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Broyles GG, Myers BM, Friedman NR, Gawin DF, Mohd-Taib FS, Sahlan PGM, Seneviratne SS, de Silva NCG, Lekamlage TTM, Hund AK, Scordato ESC. Evolutionarily labile dispersal behavior and discontinuous habitats enhance population differentiation in island versus continentally distributed swallows. Evolution 2023; 77:2656-2671. [PMID: 37801637 DOI: 10.1093/evolut/qpad179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 09/18/2023] [Accepted: 10/05/2023] [Indexed: 10/08/2023]
Abstract
The causes of population divergence in vagile groups remain a paradox in evolutionary biology: dispersive species should be able to colonize new areas, a prerequisite for allopatric speciation, but dispersal also facilitates gene flow, which erodes population differentiation. Strong dispersal ability has been suggested to enhance divergence in patchy habitats and inhibit divergence in continuous landscapes, but empirical support for this hypothesis is lacking. Here we compared patterns of population divergence in a dispersive clade of swallows distributed across both patchy and continuous habitats. The Pacific Swallow (Hirundo tahitica) has an insular distribution throughout Southeast Asia and the Pacific, while its sister species, the Welcome Swallow (H. neoxena), has a continental distribution in Australia. We used whole-genome data to demonstrate strong genetic structure and limited introgression among insular populations, but not among continental populations. Demographic models show that historic changes in habitat connectivity have contributed to population structure within the clade. Swallows appear to exhibit evolutionarily labile dispersal behavior in which they reduce dispersal propensity after island colonization despite retaining strong flight ability. Our data support the hypothesis that fragmented habitats enhance population differentiation in vagile groups, and suggest that labile dispersal behavior is a key mechanism underlying this pattern.
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Affiliation(s)
- Grant G Broyles
- Department of Biological Sciences, California State Polytechnic University, Pomona, CA, United States
| | - Brian M Myers
- Department of Biological Sciences, California State Polytechnic University, Pomona, CA, United States
- Department of Biology, Eastern Oregon University, La Grande, OR, United States
| | - Nicholas R Friedman
- Biodiversity and Biocomplexity Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Japan
- Centre for Taxonomy and Morphology, Museum of Nature Hamburg, Leibniz Institute for the Analysis of Biodiversity Change (LIB), Hamburg, Germany
| | - Dency F Gawin
- Faculty of Resource Science and Technology, Universiti Malaysia Sarawak, Kota Samarahan, Sarawak, Malaysia
| | - Farah S Mohd-Taib
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Selangor, Malaysia
| | - Penigran G M Sahlan
- Sabah Forestry Department, Forest Research Centre, Sandakan, Sabah, Malaysia
| | - Sampath S Seneviratne
- Avian Sciences and Conservation, Department of Zoology and Environment Sciences, The University of Colombo, Colombo, Sri Lanka
| | - N Chamalka G de Silva
- Avian Sciences and Conservation, Department of Zoology and Environment Sciences, The University of Colombo, Colombo, Sri Lanka
- Department of Physiology and Neurobiology, College of Liberal Arts and Sciences, University of Connecticut, Storrs, CT, United States
| | - Thilini T M Lekamlage
- Avian Sciences and Conservation, Department of Zoology and Environment Sciences, The University of Colombo, Colombo, Sri Lanka
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB, Canada
| | - Amanda K Hund
- Department of Ecology and Evolution, The University of Colorado, Boulder, CO, United States
- Department of Biology, Carleton College, Northfield, MN, United States
| | - Elizabeth S C Scordato
- Department of Biological Sciences, California State Polytechnic University, Pomona, CA, United States
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2
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Firneno TJ, Semenov G, Dopman EB, Taylor SA, Larson EL, Gompert Z. Quantitative Analyses of Coupling in Hybrid Zones. Cold Spring Harb Perspect Biol 2023; 15:a041434. [PMID: 37739809 PMCID: PMC10691479 DOI: 10.1101/cshperspect.a041434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/24/2023]
Abstract
In hybrid zones, whether barrier loci experience selection mostly independently or as a unit depends on the ratio of selection to recombination as captured by the coupling coefficient. Theory predicts a sharper transition between an uncoupled and coupled system when more loci affect hybrid fitness. However, the extent of coupling in hybrid zones has rarely been quantified. Here, we use simulations to characterize the relationship between the coupling coefficient and variance in clines across genetic loci. We then reanalyze 25 hybrid zone data sets and find that cline variances and estimated coupling coefficients form a smooth continuum from high variance and weak coupling to low variance and strong coupling. Our results are consistent with low rates of hybridization and a strong genome-wide barrier to gene flow when the coupling coefficient is much greater than 1, but also suggest that this boundary might be approached gradually and at a near constant rate over time.
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Affiliation(s)
- Thomas J Firneno
- Department of Biology, University of Denver, Denver, Colorado 80208, USA
| | - Georgy Semenov
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, Colorado 80211, USA
| | - Erik B Dopman
- Department of Biology, Tufts University, Medford, Massachusetts 02155, USA
| | - Scott A Taylor
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, Colorado 80211, USA
| | - Erica L Larson
- Department of Biology, University of Denver, Denver, Colorado 80208, USA
| | - Zachariah Gompert
- Department of Biology, Utah State University, Logan, Utah 84321, USA
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3
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Fukutani K, Matsui M, Nishikawa K. Population genetic structure and hybrid zone analyses for species delimitation in the Japanese toad ( Bufo japonicus). PeerJ 2023; 11:e16302. [PMID: 37901459 PMCID: PMC10607272 DOI: 10.7717/peerj.16302] [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: 06/26/2023] [Accepted: 09/25/2023] [Indexed: 10/31/2023] Open
Abstract
Hybridization following secondary contact may produce different outcomes depending on the extent to which genetic diversity and reproductive barriers have accumulated during isolation. The Japanese toad, Bufo japonicus, is distributed on the main islands of Japan. In the present study, we applied multiplexed inter-simple sequence repeat genotyping by sequencing to achieve the fine-scale resolution of the genetic cluster in B. j. japonicus and B. j. formosus. We also elucidated hybridization patterns and gene flow degrees across contact zones between the clusters identified. Using SNP data, we found four genetic clusters in B. j. japonicus and B. j. formosus and three contact zones of the cluster pairs among these four clusters. The two oldest diverged lineages, B. j. japonicus and B. j. formosus, formed a narrow contact zone consistent with species distinctiveness. Therefore, we recommend that these two subspecies be elevated to the species level. In contrast, the less diverged pairs of two clusters in B. j. japonicus and B. j. formosus, respectively, admixed over a hundred kilometers, suggesting that they have not yet developed strong reproductive isolation and need to be treated as conspecifics. These results will contribute to resolving taxonomic confusion in Japanese toads.
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Affiliation(s)
- Kazumi Fukutani
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto, Japan
| | - Masafumi Matsui
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto, Japan
| | - Kanto Nishikawa
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto, Japan
- Graduate School of Global Environmental Studies, Kyoto University, Kyoto, Japan
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4
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Hague MTJ, Miller LE, Stokes AN, Feldman CR, Brodie ED, Brodie ED. Conspicuous coloration of toxin-resistant predators implicates additional trophic interactions in a predator-prey arms race. Mol Ecol 2023; 32:4482-4496. [PMID: 36336815 DOI: 10.1111/mec.16772] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 10/21/2022] [Accepted: 11/03/2022] [Indexed: 08/08/2023]
Abstract
Antagonistic coevolution between natural enemies can produce highly exaggerated traits, such as prey toxins and predator resistance. This reciprocal process of adaptation and counter-adaptation may also open doors to other evolutionary novelties not directly involved in the phenotypic interface of coevolution. We tested the hypothesis that predator-prey coevolution coincided with the evolution of conspicuous coloration on resistant predators that retain prey toxins. In western North America, common garter snakes (Thamnophis sirtalis) have evolved extreme resistance to tetrodotoxin (TTX) in the coevolutionary arms race with their deadly prey, Pacific newts (Taricha spp.). TTX-resistant snakes can retain large amounts of ingested TTX, which could serve as a deterrent against the snakes' own predators if TTX toxicity and resistance are coupled with a conspicuous warning signal. We evaluated whether arms race escalation covaries with bright red coloration in snake populations across the geographic mosaic of coevolution. Snake colour variation departs from the neutral expectations of population genetic structure and covaries with escalating clines of newt TTX and snake resistance at two coevolutionary hotspots. In the Pacific Northwest, bright red coloration fits an expected pattern of an aposematic warning to avian predators: TTX-resistant snakes that consume highly toxic newts also have relatively large, reddish-orange dorsal blotches. Snake coloration also seems to have evolved with the arms race in California, but overall patterns are less intuitively consistent with aposematism. These results suggest that interactions with additional trophic levels can generate novel traits as a cascading consequence of arms race coevolution across the geographic mosaic.
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Affiliation(s)
- Michael T J Hague
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA
| | - Lauren E Miller
- Department of Biology, University of Virginia, Charlottesville, Virginia, USA
| | - Amber N Stokes
- Department of Biology, California State University, Bakersfield, California, USA
| | - Chris R Feldman
- Department of Biology, University of Nevada, Reno, Nevada, USA
| | - Edmund D Brodie
- Department of Biology, Utah State University, Logan, Utah, USA
| | - Edmund D Brodie
- Department of Biology, University of Virginia, Charlottesville, Virginia, USA
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5
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Secomandi S, Gallo GR, Sozzoni M, Iannucci A, Galati E, Abueg L, Balacco J, Caprioli M, Chow W, Ciofi C, Collins J, Fedrigo O, Ferretti L, Fungtammasan A, Haase B, Howe K, Kwak W, Lombardo G, Masterson P, Messina G, Møller AP, Mountcastle J, Mousseau TA, Ferrer Obiol J, Olivieri A, Rhie A, Rubolini D, Saclier M, Stanyon R, Stucki D, Thibaud-Nissen F, Torrance J, Torroni A, Weber K, Ambrosini R, Bonisoli-Alquati A, Jarvis ED, Gianfranceschi L, Formenti G. A chromosome-level reference genome and pangenome for barn swallow population genomics. Cell Rep 2023; 42:111992. [PMID: 36662619 PMCID: PMC10044405 DOI: 10.1016/j.celrep.2023.111992] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 07/20/2022] [Accepted: 01/04/2023] [Indexed: 01/20/2023] Open
Abstract
Insights into the evolution of non-model organisms are limited by the lack of reference genomes of high accuracy, completeness, and contiguity. Here, we present a chromosome-level, karyotype-validated reference genome and pangenome for the barn swallow (Hirundo rustica). We complement these resources with a reference-free multialignment of the reference genome with other bird genomes and with the most comprehensive catalog of genetic markers for the barn swallow. We identify potentially conserved and accelerated genes using the multialignment and estimate genome-wide linkage disequilibrium using the catalog. We use the pangenome to infer core and accessory genes and to detect variants using it as a reference. Overall, these resources will foster population genomics studies in the barn swallow, enable detection of candidate genes in comparative genomics studies, and help reduce bias toward a single reference genome.
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Affiliation(s)
- Simona Secomandi
- Department of Biosciences, University of Milan, Milan, Italy; Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | - Guido R Gallo
- Department of Biosciences, University of Milan, Milan, Italy
| | | | - Alessio Iannucci
- Department of Biology, University of Florence, Sesto Fiorentino (FI), Italy
| | - Elena Galati
- Department of Biosciences, University of Milan, Milan, Italy
| | - Linelle Abueg
- Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, USA
| | - Jennifer Balacco
- Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, USA
| | - Manuela Caprioli
- Department of Environmental Sciences and Policy, University of Milan, Milan, Italy
| | | | - Claudio Ciofi
- Department of Biology, University of Florence, Sesto Fiorentino (FI), Italy
| | | | - Olivier Fedrigo
- Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, USA
| | - Luca Ferretti
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia, Italy
| | | | - Bettina Haase
- Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, USA
| | | | - Woori Kwak
- Department of Medical and Biological Sciences, The Catholic University of Korea, Bucheon 14662, Korea
| | - Gianluca Lombardo
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia, Italy
| | - Patrick Masterson
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | | | - Anders P Møller
- Ecologie Systématique Evolution, Université Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Orsay Cedex, France
| | | | - Timothy A Mousseau
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
| | - Joan Ferrer Obiol
- Department of Environmental Sciences and Policy, University of Milan, Milan, Italy
| | - Anna Olivieri
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia, Italy
| | - Arang Rhie
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Diego Rubolini
- Department of Environmental Sciences and Policy, University of Milan, Milan, Italy
| | | | - Roscoe Stanyon
- Department of Biology, University of Florence, Sesto Fiorentino (FI), Italy
| | | | - Françoise Thibaud-Nissen
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | | | - Antonio Torroni
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia, Italy
| | | | - Roberto Ambrosini
- Department of Environmental Sciences and Policy, University of Milan, Milan, Italy
| | - Andrea Bonisoli-Alquati
- Department of Biological Sciences, California State Polytechnic University - Pomona, Pomona, CA, USA
| | - Erich D Jarvis
- Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, USA; The Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | | | - Giulio Formenti
- Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, USA.
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6
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Nikelski E, Rubtsov AS, Irwin D. High heterogeneity in genomic differentiation between phenotypically divergent songbirds: a test of mitonuclear co-introgression. Heredity (Edinb) 2023; 130:1-13. [PMID: 36463372 PMCID: PMC9814147 DOI: 10.1038/s41437-022-00580-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 11/23/2022] [Accepted: 11/23/2022] [Indexed: 12/05/2022] Open
Abstract
Comparisons of genomic variation among closely related species often show more differentiation in mitochondrial DNA (mtDNA) and sex chromosomes than in autosomes, a pattern expected due to the differing effective population sizes and evolutionary dynamics of these genomic components. Yet, introgression can cause species pairs to deviate dramatically from general differentiation trends. The yellowhammer (Emberiza citrinella) and pine bunting (E. leucocephalos) are hybridizing avian sister species that differ greatly in appearance and moderately in nuclear DNA, but that show no mtDNA differentiation. This discordance is best explained by adaptive mtDNA introgression-a process that can select for co-introgression at nuclear genes with mitochondrial functions (mitonuclear genes). To better understand these discordant differentiation patterns and characterize nuclear differentiation in this system, we investigated genome-wide differentiation between allopatric yellowhammers and pine buntings and compared it to what was seen previously in mtDNA. We found significant nuclear differentiation that was highly heterogeneous across the genome, with a particularly wide differentiation peak on the sex chromosome Z. We further investigated mitonuclear gene co-introgression between yellowhammers and pine buntings and found support for this process in the direction of pine buntings into yellowhammers. Genomic signals indicative of co-introgression were common in mitonuclear genes coding for subunits of the mitoribosome and electron transport chain complexes. Such introgression of mitochondrial DNA and mitonuclear genes provides a possible explanation for the patterns of high genomic heterogeneity in genomic differentiation seen among some species groups.
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Affiliation(s)
- Ellen Nikelski
- Department of Zoology, and Biodiversity Research Centre, 6270 University Blvd., University of British Columbia, Vancouver, BC, Canada.
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada.
| | | | - Darren Irwin
- Department of Zoology, and Biodiversity Research Centre, 6270 University Blvd., University of British Columbia, Vancouver, BC, Canada
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7
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Mandeville EG, Hall RO, Buerkle CA. Ecological outcomes of hybridization vary extensively in Catostomus fishes. Evolution 2022; 76:2697-2711. [PMID: 36097356 PMCID: PMC9801484 DOI: 10.1111/evo.14624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 07/20/2022] [Accepted: 07/26/2022] [Indexed: 01/22/2023]
Abstract
Hybridization outcomes vary geographically and can depend on the environment. Hybridization can also reshape biotic interactions, leading to ecological shifts. If hybrids function differently ecologically in ways that enhance or reduce fitness, and those ecological roles vary geographically, ecological factors might explain variation in hybridization outcomes. However, relatively few studies have focused on ecological traits of hybrids. We compared the feeding ecology of Catostomus fish species and hybrids by using stable isotopes (δ13 C and δ15 N) as a proxy for diet and habitat use, and compared two native species, an introduced species, and three interspecific hybrid crosses. We included hybrids and parental species from seven rivers where hybridization outcomes vary. Relative isotopic niches of native species varied geographically, but native species did not fully overlap in isotopic space in any river sampled, suggesting little overlap of resource use between historically sympatric species. The introduced species overlapped with one or both native species in every river, suggesting similar resource use and potential competition. Hybrids occupied intermediate, matching, or more transgressive isotopic niches, and varied within and among rivers. Ecological outcomes of hybridization varied across locations, implying that hybridization might have unpredictable, idiosyncratic ecological effects.
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Affiliation(s)
- Elizabeth G. Mandeville
- Department of Integrative Biology, University of Guelph, Guelph, Ontario Canada
- Department of Botany, University of Wyoming, Laramie, Wyoming USA
- Program in Ecology, University of Wyoming, Laramie, Wyoming USA
| | - Robert O. Hall
- Program in Ecology, University of Wyoming, Laramie, Wyoming USA
- Flathead Lake Biological Station, University of Montana, Polson, Montana USA (present address)
- Department of Zoology and Physiology, University of Wyoming, Laramie, Wyoming USA
| | - C. Alex Buerkle
- Department of Botany, University of Wyoming, Laramie, Wyoming USA
- Program in Ecology, University of Wyoming, Laramie, Wyoming USA
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8
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Lombardo G, Migliore NR, Colombo G, Capodiferro MR, Formenti G, Caprioli M, Moroni E, Caporali L, Lancioni H, Secomandi S, Gallo GR, Costanzo A, Romano A, Garofalo M, Cereda C, Carelli V, Gillespie L, Liu Y, Kiat Y, Marzal A, López-Calderón C, Balbontín J, Mousseau TA, Matyjasiak P, Møller AP, Semino O, Ambrosini R, Alquati AB, Rubolini D, Ferretti L, Achilli A, Gianfranceschi L, Olivieri A, Torroni A. The Mitogenome Relationships and Phylogeography of Barn Swallows (Hirundo rustica). Mol Biol Evol 2022; 39:6591937. [PMID: 35617136 PMCID: PMC9174979 DOI: 10.1093/molbev/msac113] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The barn swallow (Hirundo rustica) poses a number of fascinating scientific questions, including the taxonomic status of postulated subspecies. Here we obtained and assessed the sequence variation of 411 complete mitogenomes, mainly from the European H. r. rustica, but other subspecies as well. In almost every case, we observed subspecies-specific haplogroups, which we employed together with estimated radiation times to postulate a model for the geographical and temporal worldwide spread of the species. The female barn swallow carrying the Hirundo rustica ancestral mitogenome left Africa (or its vicinity) around 280 thousand years ago (kya), and her descendants expanded first into Eurasia and then, at least 51 kya, into the Americas, from where a relatively recent (< 20 kya) back migration to Asia took place. The exception to the haplogroup subspecies specificity is represented by the sedentary Levantine H. r. transitiva that extensively shares haplogroup A with the migratory European H. r. rustica and, to a lesser extent, haplogroup B with the Egyptian H. r. savignii. Our data indicate that rustica and transitiva most likely derive from a sedentary Levantine population source that split at the end of the Younger Dryas (11.7 kya). Since then, however, transitiva received genetic inputs from and admixed with both the closely related rustica and the adjacent savignii. Demographic analyses confirm this species' strong link with climate fluctuations and human activities making it an excellent indicator for monitoring and assessing the impact of current global changes on wildlife.
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Affiliation(s)
- Gianluca Lombardo
- Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", Università di Pavia, 27100 Pavia, Italy
| | - Nicola Rambaldi Migliore
- Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", Università di Pavia, 27100 Pavia, Italy
| | - Giulia Colombo
- Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", Università di Pavia, 27100 Pavia, Italy
| | - Marco Rosario Capodiferro
- Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", Università di Pavia, 27100 Pavia, Italy
| | - Giulio Formenti
- Vertebrate Genome Laboratory, The Rockefeller University, New York, NY 10065, USA
| | - Manuela Caprioli
- Dipartimento di Scienze e Politiche Ambientali, Università degli Studi di Milano, 20133 Milan, Italy
| | - Elisabetta Moroni
- Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", Università di Pavia, 27100 Pavia, Italy
| | - Leonardo Caporali
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Programma di Neurogenetica, 40139 Bologna, Italy
| | - Hovirag Lancioni
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, 06123 Perugia, Italy
| | - Simona Secomandi
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133 Milan, Italy
| | - Guido Roberto Gallo
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133 Milan, Italy
| | - Alessandra Costanzo
- Dipartimento di Scienze e Politiche Ambientali, Università degli Studi di Milano, 20133 Milan, Italy
| | - Andrea Romano
- Dipartimento di Scienze e Politiche Ambientali, Università degli Studi di Milano, 20133 Milan, Italy
| | - Maria Garofalo
- Genomic and Post-Genomic Unit, IRCCS Mondino Foundation, 27100 Pavia, Italy
| | - Cristina Cereda
- Genomic and Post-Genomic Unit, IRCCS Mondino Foundation, 27100 Pavia, Italy
| | - Valerio Carelli
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Programma di Neurogenetica, 40139 Bologna, Italy.,Dipartimento di Scienze Biomediche e Neuromotorie, Università di Bologna, 40139 Bologna, Italy
| | - Lauren Gillespie
- Department of Academic Education, Central Community College, Columbus, NE 68601, USA
| | - Yang Liu
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Guangzhou 510275, China
| | - Yosef Kiat
- Israeli Bird Ringing Center (IBRC), Israel Ornithological Center, Tel Aviv, Israel
| | - Alfonso Marzal
- Department of Zoology, University of Extremadura, 06071 Badajoz, Spain
| | - Cosme López-Calderón
- Department of Wetland Ecology, Estación Biológica de Doñana CSIC, 41092 Seville, Spain
| | - Javier Balbontín
- Department of Zoology, University of Seville, 41012 Seville, Spain
| | - Timothy A Mousseau
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
| | - Piotr Matyjasiak
- Institute of Biological Sciences, Cardinal Stefan Wyszyński University in Warsaw, 01-938 Warsaw, Poland
| | - Anders Pape Møller
- Ecologie Systématique Evolution, Université Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91405, Orsay Cedex, France
| | - Ornella Semino
- Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", Università di Pavia, 27100 Pavia, Italy
| | - Roberto Ambrosini
- Dipartimento di Scienze e Politiche Ambientali, Università degli Studi di Milano, 20133 Milan, Italy
| | - Andrea Bonisoli Alquati
- Department of Biological Sciences, California State Polytechnic University - Pomona, Pomona, CA 91767, USA
| | - Diego Rubolini
- Dipartimento di Scienze e Politiche Ambientali, Università degli Studi di Milano, 20133 Milan, Italy
| | - Luca Ferretti
- Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", Università di Pavia, 27100 Pavia, Italy
| | - Alessandro Achilli
- Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", Università di Pavia, 27100 Pavia, Italy
| | - Luca Gianfranceschi
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133 Milan, Italy
| | - Anna Olivieri
- Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", Università di Pavia, 27100 Pavia, Italy
| | - Antonio Torroni
- Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", Università di Pavia, 27100 Pavia, Italy
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9
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Turbek SP, Schield DR, Scordato ESC, Contina A, Da XW, Liu Y, Liu Y, Pagani-Núñez E, Ren QM, Smith CCR, Stricker CA, Wunder M, Zonana DM, Safran RJ. A migratory divide spanning two continents is associated with genomic and ecological divergence. Evolution 2022; 76:722-736. [PMID: 35166383 DOI: 10.1111/evo.14448] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 12/21/2021] [Accepted: 12/29/2021] [Indexed: 01/22/2023]
Abstract
Migratory divides are contact zones between breeding populations with divergent migratory strategies during the nonbreeding season. These locations provide an opportunity to evaluate the role of seasonal migration in the maintenance of reproductive isolation, particularly the relationship between population structure and features associated with distinct migratory strategies. We combine light-level geolocators, genomic sequencing, and stable isotopes to investigate the timing of migration and migratory routes of individuals breeding on either side of a migratory divide coinciding with genomic differentiation across a hybrid zone between barn swallow (Hirundo rustica) subspecies in China. Individuals west of the hybrid zone, with H. r. rustica ancestry, had comparatively enriched stable-carbon and hydrogen isotope values and overwintered in eastern Africa, whereas birds east of the hybrid zone, with H. r. gutturalis ancestry, had depleted isotope values and migrated to southern India. The two subspecies took divergent migratory routes around the high-altitude Karakoram Range and arrived on the breeding grounds over 3 weeks apart. These results indicate that assortative mating by timing of arrival and/or selection against hybrids with intermediate migratory traits may maintain reproductive isolation between the subspecies, and that inhospitable geographic features may have contributed to the diversification of Asian avifauna by influencing migratory patterns.
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Affiliation(s)
- Sheela P Turbek
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, 80309
| | - Drew R Schield
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, 80309
| | - Elizabeth S C Scordato
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, 80309.,Department of Biological Sciences, Cal Poly Pomona, Pomona, California, 91768
| | - Andrea Contina
- Department of Integrative Biology, University of Colorado, Denver, Colorado, 80217
| | - Xin-Wei Da
- College of Life Science, Wuhan University, Wuhan, 430072, China
| | - Yang Liu
- School of Ecology, Sun Yat-sen University, Guangzhou, 510275, China
| | - Yu Liu
- Key Laboratory for Biodiversity Sciences and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Emilio Pagani-Núñez
- Department of Health and Environmental Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, 215123, China
| | - Qing-Miao Ren
- School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Chris C R Smith
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, 80309
| | - Craig A Stricker
- U.S. Geological Survey, Fort Collins Science Center, Fort Collins, Colorado, 80526
| | - Michael Wunder
- Department of Integrative Biology, University of Colorado, Denver, Colorado, 80217
| | - David M Zonana
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, 80309.,Department of Biological Sciences, University of Denver, Denver, Colorado, 80210
| | - Rebecca J Safran
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, 80309
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10
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Combe FJ, Jaster L, Ricketts A, Haukos D, Hope AG. Population genomics of free-ranging Great Plains white-tailed and mule deer reflects a long history of interspecific hybridization. Evol Appl 2022; 15:111-131. [PMID: 35126651 PMCID: PMC8792484 DOI: 10.1111/eva.13330] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 09/21/2021] [Accepted: 11/22/2021] [Indexed: 12/11/2022] Open
Abstract
Hybridization is a natural process at species-range boundaries that may variably promote the speciation process or break down species barriers but minimally will influence management outcomes of distinct populations. White-tailed deer (Odocoileus virginianus) and mule deer (Odocoileus hemionus) have broad and overlapping distributions in North America and a recognized capacity for interspecific hybridization. In response to contemporary environmental change to any of one or multiple still-unknown factors, mule deer range is contracting westward accompanied by a westward expansion of white-tailed deer, leading to increasing interactions, opportunities for gene flow, and associated conservation implications. To quantify genetic diversity, phylogenomic structure, and dynamics of hybridization in sympatric populations of white-tailed and mule deer, we used mitochondrial cytochrome b data coupled with SNP loci discovered with double-digest restriction site-associated DNA sequencing. We recovered 25,018 SNPs across 92 deer samples from both species, collected from two regions of western Kansas. Eight individuals with unambiguous external morphology representing both species were of hybrid origin (8.7%), and represented the product of multi-generational backcrossing. Mitochondrial data showed both ancient and recent directional discordance with morphological species assignments, reflecting a legacy of mule deer males mating with white-tailed deer females. Mule deer had lower genetic diversity than white-tailed deer, and both mitochondrial and nuclear data suggest contemporary mule deer effective population decline. Landscape genetic analyses show relative isolation between the two study regions for white-tailed deer, but greater connectivity among mule deer, with predominant movement from north to south. Collectively, our results suggest a long history of gene flow between these species in the Great Plains and hint at evolutionary processes that purge incompatible functional genomic elements as a result of hybridization. Surviving hybrids evidently may be reproductive, but with unknown consequences for the future integrity of these species, population trajectories, or relative susceptibility to emerging pathogens.
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Affiliation(s)
- Fraser J. Combe
- Division of BiologyKansas State UniversityManhattanKansasUSA
| | - Levi Jaster
- Kansas Department of Wildlife and ParksTopekaKansasUSA
| | - Andrew Ricketts
- Department of Horticulture and Natural Sciences, Wildlife and Outdoor Enterprise ManagementKansas State UniversityManhattanKansasUSA
| | - David Haukos
- Division of BiologyU.S. Geological SurveyKansas Cooperative Fish and Wildlife Research UnitKansas State UniversityManhattanKansasUSA
| | - Andrew G. Hope
- Division of BiologyKansas State UniversityManhattanKansasUSA
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11
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Wolf JF, Bowman J, Keobouasone S, Taylor RS, Wilson PJ. A de novo genome assembly and annotation of the southern flying squirrel (Glaucomys volans). G3-GENES GENOMES GENETICS 2021; 12:6426101. [PMID: 34788821 PMCID: PMC8727995 DOI: 10.1093/g3journal/jkab373] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 10/19/2021] [Indexed: 11/24/2022]
Abstract
Northern (Glaucomys sabrinus) and southern (Glaucomys volans) flying squirrels are widespread species distributed across North America. Northern flying squirrels are common inhabitants of the boreal forest, also occurring in coniferous forest remnants farther south, whereas the southern flying squirrel range is centered in eastern temperate woodlands. These two flying squirrel species exhibit a hybrid zone across a latitudinal gradient in an area of recent secondary contact. Glaucomys hybrid offspring are viable and can successfully backcross with either parental species, however, the fitness implications of such events are currently unknown. Some populations of G. sabrinus are endangered, and thus, interspecific hybridization is a key conservation concern in flying squirrels. To provide a resource for future studies to evaluate hybridization and possible introgression, we sequenced and assembled a de novo long-read genome from a G. volans individual sampled in southern Ontario, Canada, while four short-read genomes (two G. sabrinus and two G. volans, all from Ontario) were resequenced on Illumina platforms. The final genome assembly consisted of approximately 2.40 Gb with a scaffold N50 of 455.26 Kb. Benchmarking Universal Single-Copy Orthologs reconstructed 3,742 (91.2%) complete mammalian genes and genome annotation using RNA-Seq identified the locations of 19,124 protein-coding genes. The four short-read individuals were aligned to our reference genome to investigate the demographic history of the two species. A principal component analysis clearly separated resequenced individuals, while inferring population size history using the Pairwise Sequentially Markovian Coalescent model noted an approximate species split 1 million years ago, and a single, possibly recently introgressed individual.
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Affiliation(s)
- J F Wolf
- Biology Department, Trent University, Peterborough, ON K9J 7B8, Canada.,Ontario Ministry of Northern Development, Mines, Natural Resources and Forestry, Wildlife Research and Monitoring Section, Trent University, Peterborough, ON K9J 7B8, Canada
| | - Jeff Bowman
- Biology Department, Trent University, Peterborough, ON K9J 7B8, Canada.,Ontario Ministry of Northern Development, Mines, Natural Resources and Forestry, Wildlife Research and Monitoring Section, Trent University, Peterborough, ON K9J 7B8, Canada
| | - Sonesinh Keobouasone
- Landscape Science and Technology Division, Environment and Climate Change Canada, Ottawa, ON K1S 5R1, Canada
| | - Rebecca S Taylor
- Biology Department, Trent University, Peterborough, ON K9J 7B8, Canada
| | - Paul J Wilson
- Biology Department, Trent University, Peterborough, ON K9J 7B8, Canada
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12
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Kess T, Dempson JB, Lehnert SJ, Layton KKS, Einfeldt A, Bentzen P, Salisbury SJ, Messmer AM, Duffy S, Ruzzante DE, Nugent CM, Ferguson MM, Leong JS, Koop BF, O'Connell MF, Bradbury IR. Genomic basis of deep-water adaptation in Arctic Charr (Salvelinus alpinus) morphs. Mol Ecol 2021; 30:4415-4432. [PMID: 34152667 DOI: 10.1111/mec.16033] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 05/28/2021] [Accepted: 06/03/2021] [Indexed: 12/30/2022]
Abstract
The post-glacial colonization of Gander Lake in Newfoundland, Canada, by Arctic Charr (Salvelinus alpinus) provides the opportunity to study the genomic basis of adaptation to extreme deep-water environments. Colonization of deep-water (>50 m) habitats often requires extensive adaptation to cope with novel environmental challenges from high hydrostatic pressure, low temperature, and low light, but the genomic mechanisms underlying evolution in these environments are rarely known. Here, we compare genomic divergence between a deep-water morph adapted to depths of up to 288 m and a larger, piscivorous pelagic morph occupying shallower depths. Using both a SNP array and resequencing of whole nuclear and mitochondrial genomes, we find clear genetic divergence (FST = 0.11-0.15) between deep and shallow water morphs, despite an absence of morph divergence across the mitochondrial genome. Outlier analyses identified many diverged genomic regions containing genes enriched for processes such as gene expression and DNA repair, cardiac function, and membrane transport. Detection of putative copy number variants (CNVs) uncovered 385 genes with CNVs distinct to piscivorous morphs, and 275 genes with CNVs distinct to deep-water morphs, enriched for processes associated with synapse assembly. Demographic analyses identified evidence for recent and local morph divergence, and ongoing reductions in diversity consistent with postglacial colonization. Together, these results show that Arctic Charr morph divergence has occurred through genome-wide differentiation and elevated divergence of genes underlying multiple cellular and physiological processes, providing insight into the genomic basis of adaptation in a deep-water habitat following postglacial recolonization.
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Affiliation(s)
- Tony Kess
- Fisheries and Oceans Canada, Northwest Atlantic Fisheries Centre, St. John's, NL, Canada
| | - J Brian Dempson
- Fisheries and Oceans Canada, Northwest Atlantic Fisheries Centre, St. John's, NL, Canada
| | - Sarah J Lehnert
- Fisheries and Oceans Canada, Northwest Atlantic Fisheries Centre, St. John's, NL, Canada
| | - Kara K S Layton
- School of Biological Sciences, University of Aberdeen, Aberdeen, UK
| | - Anthony Einfeldt
- Department of Biology, Dalhousie University, Halifax, NS, Canada
| | - Paul Bentzen
- Department of Biology, Dalhousie University, Halifax, NS, Canada
| | | | - Amber M Messmer
- Fisheries and Oceans Canada, Northwest Atlantic Fisheries Centre, St. John's, NL, Canada
| | - Steven Duffy
- Fisheries and Oceans Canada, Northwest Atlantic Fisheries Centre, St. John's, NL, Canada
| | | | - Cameron M Nugent
- Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
| | - Moira M Ferguson
- Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
| | - Jong S Leong
- Department of Biology, University of Victoria, Victoria, BC, Canada
| | - Ben F Koop
- Department of Biology, University of Victoria, Victoria, BC, Canada
| | - Michael F O'Connell
- Fisheries and Oceans Canada, Northwest Atlantic Fisheries Centre, St. John's, NL, Canada
| | - Ian R Bradbury
- Fisheries and Oceans Canada, Northwest Atlantic Fisheries Centre, St. John's, NL, Canada
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13
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Schield DR, Scordato ESC, Smith CCR, Carter JK, Cherkaoui SI, Gombobaatar S, Hajib S, Hanane S, Hund AK, Koyama K, Liang W, Liu Y, Magri N, Rubtsov A, Sheta B, Turbek SP, Wilkins MR, Yu L, Safran RJ. Sex-linked genetic diversity and differentiation in a globally distributed avian species complex. Mol Ecol 2021; 30:2313-2332. [PMID: 33720472 DOI: 10.1111/mec.15885] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 02/19/2021] [Accepted: 03/10/2021] [Indexed: 12/15/2022]
Abstract
Sex chromosomes often bear distinct patterns of genetic variation due to unique patterns of inheritance and demography. The processes of mutation, recombination, genetic drift and selection also influence rates of evolution on sex chromosomes differently than autosomes. Measuring such differences provides information about how these processes shape genomic variation and their roles in the origin of species. To test hypotheses and predictions about patterns of autosomal and sex-linked genomic diversity and differentiation, we measured population genetic statistics within and between populations and subspecies of the barn swallow (Hirundo rustica) and performed explicit comparisons between autosomal and Z-linked genomic regions. We first tested for evidence of low Z-linked genetic diversity and high Z-linked population differentiation relative to autosomes, then for evidence that the Z chromosome bears greater ancestry information due to faster lineage sorting. Finally, we investigated geographical clines across hybrid zones for evidence that the Z chromosome is resistant to introgression due to selection against hybrids. We found evidence that the barn swallow mating system, demographic history and linked selection each contribute to low Z-linked diversity and high Z-linked differentiation. While incomplete lineage sorting is rampant across the genome, our results indicate faster sorting of ancestral polymorphism on the Z. Finally, hybrid zone analyses indicate barriers to introgression on the Z chromosome, suggesting that sex-linked traits are important in reproductive isolation, especially in migratory divide regions. Our study highlights how selection, gene flow and demography shape sex-linked genetic diversity and underlines the relevance of the Z chromosome in speciation.
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Affiliation(s)
- Drew R Schield
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - Elizabeth S C Scordato
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA.,Department of Biological Sciences, California State Polytechnic University, Pomona, CA, USA
| | - Chris C R Smith
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - Javan K Carter
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - Sidi Imad Cherkaoui
- Ecole Supérieure de Technologie de Khénifra, Sultan Moulay Slimane University, Béni-Mellal, Morocco
| | - Sundev Gombobaatar
- National University of Mongolia and Mongolian Ornithological Society, Ulaanbaatar, Mongolia
| | - Said Hajib
- Water and Forests Department, Forest Research Center, Rabat-Agdal, Morocco
| | - Saad Hanane
- Water and Forests Department, Forest Research Center, Rabat-Agdal, Morocco
| | - Amanda K Hund
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA.,Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, MN, USA
| | | | - Wei Liang
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou, China
| | - Yang Liu
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Guangzhou, China
| | - Najib Magri
- Water and Forests Department, Forest Research Center, Rabat-Agdal, Morocco
| | | | - Basma Sheta
- Zoology Department, Faculty of Science, Damietta University, New Damietta City, Egypt
| | - Sheela P Turbek
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - Matthew R Wilkins
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA.,Collaborative for STEM Education and Outreach, Vanderbilt University, Nashville, TN, USA
| | - Liu Yu
- Key Laboratory for Biodiversity Sciences and Ecological Engineering, Ministry of Education, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Rebecca J Safran
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
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14
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Pflugbeil G, Affenzeller M, Tribsch A, Comes HP. Primary hybrid zone formation in Tephroseris helenitis (Asteraceae), following postglacial range expansion along the central Northern Alps. Mol Ecol 2021; 30:1704-1720. [PMID: 33548078 PMCID: PMC8048512 DOI: 10.1111/mec.15832] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 01/26/2021] [Accepted: 01/27/2021] [Indexed: 11/26/2022]
Abstract
Distinguishing between secondary versus primary hybrid zone formation remains a challenging task as, for instance, the time window in which these historical (vicariant) versus contemporary (environmental-selective) processes are distinguishable may be relatively narrow. Here, we examine the origin and structure of a transition zone between two subspecies of Tephroseris helenitis along the central Northern Alps, using molecular (AFLP) and morphological (achene type) data in combination with ecological niche models (ENMs) to hindcast ranges at the Last Glacial Maximum (LGM) and mid-Holocene. Samples were collected over a c. 350 km long transect, largely covered by ice during the LGM. Genetically nonadmixed individuals of subspp. helenitis versus salisburgensis dominated the westernmost versus eastern transect areas, with admixed individuals occurring in between. Clines for achene morphology and outlier loci potentially under climate-driven selection were steep, largely noncoincidental, and displaced to the east of the cline centre for neutral AFLPs. During the LGM, ssp. helenitis should have been able to persist in a refugium southwest of the transect, while suitable habitat for ssp. salisburgensis was apparently absent at this time. Together with patterns of genetic and clinal variation, our ENM data are suggestive of a primary hybrid zone that originated after the species' postglacial, eastward expansion. The observed clinal changes may thus reflect random/nonadaptive processes during expansion and selection on particular loci, and possibly achene type, in response to a long-term, west-to-east climate gradient in the direction of more stressful (e.g., wetter/cooler) conditions. Overall, this study adds to the vast hybrid zone literature a rare example of a hybrid zone caused by primary differentiation within a plant species, underlaid by historical range expansion.
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Affiliation(s)
- Georg Pflugbeil
- Department of Biosciences, University of Salzburg, Salzburg, Austria
| | | | - Andreas Tribsch
- Department of Biosciences, University of Salzburg, Salzburg, Austria
| | - Hans Peter Comes
- Department of Biosciences, University of Salzburg, Salzburg, Austria
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15
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Araki Y, Sota T. Population genetic structure underlying the geographic variation in beetle structural colour with multiple transition zones. Mol Ecol 2020; 30:670-684. [PMID: 33253446 DOI: 10.1111/mec.15758] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 11/12/2020] [Accepted: 11/24/2020] [Indexed: 11/27/2022]
Abstract
We studied the population genetic structure underlying the geographic variation in the structural colour of the geotrupid dung beetle, Phelotrupes auratus, which exhibits metallic body colours of different reflectance wavelengths perceived as red, green and indigo. These forms occur parapatrically in an area of Japan. The colour variation was not related to variation in climatic factors. Using single nucleotide polymorphisms (SNPs) from restriction-site-associated DNA sequences, we discriminated five groups of populations (west/red, south/green, south/indigo, south/red and east/red) by a combination of genetic clusters (west, south and east) and three colour forms. There were three transition zones for the colour forms: two between the red and green forms were hybrid zones with steep genetic clines, which implies the existence of barriers to gene flow between regions with different colours. The remaining transition zone between the green and indigo forms lacked genetic differentiation, despite the evident colour changes, which implies regionally specific selection on the different colours. In a genomewide association study, we identified four SNPs that were associated with the red/green or indigo colour and were not linked with one another, which implies that the coloration was controlled by multiple loci, each affecting the expression of a different colour range. These loci may have controlled the transitions between different combinations of colours. Our study demonstrates that geographic colour variation within a species can be maintained by nonuniform interactions among barriers to gene flow, locally specific selection on different colours, and the effects of different colour loci.
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Affiliation(s)
- Yoshifumi Araki
- Department of Zoology, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Teiji Sota
- Department of Zoology, Graduate School of Science, Kyoto University, Kyoto, Japan
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16
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Zolotareva KI, Belokon MM, Belokon YS, Rutovskaya MV, Hlyap LA, Starykov VP, Politov DV, Lebedev VS, Bannikova AA. Genetic diversity and structure of the hedgehogs Erinaceus europaeus and Erinaceus roumanicus: evidence for ongoing hybridization in Eastern Europe. Biol J Linn Soc Lond 2020. [DOI: 10.1093/biolinnean/blaa135] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Abstract
Secondary contact zones between related species are key to understanding speciation mechanisms. The Central European sympatry zone of West European (Erinaceus europaeus) and northern white-breasted (Erinaceus roumanicus) hedgehogs is well studied, whereas data on the Eastern European sympatry zone are scarce. We examined the genetic variation in Russian populations using the mitochondrial Cytb gene, TTR intron 1 and 11 microsatellites to assess genetic variability and distribution patterns. In contrast to the Central European sympatry zone, we found evidence of ongoing hybridization between the two species in the sympatry zone of European Russia, where the proportion of individuals with mixed ancestry was c. 20%. Our data indicate bi-directional mtDNA introgression, but with a higher frequency of E. europaeus haplotypes in hybrids. The proportion of pure specimens with introgressed mitotypes is higher in E. roumanicus than in E. europaeus. Nuclear data showed the prevalence of the genetic contribution from E. roumanicus in admixed individuals. Demographic analyses indicated recent population growth in E. europaeus and little change in E. roumanicus, suggesting that E. europaeus colonized East Europe later than E. roumanicus.
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Affiliation(s)
| | - Mariana M Belokon
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Yuri S Belokon
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Marina V Rutovskaya
- Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia
| | - Ludmila A Hlyap
- Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia
| | | | - Dmitry V Politov
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
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17
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Kirschel ANG, Nwankwo EC, Pierce DK, Lukhele SM, Moysi M, Ogolowa BO, Hayes SC, Monadjem A, Brelsford A. CYP2J19 mediates carotenoid colour introgression across a natural avian hybrid zone. Mol Ecol 2020; 29:4970-4984. [PMID: 33058329 DOI: 10.1111/mec.15691] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 10/02/2020] [Accepted: 10/05/2020] [Indexed: 02/06/2023]
Abstract
It has long been of interest to identify the phenotypic traits that mediate reproductive isolation between related species, and more recently, the genes that underpin them. Much work has focused on identifying genes associated with animal colour, with the candidate gene CYP2J19 identified in laboratory studies as the ketolase converting yellow dietary carotenoids to red ketocarotenoids in birds with red pigments. However, evidence that CYP2J19 explains variation between red and yellow feather coloration in wild populations of birds is lacking. Hybrid zones provide the opportunity to identify genes associated with specific traits. Here we investigate genomic regions associated with colour in red-fronted and yellow-fronted tinkerbirds across a hybrid zone in southern Africa. We sampled 85 individuals, measuring spectral reflectance of forecrown feathers and scoring colours from photographs, while testing for carotenoid presence with Raman spectroscopy. We performed a genome-wide association study to identify associations with carotenoid-based coloration, using double-digest RAD sequencing aligned to a short-read whole genome of a Pogoniulus tinkerbird. Admixture mapping using 104,933 single nucleotide polymorphisms (SNPs) identified a region of chromosome 8 that includes CYP2J19 as the only locus with more than two SNPs significantly associated with both crown hue and crown score, while Raman spectra provided evidence of ketocarotenoids in red feathers. Asymmetric backcrossing in the hybrid zone suggests that yellow-fronted females mate more often with red-fronted males than vice versa. Female red-fronted tinkerbirds mating assortatively with red-crowned males is consistent with the hypothesis that converted carotenoids are an honest signal of quality.
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Affiliation(s)
| | - Emmanuel C Nwankwo
- Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | - Daniel K Pierce
- Department of Evolution, Ecology, and Organismal Biology, University of California Riverside, Riverside, CA, USA
| | - Sifiso M Lukhele
- Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | - Michaella Moysi
- Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | - Bridget O Ogolowa
- Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | - Sophia C Hayes
- Department of Chemistry, University of Cyprus, Nicosia, Cyprus
| | - Ara Monadjem
- Department of Biological Sciences, University of Eswatini, Kwaluseni, Eswatini.,Department of Zoology & Entomology, Mammal Research Institute, University of Pretoria, Hatfield, South Africa
| | - Alan Brelsford
- Department of Evolution, Ecology, and Organismal Biology, University of California Riverside, Riverside, CA, USA
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18
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Turjeman S, Corl A, Wolfenden A, Tsalyuk M, Lublin A, Choi O, Kamath PL, Getz WM, Bowie RCK, Nathan R. Migration, pathogens and the avian microbiome: A comparative study in sympatric migrants and residents. Mol Ecol 2020; 29:4706-4720. [PMID: 33001530 DOI: 10.1111/mec.15660] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 09/17/2020] [Accepted: 09/18/2020] [Indexed: 12/15/2022]
Abstract
Animals generally benefit from their gastrointestinal microbiome, but the factors that influence the composition and dynamics of their microbiota remain poorly understood. Studies of nonmodel host species can illuminate how microbiota and their hosts interact in natural environments. We investigated the role of migratory behaviour in shaping the gut microbiota of free-ranging barn swallows (Hirundo rustica) by studying co-occurring migrant and resident subspecies sampled during the autumn migration at a migratory bottleneck. We found that within-host microbial richness (α-diversity) was similar between migrant and resident microbial communities. In contrast, we found that microbial communities (β-diversity) were significantly different between groups regarding both microbes present and their relative abundances. Compositional differences were found for 36 bacterial genera, with 27 exhibiting greater abundance in migrants and nine exhibiting greater abundance in residents. There was heightened abundance of Mycoplasma spp. and Corynebacterium spp. in migrants, a pattern shared by other studies of migratory species. Screens for key regional pathogens revealed that neither residents nor migrants carried avian influenza viruses and Newcastle disease virus, suggesting that the status of these diseases did not underlie observed differences in microbiome composition. Furthermore, the prevalence and abundance of Salmonella spp., as determined from microbiome data and cultural assays, were both low and similar across the groups. Overall, our results indicate that microbial composition differs between migratory and resident barn swallows, even when they are conspecific and sympatrically occurring. Differences in host origins (breeding sites) may result in microbial community divergence, and varied behaviours throughout the annual cycle (e.g., migration) could further differentiate compositional structure as it relates to functional needs.
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Affiliation(s)
- Sondra Turjeman
- Movement Ecology Laboratory, Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ammon Corl
- Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA, USA
| | - Andrew Wolfenden
- Movement Ecology Laboratory, Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Miriam Tsalyuk
- Movement Ecology Laboratory, Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Avishai Lublin
- Division of Avian Diseases, Kimron Veterinary Institute, Bet Dagan, Israel
| | - Olivia Choi
- School of Food and Agriculture, University of Maine, Orono, ME, USA
| | - Pauline L Kamath
- School of Food and Agriculture, University of Maine, Orono, ME, USA
| | - Wayne M Getz
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, USA.,School Mathematical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Rauri C K Bowie
- Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA, USA.,Department of Integrative Biology, University of California, Berkeley, CA, USA
| | - Ran Nathan
- Movement Ecology Laboratory, Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
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19
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Mimura M, Suga M. Ambiguous species boundaries: Hybridization and morphological variation in two closely related Rubus species along altitudinal gradients. Ecol Evol 2020; 10:7476-7486. [PMID: 32760542 PMCID: PMC7391560 DOI: 10.1002/ece3.6473] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Revised: 05/11/2020] [Accepted: 05/13/2020] [Indexed: 11/23/2022] Open
Abstract
Although hybridization frequently occurs among plant species, hybrid zones of divergent lineages formed at species boundaries are less common and may not be apparent in later generations of hybrids with more parental-like phenotypes, as a consequence of backcrossing. To determine the effects of dispersal and selection on species boundaries, we compared clines in leaf traits and molecular hybrid index along two hybrid zones on Yakushima Island, Japan, in which a temperate (Rubus palmatus) and subtropical (Rubus grayanus) species of wild raspberry are found. Leaf sinus depth in the two hybrid zones had narrower clines at 600 m a.s.l. than the molecular hybrid index and common garden tests confirmed that some leaf traits, including leaf sinus depth that is a major trait used in species identification, are genetically divergent between these closely related species. The sharp transition in leaf phenotypic traits compared to molecular markers indicated divergent selection pressure on the hybrid zone structure. We suggest that species boundaries based on neutral molecular data may differ from those based on observed morphological traits.
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Affiliation(s)
- Makiko Mimura
- Department of BiologyGraduate School of Natural Science and TechnologyOkayama UniversityOkayamaJapan
| | - Mihoko Suga
- Graduate School of AgricultureTamagawa UniversityTokyoJapan
- Present address:
Sacred Heart SchoolTokyoJapan
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20
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Hague MTJ, Stokes AN, Feldman CR, Brodie ED, Brodie ED. The geographic mosaic of arms race coevolution is closely matched to prey population structure. Evol Lett 2020; 4:317-332. [PMID: 32774881 PMCID: PMC7403720 DOI: 10.1002/evl3.184] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 05/11/2020] [Accepted: 05/22/2020] [Indexed: 01/09/2023] Open
Abstract
Reciprocal adaptation is the hallmark of arms race coevolution. Local coadaptation between natural enemies should generate a geographic mosaic pattern where both species have roughly matched abilities across their shared range. However, mosaic variation in ecologically relevant traits can also arise from processes unrelated to reciprocal selection, such as population structure or local environmental conditions. We tested whether these alternative processes can account for trait variation in the geographic mosaic of arms race coevolution between resistant garter snakes (Thamnophis sirtalis) and toxic newts (Taricha granulosa). We found that predator resistance and prey toxin levels are functionally matched in co-occurring populations, suggesting that mosaic variation in the armaments of both species results from the local pressures of reciprocal selection. By the same token, phenotypic and genetic variation in snake resistance deviates from neutral expectations of population genetic differentiation, showing a clear signature of adaptation to local toxin levels in newts. Contrastingly, newt toxin levels are best predicted by genetic differentiation among newt populations, and to a lesser extent, by the local environment and snake resistance. Exaggerated armaments suggest that coevolution occurs in certain hotspots, but prey population structure seems to be of particular influence on local phenotypic variation in both species throughout the geographic mosaic. Our results imply that processes other than reciprocal selection, like historical biogeography and environmental pressures, represent an important source of variation in the geographic mosaic of coevolution. Such a pattern supports the role of "trait remixing" in the geographic mosaic theory, the process by which non-adaptive forces dictate spatial variation in the interactions among species.
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Affiliation(s)
- Michael T J Hague
- Division of Biological Sciences University of Montana Missoula Montana 59812.,Department of Biology University of Virginia Charlottesville Virginia 22904
| | - Amber N Stokes
- Department of Biology California State University Bakersfield California 93311
| | - Chris R Feldman
- Department of Biology University of Nevada Reno Nevada 89557
| | - Edmund D Brodie
- Department of Biology Utah State University Logan Utah 84322
| | - Edmund D Brodie
- Department of Biology University of Virginia Charlottesville Virginia 22904
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21
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McEntee JP, Burleigh JG, Singhal S. Dispersal Predicts Hybrid Zone Widths across Animal Diversity: Implications for Species Borders under Incomplete Reproductive Isolation. Am Nat 2020; 196:9-28. [PMID: 32552108 DOI: 10.1086/709109] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Hybrid zones occur as range boundaries for many animal taxa. One model for how hybrid zones form and stabilize is the tension zone model, a version of which predicts that hybrid zone widths are determined by a balance between random dispersal into hybrid zones and selection against hybrids. Here, we examine whether random dispersal and proxies for selection against hybrids (genetic distances between hybridizing pairs) can explain variation in hybrid zone widths across 131 hybridizing pairs of animals. We show that these factors alone can explain ∼40% of the variation in zone width among animal hybrid zones, with dispersal explaining far more of the variation than genetic distances. Patterns within clades were idiosyncratic. Genetic distances predicted hybrid zone widths particularly well for reptiles, while this relationship was opposite tension zone predictions in birds. Last, the data suggest that dispersal and molecular divergence set lower bounds on hybrid zone widths in animals, indicating that there are geographic restrictions on hybrid zone formation. Overall, our analyses reinforce the fundamental importance of dispersal in hybrid zone formation and more generally in the ecology of range boundaries.
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22
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Wagner DN, Curry RL, Chen N, Lovette IJ, Taylor SA. Genomic regions underlying metabolic and neuronal signaling pathways are temporally consistent in a moving avian hybrid zone. Evolution 2020; 74:1498-1513. [PMID: 32243568 DOI: 10.1111/evo.13970] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 03/25/2020] [Accepted: 03/26/2020] [Indexed: 12/15/2022]
Abstract
The study of hybrid zones can provide insight into the genetic basis of species differences that are relevant for the maintenance of reproductive isolation. Hybrid zones can also provide insight into climate change, species distributions, and evolution. The hybrid zone between black-capped chickadees (Poecile atricapillus) and Carolina chickadees (Poecile carolinensis) is shifting northward in response to increasing winter temperatures but is not increasing in width. This pattern indicates strong selection against chickadees with admixed genomes. Using high-resolution genomic data, we identified regions of the genomes that are outliers in both time points and do not introgress between the species; these regions may be involved in the maintenance of reproductive isolation. Genes involved in metabolic regulation processes were overrepresented in this dataset. Several gene ontology categories were also temporally consistent-including glutamate signaling, synaptic transmission, and catabolic processes-but the nucleotide variants leading to this pattern were not. Our results support recent findings that hybrids between black-capped and Carolina chickadees have higher basal metabolic rates than either parental species and suffer spatial memory and problem-solving deficits. Metabolic breakdown, as well as spatial memory and problem-solving, in hybrid chickadees may act as strong postzygotic isolation mechanisms in this moving hybrid zone.
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Affiliation(s)
- Dominique N Wagner
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, Colorado, 80309
| | - Robert L Curry
- Department of Biology, Villanova University, Villanova, Pennsylvania, 19085
| | - Nancy Chen
- Department of Biology, University of Rochester, Rochester, New York, 14627
| | - Irby J Lovette
- Cornell Lab of Ornithology, Cornell University, Ithaca, New York, 14850
| | - Scott A Taylor
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, Colorado, 80309
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23
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Slager DL, Epperly KL, Ha RR, Rohwer S, Wood C, Van Hemert C, Klicka J. Cryptic and extensive hybridization between ancient lineages of American crows. Mol Ecol 2020; 29:956-969. [PMID: 32034818 DOI: 10.1111/mec.15377] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 12/30/2019] [Accepted: 02/05/2020] [Indexed: 01/02/2023]
Abstract
Most species and therefore most hybrid zones have historically been defined using phenotypic characters. However, both speciation and hybridization can occur with negligible morphological differentiation. Recently developed genomic tools provide the means to better understand cryptic speciation and hybridization. The Northwestern Crow (Corvus caurinus) and American Crow (Corvus brachyrhynchos) are continuously distributed sister taxa that lack reliable traditional characters for identification. In this first population genomic study of Northwestern and American crows, we use genomic SNPs (nuDNA) and mtDNA to investigate the degree of genetic differentiation between these crows and the extent to which they may hybridize. Our results indicate that American and Northwestern crows have distinct evolutionary histories, supported by two nuDNA ancestry clusters and two 1.1%-divergent mtDNA clades dating to the late Pleistocene, when glacial advances may have isolated crow populations in separate refugia. We document extensive hybridization, with geographic overlap of mtDNA clades and admixture of nuDNA across >900 km of western Washington and western British Columbia. This broad hybrid zone consists of late-generation hybrids and backcrosses, but not recent (e.g., F1) hybrids. Nuclear DNA and mtDNA clines had concordant widths and were both centred in southwestern British Columbia, farther north than previously postulated. Overall, our results suggest a history of reticulate evolution in American and Northwestern crows, perhaps due to recurring neutral expansion(s) from Pleistocene glacial refugia followed by lineage fusion(s). However, we do not rule out a contributing role for more recent potential drivers of hybridization, such as expansion into human-modified habitats.
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Affiliation(s)
- David L Slager
- Department of Biology, University of Washington, Seattle, WA, USA.,Burke Museum of Natural History and Culture, Seattle, WA, USA
| | - Kevin L Epperly
- Department of Biology, University of Washington, Seattle, WA, USA.,Burke Museum of Natural History and Culture, Seattle, WA, USA
| | - Renee R Ha
- Department of Psychology, University of Washington, Seattle, WA, USA
| | - Sievert Rohwer
- Department of Biology, University of Washington, Seattle, WA, USA.,Burke Museum of Natural History and Culture, Seattle, WA, USA
| | - Chris Wood
- Burke Museum of Natural History and Culture, Seattle, WA, USA
| | | | - John Klicka
- Department of Biology, University of Washington, Seattle, WA, USA.,Burke Museum of Natural History and Culture, Seattle, WA, USA
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24
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Harrison JG, Calder WJ, Shastry V, Buerkle CA. Dirichlet‐multinomial modelling outperforms alternatives for analysis of microbiome and other ecological count data. Mol Ecol Resour 2020; 20:481-497. [DOI: 10.1111/1755-0998.13128] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 11/30/2019] [Accepted: 12/16/2019] [Indexed: 12/30/2022]
Affiliation(s)
| | - W. John Calder
- Department of Botany University of Wyoming Laramie WY USA
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25
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Ebrecht AC, van der Bergh N, Harrison STL, Smit MS, Sewell BT, Opperman DJ. Biochemical and structural insights into the cytochrome P450 reductase from Candida tropicalis. Sci Rep 2019; 9:20088. [PMID: 31882753 DOI: 10.1101/711317] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 12/04/2019] [Indexed: 05/28/2023] Open
Abstract
Cytochrome P450 reductases (CPRs) are diflavin oxidoreductases that supply electrons to type II cytochrome P450 monooxygenases (CYPs). In addition, it can also reduce other proteins and molecules, including cytochrome c, ferricyanide, and different drugs. Although various CPRs have been functionally and structurally characterized, the overall mechanism and its interaction with different redox acceptors remain elusive. One of the main problems regarding electron transfer between CPRs and CYPs is the so-called "uncoupling", whereby NAD(P)H derived electrons are lost due to the reduced intermediates' (FAD and FMN of CPR) interaction with molecular oxygen. Additionally, the decay of the iron-oxygen complex of the CYP can also contribute to loss of reducing equivalents during an unproductive reaction cycle. This phenomenon generates reactive oxygen species (ROS), leading to an inefficient reaction. Here, we present the study of the CPR from Candida tropicalis (CtCPR) lacking the hydrophobic N-terminal part (Δ2-22). The enzyme supports the reduction of cytochrome c and ferricyanide, with an estimated 30% uncoupling during the reactions with cytochrome c. The ROS produced was not influenced by different physicochemical conditions (ionic strength, pH, temperature). The X-ray structures of the enzyme were solved with and without its cofactor, NADPH. Both CtCPR structures exhibited the closed conformation. Comparison with the different solved structures revealed an intricate ionic network responsible for the regulation of the open/closed movement of CtCPR.
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Affiliation(s)
- Ana C Ebrecht
- Department of Microbial, Biochemical, and Food Biotechnology, University of the Free State, Bloemfontein, 9301, South Africa
- South African DST-NRF Centre of Excellence in Catalysis (c*Change), University of Cape Town, Private Bag, Rondebosch, Cape Town, 7701, South Africa
| | - Naadia van der Bergh
- Centre for Bioprocess Engineering Research (CeBER), Department of Chemical Engineering, University of Cape Town, Rondebosch, Cape Town, 7701, South Africa
- South African DST-NRF Centre of Excellence in Catalysis (c*Change), University of Cape Town, Private Bag, Rondebosch, Cape Town, 7701, South Africa
| | - Susan T L Harrison
- Centre for Bioprocess Engineering Research (CeBER), Department of Chemical Engineering, University of Cape Town, Rondebosch, Cape Town, 7701, South Africa
- South African DST-NRF Centre of Excellence in Catalysis (c*Change), University of Cape Town, Private Bag, Rondebosch, Cape Town, 7701, South Africa
| | - Martha S Smit
- Department of Microbial, Biochemical, and Food Biotechnology, University of the Free State, Bloemfontein, 9301, South Africa
- South African DST-NRF Centre of Excellence in Catalysis (c*Change), University of Cape Town, Private Bag, Rondebosch, Cape Town, 7701, South Africa
| | - B Trevor Sewell
- Structural Biology Research Unit, Department of Integrative Biomedical Sciences, Institute for Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, 7700, South Africa.
| | - Diederik J Opperman
- Department of Microbial, Biochemical, and Food Biotechnology, University of the Free State, Bloemfontein, 9301, South Africa.
- South African DST-NRF Centre of Excellence in Catalysis (c*Change), University of Cape Town, Private Bag, Rondebosch, Cape Town, 7701, South Africa.
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26
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Scordato ESC, Smith CCR, Semenov GA, Liu Y, Wilkins MR, Liang W, Rubtsov A, Sundev G, Koyama K, Turbek SP, Wunder MB, Stricker CA, Safran RJ. Migratory divides coincide with reproductive barriers across replicated avian hybrid zones above the Tibetan Plateau. Ecol Lett 2019; 23:231-241. [DOI: 10.1111/ele.13420] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 08/25/2019] [Accepted: 10/15/2019] [Indexed: 01/02/2023]
Affiliation(s)
- Elizabeth S. C. Scordato
- Department of Ecology and Evolutionary Biology The University of Colorado Boulder CO USA
- Department of Biological Sciences California State Polytechnic University Pomona CA USA
| | - Chris C. R. Smith
- Department of Ecology and Evolutionary Biology The University of Colorado Boulder CO USA
| | - Georgy A. Semenov
- Department of Ecology and Evolutionary Biology The University of Colorado Boulder CO USA
- Institute of Ecology and Systematics of Animals Novosibirsk Russia
| | - Yu Liu
- Queen Mary University of London London England
- Beijing Normal University Beijing China
| | - Matthew R. Wilkins
- Department of Ecology and Evolutionary Biology The University of Colorado Boulder CO USA
- Vanderbilt University Center for Science Outreach Nashville TN37212 USA
| | - Wei Liang
- Ministry of Education Key Laboratory for Ecology of Tropical Islands College of Life Sciences Hainan Normal University Haikou571158 China
| | | | - Gomboobaatar Sundev
- National University of Mongolia P. O. Box 537 Ulaanbaatar210646 Mongolia
- Mongolian Ornithological Society P. O. Box 537 Ulaanbaatar210646 Mongolia
| | - Kazuo Koyama
- Japan Bird Research Association Tokyo Japan183‐0034
| | - Sheela P. Turbek
- Department of Ecology and Evolutionary Biology The University of Colorado Boulder CO USA
| | - Michael B. Wunder
- Department of Integrative Biology University of Colorado Denver Denver CO USA
| | | | - Rebecca J. Safran
- Department of Ecology and Evolutionary Biology The University of Colorado Boulder CO USA
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27
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Baiz MD, Tucker PK, Cortés-Ortiz L. Multiple forms of selection shape reproductive isolation in a primate hybrid zone. Mol Ecol 2019; 28:1056-1069. [PMID: 30582763 PMCID: PMC6888905 DOI: 10.1111/mec.14966] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 10/22/2018] [Indexed: 01/02/2023]
Abstract
Speciation occurs when populations diverge and become reproductively isolated from each other. Natural selection is commonly accepted to play a large role in this process, and it has been widely assumed that reproductive isolation often results as a by-product of divergence driven by adaptation in allopatry. When such populations come into secondary contact, reinforcement can act to strengthen reproductive isolation, but the frequency and importance of this process are still unknown. Here, we explored genomic signatures of selection in allopatry and sympatry for loci associated with reproductive isolation using a natural primate hybrid zone. By analysing reduced-representation sequencing data, we quantified admixture and population structure across a howler monkey hybrid zone and examined the relationship between locus-specific differentiation and introgression. We detected extensive admixture that was mostly limited to the narrow contact zone. Loci with reduced introgression into the heterospecific genomic background (the pattern expected for loci associated with reproductive isolation due to selection against hybrids) were significantly more differentiated between allopatric parental populations than loci with neutral and increased introgression, supporting the hypothesis that reproductive isolation is a by-product of divergence in allopatry. Further, loci with reduced introgression showed greater differentiation in sympatry than in allopatry, suggesting a role for reinforcement. Thus, our results reflect multiple forms of selection that have shaped reproductive isolation in this system. We conclude that reproductive isolation may have initially been driven by divergence in allopatry, but later reinforced by divergent selection in sympatry.
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Affiliation(s)
- Marcella D Baiz
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, Michigan
| | - Priscilla K Tucker
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, Michigan
| | - Liliana Cortés-Ortiz
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, Michigan
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28
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Taylor SA, Larson EL. Insights from genomes into the evolutionary importance and prevalence of hybridization in nature. Nat Ecol Evol 2019; 3:170-177. [DOI: 10.1038/s41559-018-0777-y] [Citation(s) in RCA: 211] [Impact Index Per Article: 42.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 12/04/2018] [Indexed: 01/27/2023]
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29
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Formenti G, Chiara M, Poveda L, Francoijs KJ, Bonisoli-Alquati A, Canova L, Gianfranceschi L, Horner DS, Saino N. SMRT long reads and Direct Label and Stain optical maps allow the generation of a high-quality genome assembly for the European barn swallow (Hirundo rustica rustica). Gigascience 2019; 8:5202456. [PMID: 30496513 PMCID: PMC6324554 DOI: 10.1093/gigascience/giy142] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 11/14/2018] [Indexed: 11/12/2022] Open
Abstract
Background The barn swallow (Hirundo rustica) is a migratory bird that has been the focus of a large number of ecological, behavioral, and genetic studies. To facilitate further population genetics and genomic studies, we present a reference genome assembly for the European subspecies (H. r. rustica). Findings As part of the Genome10K effort on generating high-quality vertebrate genomes (Vertebrate Genomes Project), we have assembled a highly contiguous genome assembly using single molecule real-time (SMRT) DNA sequencing and several Bionano optical map technologies. We compared and integrated optical maps derived from both the Nick, Label, Repair, and Stain technology and from the Direct Label and Stain (DLS) technology. As proposed by Bionano, DLS more than doubled the scaffold N50 with respect to the nickase. The dual enzyme hybrid scaffold led to a further marginal increase in scaffold N50 and an overall increase of confidence in the scaffolds. After removal of haplotigs, the final assembly is approximately 1.21 Gbp in size, with a scaffold N50 value of more than 25.95 Mbp. Conclusions This high-quality genome assembly represents a valuable resource for future studies of population genetics and genomics in the barn swallow and for studies concerning the evolution of avian genomes. It also represents one of the very first genomes assembled by combining SMRT long-read sequencing with the new Bionano DLS technology for scaffolding. The quality of this assembly demonstrates the potential of this methodology to substantially increase the contiguity of genome assemblies.
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Affiliation(s)
- Giulio Formenti
- Department of Environmental Science and Policy, University of Milan, via celoria 2, Milan, 20133, Italy
| | - Matteo Chiara
- Department of Biosciences, University of Milan, via celoria 26, Milan, 20133, Italy
| | - Lucy Poveda
- Functional Genomics Center of Zurich, University of Zurich, Winterthurerstrasse 190, Zürich, 8057, Switzerland
| | | | - Andrea Bonisoli-Alquati
- Department of Biological Sciences, California State Polytechnic University, 3801 West Temple Avenue, Pomona, California, 91768, USA
| | - Luca Canova
- Department of Biochemistry, University of Pavia, Via Taramelli 12, Pavia, 27100, Italy
| | - Luca Gianfranceschi
- Department of Biosciences, University of Milan, via celoria 26, Milan, 20133, Italy
| | - David Stephen Horner
- Department of Biosciences, University of Milan, via celoria 26, Milan, 20133, Italy
| | - Nicola Saino
- Department of Environmental Science and Policy, University of Milan, via celoria 2, Milan, 20133, Italy
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30
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Smith CCR, Flaxman SM, Scordato ESC, Kane NC, Hund AK, Sheta BM, Safran RJ. Demographic inference in barn swallows using whole-genome data shows signal for bottleneck and subspecies differentiation during the Holocene. Mol Ecol 2018; 27:4200-4212. [PMID: 30176075 DOI: 10.1111/mec.14854] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 08/27/2018] [Indexed: 12/20/2022]
Abstract
Accounting for historical demographic features is vital for many types of evolutionary inferences, including the estimation of divergence times between closely related populations. In barn swallow, Hirundo rustica, inferring historical population sizes and subspecies divergence times can shed light on the recent co-evolution of this species with humans. Pairwise sequentially Markovian coalescent uncovered population growth beginning on the order of one million years ago-which may reflect the radiation of the broader Hirundo genus-and a more recent population decline. Additionally, we used approximate Bayesian computation to evaluate hypotheses about recent timescale barn swallow demography, including population growth due to human commensalism, and a potential founder event associated with the onset of nesting on human structures. We found signal for a bottleneck event approximately 7,700 years ago, near the time that humans began building substantial structures, although there was considerable uncertainty associated with this estimate. Subspecies differentiation and subsequent growth occurred after the bottleneck in the best-supported model, an order of magnitude more recently than previous estimates in this system. We also compared results obtained from whole-genome sequencing versus reduced representation sequencing, finding many similar results despite substantial allelic dropout in the reduced representation data, which may have affected estimates of some parameters. This study presents the first genetic evidence of a potential barn swallow founder effect and subspecies divergence coinciding with the Holocene, which is an important step in analysing the biogeographical history of a well-known human commensal species.
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Affiliation(s)
- Chris C R Smith
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado
| | - Samuel M Flaxman
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado
| | - Elizabeth S C Scordato
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado.,Biological Sciences Department, California State Polytechnic University, Pomona, California
| | - Nolan C Kane
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado
| | - Amanda K Hund
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado
| | - Basma M Sheta
- Zoology Department, Faculty of Science, Damietta University, Damietta, Egypt
| | - Rebecca J Safran
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado
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31
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Semenov GA, Koblik EA, Red'kin YA, Badyaev AV. Extensive phenotypic diversification coexists with little genetic divergence and a lack of population structure in the White Wagtail subspecies complex (Motacilla alba). J Evol Biol 2018; 31:1093-1108. [PMID: 29873425 DOI: 10.1111/jeb.13305] [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: 05/02/2017] [Revised: 03/27/2018] [Accepted: 05/28/2018] [Indexed: 02/01/2023]
Abstract
Geographically clustered phenotypes often demonstrate consistent patterns in molecular markers, particularly mitochondrial DNA (mtDNA) traditionally used in phylogeographic studies. However, distinct evolutionary trajectories among traits and markers can lead to their discordance. First, geographic structure in phenotypic traits and nuclear molecular markers can be co-aligned but inconsistent with mtDNA (mito-nuclear discordance). Alternatively, phenotypic variation can have little to do with patterns in neither mtDNA nor nuclear markers. Disentangling between these distinct patterns can provide insight into the role of selection, demography and gene flow in population divergence. Here, we examined a previously reported case of strong inconsistency between geographic structure in mtDNA and plumage traits in a widespread polytypic bird species, the White Wagtail (Motacilla alba). We tested whether this pattern is due to mito-nuclear discordance or discrepancy between morphological evolution and both nuclear and mtDNA markers. We analysed population differentiation and structure across six out of nine commonly recognized subspecies using 17 microsatellite loci and a combination of microsatellites and plumage indices in a comprehensively sampled region of a contact between two subspecies. We did not find support for the mito-nuclear discordance hypothesis: nuclear markers indicated a subtle signal of genetic clustering only partially consistent with plumage groups, similar to previous findings that relied on mtDNA. We discuss evolutionary factors that could have shaped the intricate patterns of phenotypic diversification in the White wagtail and the role that repeated selection on plumage 'hotspots' and hybridization may have played.
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Affiliation(s)
- Georgy A Semenov
- Department of Ecology & Evolutionary Biology, University of Colorado, Boulder, CO, USA.,Department of Ecology & Evolutionary Biology, University of Arizona, Tucson, AZ, USA.,Institute of Systematics and Ecology of Animals, Novosibirsk, Russia
| | - Evgeniy A Koblik
- Department of Ornithology, Zoological Museum of Moscow State University, Moscow, Russia
| | - Yaroslav A Red'kin
- Department of Ornithology, Zoological Museum of Moscow State University, Moscow, Russia
| | - Alexander V Badyaev
- Department of Ecology & Evolutionary Biology, University of Arizona, Tucson, AZ, USA
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32
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Wilkins MR, Scordato ESC, Semenov GA, Karaardiç H, Shizuka D, Rubtsov A, Pap PL, Shen SF, Safran RJ. Global song divergence in barn swallows (Hirundo rustica): exploring the roles of genetic, geographical and climatic distance in sympatry and allopatry. Biol J Linn Soc Lond 2018. [DOI: 10.1093/biolinnean/bly012] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Matthew R Wilkins
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, USA
- Center for Science Outreach, Vanderbilt University, Nashville, TN, USA
| | - Elizabeth S C Scordato
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
- Biological Sciences Department, California State Polytechnic University, Pomona, CA, USA
| | - Georgy A Semenov
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
- Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | - Hakan Karaardiç
- Alanya Alaaddin Keykubat University, Education Faculty, Math and Science, Alanya, Turkey
| | - Daizaburo Shizuka
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, USA
| | | | - Peter L Pap
- Department of Taxonomy and Ecology, Babeş-Bolyai University, Cluj-Napoca, Romania
| | - Sheng-Feng Shen
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Rebecca J Safran
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
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Blackburn GS, Brunet BMT, Muirhead K, Cusson M, Béliveau C, Levesque RC, Lumley LM, Sperling FAH. Distinct sources of gene flow produce contrasting population genetic dynamics at different range boundaries of aChoristoneurabudworm. Mol Ecol 2017; 26:6666-6684. [DOI: 10.1111/mec.14386] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 09/26/2017] [Accepted: 10/07/2017] [Indexed: 12/14/2022]
Affiliation(s)
- Gwylim S. Blackburn
- Department of Biological Sciences; CW405 Biosciences Centre; University of Alberta; Edmonton AB Canada
- Laurentian Forestry Centre; Natural Resources Canada; Canadian Forest Service; Quebec City QC Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Québec QC Canada
| | - Bryan M. T. Brunet
- Department of Biological Sciences; CW405 Biosciences Centre; University of Alberta; Edmonton AB Canada
| | - Kevin Muirhead
- Department of Biological Sciences; CW405 Biosciences Centre; University of Alberta; Edmonton AB Canada
| | - Michel Cusson
- Laurentian Forestry Centre; Natural Resources Canada; Canadian Forest Service; Quebec City QC Canada
| | - Catherine Béliveau
- Laurentian Forestry Centre; Natural Resources Canada; Canadian Forest Service; Quebec City QC Canada
| | - Roger C. Levesque
- Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Québec QC Canada
| | - Lisa M. Lumley
- Department of Biological Sciences; CW405 Biosciences Centre; University of Alberta; Edmonton AB Canada
- Laurentian Forestry Centre; Natural Resources Canada; Canadian Forest Service; Quebec City QC Canada
| | - Felix A. H. Sperling
- Department of Biological Sciences; CW405 Biosciences Centre; University of Alberta; Edmonton AB Canada
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