 405 30 Gothenburg Sweden
| | - Aziz Avcı
- Department of Biology, Faculty of Arts and Sciences Adnan Menderes University 09010 Aydın Turkey
| | - Nazan Üzüm
- Department of Biology, Faculty of Arts and Sciences Adnan Menderes University 09010 Aydın Turkey
| | - Emin Bozkurt
- Department of Biology, Faculty of Arts and Sciences Adnan Menderes University 09010 Aydın Turkey
| | - Kurtuluş Olgun
- Department of Biology, Faculty of Arts and Sciences Adnan Menderes University 09010 Aydın Turkey
| | - Jan W Arntzen
- Naturalis Biodiversity Center 2300 RA Leiden The Netherlands
| |
Collapse
|
56
|
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
| |
Collapse
|
57
|
Oatley G, De Swardt DH, Nuttall RJ, Crowe TM, Bowie RCK. Phenotypic and genotypic variation across a stable white-eye (Zosterops sp.) hybrid zone in central South Africa. Biol J Linn Soc Lond 2017. [DOI: 10.1093/biolinnean/blx012] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
|
58
|
Anderson BM, Thiele KR, Krauss SL, Barrett MD. Genotyping-by-Sequencing in a Species Complex of Australian Hummock Grasses (Triodia): Methodological Insights and Phylogenetic Resolution. PLoS One 2017; 12:e0171053. [PMID: 28135342 PMCID: PMC5279811 DOI: 10.1371/journal.pone.0171053] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 01/13/2017] [Indexed: 12/16/2022] Open
Abstract
Next-generation sequencing is becoming increasingly accessible to researchers asking biosystematic questions, but current best practice in both choosing a specific approach and effectively analysing the resulting data set is still being explored. We present a case study for the use of genotyping-by-sequencing (GBS) to resolve relationships in a species complex of Australian arid and semi-arid grasses (Triodia R.Br.), highlighting our solutions to methodological challenges in the use of GBS data. We merged overlapping paired-end reads then optimised locus assembly in the program PyRAD to generate GBS data sets for phylogenetic and distance-based analyses. In addition to traditional concatenation analyses in RAxML, we also demonstrate the novel use of summary species tree analyses (taking gene trees as input) with GBS loci. We found that while species tree analyses were relatively robust to variation in PyRAD assembly parameters, our RAxML analyses resulted in well-supported but conflicting topologies under different assembly settings. Despite this conflict, multiple clades in the complex were consistently supported as distinct across analyses. Our GBS data assembly and analyses improve the resolution of taxa and phylogenetic relationships in the Triodia basedowii complex compared to our previous study based on Sanger sequencing of nuclear (ITS/ETS) and chloroplast (rps16-trnK spacer) markers. The genomic results also partly support previous evidence for hybridization between species in the complex. Our methodological insights for analysing GBS data will assist researchers using similar data to resolve phylogenetic relationships within species complexes.
Collapse
Affiliation(s)
- Benjamin M. Anderson
- School of Plant Biology, The University of Western Australia, Crawley, Western Australia, Australia
- Kings Park and Botanic Garden, Botanic Gardens and Parks Authority, Kings Park, Western Australia, Australia
| | - Kevin R. Thiele
- School of Plant Biology, The University of Western Australia, Crawley, Western Australia, Australia
- Western Australian Herbarium, Department of Parks and Wildlife, Kensington, Western Australia, Australia
| | - Siegfried L. Krauss
- School of Plant Biology, The University of Western Australia, Crawley, Western Australia, Australia
- Kings Park and Botanic Garden, Botanic Gardens and Parks Authority, Kings Park, Western Australia, Australia
| | - Matthew D. Barrett
- School of Plant Biology, The University of Western Australia, Crawley, Western Australia, Australia
- Kings Park and Botanic Garden, Botanic Gardens and Parks Authority, Kings Park, Western Australia, Australia
| |
Collapse
|
59
|
Shedding Light on the Grey Zone of Speciation along a Continuum of Genomic Divergence. PLoS Biol 2016; 14:e2000234. [PMID: 28027292 PMCID: PMC5189939 DOI: 10.1371/journal.pbio.2000234] [Citation(s) in RCA: 254] [Impact Index Per Article: 31.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 11/21/2016] [Indexed: 12/24/2022] Open
Abstract
Speciation results from the progressive accumulation of mutations that decrease the probability of mating between parental populations or reduce the fitness of hybrids—the so-called species barriers. The speciation genomic literature, however, is mainly a collection of case studies, each with its own approach and specificities, such that a global view of the gradual process of evolution from one to two species is currently lacking. Of primary importance is the prevalence of gene flow between diverging entities, which is central in most species concepts and has been widely discussed in recent years. Here, we explore the continuum of speciation thanks to a comparative analysis of genomic data from 61 pairs of populations/species of animals with variable levels of divergence. Gene flow between diverging gene pools is assessed under an approximate Bayesian computation (ABC) framework. We show that the intermediate "grey zone" of speciation, in which taxonomy is often controversial, spans from 0.5% to 2% of net synonymous divergence, irrespective of species life history traits or ecology. Thanks to appropriate modeling of among-locus variation in genetic drift and introgression rate, we clarify the status of the majority of ambiguous cases and uncover a number of cryptic species. Our analysis also reveals the high incidence in animals of semi-isolated species (when some but not all loci are affected by barriers to gene flow) and highlights the intrinsic difficulty, both statistical and conceptual, of delineating species in the grey zone of speciation. Isolated populations accumulate genetic differences across their genomes as they diverge, whereas gene flow between populations counteracts divergence and tends to restore genetic homogeneity. Speciation proceeds by the accumulation at specific loci of mutations that reduce the fitness of hybrids, therefore preventing gene flow—the so-called species barriers. Importantly, species barriers are expected to act locally within the genome, leading to the prediction of a mosaic pattern of genetic differentiation between populations at intermediate levels of divergence—the genic view of speciation. At the same time, linked selection also contributes to speed up differentiation in low-recombining and gene-dense regions. We used a modelling approach that accounts for both sources of genomic heterogeneity and explored a wide continuum of genomic divergence made by 61 pairs of species/populations in animals. Our analysis provides a unifying picture of the relationship between molecular divergence and ability to exchange genes. We show that the "grey zone" of speciation—the intermediate state in which species definition is controversial—spans from 0.5% to 2% of molecular divergence, with these thresholds being independent of species life history traits and ecology. Semi-isolated species, between which alleles can be exchanged at some but not all loci, are numerous, with the earliest species barriers being detected at divergences as low as 0.075%. These results have important implications regarding taxonomy, conservation biology, and the management of biodiversity.
Collapse
|
60
|
Friis G, Aleixandre P, Rodríguez-Estrella R, Navarro-Sigüenza AG, Milá B. Rapid postglacial diversification and long-term stasis within the songbird genus Junco: phylogeographic and phylogenomic evidence. Mol Ecol 2016; 25:6175-6195. [PMID: 27862578 DOI: 10.1111/mec.13911] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Revised: 09/01/2016] [Accepted: 11/02/2016] [Indexed: 01/04/2023]
Abstract
Natural systems composed of closely related taxa that vary in the degree of phenotypic divergence and geographic isolation provide an opportunity to investigate the rate of phenotypic diversification and the relative roles of selection and drift in driving lineage formation. The genus Junco (Aves: Emberizidae) of North America includes parapatric northern forms that are markedly divergent in plumage pattern and colour, in contrast to geographically isolated southern populations in remote areas that show moderate phenotypic divergence. Here, we quantify patterns of phenotypic divergence in morphology and plumage colour and use mitochondrial DNA genes, a nuclear intron, and genomewide SNPs to reconstruct the demographic and evolutionary history of the genus to infer relative rates of evolutionary divergence among lineages. We found that geographically isolated populations have evolved independently for hundreds of thousands of years despite little differentiation in phenotype, in sharp contrast to phenotypically diverse northern forms, which have diversified within the last few thousand years as a result of the rapid postglacial recolonization of North America. SNP data resolved young northern lineages into reciprocally monophyletic lineages, indicating low rates of gene flow even among closely related parapatric forms, and suggesting a role for strong genetic drift or multifarious selection acting on multiple loci in driving lineage divergence. Juncos represent a compelling example of speciation in action, where the combined effects of historical and selective factors have produced one of the fastest cases of speciation known in vertebrates.
Collapse
Affiliation(s)
- Guillermo Friis
- National Museum of Natural Sciences, Spanish National Research Council (CSIC), Madrid, 28006, Spain
| | - Pau Aleixandre
- National Museum of Natural Sciences, Spanish National Research Council (CSIC), Madrid, 28006, Spain
| | | | - Adolfo G Navarro-Sigüenza
- Museo de Zoología, Facultad de Ciencias, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | - Borja Milá
- National Museum of Natural Sciences, Spanish National Research Council (CSIC), Madrid, 28006, Spain
| |
Collapse
|
61
|
Baldassarre DT, Greig EI, Webster MS. The couple that sings together stays together: duetting, aggression and extra-pair paternity in a promiscuous bird species. Biol Lett 2016; 12:20151025. [PMID: 26911342 DOI: 10.1098/rsbl.2015.1025] [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] [Indexed: 11/12/2022] Open
Abstract
When individuals mate outside the pair bond, males should employ behaviours such as aggression or vocal displays (e.g. duetting) that help assure paternity of the offspring they care for. We tested whether male paternity was associated with aggression or duetting in the red-backed fairy-wren, a species exhibiting high rates of extra-pair paternity. During simulated territorial intrusions, aggression and duetting were variable among and repeatable within males, suggesting behavioural consistency of individuals. Males with quicker and stronger duet responses were cuckolded less often than males with slower and weaker responses. In contrast, physical aggression was not correlated with male paternity. These results suggest that either acoustic mate guarding or male-female vocal negotiations via duetting lead to increased paternity assurance, whereas physical aggression does not.
Collapse
Affiliation(s)
- Daniel T Baldassarre
- Cornell Lab of Ornithology, Cornell University, Ithaca, NY 14850, USA Department of Neurobiology and Behavior, Cornell University, Ithaca, NY 14850, USA
| | - Emma I Greig
- Cornell Lab of Ornithology, Cornell University, Ithaca, NY 14850, USA
| | - Michael S Webster
- Cornell Lab of Ornithology, Cornell University, Ithaca, NY 14850, USA Department of Neurobiology and Behavior, Cornell University, Ithaca, NY 14850, USA
| |
Collapse
|
62
|
Safran RJ, Scordato ESC, Wilkins MR, Hubbard JK, Jenkins BR, Albrecht T, Flaxman SM, Karaardıç H, Vortman Y, Lotem A, Nosil P, Pap P, Shen S, Chan S, Parchman T, Kane NC. Genome‐wide differentiation in closely related populations: the roles of selection and geographic isolation. Mol Ecol 2016; 25:3865-83. [DOI: 10.1111/mec.13740] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 06/08/2016] [Accepted: 06/15/2016] [Indexed: 12/19/2022]
Affiliation(s)
- R. J. Safran
- Department of Ecology and Evolutionary Biology University of Colorado Boulder CO USA
| | - E. S. C. Scordato
- Department of Ecology and Evolutionary Biology University of Colorado Boulder CO USA
| | - M. R. Wilkins
- Department of Ecology and Evolutionary Biology University of Colorado Boulder CO USA
- School of Biological Sciences University of Nebraska‐Lincoln Lincoln NE USA
| | - J. K. Hubbard
- Department of Ecology and Evolutionary Biology University of Colorado Boulder CO USA
- School of Biological Sciences University of Nebraska‐Lincoln Lincoln NE USA
| | - B. R. Jenkins
- Department of Ecology and Evolutionary Biology University of Colorado Boulder CO USA
| | - T. Albrecht
- Department of Zoology Charles University in Prague and Institute of Vertebrate Biology Academy of Sciences of the Czech Republic Prague Czech Republic
| | - S. M. Flaxman
- Department of Ecology and Evolutionary Biology University of Colorado Boulder CO USA
| | - H. Karaardıç
- Elementary Science Education Department Education Faculty Alanya Alaaddin Keykubat University Alanya Turkey
| | - Y. Vortman
- Department of Zoology Tel‐Aviv University Tel‐Aviv Israel
- Hula Research Center Department of Animal Sciences Tel‐Hai College Israel
| | - A. Lotem
- Department of Zoology Tel‐Aviv University Tel‐Aviv Israel
| | - P. Nosil
- Department of Animal and Plant Sciences University of Sheffield Sheffield UK
| | - P. Pap
- Department of Taxonomy and Ecology Babeş‐Bolyai University Cluj‐Napoca Romania
| | - S. Shen
- Biodiversity Research Center Academia Sinica Taipei Taiwan
| | - S.‐F. Chan
- Biodiversity Research Center Academia Sinica Taipei Taiwan
| | - T.L. Parchman
- Department of Biology University of Nevada Reno NV USA
| | - N. C. Kane
- Department of Ecology and Evolutionary Biology University of Colorado Boulder CO USA
| |
Collapse
|
63
|
Stankowski S, Sobel JM, Streisfeld MA. Geographic cline analysis as a tool for studying genome‐wide variation: a case study of pollinator‐mediated divergence in a monkeyflower. Mol Ecol 2016; 26:107-122. [DOI: 10.1111/mec.13645] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 04/07/2016] [Accepted: 04/08/2016] [Indexed: 01/04/2023]
Affiliation(s)
- Sean Stankowski
- Institute of Ecology and Evolution 335 Pacific Hall 5289 University of Oregon, Eugene OR 97403‐5289 USA
| | - James M. Sobel
- Department of Biological Sciences Binghamton University PO Box 6000, Binghamton NY 13902 USA
| | - Matthew A. Streisfeld
- Institute of Ecology and Evolution 335 Pacific Hall 5289 University of Oregon, Eugene OR 97403‐5289 USA
| |
Collapse
|
64
|
Greenberg R, Cammen KM, Wilson AG, Olsen BJ, Ballentine B, McInerney NC, Fleischer RC. Geographic population structure and subspecific boundaries in a tidal marsh sparrow. CONSERV GENET 2016. [DOI: 10.1007/s10592-016-0809-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
65
|
Walsh J, Shriver WG, Olsen BJ, Kovach AI. Differential introgression and the maintenance of species boundaries in an advanced generation avian hybrid zone. BMC Evol Biol 2016; 16:65. [PMID: 27000833 PMCID: PMC4802838 DOI: 10.1186/s12862-016-0635-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 03/10/2016] [Indexed: 12/31/2022] Open
Abstract
Background Evolutionary processes, including selection and differential fitness, shape the introgression of genetic material across a hybrid zone, resulting in the exchange of some genes but not others. Differential introgression of molecular or phenotypic markers can thus provide insight into factors contributing to reproductive isolation. We characterized patterns of genetic variation across a hybrid zone between two tidal marsh birds, Saltmarsh (Ammodramus caudacutus) and Nelson’s (A. nelsoni) sparrows (n = 286), and compared patterns of introgression among multiple genetic markers and phenotypic traits. Results Geographic and genomic cline analyses revealed variable patterns of introgression among marker types. Most markers exhibited gradual clines and indicated that introgression exceeds the spatial extent of the previously documented hybrid zone. We found steeper clines, indicating strong selection for loci associated with traits related to tidal marsh adaptations, including for a marker linked to a gene region associated with metabolic functions, including an osmotic regulatory pathway, as well as for a marker related to melanin-based pigmentation, supporting an adaptive role of darker plumage (salt marsh melanism) in tidal marshes. Narrow clines at mitochondrial and sex-linked markers also offer support for Haldane’s rule. We detected patterns of asymmetrical introgression toward A. caudacutus, which may be driven by differences in mating strategy or differences in population density between the two species. Conclusions Our findings offer insight into the dynamics of a hybrid zone traversing a unique environmental gradient and provide evidence for a role of ecological divergence in the maintenance of pure species boundaries despite ongoing gene flow. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0635-y) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Jennifer Walsh
- Department of Natural Resources and the Environment, University of New Hampshire, Durham, NH, USA. .,Cornell Lab of Ornithology, Cornell University, Ithaca, NY, USA.
| | - W Gregory Shriver
- Department of Entomology and Wildlife Ecology, University of Delaware, Newark, DE, USA
| | - Brian J Olsen
- School of Biology and Ecology, University of Maine, Orono, ME, USA
| | - Adrienne I Kovach
- Department of Natural Resources and the Environment, University of New Hampshire, Durham, NH, USA
| |
Collapse
|
66
|
Mao X, Zhang S, Rossiter SJ. Differential introgression suggests candidate beneficial and barrier loci between two parapatric subspecies of Pearson's horseshoe bat Rhinolophus pearsoni. Curr Zool 2016; 62:405-412. [PMID: 29491929 PMCID: PMC5829442 DOI: 10.1093/cz/zow017] [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: 09/07/2015] [Accepted: 10/05/2015] [Indexed: 11/13/2022] Open
Abstract
Observations that rates of introgression between taxa can vary across loci are
increasingly common. Here, we test for differential locus-wise introgression in 2
parapatric subspecies of Pearson′s horseshoe bat (Rhinolophus pearsoni
chinensis and R. p. pearsoni). To efficiently identify
putative speciation genes and/or beneficial genes in our current system, we used a
candidate gene approach by including loci from X chromosome that are suggested to be more
likely involved in reproductive isolation in other organisms and loci underlying hearing
that have been suggested to spread across the hybrid zone in another congeneric species.
Phylogenetic and coalescent analyses were performed at 2 X-linked, 4 hearing genes, as
well as 2 other autosomal loci individually. Likelihood ratio tests could not reject the
model of zero gene flow at 2 X-linked and 2 autosomal genes. In contrast, gene flow was
supported at 3 of 4 hearing genes. While this introgression could be adaptive, we cannot
rule out stochastic processes. Our results highlight the utility of the candidate gene
approach in searching for speciation genes and/or beneficial genes across the species
boundary in natural populations.
Collapse
Affiliation(s)
- Xiuguang Mao
- Institute of Estuarine and Coastal Research, East China Normal University, Shanghai 200062, China and.,School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK
| | - Shuyi Zhang
- Institute of Estuarine and Coastal Research, East China Normal University, Shanghai 200062, China and
| | - Stephen J Rossiter
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK
| |
Collapse
|
67
|
Sardell JM, Uy JAC. Hybridization following recent secondary contact results in asymmetric genotypic and phenotypic introgression between island species ofMyzomelahoneyeaters. Evolution 2016; 70:257-69. [DOI: 10.1111/evo.12864] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Accepted: 12/22/2015] [Indexed: 01/21/2023]
Affiliation(s)
- Jason M. Sardell
- Department of Biology; University of Miami; Coral Gables Florida 33146
| | - J. Albert C. Uy
- Department of Biology; University of Miami; Coral Gables Florida 33146
| |
Collapse
|
68
|
Grant PR, Grant BR. Introgressive hybridization and natural selection in Darwin's finches. Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12702] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Peter R. Grant
- Department of Ecology and Evolutionary Biology; Princeton University; Princeton NJ 08544-1003 USA
| | - B. Rosemary Grant
- Department of Ecology and Evolutionary Biology; Princeton University; Princeton NJ 08544-1003 USA
| |
Collapse
|
69
|
While GM, Michaelides S, Heathcote RJP, MacGregor HEA, Zajac N, Beninde J, Carazo P, Pérez i de Lanuza G, Sacchi R, Zuffi MA, Horváthová T, Fresnillo B, Schulte U, Veith M, Hochkirch A, Uller T. Sexual selection drives asymmetric introgression in wall lizards. Ecol Lett 2015; 18:1366-75. [DOI: 10.1111/ele.12531] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Revised: 06/26/2015] [Accepted: 09/09/2015] [Indexed: 01/21/2023]
Affiliation(s)
- Geoffrey M. While
- Department of Zoology; Edward Grey Institute; University of Oxford; Oxford UK
- School of Biological Sciences; University of Tasmania; Hobart Tasmania Australia
| | - Sozos Michaelides
- Department of Zoology; Edward Grey Institute; University of Oxford; Oxford UK
| | - Robert J. P. Heathcote
- Department of Zoology; Edward Grey Institute; University of Oxford; Oxford UK
- Centre for Research in Animal Behaviour; College of Life and Environmental Sciences; University of Exeter; Exeter UK
| | - Hannah E. A. MacGregor
- Department of Zoology; Edward Grey Institute; University of Oxford; Oxford UK
- School of Biological Sciences; University of Tasmania; Hobart Tasmania Australia
| | - Natalia Zajac
- Department of Zoology; Edward Grey Institute; University of Oxford; Oxford UK
| | - Joscha Beninde
- Department of Biogeography; Trier University; Trier Germany
| | - Pau Carazo
- Department of Zoology; Edward Grey Institute; University of Oxford; Oxford UK
- Cavanilles Institute of Biodiversity and Evolutionary Biology; University of Valencia; Valencia Spain
| | - Guillem Pérez i de Lanuza
- CIBIO Research Centre in Biodiversity and Genetic Resources; Universidade do Porto; Vairão, Vila do Conde Porto Portugal
| | - Roberto Sacchi
- Department of Earth and Environmental Sciences; University of Pavia; Pavia Italy
| | | | - Terézia Horváthová
- Department of Zoology; Edward Grey Institute; University of Oxford; Oxford UK
- Institute of Environmental Sciences; Jagiellonian University; Kraków Poland
| | - Belén Fresnillo
- Department of Zoology; Edward Grey Institute; University of Oxford; Oxford UK
- Department of Life Sciences; University of Alcalá; Alcalá Spain
| | - Ulrich Schulte
- Federal Agency for Nature Conservation (BfN); Bonn Germany
| | - Michael Veith
- Department of Biogeography; Trier University; Trier Germany
| | - Axel Hochkirch
- Department of Biogeography; Trier University; Trier Germany
| | - Tobias Uller
- Department of Zoology; Edward Grey Institute; University of Oxford; Oxford UK
- Department of Biology; Lund University; Lund Sweden
| |
Collapse
|
70
|
Greig EI, Baldassarre DT, Webster MS. Differential rates of phenotypic introgression are associated with male behavioral responses to multiple signals. Evolution 2015; 69:2602-12. [PMID: 26292844 DOI: 10.1111/evo.12756] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Revised: 08/04/2015] [Accepted: 08/12/2015] [Indexed: 12/26/2022]
Abstract
Sexual selection on multiple signals may lead to differential rates of signal introgression across hybrid zones if some signals contribute to reproductive isolation but others facilitate gene flow. Competition among males is one powerful form of sexual selection, but male behavioral responses to multiple traits have not been considered in a system where traits have introgressed differentially. Using playbacks, mounts, and a reciprocal experimental design, we tested the hypothesis that male responses to song and plumage in two subspecies of red-backed fairy-wren (Malurus melanocephalus) explain patterns of differential signal introgression (song has not introgressed, whereas plumage color has introgressed asymmetrically). We found that males of both subspecies discriminated symmetrically between subspecies' songs at a long range, but at a close range, we found that aggression was equal for both subspecies' plumage and songs. Taken together, our results suggest that male behavioral responses hinder the introgression of song, but allow for the observed asymmetrical introgression of plumage. Our results highlight how behavioral responses are a key component of signal evolution when recently divergent taxa come together, and how differential responses to multiple signals may lead to differential signal introgression and novel trait combinations.
Collapse
Affiliation(s)
- Emma I Greig
- Cornell Laboratory of Ornithology, Department of Neurobiology and Behavior, Cornell University, Ithaca, New York, 14850.
| | - Daniel T Baldassarre
- Cornell Laboratory of Ornithology, Department of Neurobiology and Behavior, Cornell University, Ithaca, New York, 14850.,Department of Biology, University of Miami, Coral Gables, Florida, 33146
| | - Michael S Webster
- Cornell Laboratory of Ornithology, Department of Neurobiology and Behavior, Cornell University, Ithaca, New York, 14850
| |
Collapse
|
71
|
Weir JT, Faccio MS, Pulido-Santacruz P, Barrera-Guzmán AO, Aleixo A. Hybridization in headwater regions, and the role of rivers as drivers of speciation in Amazonian birds. Evolution 2015; 69:1823-34. [DOI: 10.1111/evo.12696] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Revised: 04/29/2015] [Accepted: 04/29/2015] [Indexed: 01/19/2023]
Affiliation(s)
- Jason T. Weir
- Department of Biological Sciences; University of Toronto Scarborough; Toronto Canada
- Department of Ecology and Evolutionary Biology; University of Toronto; Toronto Canada
| | - Maya S. Faccio
- Department of Ecology and Evolutionary Biology; University of Toronto; Toronto Canada
| | | | | | - Alexandre Aleixo
- Department of Zoology; Museu Paraense Emílio Goeldi; Belém Brazil
| |
Collapse
|