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Walsh J, Billerman SM, Butcher BG, Rohwer VG, Toews DPL, Vila-Coury V, Lovette IJ. A complex genomic architecture underlies reproductive isolation in a North American oriole hybrid zone. Commun Biol 2023; 6:154. [PMID: 36747071 PMCID: PMC9902562 DOI: 10.1038/s42003-023-04532-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 01/26/2023] [Indexed: 02/08/2023] Open
Abstract
Natural hybrid zones provide powerful opportunities for identifying the mechanisms that facilitate and inhibit speciation. Documenting the extent of genomic admixture allows us to discern the architecture of reproductive isolation through the identification of isolating barriers. This approach is particularly powerful for characterizing the accumulation of isolating barriers in systems exhibiting varying levels of genomic divergence. Here, we use a hybrid zone between two species-the Baltimore (Icterus galbula) and Bullock's (I. bullockii) orioles-to investigate this architecture of reproductive isolation. We combine whole genome re-sequencing with data from an additional 313 individuals amplityped at ancestry-informative markers to characterize fine-scale patterns of admixture, and to quantify links between genes and the plumage traits. On a genome-wide scale, we document several putative barriers to reproduction, including elevated peaks of divergence above a generally high genomic baseline, a large putative inversion on the Z chromosome, and complex interactions between melanogenesis-pathway candidate genes. Concordant and coincident clines for these different genomic regions further suggest the coupling of pre- and post-mating barriers. Our findings of complex and coupled interactions between pre- and post-mating barriers suggest a relatively rapid accumulation of barriers between these species, and they demonstrate the complexities of the speciation process.
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Affiliation(s)
- Jennifer Walsh
- Fuller Evolutionary Biology Program, Cornell Lab of Ornithology, Cornell University, Ithaca, NY, USA.
| | - Shawn M. Billerman
- grid.5386.8000000041936877XFuller Evolutionary Biology Program, Cornell Lab of Ornithology, Cornell University, Ithaca, NY USA
| | - Bronwyn G. Butcher
- grid.5386.8000000041936877XFuller Evolutionary Biology Program, Cornell Lab of Ornithology, Cornell University, Ithaca, NY USA
| | - Vanya G. Rohwer
- grid.5386.8000000041936877XFuller Evolutionary Biology Program, Cornell Lab of Ornithology, Cornell University, Ithaca, NY USA
| | - David P. L. Toews
- grid.29857.310000 0001 2097 4281Department of Biology, Penn State University, University Park, Pennsylvania, USA
| | - Vicens Vila-Coury
- grid.5386.8000000041936877XFuller Evolutionary Biology Program, Cornell Lab of Ornithology, Cornell University, Ithaca, NY USA
| | - Irby J. Lovette
- grid.5386.8000000041936877XFuller Evolutionary Biology Program, Cornell Lab of Ornithology, Cornell University, Ithaca, NY USA ,grid.5386.8000000041936877XDepartment of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY USA
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2
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Wu MY, Lau CJ, Ng EYX, Baveja P, Gwee CY, Sadanandan K, Ferasyi TR, Haminuddin, Ramadhan R, Menner JK, Rheindt FE. Genomes From Historic DNA Unveil Massive Hidden Extinction and Terminal Endangerment in a Tropical Asian Songbird Radiation. Mol Biol Evol 2022; 39:6692815. [PMID: 36124912 PMCID: PMC9486911 DOI: 10.1093/molbev/msac189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Quantifying the magnitude of the global extinction crisis is important but remains challenging, as many extinction events pass unnoticed owing to our limited taxonomic knowledge of the world's organisms. The increasing rarity of many taxa renders comprehensive sampling difficult, further compounding the problem. Vertebrate lineages such as birds, which are thought to be taxonomically well understood, are therefore used as indicator groups for mapping and quantifying global extinction. To test whether extinction patterns are adequately gauged in well-studied groups, we implemented ancient-DNA protocols and retrieved whole genomes from the historic DNA of museum specimens in a widely known songbird radiation of shamas (genus Copsychus) that is assumed to be of least conservation concern. We uncovered cryptic diversity and an unexpected degree of hidden extinction and terminal endangerment. Our analyses reveal that >40% of the phylogenetic diversity of this radiation is already either extinct in the wild or nearly so, including the two genomically most distinct members of this group (omissus and nigricauda), which have so far flown under the conservation radar as they have previously been considered subspecies. Comparing the genomes of modern samples with those from roughly a century ago, we also found a significant decrease in genetic diversity and a concomitant increase in homozygosity affecting various taxa, including small-island endemics that are extinct in the wild as well as subspecies that remain widespread across the continental scale. Our application of modern genomic approaches demonstrates elevated levels of allelic and taxonomic diversity loss in a songbird clade that has not been listed as globally threatened, highlighting the importance of ongoing reassessments of extinction incidence even across well-studied animal groups. Key words: extinction, introgression, white-rumped shama, conservation.
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Affiliation(s)
- Meng Yue Wu
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Clara Jesse Lau
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Elize Ying Xin Ng
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Pratibha Baveja
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Chyi Yin Gwee
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Keren Sadanandan
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Teuku Reza Ferasyi
- Faculty of Veterinary Medicine, Universitas Syiah Kuala, Darussalam-Banda Aceh, Indonesia
| | - Haminuddin
- Faculty of Veterinary Medicine, Universitas Syiah Kuala, Darussalam-Banda Aceh, Indonesia
| | - Rezky Ramadhan
- Faculty of Veterinary Medicine, Universitas Syiah Kuala, Darussalam-Banda Aceh, Indonesia
| | | | - Frank E Rheindt
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
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3
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Driver R, Ferretti V, Burton ES, McCoy MW, Duerr KC, Curry RL. Spatiotemporal variation in hatching success and nestling sex ratios track rapid movement of a songbird hybrid zone. Am Nat 2022; 200:264-274. [DOI: 10.1086/720207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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4
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Ottenburghs J. Avian introgression patterns are consistent with Haldane's Rule. J Hered 2022; 113:363-370. [PMID: 35134952 PMCID: PMC9308041 DOI: 10.1093/jhered/esac005] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 01/27/2022] [Indexed: 11/13/2022] Open
Abstract
According to Haldane’s Rule, the heterogametic sex will show the greatest fitness reduction in a hybrid cross. In birds, where sex is determined by a ZW system, female hybrids are expected to experience lower fitness compared to male hybrids. This pattern has indeed been observed in several bird groups, but it is unknown whether the generality of Haldane’s Rule also extends to the molecular level. First, given the lower fitness of female hybrids, we can expect maternally inherited loci (i.e., mitochondrial and W-linked loci) to show lower introgression rates than biparentally inherited loci (i.e., autosomal loci) in females. Second, the faster evolution of Z-linked loci compared to autosomal loci and the hemizygosity of the Z-chromosome in females might speed up the accumulation of incompatible alleles on this sex chromosome, resulting in lower introgression rates for Z-linked loci than for autosomal loci. I tested these expectations by conducting a literature review which focused on studies that directly quantified introgression rates for autosomal, sex-linked, and mitochondrial loci. Although most studies reported introgression rates in line with Haldane’s Rule, it remains important to validate these genetic patterns with estimates of hybrid fitness and supporting field observations to rule out alternative explanations. Genomic data provide exciting opportunities to obtain a more fine-grained picture of introgression rates across the genome, which can consequently be linked to ecological and behavioral observations, potentially leading to novel insights into the genetic mechanisms underpinning Haldane’s Rule.
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Affiliation(s)
- Jente Ottenburghs
- Wildlife Ecology and Conservation, Wageningen University & Research, Wageningen, The Netherlands.,Forest Ecology and Forest Management, Wageningen University & Research, Wageningen, The Netherlands
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5
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Coman A, Potter S, Moritz C, Campbell CD, Joseph L. Biotic and abiotic drivers of evolution in some Australian thornbills (Passeriformes:
Acanthiza
) in allopatry, sympatry, and parapatry including a case of character displacement. J ZOOL SYST EVOL RES 2020. [DOI: 10.1111/jzs.12355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Amelia Coman
- Division of Ecology and Evolution Research School of Biology, and Centre for Biodiversity Analysis The Australian National University Acton ACT Australia
- Australian National Wildlife Collection CSIRO National Research Collections Australia Canberra ACT Australia
| | - Sally Potter
- Division of Ecology and Evolution Research School of Biology, and Centre for Biodiversity Analysis The Australian National University Acton ACT Australia
| | - Craig Moritz
- Division of Ecology and Evolution Research School of Biology, and Centre for Biodiversity Analysis The Australian National University Acton ACT Australia
| | - Catriona D. Campbell
- Australian National Wildlife Collection CSIRO National Research Collections Australia Canberra ACT Australia
| | - Leo Joseph
- Australian National Wildlife Collection CSIRO National Research Collections Australia Canberra ACT Australia
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6
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Saha A, Johansen T, Hedeholm R, Nielsen EE, Westgaard JI, Hauser L, Planque B, Cadrin SX, Boje J. Geographic extent of introgression in Sebastes mentella and its effect on genetic population structure. Evol Appl 2016; 10:77-90. [PMID: 28035237 PMCID: PMC5192944 DOI: 10.1111/eva.12429] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Accepted: 08/19/2016] [Indexed: 01/17/2023] Open
Abstract
Genetic population structure is often used to identify management units in exploited species, but the extent of genetic differentiation may be inflated by geographic variation in the level of hybridization between species. We identify the genetic population structure of Sebastes mentella and investigate possible introgression within the genus by analyzing 13 microsatellites in 2,562 redfish specimens sampled throughout the North Atlantic. The data support an historical divergence between the "shallow" and "deep" groups, beyond the Irminger Sea where they were described previously. A third group, "slope," has an extended distribution on the East Greenland Shelf, in addition to earlier findings on the Icelandic slope. Furthermore, S. mentella from the Northeast Arctic and Northwest Atlantic waters are genetically different populations. In both areas, interspecific introgression may influence allele frequency differences among populations. Evidence of introgression was found for almost all the identified Sebastes gene pools, but to a much lower extent than suggested earlier. Greenland waters appear to be a sympatric zone for many of the genetically independent Sebastes groups. This study illustrates that the identified groups maintain their genetic integrity in this region despite introgression.
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Affiliation(s)
- Atal Saha
- Tromsø Department Institute of Marine Research Tromsø Norway
| | - Torild Johansen
- Tromsø Department Institute of Marine Research Tromsø Norway
| | | | - Einar E Nielsen
- DTU Aqua - National Institute of Aquatic Resources Charlottenlund Denmark
| | | | - Lorenz Hauser
- School of Aquatic and Fishery Sciences University of Washington Seattle WA USA
| | - Benjamin Planque
- Tromsø Department Institute of Marine Research Tromsø Norway; Hjort Centre for Marine Ecosystem Dynamics Bergen Norway
| | - Steven X Cadrin
- School for Marine Science and Technology University of Massachusetts Darmouth Fairhaven MA USA
| | - Jesper Boje
- Greenland Institute of Natural Resources Nuuk Greenland; DTU Aqua - National Institute of Aquatic Resources Charlottenlund Denmark
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7
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Population expansion, current and past gene flow in Gould’s petrel: implications for conservation. CONSERV GENET 2016. [DOI: 10.1007/s10592-016-0886-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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8
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Sturge RJ, Cortés-Rodríguez MN, Rojas-Soto OR, Omland KE. Nuclear locus divergence at the early stages of speciation in the Orchard Oriole complex. Ecol Evol 2016; 6:4307-17. [PMID: 27386077 PMCID: PMC4930982 DOI: 10.1002/ece3.2168] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Revised: 03/30/2016] [Accepted: 04/01/2016] [Indexed: 11/29/2022] Open
Abstract
As two lineages diverge from one another, mitochondrial DNA should evolve fixed differences more rapidly than nuclear DNA due to its smaller effective population size and faster mutation rate. As a consequence, molecular systematists have focused on the criteria of reciprocal monophyly in mitochondrial DNA for delimiting species boundaries. However, mitochondrial gene trees do not necessarily reflect the evolutionary history of the taxa in question, and even mitochondrial loci are not expected to be reciprocally monophyletic when the speciation event happened very recently. The goal of this study was to examine mitochondrial paraphyly within the Orchard Oriole complex, which is composed of Icterus spurius (Orchard Oriole) and Icterus fuertesi (Fuertes' Oriole). We increased the geographic sampling, added four nuclear loci, and used a range of population genetic and coalescent methods to examine the divergence between the taxa. With increased taxon sampling, we found evidence of clear structure between the taxa for mitochondrial DNA. However, nuclear loci showed little evidence of population structure, indicating a very recent divergence between I. spurius and I. fuertesi. Another goal was to examine the genetic variation within each taxon to look for evidence of a past founder event within the I. fuertesi lineage. Based on the high amounts of genetic variation for all nuclear loci, we found no evidence of such an event – thus, we found no support for the possible founding of I. fuertesi through a change in migratory behavior, followed by peripheral isolates speciation. Our results demonstrate that these two taxa are in the earliest stages of speciation, at a point when they have fixed differences in plumage color that are not reflected in monophyly of the mitochondrial or nuclear DNA markers in this study. This very recent divergence makes them ideal for continued studies of species boundaries and the earliest stages of speciation.
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Affiliation(s)
- Rachel J Sturge
- Department of Biological Sciences University of Maryland Baltimore County 1000 Hilltop Circle Baltimore Maryland 21052
| | - M Nandadevi Cortés-Rodríguez
- Department of Biological Sciences University of Maryland Baltimore County 1000 Hilltop Circle Baltimore Maryland 21052
| | - Octavio R Rojas-Soto
- Red de Biología Evolutiva Instituto de Ecología (INECOL) Carretera antigua a Coatepec 351 Xalapa 91070 Mexico
| | - Kevin E Omland
- Department of Biological Sciences University of Maryland Baltimore County 1000 Hilltop Circle Baltimore Maryland 21052
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9
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Walsh J, Shriver WG, Olsen BJ, Kovach AI. Differential introgression and the maintenance of species boundaries in an advanced generation avian hybrid zone. BMC Evol Biol 2016; 16:65. [PMID: 27000833 PMCID: PMC4802838 DOI: 10.1186/s12862-016-0635-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 03/10/2016] [Indexed: 12/31/2022] Open
Abstract
Background Evolutionary processes, including selection and differential fitness, shape the introgression of genetic material across a hybrid zone, resulting in the exchange of some genes but not others. Differential introgression of molecular or phenotypic markers can thus provide insight into factors contributing to reproductive isolation. We characterized patterns of genetic variation across a hybrid zone between two tidal marsh birds, Saltmarsh (Ammodramus caudacutus) and Nelson’s (A. nelsoni) sparrows (n = 286), and compared patterns of introgression among multiple genetic markers and phenotypic traits. Results Geographic and genomic cline analyses revealed variable patterns of introgression among marker types. Most markers exhibited gradual clines and indicated that introgression exceeds the spatial extent of the previously documented hybrid zone. We found steeper clines, indicating strong selection for loci associated with traits related to tidal marsh adaptations, including for a marker linked to a gene region associated with metabolic functions, including an osmotic regulatory pathway, as well as for a marker related to melanin-based pigmentation, supporting an adaptive role of darker plumage (salt marsh melanism) in tidal marshes. Narrow clines at mitochondrial and sex-linked markers also offer support for Haldane’s rule. We detected patterns of asymmetrical introgression toward A. caudacutus, which may be driven by differences in mating strategy or differences in population density between the two species. Conclusions Our findings offer insight into the dynamics of a hybrid zone traversing a unique environmental gradient and provide evidence for a role of ecological divergence in the maintenance of pure species boundaries despite ongoing gene flow. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0635-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jennifer Walsh
- Department of Natural Resources and the Environment, University of New Hampshire, Durham, NH, USA. .,Cornell Lab of Ornithology, Cornell University, Ithaca, NY, USA.
| | - W Gregory Shriver
- Department of Entomology and Wildlife Ecology, University of Delaware, Newark, DE, USA
| | - Brian J Olsen
- School of Biology and Ecology, University of Maine, Orono, ME, USA
| | - Adrienne I Kovach
- Department of Natural Resources and the Environment, University of New Hampshire, Durham, NH, USA
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10
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Silva MC, Matias R, Wanless RM, Ryan PG, Stephenson BM, Bolton M, Ferrand N, Coelho MM. Understanding the mechanisms of antitropical divergence in the seabird White-faced Storm-petrel (Procellariiformes: Pelagodroma marina) using a multilocus approach. Mol Ecol 2015; 24:3122-37. [PMID: 25903359 DOI: 10.1111/mec.13212] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Revised: 04/16/2015] [Accepted: 04/21/2015] [Indexed: 11/27/2022]
Abstract
Analytical methods that apply coalescent theory to multilocus data have improved inferences of demographic parameters that are critical to understanding population divergence and speciation. In particular, at the early stages of speciation, it is important to implement models that accommodate conflicting gene trees, and benefit from the presence of shared polymorphisms. Here, we employ eleven nuclear loci and the mitochondrial control region to investigate the phylogeography and historical demography of the pelagic seabird White-faced Storm-petrel (Pelagodroma marina) by sampling subspecies across its antitropical distribution. Groups are all highly differentiated: global mitochondrial ΦST = 0.89 (P < 0.01) and global nuclear ΦST varies between 0.22 and 0.83 (all P < 0.01). The complete lineage sorting of the mitochondrial locus between hemispheres is corroborated by approximately half of the nuclear genealogies, suggesting a long-term antitropical divergence in isolation. Coalescent-based estimates of demographic parameters suggest that hemispheric divergence of P. marina occurred approximately 840 000 ya (95% HPD 582 000-1 170 000), in the absence of gene flow, and divergence within the Southern Hemisphere occurred 190 000 ya (95% HPD 96 000-600 000), both probably associated with the profound palaeo-oceanographic changes of the Pleistocene. A fledgling sampled in St Helena (tropical South Atlantic) suggests recent colonization from the Northern Hemisphere. Despite the great potential for long-distance dispersal, P. marina antitropical groups have been evolving as independent, allopatric lineages, and divergence is probably maintained by philopatry coupled with asynchronous reproductive phenology and local adaptation.
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Affiliation(s)
- Mónica C Silva
- Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, 1749-016, Lisboa, Portugal
| | - Rafael Matias
- Centre for Ecology and Conservation, School of Biosciences, University of Exeter, Penryn, TR10 9EZ, UK.,Marine and Environmental Sciences Centre, ISPA-Instituto Universitário, 1149-041, Lisboa, Portugal
| | - Ross M Wanless
- Percy FitzPatrick Institute of African Ornithology, DST-NRF Centre of Excellence, University of Cape Town, Rondebosch, 7701, South Africa.,Seabird Conservation Program, BirdLife South Africa, PO Box 7119, Roggebaai, 8012, South Africa
| | - Peter G Ryan
- Percy FitzPatrick Institute of African Ornithology, DST-NRF Centre of Excellence, University of Cape Town, Rondebosch, 7701, South Africa
| | - Brent M Stephenson
- Eco-Vista: Photography & Research Ltd, PO Box 157, Bay View, Napier, 4149, New Zealand
| | - Mark Bolton
- RSPB Centre for Conservation Science, Royal Society for the Protection of Birds, The Lodge, Sandy, Beds, SG19 2DL, UK
| | - Nuno Ferrand
- CIBIO, Universidade do Porto, Campus Agrário Vairão, 4485-661, Vairão, Portugal
| | - M Manuela Coelho
- Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, 1749-016, Lisboa, Portugal
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11
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Kutschera VE, Bidon T, Hailer F, Rodi JL, Fain SR, Janke A. Bears in a forest of gene trees: phylogenetic inference is complicated by incomplete lineage sorting and gene flow. Mol Biol Evol 2014; 31:2004-17. [PMID: 24903145 PMCID: PMC4104321 DOI: 10.1093/molbev/msu186] [Citation(s) in RCA: 140] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Ursine bears are a mammalian subfamily that comprises six morphologically and ecologically distinct extant species. Previous phylogenetic analyses of concatenated nuclear genes could not resolve all relationships among bears, and appeared to conflict with the mitochondrial phylogeny. Evolutionary processes such as incomplete lineage sorting and introgression can cause gene tree discordance and complicate phylogenetic inferences, but are not accounted for in phylogenetic analyses of concatenated data. We generated a high-resolution data set of autosomal introns from several individuals per species and of Y-chromosomal markers. Incorporating intraspecific variability in coalescence-based phylogenetic and gene flow estimation approaches, we traced the genealogical history of individual alleles. Considerable heterogeneity among nuclear loci and discordance between nuclear and mitochondrial phylogenies were found. A species tree with divergence time estimates indicated that ursine bears diversified within less than 2 My. Consistent with a complex branching order within a clade of Asian bear species, we identified unidirectional gene flow from Asian black into sloth bears. Moreover, gene flow detected from brown into American black bears can explain the conflicting placement of the American black bear in mitochondrial and nuclear phylogenies. These results highlight that both incomplete lineage sorting and introgression are prominent evolutionary forces even on time scales up to several million years. Complex evolutionary patterns are not adequately captured by strictly bifurcating models, and can only be fully understood when analyzing multiple independently inherited loci in a coalescence framework. Phylogenetic incongruence among gene trees hence needs to be recognized as a biologically meaningful signal.
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Affiliation(s)
- Verena E Kutschera
- Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany
| | - Tobias Bidon
- Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany
| | - Frank Hailer
- Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany
| | - Julia L Rodi
- Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany
| | - Steven R Fain
- National Fish and Wildlife Forensic Laboratory, Ashland, OR
| | - Axel Janke
- Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, GermanyInstitute for Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany
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12
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Rodríguez-Prieto A, Igea J, Castresana J. Development of rapidly evolving intron markers to estimate multilocus species trees of rodents. PLoS One 2014; 9:e96032. [PMID: 24804779 PMCID: PMC4012946 DOI: 10.1371/journal.pone.0096032] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Accepted: 04/03/2014] [Indexed: 11/18/2022] Open
Abstract
One of the major challenges in the analysis of closely related species, speciation and phylogeography is the identification of variable sequence markers that allow the determination of genealogical relationships in multiple genomic regions using coalescent and species tree approaches. Rodent species represent nearly half of the mammalian diversity, but so far no systematic study has been carried out to detect suitable informative markers for this group. Here, we used a bioinformatic pipeline to extract intron sequences from rodent genomes available in databases and applied a series of filters that allowed the identification of 208 introns that adequately fulfilled several criteria for these studies. The main required characteristics of the introns were that they had the maximum possible mutation rates, that they were part of single-copy genes, that they had an appropriate sequence length for amplification, and that they were flanked by exons with suitable regions for primer design. In addition, in order to determine the validity of this approach, we chose ten of these introns for primer design and tested them in a panel of eleven rodent species belonging to different representative families. We show that all these introns can be amplified in the majority of species and that, overall, 79% of the amplifications worked with minimum optimization of the annealing temperature. In addition, we confirmed for a pair of sister species the relatively high level of sequence divergence of these introns. Therefore, we provide here a set of adequate intron markers that can be applied to different species of Rodentia for their use in studies that require significant sequence variability.
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Affiliation(s)
- Ana Rodríguez-Prieto
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Javier Igea
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
- Imperial College London, Silwood Park Campus, Ascot, Berkshire, United Kingdom
| | - Jose Castresana
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
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13
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Cortés-Rodríguez N, Jacobsen F, Hernandez-Baños BE, Navarro-Siguenza AG, Peters JL, Omland KE. Coalescent analyses show isolation without migration in two closely related tropical orioles: the case of Icterus graduacauda and Icterus chrysater. Ecol Evol 2013; 3:4377-87. [PMID: 24340179 PMCID: PMC3856738 DOI: 10.1002/ece3.768] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2013] [Revised: 08/03/2013] [Accepted: 08/12/2013] [Indexed: 11/21/2022] Open
Abstract
The Isthmus of Tehuantepec has played an important role in shaping the avian diversity of Mexico, as well as the rest of the Western Hemisphere. It has been both a barrier and a land connector between North and South America for many groups of birds. Furthermore, climatic change over the Pleistocene has resulted in ecological fluctuations that led to periods of connection and isolation of the highlands in this area. Here we studied the divergence of two species of orioles whose distribution in the highlands is separated by the lowlands of the Isthmus of Tehuantepec: Icterus graduacauda (west of the Isthmus) and Icterus chrysater (east of the Isthmus). We sequenced multiple loci (one mitochondrial gene and six nuclear introns) and performed coalescent analyses (Isolation with Migration) to test whether their divergence resulted from prior occupancy of the ancestral area followed by a vicariant event or recent dispersal from one side or the other of this Isthmus. Results strongly indicate a vicariant event roughly 300,000 years ago in the Pleistocene followed by little or no gene flow. Both mitochondrial and nuclear genes show that the Isthmus of Tehuantepec is a strong barrier to gene flow. Thus, these two species appear to not exchange genes despite their recent divergence and the close geographic proximity of their ranges.
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Affiliation(s)
- Nandadevi Cortés-Rodríguez
- Department of Biological Sciences, University of Maryland-Baltimore County Baltimore, Maryland, 21250-0001
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Taylor SA, Anderson DJ, Friesen VL. Evidence for asymmetrical divergence-gene flow of nuclear loci, but not mitochondrial loci, between seabird sister species: blue-footed (Sula nebouxii) and Peruvian (S. variegata) boobies. PLoS One 2013; 8:e62256. [PMID: 23614045 PMCID: PMC3629132 DOI: 10.1371/journal.pone.0062256] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2012] [Accepted: 03/19/2013] [Indexed: 01/07/2023] Open
Abstract
Understanding the process of speciation requires understanding how gene flow influences divergence. Recent analyses indicate that divergence can take place despite gene flow and that the sex chromosomes can exhibit different levels of gene flow than autosomes and mitochondrial DNA. Using an eight marker dataset including autosomal, z-linked, and mitochondrial loci we tested the hypothesis that blue-footed (Sula nebouxii) and Peruvian (S. variegata) boobies diverged from their common ancestor with gene flow, paying specific attention to the differences in gene flow estimates from nuclear and mitochondrial markers. We found no gene flow at mitochondrial markers, but found evidence from the combined autosomal and z-linked dataset that blue-footed and Peruvian boobies experienced asymmetrical gene flow during or after their initial divergence, predominantly from Peruvian boobies into blue-footed boobies. This gene exchange may have occurred either sporadically between periods of allopatry, or regularly throughout the divergence process. Our results add to growing evidence that diverging species can remain distinct but exchange genes.
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Affiliation(s)
- Scott A Taylor
- Department of Biology, Queen's University, Kingston, Canada.
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