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Moran BM, Payne C, Langdon Q, Powell DL, Brandvain Y, Schumer M. The genomic consequences of hybridization. eLife 2021; 10:e69016. [PMID: 34346866 PMCID: PMC8337078 DOI: 10.7554/elife.69016] [Citation(s) in RCA: 84] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 07/09/2021] [Indexed: 12/29/2022] Open
Abstract
In the past decade, advances in genome sequencing have allowed researchers to uncover the history of hybridization in diverse groups of species, including our own. Although the field has made impressive progress in documenting the extent of natural hybridization, both historical and recent, there are still many unanswered questions about its genetic and evolutionary consequences. Recent work has suggested that the outcomes of hybridization in the genome may be in part predictable, but many open questions about the nature of selection on hybrids and the biological variables that shape such selection have hampered progress in this area. We synthesize what is known about the mechanisms that drive changes in ancestry in the genome after hybridization, highlight major unresolved questions, and discuss their implications for the predictability of genome evolution after hybridization.
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Affiliation(s)
- Benjamin M Moran
- Department of Biology, Stanford UniversityStanfordUnited States
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca”HidalgoMexico
| | - Cheyenne Payne
- Department of Biology, Stanford UniversityStanfordUnited States
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca”HidalgoMexico
| | - Quinn Langdon
- Department of Biology, Stanford UniversityStanfordUnited States
| | - Daniel L Powell
- Department of Biology, Stanford UniversityStanfordUnited States
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca”HidalgoMexico
| | - Yaniv Brandvain
- Department of Ecology, Evolution & Behavior and Plant and Microbial Biology, University of MinnesotaMinneapolisUnited States
| | - Molly Schumer
- Department of Biology, Stanford UniversityStanfordUnited States
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca”HidalgoMexico
- Hanna H. Gray Fellow, Howard Hughes Medical InstituteStanfordUnited States
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2
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Batalha-Filho H, Maldonado-Coelho M, Miyaki CY. Historical climate changes and hybridization shaped the evolution of Atlantic Forest spinetails (Aves: Furnariidae). Heredity (Edinb) 2019; 123:675-693. [PMID: 31123344 DOI: 10.1038/s41437-019-0234-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 05/04/2019] [Accepted: 05/09/2019] [Indexed: 01/23/2023] Open
Abstract
Combining phylogeographic approaches and hybrid zone inference in a single framework is a robust way to depict respectively the biogeographic history of lineages and the evolutionary processes responsible for speciation. Here, we studied the spatiotemporal patterns of diversification and characterize the hybrid zone between two Atlantic Forest spinetails (Synallaxis ruficapilla and Synallaxis cinerea) using mitochondrial DNA and nuclear (autosomal and Z-linked) genes. We consistently recovered divergence between and within the two species during the late Pliocene and Pleistocene using an isolation with migration model. Also, our results indicate distinct levels of introgression among lineages. Ecological niche models and demographic inferences, used to infer range distributions throughout the late Quaternary, were not consistent with the hypothesis of a large river as a primary barrier responsible for the divergence of the two species. Instead, a scenario of isolation and divergence followed by geographic expansion and admixture as a consequence of Quaternary climatic oscillations was supported. Paleomodels also were not consistent with the idea that the hybrid zone originated in primary differentiation and favor a secondary contact scenario. Model fitting indicated that clines of different loci spanning the hybrid zone are coincident and concordant. The narrow cline for one Z-linked locus could be indicative of some form of post-zygotic selection hindering genetic homogenization between the two species.
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Affiliation(s)
| | | | - Cristina Yumi Miyaki
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
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3
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Rifkin JL, Castillo AS, Liao IT, Rausher MD. Gene flow, divergent selection and resistance to introgression in two species of morning glories (Ipomoea). Mol Ecol 2019; 28:1709-1729. [PMID: 30451335 DOI: 10.1111/mec.14945] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 09/03/2018] [Accepted: 11/01/2018] [Indexed: 02/03/2023]
Abstract
Gene flow is thought to impede genetic divergence and speciation by homogenizing genomes. Recent theory and research suggest that sufficiently strong divergent selection can overpower gene flow, leading to loci that are highly differentiated compared to others. However, there are also alternative explanations for this pattern. Independent evidence that loci in highly differentiated regions are under divergent selection would allow these explanations to be distinguished, but such evidence is scarce. Here, we present multiple lines of evidence that many of the highly divergent SNPs in a pair of sister morning glory species, Ipomoea cordatotriloba and I. lacunosa, are the result of divergent selection in the face of gene flow. We analysed a SNP data set across the genome to assess the amount of gene flow, resistance to introgression and patterns of selection on loci resistant to introgression. We show that differentiation between the two species is much lower in sympatry than in allopatry, consistent with interspecific gene flow in sympatry. Gene flow appears to be substantially greater from I. lacunosa to I. cordatotriloba than in the reverse direction, resulting in sympatric and allopatric I. cordatotriloba being substantially more different than sympatric and allopatric I. lacunosa. Many SNPs highly differentiated in allopatry have experienced divergent selection, and, despite gene flow in sympatry, resist homogenization in sympatry. Finally, five out of eight floral and inflorescence characteristics measured exhibit asymmetric convergence in sympatry. Consistent with the pattern of gene flow, I. cordatotriloba traits become much more like those of I. lacunosa than the reverse. Our investigation reveals the complex interplay between selection and gene flow that can occur during the early stages of speciation.
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Affiliation(s)
- Joanna L Rifkin
- Department of Biology, Duke University, Durham, North Carolina
| | | | - Irene T Liao
- Department of Biology, Duke University, Durham, North Carolina
| | - Mark D Rausher
- Department of Biology, Duke University, Durham, North Carolina
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4
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Sciuchetti L, Dufresnes C, Cavoto E, Brelsford A, Perrin N. Dobzhansky-Muller incompatibilities, dominance drive, and sex-chromosome introgression at secondary contact zones: A simulation study. Evolution 2018; 72:1350-1361. [PMID: 29806172 DOI: 10.1111/evo.13510] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 05/08/2018] [Indexed: 11/28/2022]
Abstract
Dobzhansky-Muller (DM) incompatibilities involving sex chromosomes have been proposed to account for Haldane's rule (lowered fitness among hybrid offspring of the heterogametic sex) as well as Darwin's corollary (asymmetric fitness costs with respect to the direction of the cross). We performed simulation studies of a hybrid zone to investigate the effects of different types of DM incompatibilities on cline widths and positions of sex-linked markers. From our simulations, X-Y incompatibilities generate steep clines for both X-linked and Y-linked markers; random effects may produce strong noise in cline center positions when migration is high relative to fitness costs, but X- and Y-centers always coincide strictly. X-autosome and Y-autosome incompatibilities also generate steep clines, but systematic shifts in cline centers occur when migration is high relative to selection, as a result of a dominance drive linked to Darwin's corollary. Interestingly, sex-linked genes always show farther introgression than the associated autosomal genes. We discuss ways of disentangling the potentially confounding effects of sex biases in migration, we compare our results to those of a few documented contact zones, and we stress the need to study independent replicates of the same contact zone.
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Affiliation(s)
- Luca Sciuchetti
- Department of Ecology & Evolution, University of Lausanne, Biophore Building, Lausanne, 1015, Switzerland
| | - Christophe Dufresnes
- Department of Ecology & Evolution, University of Lausanne, Biophore Building, Lausanne, 1015, Switzerland
- Department of Animal & Plant Sciences, University of Sheffield, Alfred Denny building, Western Bank, Sheffield, S10 2TN, United Kingdom
| | - Elisa Cavoto
- Department of Ecology & Evolution, University of Lausanne, Biophore Building, Lausanne, 1015, Switzerland
| | - Alan Brelsford
- Department of Ecology & Evolution, University of Lausanne, Biophore Building, Lausanne, 1015, Switzerland
- Biology Department, University of California, Riverside, CA, 92521
| | - Nicolas Perrin
- Department of Ecology & Evolution, University of Lausanne, Biophore Building, Lausanne, 1015, Switzerland
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5
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Sung C, Bell KL, Nice CC, Martin NH. Integrating Bayesian genomic cline analyses and association mapping of morphological and ecological traits to dissect reproductive isolation and introgression in a Louisiana Iris hybrid zone. Mol Ecol 2018; 27:959-978. [DOI: 10.1111/mec.14481] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 12/14/2017] [Indexed: 01/01/2023]
Affiliation(s)
- Cheng‐Jung Sung
- Population and Conservation Biology Program Department of Biology Texas State University San Marcos TX USA
| | - Katherine L. Bell
- Population and Conservation Biology Program Department of Biology Texas State University San Marcos TX USA
| | - Chris C. Nice
- Population and Conservation Biology Program Department of Biology Texas State University San Marcos TX USA
| | - Noland H. Martin
- Population and Conservation Biology Program Department of Biology Texas State University San Marcos TX USA
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6
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Graham AM, Lavretsky P, Muñoz-Fuentes V, Green AJ, Wilson RE, McCracken KG. Migration-Selection Balance Drives Genetic Differentiation in Genes Associated with High-Altitude Function in the Speckled Teal (Anas flavirostris) in the Andes. Genome Biol Evol 2018; 10:14-32. [PMID: 29211852 PMCID: PMC5757641 DOI: 10.1093/gbe/evx253] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/30/2017] [Indexed: 12/30/2022] Open
Abstract
Local adaptation frequently occurs across populations as a result of migration-selection balance between divergent selective pressures and gene flow associated with life in heterogeneous landscapes. Studying the effects of selection and gene flow on the adaptation process can be achieved in systems that have recently colonized extreme environments. This study utilizes an endemic South American duck species, the speckled teal (Anas flavirostris), which has both high- and low-altitude populations. High-altitude speckled teal (A. f. oxyptera) are locally adapted to the Andean environment and mostly allopatric from low-altitude birds (A. f. flavirostris); however, there is occasional gene flow across altitudinal gradients. In this study, we used next-generation sequencing to explore genetic patterns associated with high-altitude adaptation in speckled teal populations, as well as the extent to which the balance between selection and migration have affected genetic architecture. We identified a set of loci with allele frequencies strongly correlated with altitude, including those involved in the insulin-like signaling pathway, bone morphogenesis, oxidative phosphorylation, responders to hypoxia-induced DNA damage, and feedback loops to the hypoxia-inducible factor pathway. These same outlier loci were found to have depressed gene flow estimates, as well as being highly concentrated on the Z-chromosome. Our results suggest a multifactorial response to life at high altitudes through an array of interconnected pathways that are likely under positive selection and whose genetic components seem to be providing an effective genomic barrier to interbreeding, potentially functioning as an avenue for population divergence and speciation.
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Affiliation(s)
| | | | - Violeta Muñoz-Fuentes
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
- Estación Biológica de Doñana, EBD-CSIC, Sevilla, Spain
| | - Andy J Green
- Estación Biológica de Doñana, EBD-CSIC, Sevilla, Spain
| | - Robert E Wilson
- Institute of Arctic Biology and University of Alaska Museum, University of Alaska, Fairbanks
| | - Kevin G McCracken
- Department of Biology, University of Miami
- Institute of Arctic Biology and University of Alaska Museum, University of Alaska, Fairbanks
- Rosenstiel School of Marine and Atmospheric Sciences, University of Miami
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine
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8
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Morales-Rozo A, Tenorio EA, Carling MD, Cadena CD. Origin and cross-century dynamics of an avian hybrid zone. BMC Evol Biol 2017; 17:257. [PMID: 29246108 PMCID: PMC5732383 DOI: 10.1186/s12862-017-1096-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 11/27/2017] [Indexed: 01/07/2023] Open
Abstract
Background Characterizations of the dynamics of hybrid zones in space and time can give insights about traits and processes important in population divergence and speciation. We characterized a hybrid zone between tanagers in the genus Ramphocelus (Aves, Thraupidae) located in southwestern Colombia. We evaluated whether this hybrid zone originated as a result of secondary contact or of primary differentiation, and described its dynamics across time using spatial analyses of molecular, morphological, and coloration data in combination with paleodistribution modeling. Results Models of potential historical distributions based on climatic data and genetic signatures of demographic expansion suggested that the hybrid zone likely originated following secondary contact between populations that expanded their ranges out of isolated areas in the Quaternary. Concordant patterns of variation in phenotypic characters across the hybrid zone and its narrow extent are suggestive of a tension zone, maintained by a balance between dispersal and selection against hybrids. Estimates of phenotypic cline parameters obtained using specimens collected over nearly a century revealed that, in recent decades, the zone appears to have moved to the east and to higher elevations, and may have become narrower. Genetic variation was not clearly structured along the hybrid zone, but comparisons between historical and contemporary specimens suggested that temporal changes in its genetic makeup may also have occurred. Conclusions Our data suggest that the hybrid zone likey resulted from secondary contact between populations. The observed changes in the hybrid zone may be a result of sexual selection, asymmetric gene flow, or environmental change. Electronic supplementary material The online version of this article (doi: 10.1186/s12862-017-1096-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Andrea Morales-Rozo
- Laboratorio de Biología Evolutiva de Vertebrados, Departamento de Ciencias Biológicas, Universidad de Los Andes, Bogotá, Colombia.,Programa de Biología y Museo de Historia Natural, Universidad de los Llanos, Sede Barcelona, Villavicencio, Colombia
| | - Elkin A Tenorio
- Laboratorio de Biología Evolutiva de Vertebrados, Departamento de Ciencias Biológicas, Universidad de Los Andes, Bogotá, Colombia.,Calima: Fundación para la Investigación de la Biodiversidad y Conservación en el Trópico, Cali, Colombia
| | - Matthew D Carling
- Cornell Laboratory of Ornithology, Cornell University, Ithaca, NY, USA.,Department of Zoology and Physiology, University of Wyoming, Laramie, WY, USA
| | - Carlos Daniel Cadena
- Laboratorio de Biología Evolutiva de Vertebrados, Departamento de Ciencias Biológicas, Universidad de Los Andes, Bogotá, Colombia.
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9
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Kenney AM, Sweigart AL. Reproductive isolation and introgression between sympatric
Mimulus
species. Mol Ecol 2016; 25:2499-517. [DOI: 10.1111/mec.13630] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Revised: 03/18/2016] [Accepted: 03/22/2016] [Indexed: 01/19/2023]
Affiliation(s)
- Amanda M. Kenney
- Department of Genetics University of Georgia Athens GA 30602 USA
- Department of Biological Sciences St. Edward's University Austin TX 78704 USA
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10
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Lavretsky P, Dacosta JM, Hernández-Baños BE, Engilis A, Sorenson MD, Peters JL. Speciation genomics and a role for the Z chromosome in the early stages of divergence between Mexican ducks and mallards. Mol Ecol 2015; 24:5364-78. [DOI: 10.1111/mec.13402] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Revised: 09/23/2015] [Accepted: 09/24/2015] [Indexed: 02/01/2023]
Affiliation(s)
- Philip Lavretsky
- Department of Biological Sciences; Wright State University; 3640 Colonel Glenn Hwy Dayton OH 45435 USA
| | | | - Blanca E. Hernández-Baños
- Departamento de Biología Evolutiva; Facultad de Ciencias; Universidad Nacional Autónoma de México; México Distrito Federal México
| | - Andrew Engilis
- Museum of Wildlife and Fish Biology; Department of Wildlife, Fish, and Conservation Biology; University of California, Davis; One Shields Avenue Davis CA 95616 USA
- Department of Wildlife, Fish and Conservation Biology; University of California, Davis; One Shields Avenue Davis CA 95616 USA
| | | | - Jeffrey L. Peters
- Department of Biological Sciences; Wright State University; 3640 Colonel Glenn Hwy Dayton OH 45435 USA
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11
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de Lafontaine G, Prunier J, Gérardi S, Bousquet J. Tracking the progression of speciation: variable patterns of introgression across the genome provide insights on the species delimitation between progenitor-derivative spruces (Picea mariana×P. rubens). Mol Ecol 2015; 24:5229-47. [DOI: 10.1111/mec.13377] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Revised: 08/05/2015] [Accepted: 09/01/2015] [Indexed: 01/17/2023]
Affiliation(s)
- Guillaume de Lafontaine
- Canada Research Chair in Forest and Environmental Genomics; Centre for Forest Research and Institute of Systems and Integrative Biology; Université Laval; 1030 Avenue de la Médecine Québec QC G1V 0A6 Canada
| | - Julien Prunier
- Canada Research Chair in Forest and Environmental Genomics; Centre for Forest Research and Institute of Systems and Integrative Biology; Université Laval; 1030 Avenue de la Médecine Québec QC G1V 0A6 Canada
| | - Sébastien Gérardi
- Canada Research Chair in Forest and Environmental Genomics; Centre for Forest Research and Institute of Systems and Integrative Biology; Université Laval; 1030 Avenue de la Médecine Québec QC G1V 0A6 Canada
| | - Jean Bousquet
- Canada Research Chair in Forest and Environmental Genomics; Centre for Forest Research and Institute of Systems and Integrative Biology; Université Laval; 1030 Avenue de la Médecine Québec QC G1V 0A6 Canada
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12
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Gante HF, Doadrio I, Alves MJ, Dowling TE. Semi-permeable species boundaries in Iberian barbels (Barbus and Luciobarbus, Cyprinidae). BMC Evol Biol 2015; 15:111. [PMID: 26066794 PMCID: PMC4465174 DOI: 10.1186/s12862-015-0392-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2015] [Accepted: 05/28/2015] [Indexed: 12/04/2022] Open
Abstract
BACKGROUND The evolution of species boundaries and the relative impact of selection and gene flow on genomic divergence are best studied in populations and species pairs exhibiting various levels of divergence along the speciation continuum. We studied species boundaries in Iberian barbels, Barbus and Luciobarbus, a system of populations and species spanning a wide degree of genetic relatedness, as well as geographic distribution and range overlap. We jointly analyze multiple types of molecular markers and morphological traits to gain a comprehensive perspective on the nature of species boundaries in these cyprinid fishes. RESULTS Intraspecific molecular and morphological differentiation is visible among many populations. Genomes of all sympatric species studied are porous to gene flow, even if they are not sister species. Compared to their allopatric counterparts, sympatric representatives of different species share alleles and show an increase in all measures of nucleotide polymorphism (S, Hd, K, π and θ). High molecular diversity is particularly striking in L. steindachneri from the Tejo and Guadiana rivers, which co-varies with other sympatric species. Interestingly, different nuclear markers introgress across species boundaries at various levels, with distinct impacts on population trees. As such, some loci exhibit limited introgression and population trees resemble the presumed species tree, while alleles at other loci introgress more freely and population trees reflect geographic affinities and interspecific gene flow. Additionally, extent of introgression decreases with increasing genetic divergence in hybridizing species pairs. CONCLUSIONS We show that reproductive isolation in Iberian Barbus and Luciobarbus is not complete and species boundaries are semi-permeable to (some) gene flow, as different species (including non-sister) are exchanging genes in areas of sympatry. Our results support a speciation-with-gene-flow scenario with heterogeneous barriers to gene flow across the genome, strengthening with genetic divergence. This is consistent with observations coming from other systems and supports the notion that speciation is not instantaneous but a gradual process, during which different species are still able to exchange some genes, while selection prevents gene flow at other loci. We also provide evidence for a hybrid origin of a barbel ecotype, L. steindachneri, suggesting that ecology plays a key role in species coexistence and hybridization in Iberian barbels. This ecotype with intermediate, yet variable, molecular, morphological, trophic and ecological characteristics is the local product of introgressive hybridization of L. comizo with up to three different species (with L. bocagei in the Tejo, with L. microcephalus and L. sclateri in the Guadiana). In spite of the homogenizing effects of ongoing gene flow, species can still be discriminated using a combination of morphological and molecular markers. Iberian barbels are thus an ideal system for the study of species boundaries, since they span a wide range of genetic divergences, with diverse ecologies and degrees of sympatry.
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Affiliation(s)
- Hugo F Gante
- School of Life Sciences, Arizona State University, 85287-4601, Tempe, AZ, USA.
- Museu Nacional de História Natural e da Ciência, Centre for Ecology, Evolution and Environmental Changes (Ce3C), Universidade de Lisboa, Rua da Escola Politécnica 58, 1250-102, Lisbon, Portugal.
- Current address: Zoological Institute, University of Basel, 4051, Basel, Switzerland.
| | - Ignacio Doadrio
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales, CSIC, c/José Gutiérrez Abascal 2, 28006, Madrid, Spain.
| | - Maria Judite Alves
- Museu Nacional de História Natural e da Ciência, Centre for Ecology, Evolution and Environmental Changes (Ce3C), Universidade de Lisboa, Rua da Escola Politécnica 58, 1250-102, Lisbon, Portugal.
| | - Thomas E Dowling
- School of Life Sciences, Arizona State University, 85287-4601, Tempe, AZ, USA.
- Current address: Department of Biological Sciences, Wayne State University, 5047 Gullen Mall, 48202, Detroit, MI, USA.
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13
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Šíchová J, Voleníková A, Dincă V, Nguyen P, Vila R, Sahara K, Marec F. Dynamic karyotype evolution and unique sex determination systems in Leptidea wood white butterflies. BMC Evol Biol 2015; 15:89. [PMID: 25981157 PMCID: PMC4436027 DOI: 10.1186/s12862-015-0375-4] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Accepted: 05/07/2015] [Indexed: 11/26/2022] Open
Abstract
Background Chromosomal rearrangements have the potential to limit the rate and pattern of gene flow within and between species and thus play a direct role in promoting and maintaining speciation. Wood white butterflies of the genus Leptidea are excellent models to study the role of chromosome rearrangements in speciation because they show karyotype variability not only among but also within species. In this work, we investigated genome architecture of three cryptic Leptidea species (L. juvernica, L. sinapis and L. reali) by standard and molecular cytogenetic techniques in order to reveal causes of the karyotype variability. Results Chromosome numbers ranged from 2n = 85 to 91 in L. juvernica and 2n = 69 to 73 in L. sinapis (both from Czech populations) to 2n = 51 to 55 in L. reali (Spanish population). We observed significant differences in chromosome numbers and localization of cytogenetic markers (rDNA and H3 histone genes) within the offspring of individual females. Using FISH with the (TTAGG)n telomeric probe we also documented the presence of multiple chromosome fusions and/or fissions and other complex rearrangements. Thus, the intraspecific karyotype variability is likely due to irregular chromosome segregation of multivalent meiotic configurations. The analysis of female meiotic chromosomes by GISH and CGH revealed multiple sex chromosomes: W1W2W3Z1Z2Z3Z4 in L. juvernica, W1W2W3Z1Z2Z3 in L. sinapis and W1W2W3W4Z1Z2Z3Z4 in L. reali. Conclusions Our results suggest a dynamic karyotype evolution and point to the role of chromosomal rearrangements in the speciation of Leptidea butterflies. Moreover, our study revealed a curious sex determination system with 3–4 W and 3–4 Z chromosomes, which is unique in the Lepidoptera and which could also have played a role in the speciation process of the three Leptidea species. Electronic supplementary material The online version of this article (doi:10.1186/s12862-015-0375-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jindra Šíchová
- Institute of Entomology, Biology Centre CAS, 370 05, České Budějovice, Czech Republic. .,Faculty of Science, University of South Bohemia, 370 05, České Budějovice, Czech Republic.
| | - Anna Voleníková
- Faculty of Science, University of South Bohemia, 370 05, České Budějovice, Czech Republic.
| | - Vlad Dincă
- Biodiversity Institute of Ontario, University of Guelph, N1G 2W1, Guelph, ON, Canada. .,Institut de Biologia Evolutiva (CSIC-Universitat Pompeu-Fabra), 08003, Barcelona, Spain.
| | - Petr Nguyen
- Institute of Entomology, Biology Centre CAS, 370 05, České Budějovice, Czech Republic. .,Faculty of Science, University of South Bohemia, 370 05, České Budějovice, Czech Republic.
| | - Roger Vila
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu-Fabra), 08003, Barcelona, Spain.
| | - Ken Sahara
- Laboratory of Applied Entomology, Faculty of Agriculture, Iwate University, Morioka, 020-8550, Japan.
| | - František Marec
- Institute of Entomology, Biology Centre CAS, 370 05, České Budějovice, Czech Republic. .,Faculty of Science, University of South Bohemia, 370 05, České Budějovice, Czech Republic.
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14
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Delmore KE, Hübner S, Kane NC, Schuster R, Andrew RL, Câmara F, Guigó R, Irwin DE. Genomic analysis of a migratory divide reveals candidate genes for migration and implicates selective sweeps in generating islands of differentiation. Mol Ecol 2015; 24:1873-88. [DOI: 10.1111/mec.13150] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Revised: 03/06/2015] [Accepted: 03/06/2015] [Indexed: 12/18/2022]
Affiliation(s)
- Kira E. Delmore
- Department of Zoology; University of British Columbia; 6270 University Blvd Vancouver BC Canada V6T1Z4
| | - Sariel Hübner
- Department of Botany; University of British Columbia; 6270 University Blvd Vancouver BC Canada V6T1Z4
| | - Nolan C. Kane
- Ecology and Evolutionary Biology; University of Colorado at Boulder; Ramaley N122 Boulder CO 80309-0334 USA
| | - Richard Schuster
- Department of Forest and Conservation Sciences; University of British Columbia; 2424 Main Mall Vancouver BC Canada V6T1Z4
| | - Rose L. Andrew
- Molecular Ecology School of Environmental and Rural Science; University of New England Armidale; Armidale NSW 2351 Australia
| | - Francisco Câmara
- Centre for Genomic Regulation and UPF; Dr Aiguader 88 Barcelona 08003 Spain
| | - Roderic Guigó
- Centre for Genomic Regulation and UPF; Dr Aiguader 88 Barcelona 08003 Spain
| | - Darren E. Irwin
- Department of Zoology; University of British Columbia; 6270 University Blvd Vancouver BC Canada V6T1Z4
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Prada C, Hellberg ME. Strong Natural Selection on Juveniles Maintains a Narrow Adult Hybrid Zone in a Broadcast Spawner. Am Nat 2014; 184:702-13. [DOI: 10.1086/678403] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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16
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Robinson JD, Bunnefeld L, Hearn J, Stone GN, Hickerson MJ. ABC inference of multi-population divergence with admixture from unphased population genomic data. Mol Ecol 2014; 23:4458-71. [PMID: 25113024 PMCID: PMC4285295 DOI: 10.1111/mec.12881] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Revised: 08/04/2014] [Accepted: 08/06/2014] [Indexed: 01/13/2023]
Abstract
Rapidly developing sequencing technologies and declining costs have made it possible to collect genome-scale data from population-level samples in nonmodel systems. Inferential tools for historical demography given these data sets are, at present, underdeveloped. In particular, approximate Bayesian computation (ABC) has yet to be widely embraced by researchers generating these data. Here, we demonstrate the promise of ABC for analysis of the large data sets that are now attainable from nonmodel taxa through current genomic sequencing technologies. We develop and test an ABC framework for model selection and parameter estimation, given histories of three-population divergence with admixture. We then explore different sampling regimes to illustrate how sampling more loci, longer loci or more individuals affects the quality of model selection and parameter estimation in this ABC framework. Our results show that inferences improved substantially with increases in the number and/or length of sequenced loci, while less benefit was gained by sampling large numbers of individuals. Optimal sampling strategies given our inferential models included at least 2000 loci, each approximately 2 kb in length, sampled from five diploid individuals per population, although specific strategies are model and question dependent. We tested our ABC approach through simulation-based cross-validations and illustrate its application using previously analysed data from the oak gall wasp, Biorhiza pallida.
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Affiliation(s)
- John D Robinson
- Department of Biology, City College of New York, 160 Convent Ave., MR 526, New York, NY, 10031, USA
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Wang W, Dai C, Alström P, Zhang C, Qu Y, Li SH, Yang X, Zhao N, Song G, Lei F. Past hybridization between two East Asian long-tailed tits (Aegithalos bonvaloti and A. fuliginosus). Front Zool 2014; 11:40. [PMID: 24883074 PMCID: PMC4040119 DOI: 10.1186/1742-9994-11-40] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Accepted: 04/28/2014] [Indexed: 11/13/2022] Open
Abstract
Introduction Incomplete lineage sorting and hybridization are two major nonexclusive causes of haplotype sharing between species. Distinguishing between these two processes is notoriously difficult as they can generate similar genetic signatures. Previous studies revealed that the mitochondrial DNA (mtDNA) differentiation between two East Asian long-tailed tits (Aegithalos bonvaloti and A. fuliginosus) was extremely low, even lower than intraspecific differentiation in some other long-tailed tits. Using a combination of multilocus and coalescent analyses, we explored the causes of the anomalous lack of mtDNA differentiation between the two species. Results The mtDNA divergence between the two species was shallow, while the nuclear DNA (nuDNA) divergence was considerably deeper. The IMa analyses based on the mtDNA dataset suggested relatively high gene flow from A. fuliginosus to A. bonvaloti, while negligible gene flow in the opposite direction. In contrast to mtDNA, the migration rates at autosomal and Z-linked nuDNA loci were negligible or much lower. The NEWHYBRIDS analysis assigned all individuals except one to pure parental species with high posterior probability. The Bayesian skyline plot showed that both species underwent population expansions during the Last Glacial Maximum (LGM), and the ecological niche modelling suggested that their ranges overlapped more during the LGM than at present. Conclusions We suggest that historical hybridization, in combination with selective sweep and/or genetic drift might be the main causes of the extremely low mtDNA differentiation between the two species. The hybridization probably occurred mainly between A. fuliginosus females and A. bonvaloti males. The LGM distribution expansion might have facilitated hybridization, while the post-LGM distribution contraction could have facilitated some mtDNA sorting. Ongoing hybridization between the two species might be very limited, but further studies with more samples from the contact zone are needed to test this conclusion.
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Affiliation(s)
- Wenjuan Wang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, No.1 Beichen West Road, Chaoyang District, 100101 Beijing, China ; Center for Watershed Ecology, Institute of Life Science, Nanchang University, 330031 Nanchang, China
| | - Chuanyin Dai
- School of Chemistry and Life Sciences, Guizhou Normal College, 550001 Guiyang, China
| | - Per Alström
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, No.1 Beichen West Road, Chaoyang District, 100101 Beijing, China ; Swedish Species Information Centre, Swedish University of Agricultural Sciences, SE-75007 Uppsala, Sweden
| | - Chunlan Zhang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, No.1 Beichen West Road, Chaoyang District, 100101 Beijing, China
| | - Yanhua Qu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, No.1 Beichen West Road, Chaoyang District, 100101 Beijing, China
| | - Shou-Hsien Li
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Xiaojun Yang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 650223 Kunming, China
| | - Na Zhao
- Key Laboratory of Ecological Impacts of Hydraulic-Projects and Restoration of Aquatic Ecosystem of Ministry of Water Resources, Institute of Hydroecology, Ministry of Water Resources and Chinese Academy of Sciences, 430079 Wuhan, China
| | - Gang Song
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, No.1 Beichen West Road, Chaoyang District, 100101 Beijing, China
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, No.1 Beichen West Road, Chaoyang District, 100101 Beijing, China
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Hamilton JA, Lexer C, Aitken SN. Differential introgression reveals candidate genes for selection across a spruce (Picea sitchensis × P. glauca) hybrid zone. THE NEW PHYTOLOGIST 2013; 197:927-938. [PMID: 23228022 DOI: 10.1111/nph.12055] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2012] [Accepted: 10/18/2012] [Indexed: 06/01/2023]
Abstract
Differential patterns of introgression between species across ecological gradients provide a fine-scale depiction of extrinsic and intrinsic factors that contribute to the maintenance of species barriers and adaptation across heterogeneous environments. Introgression was examined for 721 individuals collected from the ecological transition zone spanning maritime to continental climates within the Picea sitchensis-Picea glauca contact zone using a panel of 268 candidate gene single nucleotide polymorphisms. Geographic clines showed a strong spatial relationship between allele frequencies and both distance from the ocean along major rivers and mean annual precipitation, indicating a strong role for environmental selection. Interspecific patterns of differentiation using outlier tests revealed three candidate genes that may be targets of long-term divergent selection between the parental species, although contemporary genomic clines within the hybrid zone suggested neutral patterns of introgression for these genes. This study provides a fine-scale analysis of locus-specific introgression, identifying a suite of candidate loci that may be targets of extrinsic or intrinsic selection, with broad application in understanding local adaptation to climate.
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Affiliation(s)
- Jill A Hamilton
- Centre for Forest Conservation Genetics and Department of Forest Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Christian Lexer
- Department of Biology, Unit of Ecology and Evolution, University of Fribourg, Fribourg, Switzerland
| | - Sally N Aitken
- Centre for Forest Conservation Genetics and Department of Forest Sciences, University of British Columbia, Vancouver, BC, Canada
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Multilocus phylogeography (mitochondrial, autosomal and Z-chromosomal loci) and genetic consequence of long-distance male dispersal in Black-throated tits (Aegithalos concinnus). Heredity (Edinb) 2013; 110:457-65. [PMID: 23299099 DOI: 10.1038/hdy.2012.114] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Multilocus data from the different genomes are essential to understand the phylogeographic history of species, particularly when a species has the male-biased dispersal pattern. Although Black-throated tits (Aegithalos concinnus) are socially monogamous and cooperatively breeding birds, limited observational data suggested that males may have the ability of long-distance dispersal. We have previously detected three highly supported mitochondrial populations within two subspecies of Black-throated tits (A. c. concinnus and A. c. talifuensis). Here, we used several genetic markers with different inheritance patterns to gain insights about their phylogeographic history. Phylogenetic and individual-based Bayesian analysis showed weak geographical structure amongst nuclear sequences (autosomal and Z-chromosomal loci). Coalescent analysis revealed high levels of gene flow among mitochondrial populations, even between allopatric populations. These results strongly suggested that male-biased gene flow was responsible for the discordant cytonuclear phylogeographic patterns. Consistent with expectation on the genetic consequence of long-distance male dispersal, mantel tests revealed a significant pattern of isolation by distance for mitochondrial sequences, but failed to provide a similar pattern for nuclear genes within a continuous population; female Black-throated tits showed a stronger but not significantly different relationship of isolation by distance than males when using mitochondrial DNA alone. We discussed the contribution of male juveniles with delayed dispersal to the non-significantly different IBD patterns between sexes. Our results using multilocus genetic data revealed aspects of the complex evolutionary history of Black-throated tits and the important role of long-distance male dispersal in the population structuring.
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20
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Backström N, Saetre GP, Ellegren H. Inferring the demographic history of European Ficedula flycatcher populations. BMC Evol Biol 2013; 13:2. [PMID: 23282063 PMCID: PMC3556140 DOI: 10.1186/1471-2148-13-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Accepted: 12/22/2012] [Indexed: 12/03/2022] Open
Abstract
Background Inference of population and species histories and population stratification using genetic data is important for discriminating between different speciation scenarios and for correct interpretation of genome scans for signs of adaptive evolution and trait association. Here we use data from 24 intronic loci re-sequenced in population samples of two closely related species, the pied flycatcher and the collared flycatcher. Results We applied Isolation-Migration models, assignment analyses and estimated the genetic differentiation and diversity between species and between populations within species. The data indicate a divergence time between the species of <1 million years, significantly shorter than previous estimates using mtDNA, point to a scenario with unidirectional gene-flow from the pied flycatcher into the collared flycatcher and imply that barriers to hybridisation are still permeable in a recently established hybrid zone. Furthermore, we detect significant population stratification, predominantly between the Spanish population and other pied flycatcher populations. Conclusions Our results provide further evidence for a divergence process where different genomic regions may be at different stages of speciation. We also conclude that forthcoming analyses of genotype-phenotype relations in these ecological model species should be designed to take population stratification into account.
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Affiliation(s)
- Niclas Backström
- Department of Evolutionary Biology, Evolutionary Biology Centre (EBC), Uppsala University, Norbyvägen 18D, Uppsala, SE-752 36, Sweden.
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21
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Differences in timing of migration and response to sexual signalling drive asymmetric hybridization across a migratory divide. J Evol Biol 2012; 25:1741-50. [DOI: 10.1111/j.1420-9101.2012.02554.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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Gompert Z, Parchman TL, Buerkle CA. Genomics of isolation in hybrids. Philos Trans R Soc Lond B Biol Sci 2012; 367:439-50. [PMID: 22201173 DOI: 10.1098/rstb.2011.0196] [Citation(s) in RCA: 102] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Hybrid zones are common in nature and can offer critical insights into the dynamics and components of reproductive isolation. Hybrids between diverged lineages are particularly informative about the genetic architecture of reproductive isolation, because introgression in an admixed population is a direct measure of isolation. In this paper, we combine simulations and a new statistical model to determine the extent to which different genetic architectures of isolation leave different signatures on genome-level patterns of introgression. We found that reproductive isolation caused by one or several loci of large effect caused greater heterogeneity in patterns of introgression than architectures involving many loci with small fitness effects, particularly when isolating factors were closely linked. The same conditions that led to heterogeneous introgression often resulted in a reasonable correspondence between outlier loci and the genetic loci that contributed to isolation. However, demographic conditions affected both of these results, highlighting potential limitations to the study of the speciation genomics. Further progress in understanding the genomics of speciation will require large-scale empirical studies of introgression in hybrid zones and model-based analyses, as well as more comprehensive modelling of the expected levels of isolation with different demographies and genetic architectures of isolation.
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Affiliation(s)
- Zachariah Gompert
- Department of Botany and Program in Ecology, University of Wyoming, Laramie, WY 82071, USA.
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23
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Singhal S, Moritz C. Strong selection against hybrids maintains a narrow contact zone between morphologically cryptic lineages in a rainforest lizard. Evolution 2012; 66:1474-89. [PMID: 22519785 DOI: 10.1111/j.1558-5646.2011.01539.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Phenotypically cryptic lineages comprise an important yet understudied part of biodiversity; in particular, we have much to learn about how these lineages are formed and maintained. To better understand the evolutionary significance of such lineages, we studied a hybrid zone between two morphologically cryptic phylogeographic lineages in the rainforest lizard, Lampropholis coggeri. Analyzing a multilocus genetic dataset through cline inference, individual-based methods and population measures of disequilibrium and using simulations to explore our genetic results in context of theoretical expectations, we inferred the processes maintaining this hybrid zone. We find that these lineages meet in a hybrid zone that is narrow (≈400 m) relative to inferred dispersal rate. Further, the hybrid zone exhibits substantial genetic disequilibrium and sharply coincident and largely concordant clines. Based on our knowledge about the region's biogeography, the species' natural history, and our simulation results, we suggest that strong selection against hybrids structures this system. As all clines show a relatively narrow range of introgression, we posit that this hybrid zone might not yet be in equilibrium. Nonetheless, our results clearly show that phylogeographic lineages can evolve substantial reproductive isolation without concomitant morphological diversification, suggesting that such lineages can constitute a significant component of evolutionary diversity.
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Affiliation(s)
- Sonal Singhal
- Museum of Vertebrate Zoology, University of California, Berkeley, California 94720-3160, USA.
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24
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Hellberg ME, Dennis AB, Arbour-Reily P, Aagaard JE, Swanson WJ. The Tegula tango: a coevolutionary dance of interacting, positively selected sperm and egg proteins. Evolution 2012; 66:1681-94. [PMID: 22671539 DOI: 10.1111/j.1558-5646.2011.01530.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Reproductive proteins commonly show signs of rapid divergence driven by positive selection. The mechanisms driving these changes have remained ambiguous in part because interacting male and female proteins have rarely been examined. We isolate an egg protein the vitelline envelope receptor for lysin (VERL) from Tegula, a genus of free-spawning marine snails. Like VERL from abalone, Tegula VERL is a major component of the VE surrounding the egg, includes a conserved zona pellucida (ZP) domain at its C-terminus, and possesses a unique, negatively charged domain of about 150 amino acids implicated in interactions with the positively charged lysin. Unlike for abalone VERL, where this unique VERL domain occurs in a tandem array of 22 repeats, Tegula VERL has just one such domain. Interspecific comparisons show that both lysin and the VERL domain diverge via positive selection, whereas the ZP domain evolves neutrally. Rates of nonsynonymous substitution are correlated between lysin and the VERL domain, consistent with sexual antagonism, although lineage-specific effects, perhaps owing to different ecologies, may alter the relative evolutionary rates of sperm- and egg-borne proteins.
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Affiliation(s)
- Michael E Hellberg
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803, USA.
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The Role of Environmental Heterogeneity in Maintaining Reproductive Isolation between HybridizingPasserina(Aves: Cardinalidae) Buntings. INTERNATIONAL JOURNAL OF ECOLOGY 2012. [DOI: 10.1155/2012/295463] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Hybrid zones are useful systems in which to investigate processes important in creating and maintaining biological diversity. As they are often located in ecotones, patterns of environmental heterogeneity may influence hybridization, and may also influence the maintenance of reproductive isolation between hybridizing species. Focusing on the hybrid zone betweenPasserina amoena(Lazuli Bunting) andPasserina cyanea(Indigo Bunting), located in the eastern Rocky Mountain/western Great Plains ecotone, we examined the relationship between population-pairwise differences in the proportion of hybrids and environmental variation. Models including environmental variables explained more of the variation in hybridization rates across the ecotone than did models that only included the geographic distance between sampling localities as predictor variables (63.9% and 58.9% versus 38.8% and 39.9%, depending on how hybridization was quantified). In the models including environmental variables, the amount of rainfall during the warmest quarter had the greatest explanatory power, consistent with a hypothesis thatP. cyaneais better adapted to the mesic environments of eastern North America andP. amoenais better adapted to the xeric habitats of western North America. These results suggest that continued reproductive isolation between these species is mediated, at least partially, by differential adaptations to local environmental conditions.
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Reid N, Demboski JR, Sullivan J. Phylogeny estimation of the radiation of western North American chipmunks (Tamias) in the face of introgression using reproductive protein genes. Syst Biol 2011; 61:44-62. [PMID: 21878471 DOI: 10.1093/sysbio/syr094] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The causes and consequences of rapid radiations are major unresolved issues in evolutionary biology. This is in part because phylogeny estimation is confounded by processes such as stochastic lineage sorting and hybridization. Because these processes are expected to be heterogeneous across the genome, comparison among marker classes may provide a means of disentangling these elements. Here we use introns from nuclear-encoded reproductive protein genes expected to be resistant to introgression to estimate the phylogeny of the western chipmunks (Tamias: subgenus: Neotamias), a rapid radiation that has experienced introgressive hybridization of mitochondrial DNA (mtDNA). We analyze the nuclear loci using coalescent-based species-tree estimation methods and concatenation to estimate a species tree and we use parametric bootstraps and coalescent simulations to differentiate between phylogenetic error, coalescent stochasticity and introgressive hybridization. Results indicate that the mtDNA gene tree reflects several introgression events that have occurred between taxa of varying levels of divergence and at different time points in the tree. T. panamintinus and T. speciosus appear to be fixed for ancient mitochondrial introgressions from T. minimus. A southern Rocky Mountains clade appears well sorted (i.e., species are largely monophyletic) at multiple nuclear loci, while five of six taxa are nonmonophyletic based on cytochrome b. Our simulations reject phylogenetic error and coalescent stochasticity as causes. The results represent an advance in our understanding of the processes at work during the radiation of Tamias and suggest that sampling reproductive-protein genes may be a viable strategy for phylogeny estimation of rapid radiations in which reproductive isolation is incomplete. However, a genome-scale survey that can statistically compare heterogeneity of genealogical process at many more loci will be necessary to test this conclusion.
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Affiliation(s)
- Noah Reid
- Department of Biological Sciences, Room 105, Louisiana State University, Baton Rouge, LA 70803, USA.
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27
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Backström N, Väli U. Sex- and species-biased gene flow in a spotted eagle hybrid zone. BMC Evol Biol 2011; 11:100. [PMID: 21492478 PMCID: PMC3098175 DOI: 10.1186/1471-2148-11-100] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2010] [Accepted: 04/14/2011] [Indexed: 11/24/2022] Open
Abstract
Background Recent theoretical and empirical work points toward a significant role for sex-chromosome linked genes in the evolution of traits that induce reproductive isolation and for traits that evolve under influence of sexual selection. Empirical studies including recently diverged (Pleistocene), short-lived avian species pairs with short generation times have found that introgression occurs on the autosomes but not on the Z-chromosome. Here we study genetic differentiation and gene flow in the long-lived greater spotted eagle (Aquila clanga) and lesser spotted eagle (A. pomarina), two species with comparatively long generation times. Results Our data suggest that there is a directional bias in migration rates between hybridizing spotted eagles in eastern Europe. We find that a model including post divergence gene flow fits our data best for both autosomal and Z-chromosome linked loci but, for the Z-chromosome, the rate is reduced in the direction from A. pomarina to A. clanga. Conclusions The fact that some introgression still occurs on the Z-chromosome between these species suggests that the differentiation process is in a more premature phase in our study system than in previously studied avian species pairs and that could be explained by a shorter divergence time and/or a longer average generation time in the spotted eagles. The results are in agreement with field observations and provide further insight into the role of sex-linked loci for the build-up of barriers to gene flow among diverging populations and species.
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Affiliation(s)
- Niclas Backström
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, 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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CARLING MATTHEWD, ZUCKERBERG BENJAMIN. Spatio-temporal changes in the genetic structure of the Passerina bunting hybrid zone. Mol Ecol 2011; 20:1166-75. [DOI: 10.1111/j.1365-294x.2010.04987.x] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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PAYSEUR BRETA. Using differential introgression in hybrid zones to identify genomic regions involved in speciation. Mol Ecol Resour 2010; 10:806-20. [DOI: 10.1111/j.1755-0998.2010.02883.x] [Citation(s) in RCA: 164] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Storchová R, Reif J, Nachman MW. Female heterogamety and speciation: reduced introgression of the Z chromosome between two species of nightingales. Evolution 2010; 64:456-71. [PMID: 19796142 PMCID: PMC2911439 DOI: 10.1111/j.1558-5646.2009.00841.x] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Several lines of evidence suggest that the X chromosome plays a large role in intrinsic postzygotic isolation. The role of the Z chromosome in speciation is much less understood. To explore the role of the Z chromosome in reproductive isolation, we studied nucleotide variation in two closely related bird species, the Thrush Nightingale (Luscinia luscinia) and the Common Nightingale (L. megarhynchos). These species are isolated by incomplete prezygotic isolation and female hybrid sterility. We sequenced introns of four Z-linked and eight autosomal loci and analyzed patterns of polymorphism and divergence using a divergence-with-gene flow framework. Our results suggest that the nightingale species diverged approximately 1.8 Mya. We found strong evidence of gene flow after divergence in both directions, although more introgression occurred from L. megarhynchos into L. luscinia. Gene flow was significantly higher on the autosomes than on the Z chromosome. Our results support the idea that the Z chromosome plays an important role in intrinsic postzygotic isolation in birds, although it may also contribute to the evolution of prezygotic isolation through sexual selection. This highlights the similarities in the genetic basis of reproductive isolation between organisms with heterogametic males and organisms with heterogametic females during the early stages of speciation.
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Affiliation(s)
- Radka Storchová
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA.
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Carling MD, Lovette IJ, Brumfield RT. HISTORICAL DIVERGENCE AND GENE FLOW: COALESCENT ANALYSES OF MITOCHONDRIAL, AUTOSOMAL AND SEX-LINKED LOCI IN PASSERINA BUNTINGS. Evolution 2010; 64:1762-72. [DOI: 10.1111/j.1558-5646.2010.00954.x] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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CADENA CARLOSDANIEL, CUERVO ANDRÉSM. Molecules, ecology, morphology, and songs in concert: how many species is Arremon torquatus (Aves: Emberizidae)? Biol J Linn Soc Lond 2009. [DOI: 10.1111/j.1095-8312.2009.01333.x] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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