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Aguillon SM, Haase Cox SK, Langdon QK, Gunn TR, Baczenas JJ, Banerjee SM, Donny AE, Moran BM, Gutiérrez-Rodríguez C, Ríos-Cárdenas O, Morris MR, Powell DL, Schumer M. Pervasive gene flow despite strong and varied reproductive barriers in swordtails. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.16.589374. [PMID: 38659793 PMCID: PMC11042374 DOI: 10.1101/2024.04.16.589374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
One of the mechanisms that can lead to the formation of new species occurs through the evolution of reproductive barriers. However, recent research has demonstrated that hybridization has been pervasive across the tree of life even in the presence of strong barriers. Swordtail fishes (genus Xiphophorus) are an emerging model system for studying the interface between these barriers and hybridization. We document overlapping mechanisms that act as barriers between closely related species, X. birchmanni and X. cortezi, by combining genomic sequencing from natural hybrid populations, artificial crosses, behavioral assays, sperm performance, and developmental studies. We show that strong assortative mating plays a key role in maintaining subpopulations with distinct ancestry in natural hybrid populations. Lab experiments demonstrate that artificial F1 crosses experience dysfunction: crosses with X. birchmanni females were largely inviable and crosses with X. cortezi females had a heavily skewed sex ratio. Using F2 hybrids we identify several genomic regions that strongly impact hybrid viability. Strikingly, two of these regions underlie genetic incompatibilities in hybrids between X. birchmanni and its sister species X. malinche. Our results demonstrate that ancient hybridization has played a role in the origin of this shared genetic incompatibility. Moreover, ancestry mismatch at these incompatible regions has remarkably similar consequences for phenotypes and hybrid survival in X. cortezi × X. birchmanni hybrids as in X. malinche × X. birchmanni hybrids. Our findings identify varied reproductive barriers that shape genetic exchange between naturally hybridizing species and highlight the complex evolutionary outcomes of hybridization.
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Affiliation(s)
- Stepfanie M. Aguillon
- Department of Biology, Stanford University, Stanford, CA, USA
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca”, A.C., Calnali, Hidalgo, México
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, USA
| | | | - Quinn K. Langdon
- Department of Biology, Stanford University, Stanford, CA, USA
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca”, A.C., Calnali, Hidalgo, México
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA, USA
| | - Theresa R. Gunn
- Department of Biology, Stanford University, Stanford, CA, USA
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca”, A.C., Calnali, Hidalgo, México
| | | | - Shreya M. Banerjee
- Department of Biology, Stanford University, Stanford, CA, USA
- Center for Population Biology, University of California, Davis, Davis, CA, USA
| | | | - Benjamin M. Moran
- Department of Biology, Stanford University, Stanford, CA, USA
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca”, A.C., Calnali, Hidalgo, México
| | | | - Oscar Ríos-Cárdenas
- Red de Biología Evolutiva, Instituto de Ecología A.C., Xalapa, Veracruz, México
| | - Molly R. Morris
- Department of Biological Sciences, Ohio University, Athens, Ohio, USA
| | - Daniel L. Powell
- Department of Biology, Stanford University, Stanford, CA, USA
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca”, A.C., Calnali, Hidalgo, México
| | - Molly Schumer
- Department of Biology, Stanford University, Stanford, CA, USA
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca”, A.C., Calnali, Hidalgo, México
- Freeman Hrabowski Fellow, Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
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Thawornwattana Y, Seixas FA, Yang Z, Mallet J. OUP accepted manuscript. Syst Biol 2022; 71:1159-1177. [PMID: 35169847 PMCID: PMC9366460 DOI: 10.1093/sysbio/syac009] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 02/01/2022] [Accepted: 02/08/2022] [Indexed: 11/21/2022] Open
Abstract
Introgressive hybridization plays a key role in adaptive evolution and species diversification in many groups of species. However, frequent hybridization and gene flow between species make estimation of the species phylogeny and key population parameters challenging. Here, we show that by accounting for phasing and using full-likelihood methods, introgression histories and population parameters can be estimated reliably from whole-genome sequence data. We employ the multispecies coalescent (MSC) model with and without gene flow to infer the species phylogeny and cross-species introgression events using genomic data from six members of the erato-sara clade of Heliconius butterflies. The methods naturally accommodate random fluctuations in genealogical history across the genome due to deep coalescence. To avoid heterozygote phasing errors in haploid sequences commonly produced by genome assembly methods, we process and compile unphased diploid sequence alignments and use analytical methods to average over uncertainties in heterozygote phase resolution. There is robust evidence for introgression across the genome, both among distantly related species deep in the phylogeny and between sister species in shallow parts of the tree. We obtain chromosome-specific estimates of key population parameters such as introgression directions, times and probabilities, as well as species divergence times and population sizes for modern and ancestral species. We confirm ancestral gene flow between the sara clade and an ancestral population of Heliconius telesiphe, a likely hybrid speciation origin for Heliconius hecalesia, and gene flow between the sister species Heliconius erato and Heliconius himera. Inferred introgression among ancestral species also explains the history of two chromosomal inversions deep in the phylogeny of the group. This study illustrates how a full-likelihood approach based on the MSC makes it possible to extract rich historical information of species divergence and gene flow from genomic data. [3s; bpp; gene flow; Heliconius; hybrid speciation; introgression; inversion; multispecies coalescent]
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Affiliation(s)
- Yuttapong Thawornwattana
- Correspondence to be sent to: Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; E-mail: ; (Y.T. and J.M.); Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK; E-mail: (Z.Y.)
| | - Fernando A Seixas
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Ziheng Yang
- Correspondence to be sent to: Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; E-mail: ; (Y.T. and J.M.); Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK; E-mail: (Z.Y.)
| | - James Mallet
- Correspondence to be sent to: Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; E-mail: ; (Y.T. and J.M.); Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK; E-mail: (Z.Y.)
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Identification of Natural Hybrids between Ahlbergia frivaldszkyi (Lederer, 1853) and Callophrys rubi (Linnaeus, 1758) (Lepidoptera, Lycaenidae) Using Mitochondrial and Nuclear Markers. INSECTS 2021; 12:insects12121124. [PMID: 34940212 PMCID: PMC8706498 DOI: 10.3390/insects12121124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Revised: 12/10/2021] [Accepted: 12/14/2021] [Indexed: 11/22/2022]
Abstract
Simple Summary Butterfly specimens with unusual morphological characters (e.g., unusual wing coloration) have contradictory interpretations in the literature and have been considered by different authors either as previously undescribed taxa, putative hybrids, or aberrations of well-known species. Such individuals clearly represent a taxonomic problem that needs to be addressed by scientists. The application of molecular techniques could shed light on the origin of morphological uncertainty. Here we use a combination of mitochondrial and nuclear DNA markers to analyze three lycaenid butterflies with unusual wing pattern, which are thought to represent naturally occurring hybrids due to their intermediate phenotype. We confirm their hybrid origin and indicate that the specimens are wild-caught hybrids between females of Callophrys rubi and males of Ahlbergia frivaldszkyi. Our data indicate that gene flow across species boundaries in these butterflies can occur long after speciation. Abstract Natural hybridization is rather widespread and common in animals and can have important evolutionary consequences. In terms of taxonomy, exploring hybridization and introgression is crucial in defining species boundaries and testing taxonomic hypotheses. In the present paper, we report on natural hybrid specimens between Ahlbergia frivaldszkyi (Lederer, 1853) and Callophrys rubi (Linnaeus, 1758). To test the hypothesis of their hybrid origin, we employed the molecular mitochondrial (COI gene) and nuclear (wingless, RPS5, and Ca-ATPase genes) markers commonly used in phylogenetic studies and explored the morphology of the specimens. Our analysis revealed that hybrids bear mitochondrial haplotypes of C. rubi, while nuclear fragments are heterozygous, sharing a combination of A. frivaldszkyi and C. rubi lineages. The hybrid specimens combine morphological characters of both genera. Our results for the first time empirically demonstrate the possibility of genetic introgression between these species and between the genera Callophrys and Ahlbergia on the whole.
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Neural divergence and hybrid disruption between ecologically isolated Heliconius butterflies. Proc Natl Acad Sci U S A 2021; 118:2015102118. [PMID: 33547240 DOI: 10.1073/pnas.2015102118] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The importance of behavioral evolution during speciation is well established, but we know little about how this is manifest in sensory and neural systems. A handful of studies have linked specific neural changes to divergence in host or mate preferences associated with speciation. However, the degree to which brains are adapted to local environmental conditions, and whether this contributes to reproductive isolation between close relatives that have diverged in ecology, remains unknown. Here, we examine divergence in brain morphology and neural gene expression between closely related, but ecologically distinct, Heliconius butterflies. Despite ongoing gene flow, sympatric species pairs within the melpomene-cydno complex are consistently separated across a gradient of open to closed forest and decreasing light intensity. By generating quantitative neuroanatomical data for 107 butterflies, we show that Heliconius melpomene and Heliconius cydno clades have substantial shifts in brain morphology across their geographic range, with divergent structures clustered in the visual system. These neuroanatomical differences are mirrored by extensive divergence in neural gene expression. Differences in both neural morphology and gene expression are heritable, exceed expected rates of neutral divergence, and result in intermediate traits in first-generation hybrid offspring. Strong evidence of divergent selection implies local adaptation to distinct selective optima in each parental microhabitat, suggesting the intermediate traits of hybrids are poorly matched to either condition. Neural traits may therefore contribute to coincident barriers to gene flow, thereby helping to facilitate speciation.
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5
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Jiao X, Yang Z. Defining Species When There is Gene Flow. Syst Biol 2020; 70:108-119. [PMID: 32617579 DOI: 10.1093/sysbio/syaa052] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 06/23/2020] [Accepted: 06/23/2020] [Indexed: 12/20/2022] Open
Abstract
Whatever one's definition of species, it is generally expected that individuals of the same species should be genetically more similar to each other than they are to individuals of another species. Here, we show that in the presence of cross-species gene flow, this expectation may be incorrect. We use the multispecies coalescent model with continuous-time migration or episodic introgression to study the impact of gene flow on genetic differences within and between species and highlight a surprising but plausible scenario in which different population sizes and asymmetrical migration rates cause a genetic sequence to be on average more closely related to a sequence from another species than to a sequence from the same species. Our results highlight the extraordinary impact that even a small amount of gene flow may have on the genetic history of the species. We suggest that contrasting long-term migration rate and short-term hybridization rate, both of which can be estimated using genetic data, may be a powerful approach to detecting the presence of reproductive barriers and to define species boundaries.[Gene flow; introgression; migration; multispecies coalescent; species concept; species delimitation.].
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Affiliation(s)
- Xiyun Jiao
- Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | - Ziheng Yang
- Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK
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6
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Abstract
Introgressive hybridization can affect the evolution of populations in several important ways. It may retard or reverse divergence of species, enable the development of novel traits, enhance the potential for future evolution by elevating levels of standing variation, create new species, and alleviate inbreeding depression in small populations. Most of what is known of contemporary hybridization in nature comes from the study of pairs of species, either coexisting in the same habitat or distributed parapatrically and separated by a hybrid zone. More rarely, three species form an interbreeding complex (triad), reported in vertebrates, insects, and plants. Often, one species acts as a genetic link or conduit for the passage of genes (alleles) between two others that rarely, if ever, hybridize. Demographic and genetic consequences are unknown. Here we report results of a long-term study of interbreeding Darwin's finches on Daphne Major island, Galápagos. Geospiza fortis acted as a conduit for the passage of genes between two others that have never been observed to interbreed on Daphne: Geospiza fuliginosa, a rare immigrant, and Geospiza scandens, a resident. Microsatellite gene flow from G. fortis into G. scandens increased in frequency during 30 y of favorable ecological conditions, resulting in genetic and morphological convergence. G. fortis, G. scandens, and the derived dihybrids and trihybrids experienced approximately equal fitness. Especially relevant to young adaptive radiations, where species differ principally in ecology and behavior, these findings illustrate how new combinations of genes created by hybridization among three species can enhance the potential for evolutionary change.
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Wegener JE, Pita‐Aquino JN, Atutubo J, Moreno A, Kolbe JJ. Hybridization and rapid differentiation after secondary contact between the native green anole ( Anolis carolinensis) and the introduced green anole ( Anolis porcatus). Ecol Evol 2019; 9:4138-4148. [PMID: 31015994 PMCID: PMC6468060 DOI: 10.1002/ece3.5042] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 02/06/2019] [Accepted: 02/12/2019] [Indexed: 11/24/2022] Open
Abstract
In allopatric species, reproductive isolation evolves through the accumulation of genetic incompatibilities. The degree of divergence required for complete reproductive isolation is highly variable across taxa, which makes the outcome of secondary contact between allopatric species unpredictable. Since before the Pliocene, two species of Anolis lizards, Anolis carolinensis and Anolis porcatus, have been allopatric, yet this period of independent evolution has not led to substantial species-specific morphological differentiation, and therefore, they might not be reproductively isolated. In this study, we determined the genetic consequences of localized, secondary contact between the native green anole, A. carolinensis, and the introduced Cuban green anole, A. porcatus, in South Miami. Using 18 microsatellite markers, we found that the South Miami population formed a genetic cluster distinct from both parental species. Mitochondrial DNA revealed maternal A. porcatus ancestry for 35% of the individuals sampled from this population, indicating a high degree of cytonuclear discordance. Thus, hybridization with A. porcatus, not just population structure within A. carolinensis, may be responsible for the genetic distinctiveness of this population. Using tree-based maximum-likelihood analysis, we found support for a more recent, secondary introduction of A. porcatus to Florida. Evidence that ~33% of the nuclear DNA resulted from a secondary introduction supports the hybrid origin of the green anole population in South Miami. We used multiple lines of evidence and multiple genetic markers to reconstruct otherwise cryptic patterns of species introduction and hybridization. Genetic evidence for a lack of reproductive isolation, as well as morphological similarities between the two species, supports revising the taxonomy of A. carolinensis to include A. porcatus from western Cuba. Future studies should target the current geographic extent of introgression originating from the past injection of genetic material from Cuban green anoles and determine the consequences for the evolutionary trajectory of green anole populations in southern Florida.
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Affiliation(s)
- Johanna E. Wegener
- Department of Biological SciencesUniversity of Rhode IslandKingstonRhode Island
| | | | - Jessica Atutubo
- Department of Biological SciencesUniversity of Rhode IslandKingstonRhode Island
| | - Adam Moreno
- Department of Ecology and Evolutionary BiologyBrown UniversityProvidenceRhode Island
- Present address:
College of Veterinary MedicineOhio State UniversityColumbusOhio
| | - Jason J. Kolbe
- Department of Biological SciencesUniversity of Rhode IslandKingstonRhode Island
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8
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Southcott L, Kronforst MR. Female mate choice is a reproductive isolating barrier in Heliconius butterflies. Ethology 2018; 124:862-869. [PMID: 31024190 PMCID: PMC6475913 DOI: 10.1111/eth.12818] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 09/26/2018] [Indexed: 12/11/2022]
Abstract
In sexually reproducing organisms, speciation involves the evolution of reproductive isolating mechanisms that decrease gene flow. Premating reproductive isolation, often the result of mate choice, is a major obstacle to gene flow between species because it acts earlier in the life cycle than other isolating barriers. While female choice is often considered the default mode in animal species, research in the butterfly genus Heliconius, a frequent subject of speciation studies, has focused on male mate choice. We studied mate choice by H. cydno females by pairing them with either conspecific males or males of the closely related species H. pachinus. Significantly more intraspecific trials than interspecific trials resulted in mating. Because male courtship rates did not differ between the species when we excluded males that never courted, we attribute this difference to female choice. Females also performed more acceptance behaviours towards conspecific males. Premating isolation between these two species thus entails both male and female mate choice, and female choice may be an important factor in the origin of Heliconius species.
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Affiliation(s)
- Laura Southcott
- Committee on Evolutionary Biology, University of Chicago, Chicago, IL
- Smithsonian Tropical Research Institute, Gamboa, Panama
| | - Marcus R Kronforst
- Committee on Evolutionary Biology, University of Chicago, Chicago, IL
- Department of Ecology and Evolution, University of Chicago, Chicago, IL
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Schilling MP, Mullen SP, Kronforst M, Safran RJ, Nosil P, Feder JL, Gompert Z, Flaxman SM. Transitions from Single- to Multi-Locus Processes during Speciation with Gene Flow. Genes (Basel) 2018; 9:E274. [PMID: 29795050 PMCID: PMC6027428 DOI: 10.3390/genes9060274] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 05/16/2018] [Accepted: 05/17/2018] [Indexed: 12/20/2022] Open
Abstract
During speciation-with-gene-flow, a transition from single-locus to multi-locus processes can occur, as strong coupling of multiple loci creates a barrier to gene flow. Testing predictions about such transitions with empirical data requires building upon past theoretical work and the continued development of quantitative approaches. We simulated genomes under several evolutionary scenarios of gene flow and divergent selection, extending previous work with the additions of neutral sites and coupling statistics. We used these simulations to investigate, in a preliminary way, if and how selected and neutral sites differ in the conditions they require for transitions during speciation. For the parameter combinations we explored, as the per-locus strength of selection grew and/or migration decreased, it became easier for selected sites to show divergence-and thus to rise in linkage disequilibrium (LD) with each other as a statistical consequence-farther in advance of the conditions under which neutral sites could diverge. Indeed, even very low rates of effective gene flow were sufficient to prevent differentiation at neutral sites. However, once strong enough, coupling among selected sites eventually reduced gene flow at neutral sites as well. To explore whether similar transitions might be detectable in empirical data, we used published genome resequencing data from three taxa of Heliconius butterflies. We found that fixation index ( F S T ) outliers and allele-frequency outliers exhibited stronger patterns of within-deme LD than the genomic background, as expected. The statistical characteristics of within-deme LD-likely indicative of the strength of coupling of barrier loci-varied between chromosomes and taxonomic comparisons. Qualitatively, the patterns we observed in the empirical data and in our simulations suggest that selection drives rapid genome-wide transitions to multi-locus coupling, illustrating how divergence and gene flow interact along the speciation continuum.
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Affiliation(s)
- Martin P Schilling
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309, USA.
| | - Sean P Mullen
- Department of Biology, Boston University, Boston, MA 02215, USA.
| | - Marcus Kronforst
- Department of Ecology & Evolution, University of Chicago, Chicago, IL 60637, USA.
| | - Rebecca J Safran
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309, USA.
| | - Patrik Nosil
- Department of Biology & Ecology Center, Utah State University, Logan, UT 84322, USA.
| | - Jeffrey L Feder
- Department of Biological Sciences, University of Notre Dame, South Bend, IN 46556, USA.
| | - Zachariah Gompert
- Department of Biology & Ecology Center, Utah State University, Logan, UT 84322, USA.
| | - Samuel M Flaxman
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309, USA.
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Jasso-Martínez JM, Machkour-M’Rabet S, Vila R, Rodríguez-Arnaiz R, Castañeda-Sortibrán AN. Molecular evidence of hybridization in sympatric populations of the Enantia jethys complex (Lepidoptera: Pieridae). PLoS One 2018; 13:e0197116. [PMID: 29771959 PMCID: PMC5957354 DOI: 10.1371/journal.pone.0197116] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 04/26/2018] [Indexed: 11/19/2022] Open
Abstract
Hybridization events are frequently demonstrated in natural butterfly populations. One interesting butterfly complex species is the Enantia jethys complex that has been studied for over a century; many debates exist regarding the species composition of this complex. Currently, three species that live sympatrically in the Gulf slope of Mexico (Enantia jethys, E. mazai, and E. albania) are recognized in this complex (based on morphological and molecular studies). Where these species live in sympatry, some cases of interspecific mating have been observed, suggesting hybridization events. Considering this, we employed a multilocus approach (analyses of mitochondrial and nuclear sequences: COI, RpS5, and Wg; and nuclear dominant markers: inter-simple sequence repeat (ISSRs) to study hybridization in sympatric populations from Veracruz, Mexico. Genetic diversity parameters were determined for all molecular markers, and species identification was assessed by different methods such as analyses of molecular variance (AMOVA), clustering, principal coordinate analysis (PCoA), gene flow, and PhiPT parameters. ISSR molecular markers were used for a more profound study of hybridization process. Although species of the Enantia jethys complex have a low dispersal capacity, we observed high genetic diversity, probably reflecting a high density of individuals locally. ISSR markers provided evidence of a contemporary hybridization process, detecting a high number of hybrids (from 17% to 53%) with significant differences in genetic diversity. Furthermore, a directional pattern of hybridization was observed from E. albania to other species. Phylogenetic study through DNA sequencing confirmed the existence of three clades corresponding to the three species previously recognized by morphological and molecular studies. This study underlines the importance of assessing hybridization in evolutionary studies, by tracing the lineage separation process that leads to the origin of new species. Our research demonstrates that hybridization processes have a high occurrence in natural populations.
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Affiliation(s)
- Jovana M. Jasso-Martínez
- Laboratorio de Genética y Evolución, Departamento de Biología Celular, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Salima Machkour-M’Rabet
- Laboratorio de Ecología Molecular y Conservación, Departamento de Conservación de la Biodiversidad, El Colegio de la Frontera Sur, Chetumal, Quintana Roo, Mexico
- * E-mail: (ANCS); (SMM)
| | - Roger Vila
- Institut de Biologia Evolutiva (CSIC-UPF), Barcelona, Spain
| | - Rosario Rodríguez-Arnaiz
- Laboratorio de Genética y Evolución, Departamento de Biología Celular, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - América Nitxin Castañeda-Sortibrán
- Laboratorio de Genética y Evolución, Departamento de Biología Celular, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
- * E-mail: (ANCS); (SMM)
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11
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Leduc-Robert G, Maddison WP. Phylogeny with introgression in Habronattus jumping spiders (Araneae: Salticidae). BMC Evol Biol 2018; 18:24. [PMID: 29471785 PMCID: PMC5824460 DOI: 10.1186/s12862-018-1137-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 02/15/2018] [Indexed: 01/12/2023] Open
Abstract
Background Habronattus is a diverse clade of jumping spiders with complex courtship displays and repeated evolution of Y chromosomes. A well-resolved species phylogeny would provide an important framework to study these traits, but has not yet been achieved, in part because the few genes available in past studies gave conflicting signals. Such discordant gene trees could be the result of incomplete lineage sorting (ILS) in recently diverged parts of the phylogeny, but there are indications that introgression could be a source of conflict. Results To infer Habronattus phylogeny and investigate the cause of gene tree discordance, we assembled transcriptomes for 34 Habronattus species and 2 outgroups. The concatenated 2.41 Mb of nuclear data (1877 loci) resolved phylogeny by Maximum Likelihood (ML) with high bootstrap support (95-100%) at most nodes, with some uncertainty surrounding the relationships of H. icenoglei, H. cambridgei, H. oregonensis, and Pellenes canadensis. Species tree analyses by ASTRAL and SVDQuartets gave almost completely congruent results. Several nodes in the ML phylogeny from 12.33 kb of mitochondrial data are incongruent with the nuclear phylogeny and indicate possible mitochondrial introgression: the internal relationships of the americanus and the coecatus groups, the relationship between the altanus, decorus, banksi, and americanus group, and between H. clypeatus and the coecatus group. To determine the relative contributions of ILS and introgression, we analyzed gene tree discordance for nuclear loci longer than 1 kb using Bayesian Concordance Analysis (BCA) for the americanus group (679 loci) and the VCCR clade (viridipes/clypeatus/coecatus/roberti groups) (517 loci) and found signals of introgression in both. Finally, we tested specifically for introgression in the concatenated nuclear matrix with Patterson’s D statistics and DFOIL. We found nuclear introgression resulting in substantial admixture between americanus group species, between H. roberti and the clypeatus group, and between the clypeatus and coecatus groups. Conclusions Our results indicate that the phylogenetic history of Habronattus is predominantly a diverging tree, but that hybridization may have been common between phylogenetically distant species, especially in subgroups with complex courtship displays. Electronic supplementary material The online version of this article (10.1186/s12862-018-1137-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Wayne P Maddison
- Department of Zoology, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada. .,Department of Botany and Beaty Biodiversity Museum, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.
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12
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Mérot C, Salazar C, Merrill RM, Jiggins CD, Joron M. What shapes the continuum of reproductive isolation? Lessons from Heliconius butterflies. Proc Biol Sci 2018; 284:rspb.2017.0335. [PMID: 28592669 DOI: 10.1098/rspb.2017.0335] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 05/08/2017] [Indexed: 11/12/2022] Open
Abstract
The process by which species evolve can be illuminated by investigating barriers that limit gene flow between taxa. Recent radiations, such as Heliconius butterflies, offer the opportunity to compare isolation between pairs of taxa at different stages of ecological, geographical, and phylogenetic divergence. Here, we report a comparative analysis of existing and novel data in order to quantify the strength and direction of isolating barriers within a well-studied clade of Heliconius Our results highlight that increased divergence is associated with the accumulation of stronger and more numerous barriers to gene flow. Wing pattern is both under natural selection for Müllerian mimicry and involved in mate choice, and therefore underlies several isolating barriers. However, pairs which share a similar wing pattern also display strong reproductive isolation mediated by traits other than wing pattern. This suggests that, while wing pattern is a key factor for early stages of divergence, it may become facultative at later stages of divergence. Additional factors including habitat partitioning, hybrid sterility, and chemically mediated mate choice are associated with complete speciation. Therefore, although most previous work has emphasized the role of wing pattern, our comparative results highlight that speciation is a multi-dimensional process, whose completion is stabilized by many factors.
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Affiliation(s)
- C Mérot
- ISYEB UMR 7205, Muséum National d'Histoire Naturelle, 45 rue Buffon, Paris, France .,IBIS, Université Laval, 1030 Avenue de la Médecine, Québec, Canada
| | - C Salazar
- Biology Program, Faculty of Natural Sciences and Mathematics, Universidad del Rosario, Carrera, 24 No 63C-69, Bogota D.C., 111221, Colombia
| | - R M Merrill
- Department of Zoology, University of Cambridge, Downing Street, Cambridge, CB2 3EJ, UK.,Smithsonian Tropical Research Institute, MRC 0580-12, Unit 9100 Box 0948, DPO AA 34002-9998, Panama
| | - C D Jiggins
- Department of Zoology, University of Cambridge, Downing Street, Cambridge, CB2 3EJ, UK.,Smithsonian Tropical Research Institute, MRC 0580-12, Unit 9100 Box 0948, DPO AA 34002-9998, Panama
| | - M Joron
- ISYEB UMR 7205, Muséum National d'Histoire Naturelle, 45 rue Buffon, Paris, France .,Centre d'Ecologie Fonctionnelle et Evolutive, UMR 5175 CNRS - Université de Montpellier - Université Paul Valéry Montpellier - EPHE, 1919 route de Mende, 34293 Montpellier, France
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13
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Southcott L, Kronforst MR. A neutral view of the evolving genomic architecture of speciation. Ecol Evol 2017; 7:6358-6366. [PMID: 28861239 PMCID: PMC5574762 DOI: 10.1002/ece3.3190] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Revised: 05/18/2017] [Accepted: 05/21/2017] [Indexed: 11/18/2022] Open
Abstract
Analyses of genomewide polymorphism data have begun to shed light on speciation and adaptation. Genome scans to identify regions of the genome that are unusually different between populations or species, possibly due to divergent natural or sexual selection, are widespread in speciation genomics. Theoretical and empirical work suggests that such outlier regions may grow faster than linearly during speciation with gene flow due to a rapid transition between low and high reproductive isolation. We investigate whether this pattern could be attributed to neutral processes by simulating genomes under neutral evolution with varying amounts and timing of gene flow. Under both neutral evolution and divergent selection, simulations with little or no gene flow, or with a long allopatric period after its cessation, resulted in faster than linear growth of the proportion of the genome lying in outlier regions. Without selection, higher recent gene flow erased differentiation; with divergent selection, these same scenarios produced nonlinear growth to a plateau. Our results suggest that, given a history of gene flow, the growth of the divergent genome is informative about selection during divergence, but that in many scenarios, this pattern does not easily distinguish neutral and non-neutral processes during speciation with gene flow.
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Affiliation(s)
- Laura Southcott
- Committee on Evolutionary BiologyUniversity of ChicagoChicagoILUSA
| | - Marcus R. Kronforst
- Committee on Evolutionary BiologyUniversity of ChicagoChicagoILUSA
- Department of Ecology and EvolutionUniversity of ChicagoChicagoILUSA
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14
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Corbett-Detig R, Nielsen R. A Hidden Markov Model Approach for Simultaneously Estimating Local Ancestry and Admixture Time Using Next Generation Sequence Data in Samples of Arbitrary Ploidy. PLoS Genet 2017; 13:e1006529. [PMID: 28045893 PMCID: PMC5242547 DOI: 10.1371/journal.pgen.1006529] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 01/18/2017] [Accepted: 12/08/2016] [Indexed: 12/19/2022] Open
Abstract
Admixture-the mixing of genomes from divergent populations-is increasingly appreciated as a central process in evolution. To characterize and quantify patterns of admixture across the genome, a number of methods have been developed for local ancestry inference. However, existing approaches have a number of shortcomings. First, all local ancestry inference methods require some prior assumption about the expected ancestry tract lengths. Second, existing methods generally require genotypes, which is not feasible to obtain for many next-generation sequencing projects. Third, many methods assume samples are diploid, however a wide variety of sequencing applications will fail to meet this assumption. To address these issues, we introduce a novel hidden Markov model for estimating local ancestry that models the read pileup data, rather than genotypes, is generalized to arbitrary ploidy, and can estimate the time since admixture during local ancestry inference. We demonstrate that our method can simultaneously estimate the time since admixture and local ancestry with good accuracy, and that it performs well on samples of high ploidy-i.e. 100 or more chromosomes. As this method is very general, we expect it will be useful for local ancestry inference in a wider variety of populations than what previously has been possible. We then applied our method to pooled sequencing data derived from populations of Drosophila melanogaster on an ancestry cline on the east coast of North America. We find that regions of local recombination rates are negatively correlated with the proportion of African ancestry, suggesting that selection against foreign ancestry is the least efficient in low recombination regions. Finally we show that clinal outlier loci are enriched for genes associated with gene regulatory functions, consistent with a role of regulatory evolution in ecological adaptation of admixed D. melanogaster populations. Our results illustrate the potential of local ancestry inference for elucidating fundamental evolutionary processes.
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Affiliation(s)
- Russell Corbett-Detig
- Genomics Institute and Department of Biomolecular Engineering, UC Santa Cruz, Santa Cruz, CA, United States of America
- Department of Integrative Biology, UC Berkeley, Berkeley, CA, United States of America
| | - Rasmus Nielsen
- Department of Integrative Biology, UC Berkeley, Berkeley, CA, United States of America
- The Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
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15
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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.
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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
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16
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Zhang W, Dasmahapatra KK, Mallet J, Moreira GRP, Kronforst MR. Genome-wide introgression among distantly related Heliconius butterfly species. Genome Biol 2016; 17:25. [PMID: 26921238 PMCID: PMC4769579 DOI: 10.1186/s13059-016-0889-0] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2015] [Accepted: 01/28/2016] [Indexed: 12/30/2022] Open
Abstract
Background Although hybridization is thought to be relatively rare in animals, the raw genetic material introduced via introgression may play an important role in fueling adaptation and adaptive radiation. The butterfly genus Heliconius is an excellent system to study hybridization and introgression but most studies have focused on closely related species such as H. cydno and H. melpomene. Here we characterize genome-wide patterns of introgression between H. besckei, the only species with a red and yellow banded ‘postman’ wing pattern in the tiger-striped silvaniform clade, and co-mimetic H. melpomene nanna. Results We find a pronounced signature of putative introgression from H. melpomene into H. besckei in the genomic region upstream of the gene optix, known to control red wing patterning, suggesting adaptive introgression of wing pattern mimicry between these two distantly related species. At least 39 additional genomic regions show signals of introgression as strong or stronger than this mimicry locus. Gene flow has been on-going, with evidence of gene exchange at multiple time points, and bidirectional, moving from the melpomene to the silvaniform clade and vice versa. The history of gene exchange has also been complex, with contributions from multiple silvaniform species in addition to H. besckei. We also detect a signature of ancient introgression of the entire Z chromosome between the silvaniform and melpomene/cydno clades. Conclusions Our study provides a genome-wide portrait of introgression between distantly related butterfly species. We further propose a comprehensive and efficient workflow for gene flow identification in genomic data sets. Electronic supplementary material The online version of this article (doi:10.1186/s13059-016-0889-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Wei Zhang
- Department of Ecology & Evolution, University of Chicago, Chicago, IL, 60637, USA.
| | | | - James Mallet
- Department of Organismic & Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Gilson R P Moreira
- Departamento de Zoologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, 91501-970, Brazil
| | - Marcus R Kronforst
- Department of Ecology & Evolution, University of Chicago, Chicago, IL, 60637, USA.
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17
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Petkova D, Novembre J, Stephens M. Visualizing spatial population structure with estimated effective migration surfaces. Nat Genet 2016; 48:94-100. [PMID: 26642242 PMCID: PMC4696895 DOI: 10.1038/ng.3464] [Citation(s) in RCA: 326] [Impact Index Per Article: 40.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Accepted: 11/12/2015] [Indexed: 12/17/2022]
Abstract
Genetic data often exhibit patterns broadly consistent with 'isolation by distance'-a phenomenon where genetic similarity decays with geographic distance. In a heterogeneous habitat, this may occur more quickly in some regions than in others: for example, barriers to gene flow can accelerate differentiation between neighboring groups. We use the concept of 'effective migration' to model the relationship between genetics and geography. In this paradigm, effective migration is low in regions where genetic similarity decays quickly. We present a method to visualize variation in effective migration across a habitat from geographically indexed genetic data. Our approach uses a population genetic model to relate effective migration rates to expected genetic dissimilarities. We illustrate its potential and limitations using simulations and data from elephant, human and Arabidopsis thaliana populations. The resulting visualizations highlight important spatial features of population structure that are difficult to discern using existing methods for summarizing genetic variation.
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Affiliation(s)
- Desislava Petkova
- Department of Statistics, The University of Chicago, Chicago, Illinois, USA
- Wellcome Trust Centre for Human Genetics, Oxford, UK
| | - John Novembre
- Department of Human Genetics, The University of Chicago, Chicago, Illinois, USA
| | - Matthew Stephens
- Department of Statistics, The University of Chicago, Chicago, Illinois, USA
- Department of Human Genetics, The University of Chicago, Chicago, Illinois, USA
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18
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Efficient Strategies for Calculating Blockwise Likelihoods Under the Coalescent. Genetics 2015; 202:775-86. [PMID: 26715666 PMCID: PMC4788249 DOI: 10.1534/genetics.115.183814] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 12/15/2015] [Indexed: 01/08/2023] Open
Abstract
The inference of demographic history from genome data is hindered by a lack of efficient computational approaches. In particular, it has proved difficult to exploit the information contained in the distribution of genealogies across the genome. We have previously shown that the generating function (GF) of genealogies can be used to analytically compute likelihoods of demographic models from configurations of mutations in short sequence blocks (Lohse et al. 2011). Although the GF has a simple, recursive form, the size of such likelihood calculations explodes quickly with the number of individuals and applications of this framework have so far been mainly limited to small samples (pairs and triplets) for which the GF can be written by hand. Here we investigate several strategies for exploiting the inherent symmetries of the coalescent. In particular, we show that the GF of genealogies can be decomposed into a set of equivalence classes that allows likelihood calculations from nontrivial samples. Using this strategy, we automated blockwise likelihood calculations for a general set of demographic scenarios in Mathematica. These histories may involve population size changes, continuous migration, discrete divergence, and admixture between multiple populations. To give a concrete example, we calculate the likelihood for a model of isolation with migration (IM), assuming two diploid samples without phase and outgroup information. We demonstrate the new inference scheme with an analysis of two individual butterfly genomes from the sister species Heliconius melpomene rosina and H. cydno.
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19
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Kang S, Jung J, Kim W. Population Genetic Structure of the Malaria Vector Anopheles sinensis (Diptera: Culicidae) Sensu Stricto and Evidence for Possible Introgression in the Republic of Korea. JOURNAL OF MEDICAL ENTOMOLOGY 2015; 52:1270-1281. [PMID: 26336253 DOI: 10.1093/jme/tjv114] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Accepted: 07/17/2015] [Indexed: 06/05/2023]
Abstract
Anopheles sinensis Wiedemann sensu stricto (s.s.) is a dominant mosquito and considered a secondary malaria vector in the Republic of Korea (ROK). Despite the potential significance for malaria control, population genetics studies have been conducted using only mitochondrial DNA (mtDNA), and studies of the genetics of hybridization have never been attempted. In this study, 346 specimens from 23 localities were subject to experiments. Among them, 305 An. sinensis s.s. specimens from 20 localities were used for mtDNA analysis, and 346 specimens comprising 341 An. sinensis s.s. from 22 localities and five Anopheles kleini Rueda from one locality were examined in the microsatellite study. Neighbor-joining analysis of pairwise FST and RST based on microsatellite results showed that the populations are divided into two groups, as did the mtDNA results. However, the Bayesian analysis and factorial correspondence analysis plots showed three distinct clusters. Among the mtDNA and microsatellite results, only microsatellites represented small but positive and significant isolation-by-distance patterns. Both molecular markers show the Taebaek and Sobaek Mountain ranges as barriers between the northern and southern parts of the ROK. The newly recognized third group suggests possible introgressive hybridization of An. sinensis s.s. with closely related species. The slightly different composition of populations in each group based on different markers is probably because of different population dynamics in each group. These results imply that there is restricted gene flow of epidemiologically important malaria-related genes between the northern and southern parts of the ROK.
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Affiliation(s)
- Seunghyun Kang
- Division of Polar Life Sciences, Korea Polar Research Institute, 26 Songdomirae-ro, Yeonsu-gu, Incheon 406-840, Republic of Korea
| | - Jongwoo Jung
- Department of Science Education, Ewha Womans University, 52 Ewhayeodae-gil, Seodaemun-gu, Seoul 120-750, Republic of Korea
| | - Won Kim
- School of Biological Sciences, Seoul National University, 599 Gwanak-ro, Gwanak-gu, Seoul 151-742, Republic of Korea.
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20
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Dwyer HE, Jasieniuk M, Okada M, Shapiro AM. Molecular evidence for hybridization in Colias (Lepidoptera: Pieridae): are Colias hybrids really hybrids? Ecol Evol 2015; 5:2865-77. [PMID: 26306172 PMCID: PMC4541991 DOI: 10.1002/ece3.1574] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2015] [Revised: 05/27/2015] [Accepted: 05/28/2015] [Indexed: 11/24/2022] Open
Abstract
Gene flow and hybridization among species dramatically affect our understanding of the species as a biological unit, species relationships, and species adaptations. In North American Colias eurytheme and Colias eriphyle, there has been historical debate over the extent of hybridization occurring and the identity of phenotypically intermediate individuals as genetic hybrids. This study assesses the population structure of these two species to measure the extent of hybridization and the genetic identity of phenotypic intermediates as hybrids. Amplified fragment length polymorphism (AFLP) marker analysis was performed on 378 specimens collected from northern California and Nevada. Population structure was inferred using a Bayesian/Markov chain Monte Carlo method, which probabilistically assigns individuals to genetic clusters. Three genetic clusters provided the best fit for the data. C. eurytheme individuals were primarily assigned to two closely related clusters, and C. eriphyle individuals were mostly assigned to a third, more distantly related cluster. There appeared to be significant hybridization between the two species. Individuals of intermediate phenotype (putative hybrids) were found to be genetically indistinguishable from C. eriphyle, indicating that previous work based on the assumption that these intermediate forms are hybrids may warrant reconsideration.
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Affiliation(s)
- Heather E Dwyer
- Eberly Center for Teaching Excellence and Educational Innovation, Carnegie Mellon University Pittsburgh, Pennsylvania, 15213
| | - Marie Jasieniuk
- Department of Plant Sciences, University of California Davis, California, 95616
| | - Miki Okada
- Department of Plant Sciences, University of California Davis, California, 95616
| | - Arthur M Shapiro
- Department of Evolution and Ecology, University of California Davis, California, 95616
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21
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Zhou C, Lang X, Wang Y, Zhu C. gPGA: GPU Accelerated Population Genetics Analyses. PLoS One 2015; 10:e0135028. [PMID: 26248314 PMCID: PMC4527771 DOI: 10.1371/journal.pone.0135028] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Accepted: 07/16/2015] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND The isolation with migration (IM) model is important for studies in population genetics and phylogeography. IM program applies the IM model to genetic data drawn from a pair of closely related populations or species based on Markov chain Monte Carlo (MCMC) simulations of gene genealogies. But computational burden of IM program has placed limits on its application. METHODOLOGY With strong computational power, Graphics Processing Unit (GPU) has been widely used in many fields. In this article, we present an effective implementation of IM program on one GPU based on Compute Unified Device Architecture (CUDA), which we call gPGA. CONCLUSIONS Compared with IM program, gPGA can achieve up to 52.30X speedup on one GPU. The evaluation results demonstrate that it allows datasets to be analyzed effectively and rapidly for research on divergence population genetics. The software is freely available with source code at https://github.com/chunbaozhou/gPGA.
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Affiliation(s)
- Chunbao Zhou
- Supercomputing Center, Computer Network Information Center, Chinese Academy of Sciences, Beijing, 100190, China
| | - Xianyu Lang
- Supercomputing Center, Computer Network Information Center, Chinese Academy of Sciences, Beijing, 100190, China
| | - Yangang Wang
- Supercomputing Center, Computer Network Information Center, Chinese Academy of Sciences, Beijing, 100190, China
- * E-mail: (YGW); (CDZ)
| | - Chaodong Zhu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- * E-mail: (YGW); (CDZ)
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22
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Merrill RM, Dasmahapatra KK, Davey JW, Dell'Aglio DD, Hanly JJ, Huber B, Jiggins CD, Joron M, Kozak KM, Llaurens V, Martin SH, Montgomery SH, Morris J, Nadeau NJ, Pinharanda AL, Rosser N, Thompson MJ, Vanjari S, Wallbank RWR, Yu Q. The diversification of Heliconius butterflies: what have we learned in 150 years? J Evol Biol 2015; 28:1417-38. [PMID: 26079599 DOI: 10.1111/jeb.12672] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Revised: 06/03/2015] [Accepted: 06/07/2015] [Indexed: 11/27/2022]
Abstract
Research into Heliconius butterflies has made a significant contribution to evolutionary biology. Here, we review our understanding of the diversification of these butterflies, covering recent advances and a vast foundation of earlier work. Whereas no single group of organisms can be sufficient for understanding life's diversity, after years of intensive study, research into Heliconius has addressed a wide variety of evolutionary questions. We first discuss evidence for widespread gene flow between Heliconius species and what this reveals about the nature of species. We then address the evolution and diversity of warning patterns, both as the target of selection and with respect to their underlying genetic basis. The identification of major genes involved in mimetic shifts, and homology at these loci between distantly related taxa, has revealed a surprising predictability in the genetic basis of evolution. In the final sections, we consider the evolution of warning patterns, and Heliconius diversity more generally, within a broader context of ecological and sexual selection. We consider how different traits and modes of selection can interact and influence the evolution of reproductive isolation.
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Affiliation(s)
- R M Merrill
- Department of Zoology, University of Cambridge, Cambridge, UK.,Smithsonian Tropical Research Institute, Panama City, Panama
| | | | - J W Davey
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - D D Dell'Aglio
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - J J Hanly
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - B Huber
- Department of Biology, University of York, York, UK.,Institut de Systématique, Évolution, Biodiversité, ISYEB - UMR 7205 - CNRS, MNHN, UPMC, EPHE, Muséum national d'Histoire naturelle, Sorbonne Universités, Paris, France
| | - C D Jiggins
- Department of Zoology, University of Cambridge, Cambridge, UK.,Smithsonian Tropical Research Institute, Panama City, Panama
| | - M Joron
- Smithsonian Tropical Research Institute, Panama City, Panama.,Institut de Systématique, Évolution, Biodiversité, ISYEB - UMR 7205 - CNRS, MNHN, UPMC, EPHE, Muséum national d'Histoire naturelle, Sorbonne Universités, Paris, France.,Centre d'Ecologie Fonctionnelle et Evolutive, CEFE UMR 5175, CNRS - Université de Montpellier - Université Paul-Valéry Montpellier - EPHE, Montpellier 5, France
| | - K M Kozak
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - V Llaurens
- Institut de Systématique, Évolution, Biodiversité, ISYEB - UMR 7205 - CNRS, MNHN, UPMC, EPHE, Muséum national d'Histoire naturelle, Sorbonne Universités, Paris, France
| | - S H Martin
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - S H Montgomery
- Department of Genetics, Evolution and Environment, University College London, London, UK
| | - J Morris
- Department of Biology, University of York, York, UK
| | - N J Nadeau
- Department of Zoology, University of Cambridge, Cambridge, UK.,Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | - A L Pinharanda
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - N Rosser
- Department of Biology, University of York, York, UK
| | - M J Thompson
- Department of Zoology, University of Cambridge, Cambridge, UK.,Department of Life Sciences, Natural History Museum, London, UK
| | - S Vanjari
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - R W R Wallbank
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Q Yu
- Department of Zoology, University of Cambridge, Cambridge, UK.,School of Life Sciences, Chongqing University, Shapingba District, Chongqing, China
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23
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Arias CF, Salazar C, Rosales C, Kronforst MR, Linares M, Bermingham E, McMillan WO. Phylogeography of Heliconius cydno and its closest relatives: disentangling their origin and diversification. Mol Ecol 2014; 23:4137-52. [PMID: 24962067 DOI: 10.1111/mec.12844] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Revised: 06/14/2014] [Accepted: 06/16/2014] [Indexed: 11/28/2022]
Abstract
The origins of the extraordinary diversity within the Neotropics have long fascinated biologists and naturalists. Yet, the underlying factors that have given rise to this diversity remain controversial. To test the relative importance of Quaternary climatic change and Neogene tectonic and paleogeographic reorganizations in the generation of biodiversity, we examine intraspecific variation across the Heliconius cydno radiation and compare this variation to that within the closely related Heliconius melpomene and Heliconius timareta radiations. Our data, which consist of both mtDNA and genome-scan data from nearly 2250 amplified fragment length polymorphism (AFLP) loci, reveal a complex history of differentiation and admixture at different geographic scales. Both mtDNA and AFLP phylogenies suggest that H. timareta and H. cydno are probably geographic extremes of the same radiation that probably diverged from H. melpomene prior to the Pliocene-Pleistocene boundary, consistent with hypotheses of diversification that rely on geological events in the Pliocene. The mtDNA suggests that this radiation originated in Central America or the northwestern region of South America, with a subsequent colonization of the eastern and western slopes of the Andes. Our genome-scan data indicate significant admixture among sympatric H. cydno/H. timareta and H. melpomene populations across the extensive geographic ranges of the two radiations. Within H. cydno, both mtDNA and AFLP data indicate significant population structure at local scales, with strong genetic differences even among adjacent H. cydno colour pattern races. These genetic patterns highlight the importance of past geoclimatic events, intraspecific gene flow, and local population differentiation in the origin and establishment of new adaptive forms.
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Affiliation(s)
- Carlos F Arias
- Department of Biology, McGill University, 1205 Ave. Dr. Penfield, Montreal, QC, Canada, H3A 1B1; Smithsonian Tropical Research Institute, Apartado 0843-03092, Panamá, Panamá
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24
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Mao X, Zhu G, Zhang L, Zhang S, Rossiter SJ. Differential introgression among loci across a hybrid zone of the intermediate horseshoe bat (Rhinolophus affinis). BMC Evol Biol 2014; 14:154. [PMID: 25011626 PMCID: PMC4105523 DOI: 10.1186/1471-2148-14-154] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Accepted: 07/04/2014] [Indexed: 11/30/2022] Open
Abstract
Background Hybrid zones formed by the secondary contact of divergent lineages represent natural laboratories for studying the genetic basis of speciation. Here we tested for patterns of differential introgression among three X-linked and 11 autosomal regions to identify candidate loci related to either reproductive isolation or adaptive introgression across a hybrid zone between two Chinese mainland subspecies of the intermediate horseshoe bat Rhinolophus affinis: R. a. himalayanus and R. a. macrurus. Results Our results support the previous suggestion that macrurus formed when a third subspecies (R. a. hainanus) recolonized the mainland from Hainan Island, and that himalayanus is the ancestral taxon. However, this overall evolutionary history was not reflected in all loci examined, with considerable locus-wise heterogeneity seen in gene tree topologies, levels of polymorphism, genetic differentiation and rates of introgression. Coalescent simulations suggested levels of lineage mixing seen at some nuclear loci might result from incomplete lineage sorting. Isolation with migration models supported evidence of gene flow across the hybrid zone at one intronic marker of the hearing gene Prestin. Conclusions We suggest that phylogenetic discordance with respect to the species tree seen here is likely to arise via a combination of incomplete lineage sorting and a low incidence of introgression although we cannot rule out other explanations such as selection and recombination. Two X-linked loci and one autosomal locus were identified as candidate regions related to reproductive isolation across the hybrid zone. Our work highlights the importance of including multiple genomic regions in characterizing patterns of divergence and gene flow across a hybrid zone.
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Affiliation(s)
| | | | | | | | - Stephen J Rossiter
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK.
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Cruickshank TE, Hahn MW. Reanalysis suggests that genomic islands of speciation are due to reduced diversity, not reduced gene flow. Mol Ecol 2014; 23:3133-57. [DOI: 10.1111/mec.12796] [Citation(s) in RCA: 764] [Impact Index Per Article: 76.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Revised: 05/05/2014] [Accepted: 05/07/2014] [Indexed: 12/18/2022]
Affiliation(s)
| | - Matthew W. Hahn
- Department of Biology; Indiana University; Bloomington IN 47405 USA
- School of Informatics and Computing; Indiana University; Bloomington IN 47405 USA
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26
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Popovic I, Marko PB, Wares JP, Hart MW. Selection and demographic history shape the molecular evolution of the gamete compatibility protein bindin in Pisaster sea stars. Ecol Evol 2014; 4:1567-88. [PMID: 24967076 PMCID: PMC4063459 DOI: 10.1002/ece3.1042] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Revised: 02/15/2014] [Accepted: 02/26/2014] [Indexed: 12/18/2022] Open
Abstract
Reproductive compatibility proteins have been shown to evolve rapidly under positive selection leading to reproductive isolation, despite the potential homogenizing effects of gene flow. This process has been implicated in both primary divergence among conspecific populations and reinforcement during secondary contact; however, these two selective regimes can be difficult to discriminate from each other. Here, we describe the gene that encodes the gamete compatibility protein bindin for three sea star species in the genus Pisaster. First, we compare the full-length bindin-coding sequence among all three species and analyze the evolutionary relationships between the repetitive domains of the variable second bindin exon. The comparison suggests that concerted evolution of repetitive domains has an effect on bindin divergence among species and bindin variation within species. Second, we characterize population variation in the second bindin exon of two species: We show that positive selection acts on bindin variation in Pisaster ochraceus but not in Pisaster brevispinus, which is consistent with higher polyspermy risk in P. ochraceus. Third, we show that there is no significant genetic differentiation among populations and no apparent effect of sympatry with congeners that would suggest selection based on reinforcement. Fourth, we combine bindin and cytochrome c oxidase 1 data in isolation-with-migration models to estimate gene flow parameter values and explore the historical demographic context of our positive selection results. Our findings suggest that positive selection on bindin divergence among P. ochraceus alleles can be accounted for in part by relatively recent northward population expansions that may be coupled with the potential homogenizing effects of concerted evolution.
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Affiliation(s)
- Iva Popovic
- Department of Biological Sciences, Simon Fraser UniversityBurnaby, British Columbia, Canada
| | - Peter B Marko
- Department of Biology, University of Hawai'iMānoa, Hawaii
| | - John P Wares
- Department of Genetics, University of GeorgiaAthens, Georgia
| | - Michael W Hart
- Department of Biological Sciences, Simon Fraser UniversityBurnaby, British Columbia, Canada
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27
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Sovic MG, Kubatko LS, Fuerst PA. The effects of locus number, genetic divergence, and genotyping error on the utility of dominant markers for hybrid identification. Ecol Evol 2014; 4:462-73. [PMID: 24634730 PMCID: PMC3936392 DOI: 10.1002/ece3.833] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Revised: 09/03/2013] [Accepted: 09/06/2013] [Indexed: 11/27/2022] Open
Abstract
In surveys of hybrid zones, dominant genetic markers are often used to identify individuals of hybrid origin and assign these individuals to one of several potential hybrid classes. Quantitative analyses that address the statistical power of dominant markers in such inference are scarce. In this study, dominant genotype data were simulated to evaluate the effects of, first, the number of loci analyzed, second, the magnitude of differentiation between the markers scored in the groups that are hybridizing, and third, the level of genotyping error associated with the data when assigning individuals to various parental and hybrid categories. The overall performance of the assignment methods was relatively modest at the lowest level of divergence examined (Fst ˜ 0.4), but improved substantially at higher levels of differentiation (Fst ˜ 0.67 or 0.8). The effect of genotyping error was dependent on the level of divergence between parental taxa, with larger divergences tempering the effects of genotyping error. These results highlight the importance of considering the effects of each of the variables when assigning individuals to various parental and hybrid categories, and can help guide decisions regarding the number of loci employed in future hybridization studies to achieve the power and level of resolution desired.
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Affiliation(s)
- Michael G Sovic
- Department of Evolution, Ecology, and Organismal Biology, 314 Aronoff Laboratory, The Ohio State University 318 W. 12th Ave, Columbus, Ohio, 43210
| | - Laura S Kubatko
- Departments of Statistics and Evolution, Ecology, and Organismal Biology, The Ohio State University 404 Cockins Hall, 1958 Neil Ave., Columbus, Ohio, 43210
| | - Paul A Fuerst
- Department of Evolution, Ecology, and Organismal Biology, 386 Aronoff Laboratory, The Ohio State University 318 W. 12th Ave, Columbus, Ohio, 43210
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28
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Kol-Maimon H, Ghanim M, Franco JC, Mendel Z. Evidence for gene flow between two sympatric mealybug species (Insecta; Coccoidea; Pseudococcidae). PLoS One 2014; 9:e88433. [PMID: 24523894 PMCID: PMC3921159 DOI: 10.1371/journal.pone.0088433] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Accepted: 01/07/2014] [Indexed: 11/27/2022] Open
Abstract
Occurrence of inter-species hybrids in natural populations might be evidence of gene flow between species. In the present study we found evidence of gene flow between two sympatric, genetically related scale insect species--the citrus mealybug Planococcus citri (Risso) and the vine mealybug Planococcus ficus (Signoret). These species can be distinguished by morphological, behavioral, and molecular traits. We employed the sex pheromones of the two respective species to study their different patterns of male attraction. We also used nuclear ITS2 (internal transcribed spacer 2) and mitochondrial COI (Cytochrome c oxidase sub unit 1) DNA sequences to characterize populations of the two species, in order to demonstrate the outcome of a possible gene flow between feral populations of the two species. Our results showed attraction to P. ficus pheromones of all tested populations of P. citri males but not vice versa. Furthermore, ITS2 sequences revealed the presence of 'hybrid females' among P. citri populations but not among those of P. ficus. 'hybrid females' from P. citri populations identified as P. citri females according to COI sequences. We offer two hypotheses for these results. 1) The occurrence of phenotypic and genotypic traits of P. ficus in P. citri populations may be attributed to both ancient and contemporary gene flow between their populations; and 2) we cannot rule out that an ancient sympatric speciation by which P. ficus emerged from P. citri might have led to the present situation of shared traits between these species. In light of these findings we also discuss the origin of the studied species and the importance of the pherotype phenomenon as a tool with which to study genetic relationships between congener scale insects.
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Affiliation(s)
- Hofit Kol-Maimon
- Department of Entomology, Volcani Center (ARO), Bet Dagan, Israel
| | - Murad Ghanim
- Department of Entomology, Volcani Center (ARO), Bet Dagan, Israel
| | - José Carlos Franco
- Departamento de Ciências e Engenharia de Biossistemas/Centro de Estudos Florestais, Instituto Superior de Agronomia, Universidade de Lisboa, Lisboa, Portugal
| | - Zvi Mendel
- Department of Entomology, Volcani Center (ARO), Bet Dagan, Israel
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29
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Kronforst MR, Hansen MEB, Crawford NG, Gallant JR, Zhang W, Kulathinal RJ, Kapan DD, Mullen SP. Hybridization reveals the evolving genomic architecture of speciation. Cell Rep 2013; 5:666-77. [PMID: 24183670 PMCID: PMC4388300 DOI: 10.1016/j.celrep.2013.09.042] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Revised: 08/09/2013] [Accepted: 09/25/2013] [Indexed: 11/30/2022] Open
Abstract
The rate at which genomes diverge during speciation is unknown, as are the physical dynamics of the process. Here, we compare full genome sequences of 32 butterflies, representing five species from a hybridizing Heliconius butterfly community, to examine genome-wide patterns of introgression and infer how divergence evolves during the speciation process. Our analyses reveal that initial divergence is restricted to a small fraction of the genome, largely clustered around known wing-patterning genes. Over time, divergence evolves rapidly, due primarily to the origin of new divergent regions. Furthermore, divergent genomic regions display signatures of both selection and adaptive introgression, demonstrating the link between microevolutionary processes acting within species and the origin of species across macroevolutionary timescales. Our results provide a uniquely comprehensive portrait of the evolving species boundary due to the role that hybridization plays in reducing the background accumulation of divergence at neutral sites.
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Affiliation(s)
- Marcus R Kronforst
- Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA.
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30
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Martin SH, Dasmahapatra KK, Nadeau NJ, Salazar C, Walters JR, Simpson F, Blaxter M, Manica A, Mallet J, Jiggins CD. Genome-wide evidence for speciation with gene flow in Heliconius butterflies. Genome Res 2013; 23:1817-28. [PMID: 24045163 PMCID: PMC3814882 DOI: 10.1101/gr.159426.113] [Citation(s) in RCA: 440] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Most speciation events probably occur gradually, without complete and immediate reproductive isolation, but the full extent of gene flow between diverging species has rarely been characterized on a genome-wide scale. Documenting the extent and timing of admixture between diverging species can clarify the role of geographic isolation in speciation. Here we use new methodology to quantify admixture at different stages of divergence in Heliconius butterflies, based on whole-genome sequences of 31 individuals. Comparisons between sympatric and allopatric populations of H. melpomene, H. cydno, and H. timareta revealed a genome-wide trend of increased shared variation in sympatry, indicative of pervasive interspecific gene flow. Up to 40% of 100-kb genomic windows clustered by geography rather than by species, demonstrating that a very substantial fraction of the genome has been shared between sympatric species. Analyses of genetic variation shared over different time intervals suggested that admixture between these species has continued since early in speciation. Alleles shared between species during recent time intervals displayed higher levels of linkage disequilibrium than those shared over longer time intervals, suggesting that this admixture took place at multiple points during divergence and is probably ongoing. The signal of admixture was significantly reduced around loci controlling divergent wing patterns, as well as throughout the Z chromosome, consistent with strong selection for Müllerian mimicry and with known Z-linked hybrid incompatibility. Overall these results show that species divergence can occur in the face of persistent and genome-wide admixture over long periods of time.
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Affiliation(s)
- Simon H Martin
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, United Kingdom
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31
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Merrill RM, Naisbit RE, Mallet J, Jiggins CD. Ecological and genetic factors influencing the transition between host-use strategies in sympatric Heliconius butterflies. J Evol Biol 2013; 26:1959-67. [PMID: 23961921 DOI: 10.1111/jeb.12194] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Revised: 05/06/2013] [Accepted: 05/07/2013] [Indexed: 11/27/2022]
Abstract
Shifts in host-plant use by phytophagous insects have played a central role in their diversification. Evolving host-use strategies will reflect a trade-off between selection pressures. The ecological niche of herbivorous insects is partitioned along several dimensions, and if populations remain in contact, recombination will break down associations between relevant loci. As such, genetic architecture can profoundly affect the coordinated divergence of traits and subsequently the ability to exploit novel habitats. The closely related species Heliconius cydno and H. melpomene differ in mimetic colour pattern, habitat and host-plant use. We investigate the selection pressures and genetic basis underlying host-use differences in these two species. Host-plant surveys reveal that H. melpomene specializes on a single species of Passiflora. This is also true for the majority of other Heliconius species in secondary growth forest at our study site, as expected under a model of interspecific competition. In contrast, H. cydno, which uses closed-forest habitats where both Heliconius and Passiflora are less common, appears not to be restricted by competition and uses a broad selection of the available Passiflora. However, other selection pressures are likely involved, and field experiments reveal that early larval survival of both butterfly species is highest on Passiflora menispermifolia, but most markedly so for H. melpomene, the specialist on that host. Finally, we demonstrate an association between host-plant acceptance and colour pattern amongst interspecific hybrids, suggesting that major loci underlying these important ecological traits are physically linked in the genome. Together, our results reveal ecological and genetic associations between shifts in habitat, host use and mimetic colour pattern that have likely facilitated both speciation and coexistence.
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Affiliation(s)
- R M Merrill
- Department of Zoology, University of Cambridge, Cambridge, UK.
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32
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Abstract
Hybridization has the potential to transfer beneficial alleles across species boundaries, and there are a growing number of examples in which this has apparently occurred. Recent studies suggest that Heliconius butterflies have transferred wing pattern mimicry alleles between species via hybridization, but ancestral polymorphism could also produce a signature of shared ancestry around mimicry genes. To distinguish between these alternative hypotheses, we measured DNA sequence divergence around putatively introgressed mimicry loci and compared this with the rest of the genome. Our results reveal that putatively introgressed regions show strongly reduced sequence divergence between co-mimetic species, suggesting that their divergence times are younger than the rest of the genome. This is consistent with introgression and not ancestral variation. We further show that this signature of introgression occurs at sites throughout the genome, not just around mimicry genes.
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Affiliation(s)
- Joel Smith
- Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA
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33
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Abstract
When divergence occurs in the presence of gene flow, there can arise an interesting dynamic in which selection against gene flow, at sites associated with population-specific adaptations or genetic incompatibilities, can cause net gene flow to vary across the genome. Loci linked to sites under selection may experience reduced gene flow and may experience genetic bottlenecks by the action of nearby selective sweeps. Data from histories such as these may be poorly fitted by conventional neutral model approaches to demographic inference, which treat all loci as equally subject to forces of genetic drift and gene flow. To allow for demographic inference in the face of such histories, as well as the identification of loci affected by selection, we developed an isolation-with-migration model that explicitly provides for variation among genomic regions in migration rates and/or rates of genetic drift. The method allows for loci to fall into any of multiple groups, each characterized by a different set of parameters, thus relaxing the assumption that all loci share the same demography. By grouping loci, the method can be applied to data with multiple loci and still have tractable dimensionality and statistical power. We studied the performance of the method using simulated data, and we applied the method to study the divergence of two subspecies of European rabbits (Oryctolagus cuniculus).
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34
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Jeratthitikul E, Hara T, Yago M, Itoh T, Wang M, Usami SI, Hikida T. Phylogeography of Fischer’s blue, Tongeia fischeri, in Japan: Evidence for introgressive hybridization. Mol Phylogenet Evol 2013; 66:316-26. [DOI: 10.1016/j.ympev.2012.10.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2012] [Revised: 08/24/2012] [Accepted: 10/06/2012] [Indexed: 11/27/2022]
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35
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DUPUIS JULIANR, ROE AMANDAD, SPERLING FELIXAH. Multi-locus species delimitation in closely related animals and fungi: one marker is not enough. Mol Ecol 2012; 21:4422-36. [DOI: 10.1111/j.1365-294x.2012.05642.x] [Citation(s) in RCA: 232] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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36
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Affiliation(s)
- Marcus R Kronforst
- FAS Center for Systems Biology, Harvard University, Cambridge, Massachusetts, United States of America.
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37
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Hahn MW, White BJ, Muir CD, Besansky NJ. No evidence for biased co-transmission of speciation islands in Anopheles gambiae. Philos Trans R Soc Lond B Biol Sci 2012; 367:374-84. [PMID: 22201167 DOI: 10.1098/rstb.2011.0188] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Genome-scale scans have revealed highly heterogeneous levels of divergence between closely related taxa in many systems. Generally, a small number of regions show high differentiation, with the rest of the genome showing no or only low levels of divergence. These patterns have been interpreted as evidence for ongoing speciation-with-gene-flow, with introgression homogenizing the whole genome except loci involved in reproductive isolation. However, as the number of selected loci increases, the probability of introgression at unselected loci decreases unless there is a transmission ratio distortion causing an over-representation of specific combinations of alleles. Here we examine the transmission of three 'speciation islands' that contain fixed differences between the M and S forms of the mosquito, Anopheles gambiae. We made reciprocal crosses between M and S parents and genotyped over 2000 F(2) individuals, developing a hierarchical likelihood model to identify specific genotypes that are under- or over-represented among the recombinant offspring. Though our overall results did not match the expected number of F(2) genotypes, we found no biased co-transmission among M or S alleles in the three islands. Our likelihood model did identify transmission ratio distortion at two of the three islands, but this distortion was small (approx. 3%) and in opposite directions for the two islands. We discuss how our results impinge on hypotheses of current gene flow between M and S and ongoing speciation-with-gene-flow in this system.
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Affiliation(s)
- Matthew W Hahn
- Department of Biology, Indiana University, Bloomington, IN 47405, USA.
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38
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Monahan WB, Pereira RJ, Wake DB. Ring distributions leading to species formation: a global topographic analysis of geographic barriers associated with ring species. BMC Biol 2012; 10:20. [PMID: 22410314 PMCID: PMC3320551 DOI: 10.1186/1741-7007-10-20] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2011] [Accepted: 03/12/2012] [Indexed: 11/10/2022] Open
Abstract
Background In the mid 20th century, Ernst Mayr and Theodosius Dobzhansky championed the significance of circular overlaps or ring species as the perfect demonstration of speciation, yet in the over 50 years since, only a handful of such taxa are known. We developed a topographic model to evaluate whether the geographic barriers that favor processes leading to ring species are common or rare, and to predict where other candidate ring barriers might be found. Results Of the 952,147 geographic barriers identified on the planet, only about 1% are topographically similar to barriers associated with known ring taxa, with most of the likely candidates occurring in under-studied parts of the world (for example, marine environments, tropical latitudes). Predicted barriers separate into two distinct categories: (i) single cohesive barriers (< 50,000 km2), associated with taxa that differentiate at smaller spatial scales (salamander: Ensatina eschscholtzii; tree: Acacia karroo); and (ii) composite barriers - formed by groups of barriers (each 184,000 to 1.7 million km2) in close geographic proximity (totaling 1.9 to 2.3 million km2) - associated with taxa that differentiate at larger spatial scales (birds: Phylloscopus trochiloides and Larus (sp. argentatus and fuscus)). When evaluated globally, we find a large number of cohesive barriers that are topographically similar to those associated with known ring taxa. Yet, compared to cohesive barriers, an order of magnitude fewer composite barriers are similar to those that favor ring divergence in species with higher dispersal. Conclusions While these findings confirm that the topographic conditions that favor evolutionary processes leading to ring speciation are, in fact, rare, they also suggest that many understudied natural systems could provide valuable demonstrations of continuous divergence towards the formation of new species. Distinct advantages of the model are that it (i) requires no a priori information on the relative importance of features that define barriers, (ii) can be replicated using any kind of continuously distributed environmental variable, and (iii) generates spatially explicit hypotheses of geographic species formation. The methods developed here - combined with study of the geographical ecology and genetics of taxa in their environments - should enable recognition of ring species phenomena throughout the world.
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Aguila RN, Plasencia EO, Maravi PFM, Wahlberg N. Cuban Calisto (Lepidoptera, Nymphalidae, Satyrinae), a review based on morphological and DNA data. Zookeys 2012:57-105. [PMID: 22328857 PMCID: PMC3272634 DOI: 10.3897/zookeys.165.2206] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2011] [Accepted: 12/28/2011] [Indexed: 11/12/2022] Open
Abstract
The Cuban species of Calisto are reviewed based on the morphology of adult and immature stages, as well as DNA sequences of six genes (COI, EF1α, wingless, GAPDH, RpS5, CAD). A new species, Calisto occultasp. n., is described from the northeastern Cuban mountains. Calisto smintheus Bates, 1935 and Calisto bruneri, Michener 1949 are revised and revalidated. A new status, the species level, is proposed for Calisto brochei, Torre 1973, Calisto muripetens, Bates 1939 and Calisto bradleyi, Munroe 1950. The immature stages of Calisto smintheus, Calisto brochei,and Calisto occulta are described for the first time, and those of Calisto herophile, Hübner 1823 are redescribed. Useful morphological characters for adults are the shape and conspicuousness of androconial patch, the number and relative size of white dots on underside of hindwing, the shape of aedeagus, the shape of digitiform projection of genitalia valve, the shape and relative size of tegumen and uncus, the relative size of female genitalia, the height of sterigmal ring dorsal crown of the latter, and the relative size of corpus bursae and ductus bursae. For the immature stages, the most important characters are the color pattern of head capsule, the number and width of longitudinal lines of body, in the larvae; and the color pattern and the absence or presence of dorsal ridges on the abdomen of pupae. The phylogenetic relationships between the Cuban Calisto species are quite robust and well-supported; however, conflict between mitochondrial and nuclear datasets was detected in Calisto brochei, Calisto muripetens and to a lesser degree in Calisto bradleyi.
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Affiliation(s)
- Rayner Núñez Aguila
- División de Colecciones Zoológicas y Sistemática, Instituto de Ecología y Sistemática, Carretera de Varona km 3.5, Capdevila, Boyeros, Ciudad de La Habana, Cuba
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40
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DeVries PJ, Alexander LG, Chacon IA, Fordyce JA. Similarity and difference among rainforest fruit-feeding butterfly communities in Central and South America. J Anim Ecol 2011; 81:472-82. [DOI: 10.1111/j.1365-2656.2011.01922.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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41
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Chamberlain NL, Hill RI, Baxter SW, Jiggins CD, Kronforst MR. Comparative population genetics of a mimicry locus among hybridizing Heliconius butterfly species. Heredity (Edinb) 2011; 107:200-4. [PMID: 21304546 PMCID: PMC3119732 DOI: 10.1038/hdy.2011.3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2010] [Revised: 11/16/2010] [Accepted: 12/20/2010] [Indexed: 11/09/2022] Open
Abstract
The comimetic Heliconius butterfly species pair, H. erato and H. melpomene, appear to use a conserved Mendelian switch locus to generate their matching red wing patterns. Here we investigate whether H. cydno and H. pachinus, species closely related to H. melpomene, use this same switch locus to generate their highly divergent red and brown color pattern elements. Using an F2 intercross between H. cydno and H. pachinus, we first map the genomic positions of two novel red/brown wing pattern elements; the G locus, which controls the presence of red vs brown at the base of the ventral wings, and the Br locus, which controls the presence vs absence of a brown oval pattern on the ventral hind wing. The results reveal that the G locus is tightly linked to markers in the genomic interval that controls red wing pattern elements of H. erato and H. melpomene. Br is on the same linkage group but approximately 26 cM away. Next, we analyze fine-scale patterns of genetic differentiation and linkage disequilibrium throughout the G locus candidate interval in H. cydno, H. pachinus and H. melpomene, and find evidence for elevated differentiation between H. cydno and H. pachinus, but no localized signature of association. Overall, these results indicate that the G locus maps to the same interval as the locus controlling red patterning in H. melpomene and H. erato. This, in turn, suggests that the genes controlling red pattern elements may be homologous across Heliconius, supporting the hypothesis that Heliconius butterflies use a limited suite of conserved genetic switch loci to generate both convergent and divergent wing patterns.
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Affiliation(s)
- N L Chamberlain
- FAS Center for Systems Biology, Harvard University, Cambridge, MA, USA
| | - R I Hill
- FAS Center for Systems Biology, Harvard University, Cambridge, MA, USA
| | - S W Baxter
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - C D Jiggins
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - M R Kronforst
- FAS Center for Systems Biology, Harvard University, Cambridge, MA, USA
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42
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Brower AVZ. Hybrid speciation in Heliconius butterflies? A review and critique of the evidence. Genetica 2011; 139:589-609. [PMID: 21113790 PMCID: PMC3089819 DOI: 10.1007/s10709-010-9530-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2010] [Accepted: 11/15/2010] [Indexed: 11/24/2022]
Abstract
The evidence supporting the recent hypothesis of a homoploid hybrid origin for the butterfly species Heliconius heurippa is evaluated. Data from selective breeding experiments, mate-choice studies, and a wide variety of DNA markers are reviewed, and an alternative hypothesis for the origin of the species and its close relatives is proposed. A scenario of occasional red wing-pattern mutations in peripheral populations of Heliconius cydno with subsequent adaptive convergence towards sympatric mimicry rings involving H. melpomene and H. erato is offered as an alternative to the HHS hypothesis. Recent twists of this tale are addressed in a postscript.
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Affiliation(s)
- Andrew V Z Brower
- Evolution and Ecology Group, Department of Biology, Middle Tennessee State University, Murfreesboro, TN 37132, USA.
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Dufková P, Macholán M, Piálek J. Inference of selection and stochastic effects in the house mouse hybrid zone. Evolution 2011; 65:993-1010. [PMID: 21463294 DOI: 10.1111/j.1558-5646.2011.01222.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
We explored the transition of 13 X-linked markers across two separate portions of the house mouse hybrid zone, asking whether such a comparison can distinguish the effects of selection from random factors. A heuristic search in the likelihood landscape revealed more complex likelihood profiles for data sampled in two-dimensional (2D) space relative to data sampled along a linear transect. Randomized resampling of localities analyzed for individual loci showed that deletion of sites away from the zone center can decrease cline width estimates whereas deletion of sites close to the center can significantly increase the width estimates. Deleting localities for all loci resulted in wider clines if the number of samples from the center was limited. The results suggest that, given the great variation in width estimates resulting from inclusion/exclusion of sampling sites, the geographic sampling design is important in hybrid zone studies and that our inferences should take into account measures of uncertainty such as support intervals. The comparison of the two transects indicates cline widths are narrower for loci in the central part of the X chromosome, suggesting selection is stronger in this region and genetic incompatibilities may have at least partly common architecture in the house mouse hybrid zone.
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Affiliation(s)
- Petra Dufková
- Institute of Vertebrate Biology, Academy of Science of the Czech Republic, Brno, Czech Republic.
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Merrill RM, Gompert Z, Dembeck LM, Kronforst MR, McMillan WO, Jiggins CD. Mate preference across the speciation continuum in a clade of mimetic butterflies. Evolution 2011; 65:1489-500. [PMID: 21521198 DOI: 10.1111/j.1558-5646.2010.01216.x] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Premating behavioral isolation is increasingly recognized as an important part of ecological speciation, where divergent natural selection causes the evolution of reproductive barriers. A number of studies have now demonstrated that traits under divergent natural selection also affect mate preferences. However, studies of single species pairs only capture a snapshot of the speciation process, making it difficult to assess the role of mate preferences throughout the entire process. Heliconius butterflies are well known for their brightly colored mimetic warning patterns, and previous studies have shown that these patterns are also used as mate recognition cues. Here, we present mate preference data for four pairs of sister taxa, representing different stages of divergence, which together allow us to compare diverging mate preferences across the continuum of Heliconius speciation. Using a novel Bayesian approach, our results support a model of ecological speciation in which strong premating isolation arises early, but continues to increase throughout the continuum from polymorphic populations through to "good," sympatric ecologically divergent species.
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Affiliation(s)
- Richard M Merrill
- Department of Zoology, University of Cambridge, Downing Street, Cambridge, CB2 3EJ, United Kingdom.
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Schilthuizen M, Giesbers MCWG, Beukeboom LW. Haldane's rule in the 21st century. Heredity (Edinb) 2011; 107:95-102. [PMID: 21224879 DOI: 10.1038/hdy.2010.170] [Citation(s) in RCA: 100] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Haldane's Rule (HR), which states that 'when in the offspring of two different animal races one sex is absent, rare, or sterile, that sex is the heterozygous (heterogametic) sex', is one of the most general patterns in speciation biology. We review the literature of the past 15 years and find that among the ∼85 new studies, many consider taxa that traditionally have not been the focus for HR investigations. The new studies increased to nine, the number of 'phylogenetically independent' groups that comply with HR. They continue to support the dominance and faster-male theories as explanations for HR, although due to increased reliance on indirect data (from, for example, differential introgression of cytoplasmic versus chromosomal loci in natural hybrid zones) unambiguous novel results are rare. We further highlight how research on organisms with sex determination systems different from those traditionally considered may lead to more insight in the underlying causes of HR. In particular, haplodiploid organisms provide opportunities for testing specific predictions of the dominance and faster X chromosome theory, and we present new data that show that the faster-male component of HR is supported in hermaphrodites, suggesting that genes involved in male function may evolve faster than those expressed in the female function.
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Affiliation(s)
- M Schilthuizen
- Netherlands Centre for Biodiversity, Naturalis, Leiden, The Netherlands.
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BROWER ANDREWVZ. Alleviating the taxonomic impediment of DNA barcoding and setting a bad precedent: names for ten species of ‘Astraptes fulgerator’ (Lepidoptera: Hesperiidae: Eudaminae) with DNA-based diagnoses. SYST BIODIVERS 2010. [DOI: 10.1080/14772000.2010.534512] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Nydam ML, Harrison RG. INTROGRESSION DESPITE SUBSTANTIAL DIVERGENCE IN A BROADCAST SPAWNING MARINE INVERTEBRATE. Evolution 2010; 65:429-42. [DOI: 10.1111/j.1558-5646.2010.01153.x] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Merrill RM, Van Schooten B, Scott JA, Jiggins CD. Pervasive genetic associations between traits causing reproductive isolation in Heliconius butterflies. Proc Biol Sci 2010; 278:511-8. [PMID: 20810445 PMCID: PMC3025683 DOI: 10.1098/rspb.2010.1493] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Ecological speciation proceeds through the accumulation of divergent traits that contribute to reproductive isolation, but in the face of gene flow traits that characterize incipient species may become disassociated through recombination. Heliconius butterflies are well known for bright mimetic warning patterns that are also used in mate recognition and cause both pre- and post-mating isolation between divergent taxa. Sympatric sister taxa representing the final stages of speciation, such as Heliconius cydno and Heliconius melpomene, also differ in ecology and hybrid fertility. We examine mate preference and sterility among offspring of crosses between these species and demonstrate the clustering of Mendelian colour pattern loci and behavioural loci that contribute to reproductive isolation. In particular, male preference for red patterns is associated with the locus responsible for the red forewing band. Two further colour pattern loci are associated, respectively, with female mating outcome and hybrid sterility. This genetic architecture in which ‘speciation genes’ are clustered in the genome can facilitate two controversial models of speciation, namely divergence in the face of gene flow and hybrid speciation.
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Affiliation(s)
- Richard M Merrill
- Department of Zoology, University of Cambridge, , Downing Street, Cambridge CB2 3EJ, UK.
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Discordant molecular and morphological evolution in buffalofishes (Actinopterygii: Catostomidae). Mol Phylogenet Evol 2010; 56:808-20. [DOI: 10.1016/j.ympev.2010.04.029] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2009] [Revised: 04/18/2010] [Accepted: 04/20/2010] [Indexed: 11/21/2022]
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McCormack JE, Heled J, Delaney KS, Peterson AT, Knowles LL. CALIBRATING DIVERGENCE TIMES ON SPECIES TREES VERSUS GENE TREES: IMPLICATIONS FOR SPECIATION HISTORY OF APHELOCOMA JAYS. Evolution 2010; 65:184-202. [DOI: 10.1111/j.1558-5646.2010.01097.x] [Citation(s) in RCA: 210] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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