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Reeve AH, Kennedy JD, Pujolar JM, Petersen B, Blom MPK, Alström P, Haryoko T, Ericson PGP, Irestedt M, Nylander JAA, Jønsson KA. The formation of the Indo-Pacific montane avifauna. Nat Commun 2023; 14:8215. [PMID: 38081809 PMCID: PMC10713610 DOI: 10.1038/s41467-023-43964-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 11/24/2023] [Indexed: 12/18/2023] Open
Abstract
The processes generating the earth's montane biodiversity remain a matter of debate. Two contrasting hypotheses have been advanced to explain how montane populations form: via direct colonization from other mountains, or, alternatively, via upslope range shifts from adjacent lowland areas. We seek to reconcile these apparently conflicting hypotheses by asking whether a species' ancestral geographic origin determines its mode of mountain colonization. Island-dwelling passerine birds at the faunal crossroads between Eurasia and Australo-Papua provide an ideal study system. We recover the phylogenetic relationships of the region's montane species and reconstruct their ancestral geographic ranges, elevational ranges, and migratory behavior. We also perform genomic population studies of three super-dispersive montane species/clades with broad island distributions. Eurasian-origin species populated archipelagos via direct colonization between mountains. This mode of colonization appears related to ancestral adaptations to cold and seasonal climates, specifically short-distance migration. Australo-Papuan-origin mountain populations, by contrast, evolved from lowland ancestors, and highland distribution mostly precludes their further colonization of island mountains. Our study explains much of the distributional variation within a complex biological system, and provides a synthesis of two seemingly discordant hypotheses for montane community formation.
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Affiliation(s)
- Andrew Hart Reeve
- Natural History Museum of Denmark, University of Copenhagen, DK-2100, Copenhagen Ø, Denmark.
| | - Jonathan David Kennedy
- Natural History Museum of Denmark, University of Copenhagen, DK-2100, Copenhagen Ø, Denmark
| | - José Martín Pujolar
- Natural History Museum of Denmark, University of Copenhagen, DK-2100, Copenhagen Ø, Denmark
- Centre for Gelatinous Plankton Ecology and Evolution, DTU Aqua, Kemitorvet, Building 202, DK-2800, Kongens Lyngby, Denmark
| | - Bent Petersen
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, DK-1353, Copenhagen, Denmark
- Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, AIMST University, Kedah, Malaysia
| | - Mozes P K Blom
- Museum für Naturkunde Berlin, Leibniz Institut für Evolutions- und Biodiversitätsforschung, 10115, Berlin, Germany
| | - Per Alström
- Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Tri Haryoko
- Museum Zoologicum Bogoriense, Research Center for Biosystematics and Evolution, National Research and Innovation Agency (BRIN), Cibinong, 16911, Indonesia
| | - Per G P Ericson
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, P.O. Box 50007, SE-104 05, Stockholm, Sweden
| | - Martin Irestedt
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, P.O. Box 50007, SE-104 05, Stockholm, Sweden
| | - Johan A A Nylander
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, P.O. Box 50007, SE-104 05, Stockholm, Sweden
| | - Knud Andreas Jønsson
- Natural History Museum of Denmark, University of Copenhagen, DK-2100, Copenhagen Ø, Denmark
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, P.O. Box 50007, SE-104 05, Stockholm, Sweden
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2
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Camacho-Sanchez M, Leonard JA. Mitogenomes Reveal Multiple Colonization of Mountains by Rattus in Sundaland. J Hered 2021; 111:392-404. [PMID: 32485737 PMCID: PMC7423070 DOI: 10.1093/jhered/esaa014] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 05/25/2020] [Indexed: 01/16/2023] Open
Abstract
Tropical mountains are cradles of biodiversity and endemism. Sundaland, tropical Southeast Asia, hosts 3 species of Rattus endemic to elevations above 2000 m with an apparent convergence in external morphology: Rattus korinchi and R. hoogerwerfi from Sumatra, and R. baluensis from Borneo. A fourth one, R. tiomanicus, is restricted to lowland elevations across the whole region. The origins of these endemics are little known due to the absence of a robust phylogenetic framework. We use complete mitochondrial genomes from the 3 high altitude Rattus, and several related species to determine their relationships, date divergences, reconstruct their history of colonization, and test for selection on the mitochondrial DNA. We show that mountain colonization happened independently in Borneo (<390 Kya) and Sumatra (~1.38 Mya), likely from lowland lineages. The origin of the Bornean endemic R. baluensis is very recent and its genetic diversity is nested within the diversity of R. tiomanicus. We found weak evidence of positive selection in the high-elevation lineages and attributed the greater nonsynonymous mutations on these branches (specially R. baluensis) to lesser purifying selection having acted on the terminal branches in the phylogeny.
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Affiliation(s)
- Miguel Camacho-Sanchez
- Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana (EBD-CSIC), Sevilla, Spain
| | - Jennifer A Leonard
- Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana (EBD-CSIC), Sevilla, Spain
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3
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Linck E, Freeman BG, Dumbacher JP. Speciation and gene flow across an elevational gradient in New Guinea kingfishers. J Evol Biol 2020; 33:1643-1652. [PMID: 32916016 DOI: 10.1111/jeb.13698] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 07/24/2020] [Accepted: 08/29/2020] [Indexed: 01/01/2023]
Abstract
Closely related species with parapatric elevational ranges are ubiquitous in tropical mountains worldwide. The gradient speciation hypothesis proposes that these series are the result of in situ ecological speciation driven by divergent selection across elevation. Direct tests of this scenario have been hampered by the difficulty inferring the geographic arrangement of populations at the time of divergence. In cichlids, sticklebacks and Timema stick insects, support for ecological speciation driven by other selective pressures has come from demonstrating parallel speciation, where divergence proceeds independently across replicated environmental gradients. Here, we take advantage of the unique geography of the island of New Guinea to test for parallel gradient speciation in replicated populations of Syma kingfishers that show extremely subtle differentiation across elevation and between historically isolated mountain ranges. We find that currently described high-elevation and low-elevation species have reciprocally monophyletic gene trees and form nuclear DNA clusters, rejecting this hypothesis. However, demographic modelling suggests selection has likely maintained species boundaries in the face of gene flow following secondary contact. We compile evidence from the published literature to show that although in situ gradient speciation in labile organisms such as birds appears rare, divergent selection and post-speciation gene flow may be an underappreciated force in the origin of elevational series and tropical beta diversity along mountain slopes.
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Affiliation(s)
- Ethan Linck
- Department of Biology & Burke Museum of Natural History & Culture, University of Washington, Seattle, WA, USA
| | - Benjamin G Freeman
- Beaty Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - John P Dumbacher
- Ornithology & Mammalogy, California Academy of Sciences, San Francisco, CA, USA
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4
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Liew TS, Marzuki ME, Schilthuizen M, Chen Y, Vermeulen JJ, Mohd-Azlan J. Molecular phylogenetics and evolutionary history of the endemic land snail genus Everettia in northern Borneo. PeerJ 2020; 8:e9416. [PMID: 32714659 PMCID: PMC7354840 DOI: 10.7717/peerj.9416] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 06/03/2020] [Indexed: 11/20/2022] Open
Abstract
Borneo has gone through dramatic changes in geology and topography from the early Eocene until the early Pliocene and experienced climatic cycling during the Pleistocene. However, how these changes have shaped the present-day patterns of high diversity and complex distribution are still poorly understood. In this study, we use integrative approaches by estimating phylogenetic relationships, divergence time, and current and past niche suitability for the Bornean endemic land snail genus Everettia to provide additional insight into the evolutionary history of this genus in northern Borneo in the light of the geological vicariance events and climatic fluctuations in the Pleistocene. Our results show that northern Borneo Everettia species belong to two deeply divergent lineages: one contains the species that inhabit high elevation at the central mountain range, while the other contains lowland species. Species diversification in these lineages has taken place before the Pliocene. Climate changes during the Pleistocene did not play a significant role in species diversification but could have shaped contemporary species distribution patterns. Our results also show that the species-rich highland habitats have acted as interglacial refugia for highland species. This study of a relatively sedentary invertebrate supports and enhances the growing understanding of the evolutionary history of Borneo. Species diversification in Everettia is caused by geological vicariance events between the early Miocene and the Pliocene, and the distribution patterns were subsequently determined by climatic fluctuations in the Pleistocene.
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Affiliation(s)
- Thor-Seng Liew
- Institute for Tropical Biology and Conservation, Universiti Malaysia Sabah, Kota Kinabalu, Sabah, Malaysia
| | - Mohammad Effendi Marzuki
- Institute of Biodiversity and Environmental Conservation, Universiti Malaysia Sarawak, Kota Samarahan, Sarawak, Malaysia
| | - Menno Schilthuizen
- Institute for Tropical Biology and Conservation, Universiti Malaysia Sabah, Kota Kinabalu, Sabah, Malaysia.,Naturalis Biodiversity Center, Leiden, The Netherlands.,Institute Biology Leiden, Leiden Univerisity, Leiden, The Netherlands
| | - Yansen Chen
- Independent Researcher, Medan, North Sumatra, Indonesia
| | - Jaap J Vermeulen
- Naturalis Biodiversity Center, Leiden, The Netherlands.,JK Art and Science, Leiden, The Netherlands
| | - Jayasilan Mohd-Azlan
- Institute of Biodiversity and Environmental Conservation, Universiti Malaysia Sarawak, Kota Samarahan, Sarawak, Malaysia
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5
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Origin of Elevational Replacements in a Clade of Nearly Flightless Birds: Most Diversity in Tropical Mountains Accumulates via Secondary Contact Following Allopatric Speciation. NEOTROPICAL DIVERSIFICATION: PATTERNS AND PROCESSES 2020. [DOI: 10.1007/978-3-030-31167-4_23] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Camacho-Sanchez M, Hawkins MTR, Tuh Yit Yu F, Maldonado JE, Leonard JA. Endemism and diversity of small mammals along two neighboring Bornean mountains. PeerJ 2019; 7:e7858. [PMID: 31608182 PMCID: PMC6788440 DOI: 10.7717/peerj.7858] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 09/09/2019] [Indexed: 11/20/2022] Open
Abstract
Mountains offer replicated units with large biotic and abiotic gradients in a reduced spatial scale. This transforms them into well-suited scenarios to evaluate biogeographic theories. Mountain biogeography is a hot topic of research and many theories have been proposed to describe the changes in biodiversity with elevation. Geometric constraints, which predict the highest diversity to occur in mid-elevations, have been a focal part of this discussion. Despite this, there is no general theory to explain these patterns, probably because of the interaction among different predictors with the local effects of historical factors. We characterize the diversity of small non-volant mammals across the elevational gradient on Mount (Mt.) Kinabalu (4,095 m) and Mt. Tambuyukon (2,579 m), two neighboring mountains in Borneo, Malaysia. We documented a decrease in species richness with elevation which deviates from expectations of the geometric constraints and suggests that spatial factors (e.g., larger diversity in larger areas) are important. The lowland small mammal community was replaced in higher elevations (from above ~1,900 m) with montane communities consisting mainly of high elevation Borneo endemics. The positive correlation we find between elevation and endemism is concordant with a hypothesis that predicts higher endemism with topographical isolation. This supports lineage history and geographic history could be important drivers of species diversity in this region.
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Affiliation(s)
- Miguel Camacho-Sanchez
- Conservation and Evolutionary Genetics Group, Doñana Biological Station (EBD-CSIC), Sevilla, Spain.,CiBIO-Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto, Vairão, Portugal
| | - Melissa T R Hawkins
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC, USA.,Department of Biological Sciences, Humboldt State University, Arcata, CA, USA.,Division of Mammals, National Museum of Natural History, Washington, DC, USA
| | | | - Jesus E Maldonado
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC, USA
| | - Jennifer A Leonard
- Conservation and Evolutionary Genetics Group, Doñana Biological Station (EBD-CSIC), Sevilla, Spain
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7
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Maxwell CS, Mattox K, Turissini DA, Teixeira MM, Barker BM, Matute DR. Gene exchange between two divergent species of the fungal human pathogen, Coccidioides. Evolution 2019; 73:42-58. [PMID: 30414183 PMCID: PMC6430640 DOI: 10.1111/evo.13643] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 10/15/2018] [Accepted: 10/18/2018] [Indexed: 12/12/2022]
Abstract
The fungal genus Coccidioides is composed of two species, Coccidioides immitis and Coccidioides posadasii. These two species are the causal agents of coccidioidomycosis, a pulmonary disease also known as valley fever. The two species are thought to have shared genetic material due to gene exchange in spite of their long divergence. To quantify the magnitude of shared ancestry between them, we analyzed the genomes of a population sample from each species. Next, we inferred what is the expected size of shared haplotypes that might be inherited from the last common ancestor of the two species and find a cutoff to find what haplotypes have conclusively been exchanged between species. Finally, we precisely identified the breakpoints of the haplotypes that have crossed the species boundary and measure the allele frequency of each introgression in this sample. We find that introgressions are not uniformly distributed across the genome. Most, but not all, of the introgressions segregate at low frequency. Our results show that divergent species can share alleles, that species boundaries can be porous, and highlight the need for a systematic exploration of gene exchange in fungal species.
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Affiliation(s)
- Colin S Maxwell
- Biology Department, University of North Carolina, Chapel Hill, North Carolina
| | - Kathleen Mattox
- Biology Department, University of North Carolina, Chapel Hill, North Carolina
| | - David A Turissini
- Biology Department, University of North Carolina, Chapel Hill, North Carolina
| | - Marcus M Teixeira
- Núcleo de Medicina Tropical, Faculdade de Medicina, University of Brasília, Brasília, Brazil
| | - Bridget M Barker
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona
| | - Daniel R Matute
- Biology Department, University of North Carolina, Chapel Hill, North Carolina
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8
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Hosner PA, Campillo LC, Andersen MJ, Sánchez-González LA, Oliveros CH, Urriza RC, Moyle RG. An integrative species delimitation approach reveals fine-scale endemism and substantial unrecognized avian diversity in the Philippine Archipelago. CONSERV GENET 2018. [DOI: 10.1007/s10592-018-1085-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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9
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Shakya SB, Haryoko T, Burner RC, Prawiradilaga DM, Sheldon FH. Preliminary assessment of community composition and phylogeographic relationships of the birds of the Meratus Mountains, south-east borneo, Indonesia. ACTA ACUST UNITED AC 2018. [DOI: 10.25226/bboc.v138i1.2018.a6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Subir B. Shakya
- Subir B. Shakya, Dept. of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, Louisiana 70803, USA,
| | - Tri Haryoko
- Tri Haryoko, Division of Zoology, Research Centre for Biology-LIPI, Jalan Raya Bogor km 46, Cibinong-Bogor 16911, Indonesia,
| | - Ryan C. Burner
- Ryan C. Burner, Dept. of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, Louisiana 70803, USA,
| | - Dewi M. Prawiradilaga
- Dewi Prawiradilaga, Division of Zoology, Research Centre for Biology-LIPI, Jalan Raya Bogor km 46, Cibinong-Bogor 16911, Indonesia,
| | - Frederick H. Sheldon
- Frederick H. Sheldon, Dept. of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, Louisiana 70803, USA,
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Chattopadhyay B, Garg KM, Gwee CY, Edwards SV, Rheindt FE. Gene flow during glacial habitat shifts facilitates character displacement in a Neotropical flycatcher radiation. BMC Evol Biol 2017; 17:210. [PMID: 28863778 PMCID: PMC5580441 DOI: 10.1186/s12862-017-1047-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 08/10/2017] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND Pleistocene climatic fluctuations are known to be an engine of biotic diversification at higher latitudes, but their impact on highly diverse tropical areas such as the Andes remains less well-documented. Specifically, while periods of global cooling may have led to fragmentation and differentiation at colder latitudes, they may - at the same time - have led to connectivity among insular patches of montane tropical habitat with unknown consequences on diversification. In the present study we utilized ~5.5 kb of DNA sequence data from eight nuclear loci and one mitochondrial gene alongside diagnostic morphological and bioacoustic markers to test the effects of Pleistocene climatic fluctuations on diversification in a complex of Andean tyrant-flycatchers of the genus Elaenia. RESULTS Population genetic and phylogenetic approaches coupled with coalescent simulations demonstrated disparate levels of gene flow between the taxon chilensis and two parapatric Elaenia taxa predominantly during the last glacial period but not thereafter, possibly on account of downward shifts of montane forest habitat linking the populations of adjacent ridges. Additionally, morphological and bioacoustic analyses revealed a distinct pattern of character displacement in coloration and vocal traits between the two sympatric taxa albiceps and pallatangae, which were characterized by a lack of gene flow. CONCLUSION Our study demonstrates that global periods of cooling are likely to have facilitated gene flow among Andean montane Elaenia flycatchers that are more isolated from one another during warm interglacial periods such as the present era. We also identify a hitherto overlooked case of plumage and vocal character displacement, underpinning the complexities of gene flow patterns caused by Pleistocene climate change across the Andes.
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Affiliation(s)
- Balaji Chattopadhyay
- Department of Biological Sciences, National University of Singapore, 117543, Singapore, Republic of Singapore.
| | - Kritika M Garg
- Department of Biological Sciences, National University of Singapore, 117543, Singapore, Republic of Singapore
| | - Chyi Yin Gwee
- Department of Biological Sciences, National University of Singapore, 117543, Singapore, Republic of Singapore
| | - Scott V Edwards
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, 02138, MA, USA
| | - Frank E Rheindt
- Department of Biological Sciences, National University of Singapore, 117543, Singapore, Republic of Singapore.
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Turissini DA, Matute DR. Fine scale mapping of genomic introgressions within the Drosophila yakuba clade. PLoS Genet 2017; 13:e1006971. [PMID: 28873409 PMCID: PMC5600410 DOI: 10.1371/journal.pgen.1006971] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Revised: 09/15/2017] [Accepted: 08/09/2017] [Indexed: 12/15/2022] Open
Abstract
The process of speciation involves populations diverging over time until they are genetically and reproductively isolated. Hybridization between nascent species was long thought to directly oppose speciation. However, the amount of interspecific genetic exchange (introgression) mediated by hybridization remains largely unknown, although recent progress in genome sequencing has made measuring introgression more tractable. A natural place to look for individuals with admixed ancestry (indicative of introgression) is in regions where species co-occur. In west Africa, D. santomea and D. yakuba hybridize on the island of São Tomé, while D. yakuba and D. teissieri hybridize on the nearby island of Bioko. In this report, we quantify the genomic extent of introgression between the three species of the Drosophila yakuba clade (D. yakuba, D. santomea), D. teissieri). We sequenced the genomes of 86 individuals from all three species. We also developed and applied a new statistical framework, using a hidden Markov approach, to identify introgression. We found that introgression has occurred between both species pairs but most introgressed segments are small (on the order of a few kilobases). After ruling out the retention of ancestral polymorphism as an explanation for these similar regions, we find that the sizes of introgressed haplotypes indicate that genetic exchange is not recent (>1,000 generations ago). We additionally show that in both cases, introgression was rarer on X chromosomes than on autosomes which is consistent with sex chromosomes playing a large role in reproductive isolation. Even though the two species pairs have stable contemporary hybrid zones, providing the opportunity for ongoing gene flow, our results indicate that genetic exchange between these species is currently rare.
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Affiliation(s)
- David A. Turissini
- Biology Department, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Daniel R. Matute
- Biology Department, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina, United States of America
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