1
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Gyllenhaal EF, Brady SS, DeCicco LH, Naikatini A, Hime PM, Manthey JD, Kelly J, Moyle RG, Andersen MJ. Waves of Colonization and Gene Flow in a Great Speciator. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.18.603796. [PMID: 39091784 PMCID: PMC11291091 DOI: 10.1101/2024.07.18.603796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
Secondary contact between previously allopatric lineages offers a test of reproductive isolating mechanisms that may have accrued in isolation. Such instances of contact can produce stable hybrid zones-where reproductive isolation can further develop via reinforcement or phenotypic displacement-or result in the lineages merging. Ongoing secondary contact is most visible in continental systems, where steady input from parental taxa can occur readily. In oceanic island systems, however, secondary contact between closely related species of birds is relatively rare. When observed on sufficiently small islands, relative to population size, secondary contact likely represents a recent phenomenon. Here, we examine the dynamics of a group of birds whose apparent widespread hybridization influenced Ernst Mayr's foundational work on allopatric speciation: the whistlers of Fiji (Aves: Pachycephala ). We demonstrate two clear instances of secondary contact within the Fijian archipelago, one resulting in a hybrid zone on a larger island, and the other resulting in a wholly admixed population on a smaller, adjacent island. We leveraged low genome-wide divergence in the hybrid zone to pinpoint a single genomic region associated with observed phenotypic differences. We use genomic data to present a new hypothesis that emphasizes rapid plumage evolution and post-divergence gene flow.
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2
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DeCicco LH, DeRaad DA, Ostrow EN, Moyle RG. A complete species-level phylogeny of the Erythrura parrotfinches (Aves: Estrildidae). Mol Phylogenet Evol 2023; 187:107883. [PMID: 37481145 DOI: 10.1016/j.ympev.2023.107883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 07/10/2023] [Accepted: 07/14/2023] [Indexed: 07/24/2023]
Abstract
Identifying species boundaries and phylogenetic relationships among groups of closely related species provides a necessary framework for understanding how biodiversity evolves in natural systems. Here we present a complete phylogeny of the avian genus Erythrura (family Estrildidae) commonly known as parrotfinches, which includes species threatened by habitat loss and the pet trade. Using both mitogenome and reduced-representation genome-wide nuclear DNA sequence data, we reconstructed the evolutionary history of the group by sampling all 12 recognized species, four of which had not previously been studied in a phylogenetic context. We included intra-species geographic sampling that allowed us to comment on species limits in some taxa. We recovered the Gouldian Finch (Chloebia gouldiae) of Australia which has often been placed in the monotypic genus Chloebia, as being sister to a clade comprising all Erythrura species. In addition, we recovered a well-supported clade comprising eight species distributed throughout the Pacific Island eco-region, whereas those species occurring in continental southeast Asia, the Greater Sundas, and the Philippines, were recovered as earlier branching lineages. Of note was the early branching of the Fiji-endemic E. kleinschmidti which corroborates its unique phenotype. We also found a deep phylogenetic split (8.59% corrected, 7.89% uncorrected divergence in the mitochondrial gene ND2) between the Java and Philippine populations of E. hyperythra, indicating unrecognized species-level diversity within this taxon. In contrast, genome-wide nuclear data suggested that the New Guinea endemic species E. papuana is embedded within the widespread species E. trichroa in all phylogenetic reconstructions, corroborating previously published mitochondrial data that suggested a similar pattern. By generating a phylogenetic hypothesis for the relationships among all species of Erythrura parrotfinches, we provide a framework for better understanding the extant diversity and evolutionary history of this group.
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Affiliation(s)
- Lucas H DeCicco
- Biodiversity Institute and Natural History Museum, University of Kansas, Lawrence, KS, USA.
| | - Devon A DeRaad
- Biodiversity Institute and Natural History Museum, University of Kansas, Lawrence, KS, USA
| | - Emily N Ostrow
- Biodiversity Institute and Natural History Museum, University of Kansas, Lawrence, KS, USA
| | - Robert G Moyle
- Biodiversity Institute and Natural History Museum, University of Kansas, Lawrence, KS, USA
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3
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Cowles SA, Witt CC, Bonaccorso E, Grewe F, Uy JAC. Early stages of speciation with gene flow in the Amazilia Hummingbird (
Amazilis amazilia
) subspecies complex of Western South America. Ecol Evol 2022; 12:e8895. [PMID: 35592064 PMCID: PMC9102506 DOI: 10.1002/ece3.8895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 03/22/2022] [Accepted: 04/14/2022] [Indexed: 11/06/2022] Open
Affiliation(s)
- Sarah A. Cowles
- Department of Biology University of Miami Coral Gables Florida USA
| | - Christopher C. Witt
- Department of Biology and Museum of Southwestern Biology University of New Mexico Albuquerque New Mexico USA
| | - Elisa Bonaccorso
- Laboratorio de Biología Evolutiva, Colegio de Ciencias Biológicas y Ambientales Universidad San Francisco de Quito Quito Ecuador
- Centro de Investigación de la Biodiversidad y Cambio Climático Universidad Tecnológica Indoamérica Quito Ecuador
| | - Felix Grewe
- Grainger Bioinformatics Center Field Museum Chicago Illinois USA
| | - J. Albert C. Uy
- Department of Biology University of Miami Coral Gables Florida USA
- Department of Biology University of Rochester Rochester New York USA
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4
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Abstract
Many species of plants, animals, and microorganisms exchange genes well after the point of evolutionary divergence at which taxonomists recognize them as species. Genomes contain signatures of past gene exchange and, in some cases, they reveal a legacy of lineages that no longer exist. But genomic data are not available for many organisms, and particularly problematic for reconstructing and interpreting evolutionary history are communities that have been depleted by extinctions. For these, morphology may substitute for genes, as exemplified by the history of Darwin's finches on the Galápagos islands of Floreana and San Cristóbal. Darwin and companions collected seven specimens of a uniquely large form of Geospiza magnirostris in 1835. The populations became extinct in the next few decades, partly due to destruction of Opuntia cactus by introduced goats, whereas Geospiza fortis has persisted to the present. We used measurements of large samples of G. fortis collected for museums in the period 1891 to 1906 to test for unusually large variances and skewed distributions of beak and body size resulting from introgression. We found strong evidence of hybridization on Floreana but not on San Cristóbal. The skew is in the direction of the absent G. magnirostris We estimate introgression influenced 6% of the frequency distribution that was eroded by selection after G. magnirostris became extinct on these islands. The genetic residuum of an extinct species in an extant one has implications for its future evolution, as well as for a conservation program of reintroductions in extinction-depleted communities.
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Guo K, Zhong J, Xie F, Zhu L, Qu Y, Ji X. Climate warming will increase chances of hybridization and introgression between two Takydromus lizards (Lacertidae). Ecol Evol 2021; 11:8573-8584. [PMID: 34257917 PMCID: PMC8258214 DOI: 10.1002/ece3.7671] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 04/23/2021] [Accepted: 04/27/2021] [Indexed: 11/06/2022] Open
Abstract
Coexisting species may experience population and range changes alone or jointly in response to environmental change. Here, we used six climate variables and ten modeling algorithms to predict the distribution of two Takydromus species (T. septentrionalis and T. sexlineatus) in China. We identified the sympatric and allopatric areas by comparing projections between the two species based on habitat suitability under present and future climate scenarios. We constructed the hypervolumes of six climate variables for the two species and then evaluated overlaps between hypervolumes. From this study, we know the following. First, minimum temperature of coldest month contributes the most to the prediction of habitat suitability. Second, habitats suitable for the two species will shift northward in response to climate warming. Third, the range of T. sexlineatus will expand across the four future time intervals before 2,100, namely the 2021-2040, 2041-2060, 2061-2080, and 2081-2100 intervals, under both Shared socioeconomic pathway (SSP) 245 and SSP585 scenarios, and the range of T. septentrionalis will also expand in the future except at the 2081-2100 interval under the SSP585 scenario. Fourth, the sympatric areas will contract or expand under the SSP245 scenario and expand across the four future time intervals before 2,100 under the SSP585 scenario. Fifth, the niche hypervolumes of the two species partially overlapped, and the differences in niche centroid show some degree of niche differentiation between the two species. These results allow to conclude that climate warming will not only drive the northward drift of sympatric areas but also increase the size of these areas if nothing is done to limit the emission of greenhouse gases. Given the existence of hybridization and introgression between T. septentrionalis and T. sexlineatus in the field where they coexist, we also conclude that climate warming will increase chances of hybridization and introgression between the two species.
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Affiliation(s)
- Kun Guo
- Jiangsu Key Laboratory for Biodiversity and BiotechnologyCollege of Life SciencesNanjing Normal UniversityNanjingChina
- College of Life and Environmental SciencesWenzhou UniversityWenzhouChina
| | - Jun Zhong
- Jiangsu Key Laboratory for Biodiversity and BiotechnologyCollege of Life SciencesNanjing Normal UniversityNanjingChina
- College of Life and Environmental SciencesWenzhou UniversityWenzhouChina
| | - Fan Xie
- Jiangsu Key Laboratory for Biodiversity and BiotechnologyCollege of Life SciencesNanjing Normal UniversityNanjingChina
| | - Lin Zhu
- Jiangsu Key Laboratory for Biodiversity and BiotechnologyCollege of Life SciencesNanjing Normal UniversityNanjingChina
| | - Yan‐Fu Qu
- Jiangsu Key Laboratory for Biodiversity and BiotechnologyCollege of Life SciencesNanjing Normal UniversityNanjingChina
| | - Xiang Ji
- Jiangsu Key Laboratory for Biodiversity and BiotechnologyCollege of Life SciencesNanjing Normal UniversityNanjingChina
- College of Life and Environmental SciencesWenzhou UniversityWenzhouChina
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6
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O'Connell KA, Prates I, Scheinberg LA, Mulder KP, Bell RC. Speciation and secondary contact in a fossorial island endemic, the São Tomé caecilian. Mol Ecol 2021; 30:2859-2871. [PMID: 33969550 DOI: 10.1111/mec.15928] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 04/07/2021] [Accepted: 04/14/2021] [Indexed: 02/06/2023]
Abstract
A period of isolation in allopatry typically precedes local adaptation and subsequent divergence among lineages. Alternatively, locally adapted phenotypes may arise and persist in the face of gene flow, resulting in strong correlations between ecologically-relevant phenotypic variation and corresponding environmental gradients. Quantifying genetic, ecological, and phenotypic divergence in such lineages can provide insights into the abiotic and biotic mechanisms that structure populations and drive the accumulation of phenotypic and taxonomic diversity. Low-vagility organisms whose distributions span ephemeral geographic barriers present the ideal evolutionary context within which to address these questions. Here, we combine genetic (mtDNA and genome-wide SNPs) and phenotypic data to investigate the divergence history of caecilians (Amphibia: Gymnophiona) endemic to the oceanic island of São Tomé in the Gulf of Guinea archipelago. Consistent with a previous mtDNA study, we find two phenotypically and genetically distinct lineages that occur along a north-to-south axis with extensive admixture in the centre of the island. Demographic modelling supports divergence in allopatry (~300 kya) followed by secondary contact (~95 kya). Consequently, in contrast to a morphological study that interpreted latitudinal phenotypic variation in these caecilians as a cline within a single widespread species, our analyses suggest a history of allopatric lineage divergence and subsequent hybridization that may have blurred species boundaries. We propose that late Pleistocene volcanic activity favoured allopatric divergence between these lineages with local adaptation to climate maintaining a stable hybrid zone in the centre of São Tomé Island. Our study joins a growing number of systems demonstrating lineage divergence on volcanic islands with stark environmental transitions across small geographic distances.
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Affiliation(s)
- Kyle A O'Connell
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA.,Global Genome Initiative, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA.,Department of Biological Sciences, George Washington University, Washington, DC, USA
| | - Ivan Prates
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA.,Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, MI, USA
| | - Lauren A Scheinberg
- Department of Herpetology, California Academy of Sciences, San Francisco, CA, USA
| | - Kevin P Mulder
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA.,CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal.,Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC, USA
| | - Rayna C Bell
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA.,Department of Herpetology, California Academy of Sciences, San Francisco, CA, USA
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7
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Hybridization increases population variation during adaptive radiation. Proc Natl Acad Sci U S A 2019; 116:23216-23224. [PMID: 31659024 DOI: 10.1073/pnas.1913534116] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Adaptive radiations are prominent components of the world's biodiversity. They comprise many species derived from one or a small number of ancestral species in a geologically short time that have diversified into a variety of ecological niches. Several authors have proposed that introgressive hybridization has been important in the generation of new morphologies and even new species, but how that happens throughout evolutionary history is not known. Interspecific gene exchange is expected to have greatest impact on variation if it occurs after species have diverged genetically and phenotypically but before genetic incompatibilities arise. We use a dated phylogeny to infer that populations of Darwin's finches in the Galápagos became more variable in morphological traits through time, consistent with the hybridization hypothesis, and then declined in variation after reaching a peak. Some species vary substantially more than others. Phylogenetic inferences of hybridization are supported by field observations of contemporary hybridization. Morphological effects of hybridization have been investigated on the small island of Daphne Major by documenting changes in hybridizing populations of Geospiza fortis and Geospiza scandens over a 30-y period. G. scandens showed more evidence of admixture than G. fortis Beaks of G. scandens became progressively blunter, and while variation in length increased, variation in depth decreased. These changes imply independent effects of introgression on 2, genetically correlated, beak dimensions. Our study shows how introgressive hybridization can alter ecologically important traits, increase morphological variation as a radiation proceeds, and enhance the potential for future evolution in changing environments.
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8
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Cowles SA, Uy JAC. Rapid, complete reproductive isolation in two closely related
Zosterops
White‐eye bird species despite broadly overlapping ranges*. Evolution 2019; 73:1647-1662. [DOI: 10.1111/evo.13797] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 06/06/2019] [Indexed: 12/13/2022]
Affiliation(s)
- Sarah A. Cowles
- Department of BiologyUniversity of Miami Coral Gables Florida 33146
| | - J. Albert C. Uy
- Department of BiologyUniversity of Miami Coral Gables Florida 33146
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9
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Pacheco-Sierra G, Vázquez-Domínguez E, Pérez-Alquicira J, Suárez-Atilano M, Domínguez-Laso J. Ancestral Hybridization Yields Evolutionary Distinct Hybrids Lineages and Species Boundaries in Crocodiles, Posing Unique Conservation Conundrums. Front Ecol Evol 2018. [DOI: 10.3389/fevo.2018.00138] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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10
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Diedericks G, Henriques R, von der Heyden S, Weyl OLF, Hui C. Sleeping with the enemy: introgressive hybridization in two invasive centrarchids. JOURNAL OF FISH BIOLOGY 2018; 93:405-410. [PMID: 29959774 DOI: 10.1111/jfb.13730] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2017] [Accepted: 06/15/2018] [Indexed: 05/25/2023]
Abstract
Introgressive hybridization between Micropterus dolomieu and Micropterus salmoides was assessed in their invaded South African range using nine microsatellite markers and two mtDNA gene regions. Although M. dolomieu and M. salmoides are distantly related, indicated by the large uncorrected pairwise distances observed between the two species, mitochondrial introgression and unidirectional admixture was detected.
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Affiliation(s)
- Genevieve Diedericks
- Centre for Invasion Biology, Department of Botany and Zoology, Stellenbosch University, Matieland, Stellenbosch, South Africa
- Evolutionary Genomics Group, Department of Botany and Zoology, Stellenbosch University, Matieland, Stellenbosch, South Africa
| | - Romina Henriques
- Section for Marine Living Resources, National Institute of Aquatic Resources, Technical University of Denmark, Lyngby, Denmark
| | - Sophie von der Heyden
- Evolutionary Genomics Group, Department of Botany and Zoology, Stellenbosch University, Matieland, Stellenbosch, South Africa
| | - Olaf L F Weyl
- DST/NRF Research Chair in Inland Fisheries and Freshwater Ecology, South African Institute for Aquatic Biodiversity (SAIAB), Grahamstown, South Africa
- Centre for Invasion Biology, South African Institute for Aquatic Biodiversity (SAIAB), Grahamstown, South Africa
| | - Cang Hui
- Centre for Invasion Biology, Department of Mathematical Sciences, Stellenbosch University, Matieland, Stellenbosch, South Africa
- Mathematical Biosciences Group, African Institute for Mathematical Sciences, Cape Town, South Africa
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11
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Semenov GA, Scordato ESC, Khaydarov DR, Smith C, Kane NC, Safran RJ. Effects of assortative mate choice on the genomic and morphological structure of a hybrid zone between two bird subspecies. Mol Ecol 2017; 26:6430-6444. [DOI: 10.1111/mec.14376] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Revised: 08/15/2017] [Accepted: 09/27/2017] [Indexed: 12/20/2022]
Affiliation(s)
- Georgy A. Semenov
- Department of Ecology & Evolutionary Biology The University of Arizona Tucson AZ USA
- Institute of Systematics and Ecology of Animals Novosibirsk Russia
| | | | | | - Chris C. R. Smith
- Department of Ecology and Evolutionary Biology The University of Colorado Boulder CO USA
| | - Nolan C. Kane
- Department of Ecology and Evolutionary Biology The University of Colorado Boulder CO USA
| | - Rebecca J. Safran
- Department of Ecology and Evolutionary Biology The University of Colorado Boulder CO USA
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12
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Scordato ESC, Wilkins MR, Semenov G, Rubtsov AS, Kane NC, Safran RJ. Genomic variation across two barn swallow hybrid zones reveals traits associated with divergence in sympatry and allopatry. Mol Ecol 2017; 26:5676-5691. [DOI: 10.1111/mec.14276] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 07/19/2017] [Accepted: 07/24/2017] [Indexed: 12/31/2022]
Affiliation(s)
| | - Matthew R. Wilkins
- Department of Ecology and Evolutionary Biology The University of Colorado Boulder CO USA
- School of Biological Sciences University of Nebraska‐Lincoln Lincoln NE USA
| | - Georgy Semenov
- Department of Ecology & Evolutionary Biology University of Arizona Tucson AZ USA
- Institute of Systematics and Ecology of Animals Novosibirsk Russia
| | | | - Nolan C. Kane
- Department of Ecology and Evolutionary Biology The University of Colorado Boulder CO USA
| | - Rebecca J. Safran
- Department of Ecology and Evolutionary Biology The University of Colorado Boulder CO USA
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13
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14
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Purcell J, Zahnd S, Athanasiades A, Türler R, Chapuisat M, Brelsford A. Ants exhibit asymmetric hybridization in a mosaic hybrid zone. Mol Ecol 2016; 25:4866-74. [PMID: 27506180 DOI: 10.1111/mec.13799] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2016] [Revised: 07/13/2016] [Accepted: 07/14/2016] [Indexed: 02/06/2023]
Abstract
Research on hybridization between species provides unparalleled insights into the pre- and postzygotic isolating mechanisms that drive speciation. In social organisms, colony-level incompatibilities may provide additional reproductive barriers not present in solitary species, and hybrid zones offer an opportunity to identify these barriers. Here, we use genotyping-by-sequencing to sequence hundreds of markers in a hybrid zone between two socially polymorphic ant species, Formica selysi and Formica cinerea. We characterize the zone, determine the frequency of hybrid workers, infer whether hybrid queens or males are produced and investigate whether hybridization is influenced by colony social organization. We also compare cuticular hydrocarbon profiles and aggression levels between the two species. The hybrid zone exhibits a mosaic structure. The asymmetric distribution of hybrids skewed towards F. cinerea suggests a pattern of unidirectional nuclear gene flow from F. selysi into F. cinerea. The occurrence of backcrossed individuals indicates that hybrid queens and/or males are fertile, and the presence of the F. cinerea mitochondrial haplotype in 97% of hybrids shows that successful F1 hybrids will generally have F. cinerea mothers and F. selysi fathers. We found no evidence that social organization contributes to speciation, because hybrids occur in both single-queen and multiple-queen colonies. Strongly differentiated cuticular hydrocarbon profiles and heightened interspecific aggression further reveal that species recognition cues are both present and perceived. The discovery of fertile hybrids and asymmetrical gene flow is unusual in ants, and this hybrid zone will therefore provide an ideal system with which to investigate speciation in social insects.
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Affiliation(s)
- Jessica Purcell
- Department of Ecology and Evolution, University of Lausanne, 1015, Lausanne, Switzerland. .,Department of Entomology, University of California, Riverside, Riverside, CA, 92521, USA.
| | - Sacha Zahnd
- Department of Ecology and Evolution, University of Lausanne, 1015, Lausanne, Switzerland
| | - Anouk Athanasiades
- Department of Ecology and Evolution, University of Lausanne, 1015, Lausanne, Switzerland
| | - Rebecca Türler
- Department of Ecology and Evolution, University of Lausanne, 1015, Lausanne, Switzerland
| | - Michel Chapuisat
- Department of Ecology and Evolution, University of Lausanne, 1015, Lausanne, Switzerland
| | - Alan Brelsford
- Department of Ecology and Evolution, University of Lausanne, 1015, Lausanne, Switzerland.,Department of Biology, University of California, Riverside, Riverside, CA, 92521, USA
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