1
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Chaplin K, Smith Date K, Bray RD, Miller KA, Lutz ML, Razeng E, Thompson MB, Chapple DG. Intraspecific hybridisation of an invasive lizard on Lord Howe Island. AUST J ZOOL 2022. [DOI: 10.1071/zo21045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Human-mediated dispersal of animals often acts to bring populations that have been separated for substantial periods of evolutionary time (e.g. millions of years) in their native range into contact in their introduced range. Whether these taxa successfully interbreed in the introduced range provides information on the strength of reproductive isolation amongst them. The invasive delicate skink (Lampropholis delicata) has been accidentally introduced to Lord Howe Island from four genetically divergent (>2 million years) regions of the species’ native range in eastern Australia. We used mitochondrial DNA and microsatellite data to investigate whether the individuals from four of the native-range source regions are interbreeding on Lord Howe Island. Our analyses indicate that intraspecific hybridisation among individuals from all four native-range source regions is occurring. Although there is little evidence for hybrids in the northern end of Lord Howe Island (proportion of hybrids: 0–0.02; n = 31), there is a high proportion of hybrids in the central (0.33–0.69; n = 59) and southern regions (0.38–0.75; n = 8) of the island. Given the strong evidence for interbreeding among all four native-range source regions examined, and the relatively minor morphological, life-history and phenotypic variation among them, we suggest that the delicate skink should continue to be treated as a single, widespread, but variable species.
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2
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Hager ER, Harringmeyer OS, Wooldridge TB, Theingi S, Gable JT, McFadden S, Neugeboren B, Turner KM, Jensen JD, Hoekstra HE. A chromosomal inversion contributes to divergence in multiple traits between deer mouse ecotypes. Science 2022; 377:399-405. [PMID: 35862520 DOI: 10.1126/science.abg0718] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
How locally adapted ecotypes are established and maintained within a species is a long-standing question in evolutionary biology. Using forest and prairie ecotypes of deer mice (Peromyscus maniculatus), we characterized the genetic basis of variation in two defining traits-tail length and coat color-and discovered a 41-megabase chromosomal inversion linked to both. The inversion frequency is 90% in the dark, long-tailed forest ecotype; decreases across a habitat transition; and is absent from the light, short-tailed prairie ecotype. We implicate divergent selection in maintaining the inversion at frequencies observed in the wild, despite high levels of gene flow, and explore fitness benefits that arise from suppressed recombination within the inversion. We uncover a key role for a large, previously uncharacterized inversion in the evolution and maintenance of classic mammalian ecotypes.
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Affiliation(s)
- Emily R Hager
- Department of Molecular and Cellular Biology, Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, and Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
| | - Olivia S Harringmeyer
- Department of Molecular and Cellular Biology, Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, and Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
| | - T Brock Wooldridge
- Department of Molecular and Cellular Biology, Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, and Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
| | - Shunn Theingi
- Department of Molecular and Cellular Biology, Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, and Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
| | - Jacob T Gable
- Department of Molecular and Cellular Biology, Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, and Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
| | - Sade McFadden
- Department of Molecular and Cellular Biology, Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, and Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
| | - Beverly Neugeboren
- Department of Molecular and Cellular Biology, Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, and Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
| | - Kyle M Turner
- Department of Molecular and Cellular Biology, Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, and Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
| | - Jeffrey D Jensen
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Hopi E Hoekstra
- Department of Molecular and Cellular Biology, Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, and Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
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3
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Del-Rio G, Rego MA, Whitney BM, Schunck F, Silveira LF, Faircloth BC, Brumfield RT. Displaced clines in an avian hybrid zone (Thamnophilidae: Rhegmatorhina) within an Amazonian interfluve. Evolution 2021; 76:455-475. [PMID: 34626500 DOI: 10.1111/evo.14377] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 08/25/2021] [Accepted: 09/01/2021] [Indexed: 12/24/2022]
Abstract
Secondary contact between species often results in the formation of a hybrid zone, with the eventual fates of the hybridizing species dependent on evolutionary and ecological forces. We examine this process in the Amazon Basin by conducting the first genomic and phenotypic characterization of the hybrid zone formed after secondary contact between two obligate army-ant-followers: the White-breasted Antbird (Rhegmatorhina hoffmannsi) and the Harlequin Antbird (Rhegmatorhina berlepschi). We found a major geographic displacement (∼120 km) between the mitochondrial and nuclear clines, and we explore potential hypotheses for the displacement, including sampling error, genetic drift, and asymmetric cytonuclear incompatibilities. We cannot exclude roles for sampling error and genetic drift in contributing to the discordance; however, the data suggest expansion and unidirectional introgression of hoffmannsi into the distribution of berlepschi.
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Affiliation(s)
- Glaucia Del-Rio
- Museum of Natural Science, Louisiana State University, Baton Rouge, Louisiana, 70803.,Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, 70803
| | - Marco A Rego
- Museum of Natural Science, Louisiana State University, Baton Rouge, Louisiana, 70803.,Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, 70803
| | - Bret M Whitney
- Museum of Natural Science, Louisiana State University, Baton Rouge, Louisiana, 70803.,Museu de Zoologia, Universidade de São Paulo, São Paulo, SP, 04263-000, Brazil
| | - Fabio Schunck
- Museu de Zoologia, Universidade de São Paulo, São Paulo, SP, 04263-000, Brazil
| | - Luís F Silveira
- Museu de Zoologia, Universidade de São Paulo, São Paulo, SP, 04263-000, Brazil
| | - Brant C Faircloth
- Museum of Natural Science, Louisiana State University, Baton Rouge, Louisiana, 70803.,Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, 70803
| | - Robb T Brumfield
- Museum of Natural Science, Louisiana State University, Baton Rouge, Louisiana, 70803.,Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, 70803
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4
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Stankowski S, Ravinet M. Defining the speciation continuum. Evolution 2021; 75:1256-1273. [PMID: 33754340 DOI: 10.1111/evo.14215] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 03/01/2021] [Accepted: 03/13/2021] [Indexed: 02/06/2023]
Abstract
A primary roadblock to our understanding of speciation is that it usually occurs over a timeframe that is too long to study from start to finish. The idea of a speciation continuum provides something of a solution to this problem; rather than observing the entire process, we can simply reconstruct it from the multitude of speciation events that surround us. But what do we really mean when we talk about the speciation continuum, and can it really help us understand speciation? We explored these questions using a literature review and online survey of speciation researchers. Although most researchers were familiar with the concept and thought it was useful, our survey revealed extensive disagreement about what the speciation continuum actually tells us. This is due partly to the lack of a clear definition. Here, we provide an explicit definition that is compatible with the Biological Species Concept. That is, the speciation continuum is a continuum of reproductive isolation. After outlining the logic of the definition in light of alternatives, we explain why attempts to reconstruct the speciation process from present-day populations will ultimately fail. We then outline how we think the speciation continuum concept can continue to act as a foundation for understanding the continuum of reproductive isolation that surrounds us.
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Affiliation(s)
- Sean Stankowski
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, United Kingdom.,Current Address: Sean Stankowski, IST Austria, Klosterneuburg, 3400, Austria
| | - Mark Ravinet
- Centre for Ecological and Evolutionary Synthesis, University of Oslo, Oslo, 0316, Norway.,School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, United Kingdom
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5
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Damasceno RP, Carnaval AC, Sass C, Sousa Recoder R, Moritz C, Trefaut Rodrigues M. Geographic restriction, genetic divergence, and morphological disparity in the Brazilian Atlantic Forests: Insights from Leposoma lizards (Gymnophthalmidae, Squamata). Mol Phylogenet Evol 2020; 154:106993. [PMID: 33148523 DOI: 10.1016/j.ympev.2020.106993] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 09/01/2020] [Accepted: 09/28/2020] [Indexed: 10/23/2022]
Abstract
Lineage differentiation, long-term persistence, and range limitation promote high levels of phylogenetic and phylogeographic endemisms and likely underlie the abundant morphologically cryptic diversity observed in the Brazilian Atlantic Forests (AF). We explore lineage differentiation and range restriction in the AF and ask if genetic divergence and morphological disparity are correlated by integrating coalescent-based species delimitation, molecular phylogenetic, and morphological analyses in the lizard genus Leposoma. We present the first species tree for Leposoma and of their tribe, the Ecpleopodini. The analyses are based on the largest dataset ever assembled for Leposoma in terms of number of species (all represented), genetic markers (12 loci), and geographic coverage (~2,500 km). The exercise allows us to robustly delimit species within the genus and phylogeographic lineages within all species. We find support for the monophyly of the genus and for the recognition of a yet undescribed species around the Baía de Todos-os-Santos, in the state of Bahia; this form is distinct from all other congeners, both genetically and morphologically. We find that L. baturitensis, from the northeastern state of Ceará, is basal to the genus - and sister to a clade of six species restricted to the AF across the eastern coast of Brazil. Relationships within this coastal clade are ((((L. annectans, Leposoma sp.), L. scincoides), L. puk) (L. nanodactylus, L. sinepollex)). Phylogenetic and phylogeographic analyses, together with precise distribution data, allowed us to update the ranges of species and phylogeographic lineages. We reveal pervasive geographic restriction of divergent lineages in Leposoma at and below species level and discuss how forest refuges and rivers might have contributed to it. We find that morphological disparity lags behind genetic divergence in the genus because although they are correlated, the first accumulates at a much slower rate than the latter. We hope to encourage new studies in the area of AF north of the Doce river; phylogeographic sampling in that region has been much less common relative to southern sites, yet it may hold the key to several important processes defining biodiversity patterns in eastern Brazil. This appears to specially apply to processes underlying geographic restriction of morphologically cryptic, yet genetic divergent lineages, as the case of Leposoma.
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Affiliation(s)
- Roberta P Damasceno
- Instituto de Biociências, Universidade de São Paulo, Rua do Matão, trav. 14, n. 321, Cidade Universitária, São Paulo, SP 05508-090, Brazil; Museum of Vertebrate Zoology, University of California, Berkeley, 3101 Valley Life Sciences Building, Berkeley, CA 94720, USA.
| | - Ana Carolina Carnaval
- Department of Biology, City College of New York and the Biology Program at the Graduate Center of CUNY, 160 Convent Avenue, Marshak Life Science Building J-526, New York, NY 10031, USA.
| | - Chodon Sass
- Museum of Vertebrate Zoology, University of California, Berkeley, 3101 Valley Life Sciences Building, Berkeley, CA 94720, USA; University and Jepson Herbaria, University of California, Berkeley, 1001 Valley Life Sciences Building, Berkeley, CA 94720, USA.
| | - Renato Sousa Recoder
- Instituto de Biociências, Universidade de São Paulo, Rua do Matão, trav. 14, n. 321, Cidade Universitária, São Paulo, SP 05508-090, Brazil
| | - Craig Moritz
- Museum of Vertebrate Zoology, University of California, Berkeley, 3101 Valley Life Sciences Building, Berkeley, CA 94720, USA; Division of Ecology and Evolution, Research School of Biology, and Centre for Biodiversity Analysis, The Australian National University, 46 Sullivans Creek Road, Acton, ACT 2601, Australia.
| | - Miguel Trefaut Rodrigues
- Instituto de Biociências, Universidade de São Paulo, Rua do Matão, trav. 14, n. 321, Cidade Universitária, São Paulo, SP 05508-090, Brazil.
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6
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Curran EV, Stankowski S, Pardo‐Diaz C, Salazar C, Linares M, Nadeau NJ. Müllerian mimicry of a quantitative trait despite contrasting levels of genomic divergence and selection. Mol Ecol 2020; 29:2016-2030. [DOI: 10.1111/mec.15460] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 03/24/2020] [Accepted: 04/24/2020] [Indexed: 11/26/2022]
Affiliation(s)
- Emma V. Curran
- Department of Animal and Plant Sciences University of Sheffield Sheffield UK
| | - Sean Stankowski
- Department of Animal and Plant Sciences University of Sheffield Sheffield UK
| | - Carolina Pardo‐Diaz
- Biology Program Faculty of Natural Sciences and Mathematics Universidad del Rosario Bogota Colombia
| | - Camilo Salazar
- Biology Program Faculty of Natural Sciences and Mathematics Universidad del Rosario Bogota Colombia
| | - Mauricio Linares
- Biology Program Faculty of Natural Sciences and Mathematics Universidad del Rosario Bogota Colombia
| | - Nicola J. Nadeau
- Department of Animal and Plant Sciences University of Sheffield Sheffield UK
- The Smithsonian Tropical Research Institute Panama City Republic of Panama
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7
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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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8
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Wong ELY, Nevado B, Osborne OG, Papadopulos AST, Bridle JR, Hiscock SJ, Filatov DA. Strong divergent selection at multiple loci in two closely related species of ragworts adapted to high and low elevations on Mount Etna. Mol Ecol 2019; 29:394-412. [PMID: 31793091 DOI: 10.1111/mec.15319] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 11/28/2019] [Accepted: 11/28/2019] [Indexed: 12/20/2022]
Abstract
Recently diverged species present particularly informative systems for studying speciation and maintenance of genetic divergence in the face of gene flow. We investigated speciation in two closely related Senecio species, S. aethnensis and S. chrysanthemifolius, which grow at high and low elevations, respectively, on Mount Etna, Sicily and form a hybrid zone at intermediate elevations. We used a newly generated genome-wide single nucleotide polymorphism (SNP) dataset from 192 individuals collected over 18 localities along an elevational gradient to reconstruct the likely history of speciation, identify highly differentiated SNPs, and estimate the strength of divergent selection. We found that speciation in this system involved heterogeneous and bidirectional gene flow along the genome, and species experienced marked population size changes in the past. Furthermore, we identified highly-differentiated SNPs between the species, some of which are located in genes potentially involved in ecological differences between species (such as photosynthesis and UV response). We analysed the shape of these SNPs' allele frequency clines along the elevational gradient. These clines show significantly variable coincidence and concordance, indicative of the presence of multifarious selective forces. Selection against hybrids is estimated to be very strong (0.16-0.78) and one of the highest reported in literature. The combination of strong cumulative selection across the genome and previously identified intrinsic incompatibilities probably work together to maintain the genetic and phenotypic differentiation between these species - pointing to the importance of considering both intrinsic and extrinsic factors when studying divergence and speciation.
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Affiliation(s)
- Edgar L Y Wong
- Department of Plant Sciences, University of Oxford, Oxford, UK
| | - Bruno Nevado
- Department of Plant Sciences, University of Oxford, Oxford, UK
| | - Owen G Osborne
- Department of Plant Sciences, University of Oxford, Oxford, UK
| | | | - Jon R Bridle
- School of Biological Sciences, University of Bristol, Bristol, UK
| | - Simon J Hiscock
- Department of Plant Sciences, University of Oxford, Oxford, UK
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9
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van Riemsdijk I, Butlin RK, Wielstra B, Arntzen JW. Testing an hypothesis of hybrid zone movement for toads in France. Mol Ecol 2019; 28:1070-1083. [PMID: 30609055 DOI: 10.1111/mec.15005] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 12/08/2018] [Accepted: 12/19/2018] [Indexed: 02/06/2023]
Abstract
Hybrid zone movement may result in substantial unidirectional introgression of selectively neutral material from the local to the advancing species, leaving a genetic footprint. This genetic footprint is represented by a trail of asymmetric tails and displaced cline centres in the wake of the moving hybrid zone. A peak of admixture linkage disequilibrium is predicted to exist ahead of the centre of the moving hybrid zone. We test these predictions of the movement hypothesis in a hybrid zone between common (Bufo bufo) and spined toads (B. spinosus), using 31 nuclear and one mtDNA SNPs along a transect in the northwest of France. Average effective selection in Bufo hybrids is low and clines vary in shape and centre. A weak pattern of asymmetric introgression is inferred from cline discordance of seven nuclear markers. The dominant direction of gene flow is from B. spinosus to B. bufo and is in support of southward movement of the hybrid zone. Conversely, a peak of admixture linkage disequilibrium north of the hybrid zone suggests northward movement. These contrasting results can be explained by reproductive isolation of the B. spinosus and B. bufo gene pools at the southern (B. spinosus) side of the hybrid zone. The joint occurrence of asymmetric introgression and admixture linkage disequilibrium can also be explained by the combination of low dispersal and random genetic drift due to low effective population sizes.
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Affiliation(s)
- Isolde van Riemsdijk
- Taxonomy and Systematics, Naturalis Biodiversity Center, Leiden, The Netherlands.,Institute of Biology Leiden, Leiden University, Leiden, The Netherlands
| | - Roger K Butlin
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK.,Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Ben Wielstra
- Taxonomy and Systematics, Naturalis Biodiversity Center, Leiden, The Netherlands.,Institute of Biology Leiden, Leiden University, Leiden, The Netherlands.,Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK.,Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California
| | - Jan W Arntzen
- Taxonomy and Systematics, Naturalis Biodiversity Center, Leiden, The Netherlands
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10
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Sequeira F, Bessa-Silva A, Tarroso P, Sousa-Neves T, Vallinoto M, Gonçalves H, Martínez-Solano I. Discordant patterns of introgression across a narrow hybrid zone between two cryptic lineages of an Iberian endemic newt. J Evol Biol 2019; 33:202-216. [PMID: 31677317 DOI: 10.1111/jeb.13562] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 10/15/2019] [Accepted: 10/25/2019] [Indexed: 11/30/2022]
Abstract
The study of natural hybrid zones can illuminate aspects of lineage divergence and speciation in morphologically cryptic taxa. We studied a hybrid zone between two highly divergent but morphologically similar lineages (south-western and south-eastern) of the Iberian endemic Bosca's newt (Lissotriton boscai) in SW Iberia with a multilocus dataset (microsatellites, nuclear and mitochondrial genes). STRUCTURE and NEWHYBRIDS analyses retrieved few admixed individuals, which classified as backcrosses involving parental individuals of the south-western lineage. Our results show asymmetric introgression of mtDNA beyond the contact from this lineage into the south-eastern lineage. Analysis of nongeographic introgression patterns revealed asymmetries in the direction of introgression, but except for mtDNA, we did not find evidence for nonconcordant introgression patterns across nuclear loci. Analysis of a 150-km transect across the hybrid zone showed broadly coincident cline widths (ca. 3.2-27.9 km), and concordant cline centres across all markers, except for mtDNA that is displaced ca. 60 km northward. Results from ecological niche modelling show that the hybrid zone is in a climatically homogenous area with suitable habitat for the species, suggesting that contact between the two lineages is unlikely to occur further south as their distributions are currently separated by an extensive area of unfavourable habitat. Taken together, our findings suggest the genetic structure of this hybrid zone results from the interplay of historical (biogeographic) and population-level processes. The narrowness and coincidence of genetic clines can be explained by weak selection against hybrids and reflect a degree of reproductive isolation that is consistent with cryptic speciation.
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Affiliation(s)
- Fernando Sequeira
- Laboratorio Associado, CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Universidade do Porto, Vairão, Portugal
| | - Adam Bessa-Silva
- Laboratório de Evolução (LEVO), Instituto de Estudos Costeiros (IECOS), Universidade Federal do Pará, Pará, Brasil
| | - Pedro Tarroso
- Laboratorio Associado, CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Universidade do Porto, Vairão, Portugal
| | - Tiago Sousa-Neves
- Laboratorio Associado, CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Universidade do Porto, Vairão, Portugal.,Museu Paraense Emílio Goeldi, Coordenação de Zoologia, Pará, Brasil
| | - Marcelo Vallinoto
- Laboratorio Associado, CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Universidade do Porto, Vairão, Portugal.,Laboratório de Evolução (LEVO), Instituto de Estudos Costeiros (IECOS), Universidade Federal do Pará, Pará, Brasil
| | - Helena Gonçalves
- Laboratorio Associado, CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Universidade do Porto, Vairão, Portugal.,Museu de História Natural e da Ciência, Universidade do Porto, Porto, Portugal
| | - Iñigo Martínez-Solano
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales, CSIC (MNCN-CSIC), Madrid, Spain
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11
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Thurman TJ, Szejner-Sigal A, McMillan WO. Movement of a Heliconius hybrid zone over 30 years: A Bayesian approach. J Evol Biol 2019; 32:974-983. [PMID: 31216075 DOI: 10.1111/jeb.13499] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 05/29/2019] [Accepted: 06/10/2019] [Indexed: 11/27/2022]
Abstract
Hybrid zones have long been of interest to biologists as natural laboratories where we can gain insight into the processes of adaptation and speciation. Repeated sampling of individual hybrid zones has been particularly useful in elucidating the dynamic balance between selection and dispersal that maintains most hybrid zones. Here, we revisit a hybrid zone between Heliconius erato butterflies in Panamá for a third time over more than 30 years. We combine a novel Bayesian extension of stepped-cline hybrid zone models with environmental data to understand the genetic and environmental causes of cline dynamics in this species. The cline has continued to move west, likely due to dominance drive, but has slowed and broadened. Environmental analyses suggest that widespread deforestation in Panamá could be leading to decreased avian predation and relaxed selection, causing the observed changes in cline dynamics.
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Affiliation(s)
- Timothy J Thurman
- Smithsonian Tropical Research Institute, Panamá, República de Panamá.,Redpath Museum and Department of Biology, McGill University, Montréal, Québec, Canada
| | - Andre Szejner-Sigal
- Smithsonian Tropical Research Institute, Panamá, República de Panamá.,Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, USA
| | - W Owen McMillan
- Smithsonian Tropical Research Institute, Panamá, República de Panamá
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12
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Saxenhofer M, Schmidt S, Ulrich RG, Heckel G. Secondary contact between diverged host lineages entails ecological speciation in a European hantavirus. PLoS Biol 2019; 17:e3000142. [PMID: 30785873 PMCID: PMC6382107 DOI: 10.1371/journal.pbio.3000142] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 01/22/2019] [Indexed: 11/19/2022] Open
Abstract
The diversity of viruses probably exceeds biodiversity of eukaryotes, but little is known about the origin and emergence of novel virus species. Experimentation and disease outbreak investigations have allowed the characterization of rapid molecular virus adaptation. However, the processes leading to the establishment of functionally distinct virus taxa in nature remain obscure. Here, we demonstrate that incipient speciation in a natural host species has generated distinct ecological niches leading to adaptive isolation in an RNA virus. We found a very strong association between the distributions of two major phylogenetic clades in Tula orthohantavirus (TULV) and the rodent host lineages in a natural hybrid zone of the European common vole (Microtus arvalis). The spatial transition between the virus clades in replicated geographic clines is at least eight times narrower than between the hybridizing host lineages. This suggests a strong barrier for effective virus transmission despite frequent dispersal and gene flow among local host populations, and translates to a complete turnover of the adaptive background of TULV within a few hundred meters in the open, unobstructed landscape. Genetic differences between TULV clades are homogenously distributed in the genomes and mostly synonymous (93.1%), except for a cluster of nonsynonymous changes in the 5' region of the viral envelope glycoprotein gene, potentially involved in host-driven isolation. Evolutionary relationships between TULV clades indicate an emergence of these viruses through rapid differential adaptation to the previously diverged host lineages that resulted in levels of ecological isolation exceeding the progress of speciation in their vertebrate hosts.
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Affiliation(s)
- Moritz Saxenhofer
- Institute of Ecology and Evolution, University of Bern, Switzerland
- Swiss Institute of Bioinformatics, Quartier Sorge, Bâtiment Génopode, Lausanne, Switzerland
| | - Sabrina Schmidt
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Novel and Emerging Infectious Diseases, Greifswald-Insel Riems, Germany
| | - Rainer G. Ulrich
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Novel and Emerging Infectious Diseases, Greifswald-Insel Riems, Germany
- German Center for Infection Research (DZIF), partner site Hamburg-Luebeck-Borstel-Insel Riems, Germany
| | - Gerald Heckel
- Institute of Ecology and Evolution, University of Bern, Switzerland
- Swiss Institute of Bioinformatics, Quartier Sorge, Bâtiment Génopode, Lausanne, Switzerland
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13
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A dated molecular phylogeny of mite harvestmen (Arachnida: Opiliones: Cyphophthalmi) elucidates ancient diversification dynamics in the Australian Wet Tropics. Mol Phylogenet Evol 2018; 127:813-822. [DOI: 10.1016/j.ympev.2018.06.029] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 06/04/2018] [Accepted: 06/15/2018] [Indexed: 11/20/2022]
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14
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Singhal S, Hoskin CJ, Couper P, Potter S, Moritz C. A Framework for Resolving Cryptic Species: A Case Study from the Lizards of the Australian Wet Tropics. Syst Biol 2018; 67:1061-1075. [DOI: 10.1093/sysbio/syy026] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 03/27/2018] [Indexed: 12/19/2022] Open
Affiliation(s)
- Sonal Singhal
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Biology, California State University—Dominguez Hills, Carson, CA 90747, USA
| | - Conrad J Hoskin
- College of Science & Engineering, James Cook University, Townsville, Queensland 4811, Australia
| | - Patrick Couper
- Biodiversity Program, Queensland Museum, South Brisbane, Queensland 4101, Australia
| | - Sally Potter
- Division of Ecology and Evolution, Research School of Biology and Centre for Biodiversity Analysis, Australian National University, Acton, ACT 2601, Australia
| | - Craig Moritz
- Division of Ecology and Evolution, Research School of Biology and Centre for Biodiversity Analysis, Australian National University, Acton, ACT 2601, Australia
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15
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Afonso Silva AC, Santos N, Ogilvie HA, Moritz C. Validation and description of two new north-western Australian Rainbow skinks with multispecies coalescent methods and morphology. PeerJ 2017; 5:e3724. [PMID: 28875076 PMCID: PMC5580384 DOI: 10.7717/peerj.3724] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 08/01/2017] [Indexed: 11/20/2022] Open
Abstract
While methods for genetic species delimitation have noticeably improved in the last decade, this remains a work in progress. Ideally, model based approaches should be applied and considered jointly with other lines of evidence, primarily morphology and geography, in an integrative taxonomy framework. Deep phylogeographic divergences have been reported for several species of Carlia skinks, but only for some eastern taxa have species boundaries been formally tested. The present study does this and revises the taxonomy for two species from northern Australia, Carlia johnstonei and C. triacantha. We introduce an approach that is based on the recently published method StarBEAST2, which uses multilocus data to explore the support for alternative species delimitation hypotheses using Bayes Factors (BFD). We apply this method, jointly with two other multispecies coalescent methods, using an extensive (from 2,163 exons) data set along with measures of 11 morphological characters. We use this integrated approach to evaluate two new candidate species previously revealed in phylogeographic analyses of rainbow skinks (genus Carlia) in Western Australia. The results based on BFD StarBEAST2, BFD* SNAPP and BPP genetic delimitation, together with morphology, support each of the four recently identified Carlia lineages as separate species. The BFD StarBEAST2 approach yielded results highly congruent with those from BFD* SNAPP and BPP. This supports use of the robust multilocus multispecies coalescent StarBEAST2 method for species delimitation, which does not require a priori resolved species or gene trees. Compared to the situation in C. triacantha, morphological divergence was greater between the two lineages within Kimberley endemic C. johnstonei, which also had deeper divergent histories. This congruence supports recognition of two species within C. johnstonei. Nevertheless, the combined evidence also supports recognition of two taxa within the more widespread C. triacantha. With this work, we describe two new species, Carlia insularis sp. nov and Carlia isostriacantha sp. nov. in the northwest of Australia. This contributes to increasing recognition that this region of tropical Australia has a rich and unique fauna.
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Affiliation(s)
- Ana C. Afonso Silva
- Division of Ecology and Evolution, Research School of Biology and Centre for Biodiversity Analysis, Australian National University, Acton, ACT, Australia
- cE3c—Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Natali Santos
- Universidade Federal do ABC, Santo André, SP, Brazil
| | - Huw A. Ogilvie
- Division of Ecology and Evolution, Research School of Biology and Centre for Biodiversity Analysis, Australian National University, Acton, ACT, Australia
- Centre for Computational Evolution, University of Auckland, Auckland, New Zealand
| | - Craig Moritz
- Division of Ecology and Evolution, Research School of Biology and Centre for Biodiversity Analysis, Australian National University, Acton, ACT, Australia
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16
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Afonso Silva AC, Bragg JG, Potter S, Fernandes C, Coelho MM, Moritz C. Tropical specialist vs. climate generalist: Diversification and demographic history of sister species of
Carlia
skinks from northwestern Australia. Mol Ecol 2017; 26:4045-4058. [DOI: 10.1111/mec.14185] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 04/29/2016] [Accepted: 05/02/2017] [Indexed: 01/05/2023]
Affiliation(s)
- Ana C. Afonso Silva
- Research School of Biology and Centre for Biodiversity Analysis Australian National University Acton ACT Australia
- cE3c ‐ Centre for Ecology, Evolution and Environmental Changes Departamento de Biologia Animal Faculdade de Ciências Universidade de Lisboa Lisboa Portugal
| | - Jason G. Bragg
- Research School of Biology and Centre for Biodiversity Analysis Australian National University Acton ACT Australia
- Royal Botanic Garden Sydney NSW Australia
| | - Sally Potter
- Research School of Biology and Centre for Biodiversity Analysis Australian National University Acton ACT Australia
| | - Carlos Fernandes
- cE3c ‐ Centre for Ecology, Evolution and Environmental Changes Departamento de Biologia Animal Faculdade de Ciências Universidade de Lisboa Lisboa Portugal
| | - Maria Manuela Coelho
- cE3c ‐ Centre for Ecology, Evolution and Environmental Changes Departamento de Biologia Animal Faculdade de Ciências Universidade de Lisboa Lisboa Portugal
| | - Craig Moritz
- Research School of Biology and Centre for Biodiversity Analysis Australian National University Acton ACT Australia
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17
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Singhal S, Bi K. History cleans up messes: The impact of time in driving divergence and introgression in a tropical suture zone. Evolution 2017; 71:1888-1899. [DOI: 10.1111/evo.13278] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 05/04/2017] [Indexed: 02/01/2023]
Affiliation(s)
- Sonal Singhal
- Department of Ecology and Evolutionary Biology University of Michigan, 830 North University Ann Arbor Michigan 48109
- Museum of Zoology University of Michigan, 1109 Geddes Avenue Ann Arbor Michigan 48109
| | - Ke Bi
- Museum of Vertebrate Zoology University of California, Berkeley, 3101 Valley Life Sciences Building Berkeley California 94720
- Computational Genomics Resource Laboratory, California Institute for Quantitative Biosciences University of California Berkeley California 94720
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18
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Bryant LM, Krosch MN. Lines in the land: a review of evidence for eastern Australia's major biogeographical barriers to closed forest taxa. Biol J Linn Soc Lond 2016. [DOI: 10.1111/bij.12821] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Litticia M. Bryant
- School of Earth, Environmental and Biological Sciences; Queensland University of Technology; Brisbane Qld 4000 Australia
| | - Matt N. Krosch
- School of Earth, Environmental and Biological Sciences; Queensland University of Technology; Brisbane Qld 4000 Australia
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19
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Stankowski S, Sobel JM, Streisfeld MA. The geography of divergence with gene flow facilitates multitrait adaptation and the evolution of pollinator isolation inMimulus aurantiacus. Evolution 2015; 69:3054-68. [DOI: 10.1111/evo.12807] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Revised: 09/16/2015] [Accepted: 10/18/2015] [Indexed: 01/07/2023]
Affiliation(s)
- Sean Stankowski
- Institute of Ecology and Evolution; University of Oregon; Eugene Oregon 97401
| | - James M. Sobel
- Department of Biological Sciences; Binghamton University; Binghamton New York 13902
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20
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Chávez-Galarza J, Henriques D, Johnston JS, Carneiro M, Rufino J, Patton JC, Pinto MA. Revisiting the Iberian honey bee (Apis mellifera iberiensis) contact zone: maternal and genome-wide nuclear variations provide support for secondary contact from historical refugia. Mol Ecol 2015; 24:2973-92. [PMID: 25930679 DOI: 10.1111/mec.13223] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2014] [Revised: 04/16/2015] [Accepted: 04/21/2015] [Indexed: 12/30/2022]
Abstract
Dissecting diversity patterns of organisms endemic to Iberia has been truly challenging for a variety of taxa, and the Iberian honey bee is no exception. Surveys of genetic variation in the Iberian honey bee are among the most extensive for any honey bee subspecies. From these, differential and complex patterns of diversity have emerged, which have yet to be fully resolved. Here, we used a genome-wide data set of 309 neutrally tested single nucleotide polymorphisms (SNPs), scattered across the 16 honey bee chromosomes, which were genotyped in 711 haploid males. These SNPs were analysed along with an intergenic locus of the mtDNA, to reveal historical patterns of population structure across the entire range of the Iberian honey bee. Overall, patterns of population structure inferred from nuclear loci by multiple clustering approaches and geographic cline analysis were consistent with two major clusters forming a well-defined cline that bisects Iberia along a northeastern-southwestern axis, a pattern that remarkably parallels that of the mtDNA. While a mechanism of primary intergradation or isolation by distance could explain the observed clinal variation, our results are more consistent with an alternative model of secondary contact between divergent populations previously isolated in glacial refugia, as proposed for a growing list of other Iberian taxa. Despite current intense honey bee management, human-mediated processes have seemingly played a minor role in shaping Iberian honey bee genetic structure. This study highlights the complexity of the Iberian honey bee patterns and reinforces the importance of Iberia as a reservoir of Apis mellifera diversity.
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Affiliation(s)
- Julio Chávez-Galarza
- Mountain Research Centre (CIMO), Polytechnic Institute of Bragança, Campus de Sta. Apolónia, Apartado 1172, 5301-855, Bragança, Portugal.,Centre of Molecular and Environmental Biology (CBMA), University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Dora Henriques
- Mountain Research Centre (CIMO), Polytechnic Institute of Bragança, Campus de Sta. Apolónia, Apartado 1172, 5301-855, Bragança, Portugal.,Centre of Molecular and Environmental Biology (CBMA), University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - J Spencer Johnston
- Department of Entomology, Texas A&M University, College Station, TX, 77843-2475, USA
| | - Miguel Carneiro
- CIBIO/InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, Campus Agrário de Vairão, 4485-661, Vairão, Portugal
| | - José Rufino
- Polytechnic Institute of Bragança, 5301-857, Bragança, Portugal
| | - John C Patton
- Department of Forestry and Natural Resources, Purdue University, 715 W State St., West Lafayette, IN, 4797-2061, USA
| | - M Alice Pinto
- Mountain Research Centre (CIMO), Polytechnic Institute of Bragança, Campus de Sta. Apolónia, Apartado 1172, 5301-855, Bragança, Portugal
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21
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Cliff HB, Wapstra E, Burridge CP. Persistence and dispersal in a Southern Hemisphere glaciated landscape: the phylogeography of the spotted snow skink (Niveoscincus ocellatus) in Tasmania. BMC Evol Biol 2015; 15:121. [PMID: 26111715 PMCID: PMC4482293 DOI: 10.1186/s12862-015-0397-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2014] [Accepted: 05/29/2015] [Indexed: 11/10/2022] Open
Abstract
Background The aim of this research was to identify the effects of Pleistocene climate change on the distribution of fauna in Tasmania, and contrast this with biotic responses in other temperate regions in the Northern and Southern Hemisphere that experienced glacial activity during this epoch. This was achieved by examining the phylogeographic patterns in a widely distributed Tasmanian endemic reptile, Niveoscincus ocellatus. 204 individuals from 29 populations across the distributional range of N. ocellatus were surveyed for variation at two mitochondrial genes (ND2, ND4), and two nuclear genes (β-globin, RPS8). Phylogenetic relationships were reconstructed using a range of methods (maximum parsimony, Bayesian inference and haplotype networks), and the demographic histories of populations were assessed (AMOVA, Tajima’s D, Fu’s Fs, mismatch distributions, extended Bayesian skyline plots, and relaxed random walk analyses). Results There was a high degree of mitochondrial haplotype diversity (96 unique haplotypes) and phylogeographic structure, where spatially distinct groups were associated with Tasmania’s Northeast and a large area covering Southeast and Central Tasmania. Phylogeographic structure was also present within each major group, but the degree varied regionally, being highest in the Northeast. Only the Southeastern group had a signature of demographic expansion, occurring during the Pleistocene but post-dating the Last Glacial Maximum. In contrast, nuclear DNA had low levels of variation and a lack of phylogeographic structure, and further loci should be surveyed to corroborate the mitochondrial inferences. Conclusions The phylogeographic patterns of N. ocellatus indicate Pleistocene range and demographic expansion in N. ocellatus, particularly in the Southeast and Central areas of Tasmania. Expansion in Central and Southeastern areas appears to have been more recent in both demographic and spatial contexts, than in Northeast Tasmania, which is consistent with inferences for other taxa of greater stability and persistence in Northeast Tasmania during the Last Glacial Maximum. These phylogeographic patterns indicate contrasting demographic histories of populations in close proximity to areas directly affected by glaciers in the Southern Hemisphere during the LGM. Electronic supplementary material The online version of this article (doi:10.1186/s12862-015-0397-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- H B Cliff
- School of Biological Sciences, University of Tasmania, Private Bag 55, Hobart, Tasmania, 7001, Australia.
| | - E Wapstra
- School of Biological Sciences, University of Tasmania, Private Bag 55, Hobart, Tasmania, 7001, Australia.
| | - C P Burridge
- School of Biological Sciences, University of Tasmania, Private Bag 55, Hobart, Tasmania, 7001, Australia.
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22
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Rosauer DF, Catullo RA, VanDerWal J, Moussalli A, Moritz C. Lineage range estimation method reveals fine-scale endemism linked to Pleistocene stability in Australian rainforest herpetofauna. PLoS One 2015; 10:e0126274. [PMID: 26020936 PMCID: PMC4447262 DOI: 10.1371/journal.pone.0126274] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Accepted: 03/31/2015] [Indexed: 12/03/2022] Open
Abstract
Areas of suitable habitat for species and communities have arisen, shifted, and disappeared with Pleistocene climate cycles, and through this shifting landscape, current biodiversity has found paths to the present. Evolutionary refugia, areas of relative habitat stability in this shifting landscape, support persistence of lineages through time, and are thus crucial to the accumulation and maintenance of biodiversity. Areas of endemism are indicative of refugial areas where diversity has persisted, and endemism of intraspecific lineages in particular is strongly associated with late-Pleistocene habitat stability. However, it remains a challenge to consistently estimate the geographic ranges of intraspecific lineages and thus infer phylogeographic endemism, because spatial sampling for genetic analyses is typically sparse relative to species records. We present a novel technique to model the geographic distribution of intraspecific lineages, which is informed by the ecological niche of a species and known locations of its constituent lineages. Our approach allows for the effects of isolation by unsuitable habitat, and captures uncertainty in the extent of lineage ranges. Applying this method to the arc of rainforest areas spanning 3500 km in eastern Australia, we estimated lineage endemism for 53 species of rainforest dependent herpetofauna with available phylogeographic data. We related endemism to the stability of rainforest habitat over the past 120,000 years and identified distinct concentrations of lineage endemism that can be considered putative refugia. These areas of lineage endemism are strongly related to historical stability of rainforest habitat, after controlling for the effects of current environment. In fact, a dynamic stability model that allows movement to track suitable habitat over time was the most important factor in explaining current patterns of endemism. The techniques presented here provide an objective, practical method for estimating geographic ranges below the species level, and including them in spatial analyses of biodiversity.
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Affiliation(s)
- Dan F. Rosauer
- Research School of Biology & Centre for Biodiversity Analysis, Australian National University, Canberra, Australian Capital Territory, Australia
- * E-mail:
| | - Renee A. Catullo
- Research School of Biology & Centre for Biodiversity Analysis, Australian National University, Canberra, Australian Capital Territory, Australia
- CSIRO Land and Water Flagship, Canberra, Australian Capital Territory, Australia
| | - Jeremy VanDerWal
- Centre for Tropical Biodiversity & Climate Change, College of Marine and Environmental Sciences, James Cook University, Townsville, Queensland, Australia
- eResearch Centre, Division of Research and Innovation, James Cook University, Townsville, Queensland, Australia
| | - Adnan Moussalli
- Sciences Department, Museum Victoria, Melbourne, Victoria, Australia
| | - Craig Moritz
- Research School of Biology & Centre for Biodiversity Analysis, Australian National University, Canberra, Australian Capital Territory, Australia
- CSIRO Land and Water Flagship, Canberra, Australian Capital Territory, Australia
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23
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Baldassarre DT, White TA, Karubian J, Webster MS. GENOMIC AND MORPHOLOGICAL ANALYSIS OF A SEMIPERMEABLE AVIAN HYBRID ZONE SUGGESTS ASYMMETRICAL INTROGRESSION OF A SEXUAL SIGNAL. Evolution 2014; 68:2644-57. [DOI: 10.1111/evo.12457] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Accepted: 05/22/2014] [Indexed: 12/14/2022]
Affiliation(s)
- Daniel T. Baldassarre
- Department of Neurobiology and Behavior; Cornell University; Ithaca New York 14850
- Macaulay Library; Cornell Lab of Ornithology; Ithaca New York 14853
| | - Thomas A. White
- Department of Ecology and Evolutionary Biology; Cornell University; Ithaca New York 14850
| | - Jordan Karubian
- Department of Ecology and Evolutionary Biology; Tulane University; New Orleans Louisiana 70118
| | - Michael S. Webster
- Department of Neurobiology and Behavior; Cornell University; Ithaca New York 14850
- Macaulay Library; Cornell Lab of Ornithology; Ithaca New York 14853
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24
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Beysard M, Heckel G. Structure and dynamics of hybrid zones at different stages of speciation in the common vole (Microtus arvalis). Mol Ecol 2014; 23:673-87. [DOI: 10.1111/mec.12613] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2013] [Revised: 11/21/2013] [Accepted: 11/25/2013] [Indexed: 11/30/2022]
Affiliation(s)
- Mathias Beysard
- Computational and Molecular Population Genetics; Institute of Ecology and Evolution; University of Bern; CH 3012 Bern Switzerland
- Swiss Institute of Bioinformatics; Genopode CH 1015 Lausanne Switzerland
| | - Gerald Heckel
- Computational and Molecular Population Genetics; Institute of Ecology and Evolution; University of Bern; CH 3012 Bern Switzerland
- Swiss Institute of Bioinformatics; Genopode CH 1015 Lausanne Switzerland
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25
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Derryberry EP, Derryberry GE, Maley JM, Brumfield RT. hzar: hybrid zone analysis using an R software package. Mol Ecol Resour 2013; 14:652-63. [DOI: 10.1111/1755-0998.12209] [Citation(s) in RCA: 200] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2012] [Revised: 11/27/2013] [Accepted: 11/29/2013] [Indexed: 11/30/2022]
Affiliation(s)
- Elizabeth P. Derryberry
- Department of Ecology and Evolutionary Biology; Tulane University; New Orleans LA 70118 USA
- Museum of Natural Science and Department of Biological Sciences; Louisiana State University; Baton Rouge LA 70803 USA
| | | | - James M. Maley
- Museum of Natural Science and Department of Biological Sciences; Louisiana State University; Baton Rouge LA 70803 USA
- Moore Laboratory of Zoology; Occidental College; 1600 Campus Road Los Angeles, CA 90041 USA
| | - Robb T. Brumfield
- Museum of Natural Science and Department of Biological Sciences; Louisiana State University; Baton Rouge LA 70803 USA
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26
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Larson EL, White TA, Ross CL, Harrison RG. Gene flow and the maintenance of species boundaries. Mol Ecol 2013; 23:1668-78. [DOI: 10.1111/mec.12601] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Erica L. Larson
- Department of Ecology and Evolutionary Biology; Cornell University; Ithaca NY 14853 USA
- Division of Biological Sciences; University of Montana; Missoula MT 59812 USA
| | - Thomas A. White
- Department of Ecology and Evolutionary Biology; Cornell University; Ithaca NY 14853 USA
- CMPG Lab; Institute of Ecology and Evolution; University of Bern; Baltzerstrasse 6 3012 Bern Switzerland
| | - Charles L. Ross
- School of Natural Science; Hampshire College; Amherst MA 01002 USA
| | - Richard G. Harrison
- Department of Ecology and Evolutionary Biology; Cornell University; Ithaca NY 14853 USA
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27
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Stewart KA, Lougheed SC. Testing for intraspecific postzygotic isolation between cryptic lineages of Pseudacris crucifer. Ecol Evol 2013; 3:4621-30. [PMID: 24363891 PMCID: PMC3867898 DOI: 10.1002/ece3.851] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Revised: 09/14/2013] [Accepted: 09/17/2013] [Indexed: 12/01/2022] Open
Abstract
Phenotypically cryptic lineages appear common in nature, yet little is known about the mechanisms that initiate and/or maintain barriers to gene flow, or how secondary contact between them might influence evolutionary trajectories. The consequences of such contact between diverging lineages depend on hybrid fitness, highlighting the potential for postzygotic isolating barriers to play a role in the origins of biological species. Previous research shows that two cryptic, deeply diverged intraspecific mitochondrial lineages of a North American chorus frog, the spring peeper (Pseudacris crucifer), meet in secondary contact in Southwestern Ontario, Canada. Our study quantified hatching success, tadpole survival, size at metamorphosis, and development time for experimentally generated pure lineage and hybrid tadpoles. Results suggest that lineages differ in tadpole survival and that F1 hybrids may have equal fitness and higher than average mass at metamorphosis compared with pure parental crosses. These findings imply hybrid early life viability may not be the pivotal reproductive isolation barrier helping to maintain lineage boundaries. However, we observed instances of tadpole gigantism, failure to metamorphose, and bent tails in some tadpoles from hybrid families. We also speculate and provide some evidence that apparent advantages or similarities of hybrids compared with pure lineage tadpoles may disappear when tadpoles are raised with competitors of different genetic makeup. This pilot study implies that ecological context and consideration of extrinsic factors may be a key to revealing mechanisms causing negative hybrid fitness during early life stages, a provocative avenue for future investigations on barriers to gene flow among these intraspecific lineages.
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Affiliation(s)
- Kathryn A Stewart
- Department of Biology, Queen's University Kingston, Ontario, Canada, K7L 3N6
| | - Stephen C Lougheed
- Department of Biology, Queen's University Kingston, Ontario, Canada, K7L 3N6
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28
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Singhal S, Moritz C. Reproductive isolation between phylogeographic lineages scales with divergence. Proc Biol Sci 2013; 280:20132246. [PMID: 24107536 DOI: 10.1098/rspb.2013.2246] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Phylogeographic studies frequently reveal multiple morphologically cryptic lineages within species. What is not yet clear is whether such lineages represent nascent species or evolutionary ephemera. To address this question, we compare five contact zones, each of which occurs between ecomorphologically cryptic lineages of skinks from the rainforests of the Australian Wet Tropics. Although the contacts probably formed concurrently in response to Holocene expansion from glacial refugia, we estimate that the divergence times (τ) of the lineage pairs range from 3.1 to 11.5 Ma. Multi-locus analyses of the contact zones yielded estimates of reproductive isolation that are tightly correlated with divergence time and, for lineages with older divergence times (τ > 5 Myr), substantial. These results show that phylogeographic splits of increasing depth represent stages along the speciation continuum, even in the absence of overt change in ecologically relevant morphology.
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Affiliation(s)
- Sonal Singhal
- Museum of Vertebrate Zoology, University of California, , 3101 Valley Life Sciences Building, Berkeley, CA 94720-3160, USA, Department of Integrative Biology, University of California, , 1005 Valley Life Sciences Building, Berkeley, CA 94720-3140, USA, Research School of Biology, The Australian National University, , Building 116, Acton, Australian Capital Territory 0200, Australia
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29
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Delmore KE, Brenneman RA, Lei R, Bailey CA, Brelsford A, Louis EE, Johnson SE. Clinal variation in a brown lemur (Eulemur
spp.) hybrid zone: Combining morphological, genetic and climatic data to examine stability. J Evol Biol 2013; 26:1677-90. [DOI: 10.1111/jeb.12178] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Revised: 02/15/2013] [Accepted: 03/26/2013] [Indexed: 11/27/2022]
Affiliation(s)
- K. E. Delmore
- Department of Anthropology; University of Calgary; Calgary AB Canada
| | - R. A. Brenneman
- Center for Conservation and Research; Omaha's Henry Doorly Zoo; Omaha NE USA
| | - R. Lei
- Center for Conservation and Research; Omaha's Henry Doorly Zoo; Omaha NE USA
| | - C. A. Bailey
- Center for Conservation and Research; Omaha's Henry Doorly Zoo; Omaha NE USA
| | - A. Brelsford
- Department of Ecology and Evolution; University of Lausanne; Lausanne Switzerland
| | - E. E. Louis
- Center for Conservation and Research; Omaha's Henry Doorly Zoo; Omaha NE USA
| | - S. E. Johnson
- Department of Anthropology; University of Calgary; Calgary AB Canada
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30
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Lindell J, Murphy RW. Simple identification of mitochondrial lineages in contact zones based on lineage-selective primers. Mol Ecol Resour 2013; 8:66-73. [PMID: 21585720 DOI: 10.1111/j.1471-8286.2007.01894.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A variety of research projects focus on genetic variation among and within maternal lineages as encompassed by mitochondrial DNA (mtDNA). While mtDNA often differs substantially between species, large differences may also be found within species. The evaluation of such divergent lineages, for example in intraspecific contact zones (hybrid zones), commonly involves sequencing numerous individuals. Large-scale sequencing is both expensive and labour-intensive. Based on sequences from 15 individuals, we devised a simple and quick polymerase chain reaction assay for identification of divergent mtDNA lineages in a secondary contact zone of the side-blotched lizard (Uta stansburiana). The application uses lineage-selective primers to amplify a lineage-diagnostic product, and is based on each group of mtDNA haplotypes being a monophyletic assemblage of haplotypes sharing the same maternal ancestry, deeply divergent from the other group. The assay was tested on a larger sample (n = 147) of specimens from the contact zone, confirming its usefulness in quick and reliable identification of mtDNA lineages. This approach can be modified for other species, provided diagnostic lineage variation is available, and may also be performed in simple laboratory settings while conducting fieldwork.
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Affiliation(s)
- Johan Lindell
- Department of Ecology & Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, Ontario, Canada M5S 3B2, and Department of Natural History, Royal Ontario Museum, 100 Queen's Park, Toronto, Ontario, Canada M5S 2C6
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Carneiro M, Baird SJE, Afonso S, Ramirez E, Tarroso P, Teotónio H, Villafuerte R, Nachman MW, Ferrand N. Steep clines within a highly permeable genome across a hybrid zone between two subspecies of the European rabbit. Mol Ecol 2013; 22:2511-25. [PMID: 23530594 DOI: 10.1111/mec.12272] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2012] [Revised: 01/09/2013] [Accepted: 01/11/2013] [Indexed: 11/27/2022]
Abstract
Maintenance of genetic distinction in the face of gene flow is an important aspect of the speciation process. Here, we provide a detailed spatial and genetic characterization of a hybrid zone between two subspecies of the European rabbit. We examined patterns of allele frequency change for 22 markers located on the autosomes, X-chromosome, Y-chromosome and mtDNA in 1078 individuals sampled across the hybrid zone. While some loci revealed extremely wide clines (w ≥ 300 km) relative to an estimated dispersal of 1.95-4.22 km/generation, others showed abrupt transitions (w ≈ 10 km), indicating localized genomic regions of strong selection against introgression. The subset of loci showing steep clines had largely coincident centers and stepped changes in allele frequency that did not co-localize with any physical barrier or ecotone, suggesting that the rabbit hybrid zone is a tension zone. The steepest clines were for X- and Y-chromosome markers. Our results are consistent with previous inference based on DNA sequence variation of individuals sampled in allopatry in suggesting that a large proportion of each genome has escaped the overall barrier to gene flow in the middle of the hybrid zone. These results imply an old history of hybridization and high effective gene flow and anticipate that isolation factors should often localize to small genomic regions.
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Affiliation(s)
- Miguel Carneiro
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Universidade do Porto, Vairão, Portugal.
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Sex-specific clines support incipient speciation in a common European mammal. Heredity (Edinb) 2013; 110:398-404. [PMID: 23340600 DOI: 10.1038/hdy.2012.124] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Hybrid zones provide excellent opportunities to study processes and mechanisms underlying reproductive isolation and speciation. Here we investigated sex-specific clines of molecular markers in hybrid zones of morphologically cryptic yet genetically highly-diverged evolutionary lineages of the European common vole (Microtus arvalis). We analyzed the position and width of four secondary contact zones along three independent transects in the region of the Alps using maternally (mitochondrial DNA) and paternally (Y-chromosome) inherited genetic markers. Given male-biased dispersal in the common vole, a selectively neutral secondary contact would show broader paternal marker clines than maternal ones. In a selective case, for example, involving a form of Haldane's rule, Y-chromosomal clines would not be expected to be broader than maternal markers because they are transmitted by the heterogametic sex and thus gene flow would be restricted. Consistent with the selective case, paternal clines were significantly narrower or at most equal in width to maternal clines in all contact zones. In addition, analyses using maximum likelihood cline-fitting detected a shift of paternal relative to maternal clines in three of four contact zones. These patterns suggest that processes at the contact zones in the common vole are not selectively neutral, and that partial reproductive isolation is already established between these evolutionary lineages. We conclude that hybrid zone movement, sexual selection and/or genetic incompatibilities are likely associated with an unusual unidirectional manifestation of Haldane's rule in this common European mammal.
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Roy JS, O’Connor D, Green DM. Oscillation of an anuran hybrid zone: morphological evidence spanning 50 years. PLoS One 2013; 7:e52819. [PMID: 23300785 PMCID: PMC3530495 DOI: 10.1371/journal.pone.0052819] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2012] [Accepted: 11/23/2012] [Indexed: 11/19/2022] Open
Abstract
Background The hybrid zone between the primarily forest-dwelling American toad, Anaxyrus americanus, and the prairie-adapted Canadian toad, A. hemiophrys, in southeastern Manitoba is known to have shifted its position during the past 50 years. Hybrid zones are areas of interbreeding between species and their movement across a landscape should reflect their underlying dynamics and environmental change. However, empirical demonstrations of hybrid zone movements over long periods of time are rare. This hybrid zone is dominated by individuals of intermediate morphology and genetic composition. We sought to determine if it had continued to move and if that movement was associated with shifts in habitat, as predicted. Methodology/Principle Findings We used variation in the toads’ most diagnostic morphological feature, the separation between their interorbital cranial crests, to determine the geographic position of the hybrid zone center at four times between 1960 and 2009 using maximum likelihood methods. The hybrid zone center moved west by 38 km over 19 years and then east again by 10 km over the succeeding 29 years. The position of the hybrid zone did not track either the direction or the magnitude of movement of the forest-prairie habitat transition over the same time period. Conclusions/Significance This is the first reported evidence of oscillation in the position of a hybrid zone. The back and forth movement indicates that neither species maintains a selective advantage over the other in the long term. However, the movement of the hybrid zone was not bounded by the breadth of the habitat transition. Its oscillation suggests that the hybrid zone is better described as being elastically tethered to the habitat transition.
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Affiliation(s)
| | - David O’Connor
- Redpath Museum, McGill University, Montréal, Québec, Canada
| | - David M. Green
- Redpath Museum, McGill University, Montréal, Québec, Canada
- * E-mail:
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Recipient of the 2012 molecular ecology prize: Craig Moritz. Mol Ecol 2012; 22:15-8. [PMID: 23252576 DOI: 10.1111/mec.12148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Geographical patterns of genetic divergence in the widespread Mesoamerican bumble bee Bombus ephippiatus (Hymenoptera: Apidae). Mol Phylogenet Evol 2012; 64:219-31. [PMID: 22521295 DOI: 10.1016/j.ympev.2012.03.018] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2011] [Revised: 03/19/2012] [Accepted: 03/30/2012] [Indexed: 11/20/2022]
Abstract
Bumble bees (Bombus Latreille) are an important group of social insects, well recognized throughout northern temperate regions as important pollinators of wild and agricultural plants. Little is known about the biology of this group in southern portions of the Americas, especially in Mesoamerica, a region of geological and ecological complexity from Mexico through Central America. One ubiquitous Mesoamerican species, Bombus ephippiatus, is enigmatic. Like many other Bombus, this species is homogeneous in body structure yet exhibits striking intraspecific color pattern polymorphism across its range, leading to uncertainty about its genealogical boundaries. It has been grouped taxonomically with B. wilmattae, a species narrowly restricted to southern Mexico and northern Guatamala. Furthermore, the relationships between these two taxa and a third species, B. impatiens, found only in America north of Mexico, have been controversial. Our phylogenetic analysis of DNA sequences from mitochondrial COI and nuclear PEPCK and CAD resolves the phylogeny of these three taxa as (B. impatiens, (B. ephippiatus, B. wilmattae)). Additional data from eight nuclear microsatellite markers reveal complex patterns of genetic divergence and isolation among populations of B. ephippiatus across its extensive geographic range, providing evidence for multiple independent evolutionary lineages. These lineages correspond not only to geographic and habitat variation across their range, but also to distinct color pattern groups present in the species. Knowledge of the phylogeny and genetic divergence of the B. ephippiatus group will provide a framework for understanding evolutionary and ecological origins of color pattern polymorphism in bumble bees, as well as providing insight into geographical factors enhancing speciation in Mesoamerica.
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Fitness J, Hitchmough RA, Morgan-Richards M. Little and large: body size and genetic clines in a New Zealand gecko (Woodworthia maculata) along a coastal transect. Ecol Evol 2012; 2:273-85. [PMID: 22423323 PMCID: PMC3298942 DOI: 10.1002/ece3.64] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2011] [Revised: 10/05/2011] [Accepted: 10/06/2011] [Indexed: 11/17/2022] Open
Abstract
Clinal variation can result from primary differentiation or secondary contact and determining which of these two processes is responsible for the existence of a cline is not a trivial problem. Samples from a coastal transect of New Zealand geckos (Woodworthia maculata) identified for the first time a body size cline 7–10 km wide. The larger geckos are almost twice the mass of the small adult geckos. Clines in allele and haplotype frequency were found at two of the four genetic loci examined. Estimated width of the morphological cline was concordant with neither the narrower mtDNA cline (3–7 m) nor the wider nuclear cline (RAG-2; 34–42 km), and cline centers were not coincident. Although the body size cline is narrow compared to the entire range of the species, it is 2–3 orders of magnitude greater than estimates of dispersal distance per generation for these geckos. No evidence of assortative mating, nor of hybrid disadvantage was identified, thus there is little evidence to infer that endogenous selection is maintaining a hybrid zone. We cannot distinguish secondary contact from primary origin of this body size cline but conclude that secondary contact is likely due to the occurrence of mtDNA haplotypes from three distinct clades within the coastal transect and the presence of two frequency clines within this region.
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Affiliation(s)
- Josephine Fitness
- Ecology, Institute of Natural Resources, Massey UniversityPalmerston North, New Zealand
| | | | - Mary Morgan-Richards
- Ecology, Institute of Natural Resources, Massey UniversityPalmerston North, New Zealand
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Singhal S, Moritz C. Strong selection against hybrids maintains a narrow contact zone between morphologically cryptic lineages in a rainforest lizard. Evolution 2012; 66:1474-89. [PMID: 22519785 DOI: 10.1111/j.1558-5646.2011.01539.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Phenotypically cryptic lineages comprise an important yet understudied part of biodiversity; in particular, we have much to learn about how these lineages are formed and maintained. To better understand the evolutionary significance of such lineages, we studied a hybrid zone between two morphologically cryptic phylogeographic lineages in the rainforest lizard, Lampropholis coggeri. Analyzing a multilocus genetic dataset through cline inference, individual-based methods and population measures of disequilibrium and using simulations to explore our genetic results in context of theoretical expectations, we inferred the processes maintaining this hybrid zone. We find that these lineages meet in a hybrid zone that is narrow (≈400 m) relative to inferred dispersal rate. Further, the hybrid zone exhibits substantial genetic disequilibrium and sharply coincident and largely concordant clines. Based on our knowledge about the region's biogeography, the species' natural history, and our simulation results, we suggest that strong selection against hybrids structures this system. As all clines show a relatively narrow range of introgression, we posit that this hybrid zone might not yet be in equilibrium. Nonetheless, our results clearly show that phylogeographic lineages can evolve substantial reproductive isolation without concomitant morphological diversification, suggesting that such lineages can constitute a significant component of evolutionary diversity.
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Affiliation(s)
- Sonal Singhal
- Museum of Vertebrate Zoology, University of California, Berkeley, California 94720-3160, USA.
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Hoskin CJ, Tonione M, Higgie M, MacKenzie JB, Williams SE, VanDerWal J, Moritz C. Persistence in Peripheral Refugia Promotes Phenotypic Divergence and Speciation in a Rainforest Frog. Am Nat 2011; 178:561-78. [DOI: 10.1086/662164] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Devitt TJ, Baird SJE, Moritz C. Asymmetric reproductive isolation between terminal forms of the salamander ring species Ensatina eschscholtzii revealed by fine-scale genetic analysis of a hybrid zone. BMC Evol Biol 2011; 11:245. [PMID: 21859447 PMCID: PMC3175475 DOI: 10.1186/1471-2148-11-245] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2011] [Accepted: 08/22/2011] [Indexed: 11/29/2022] Open
Abstract
Background Ring species, exemplified by salamanders of the Ensatina eschscholtzii complex, represent a special window into the speciation process because they allow the history of species formation to be traced back in time through the geographically differentiated forms connecting the two terminal forms of the ring. Of particular interest is the nature and extent of reproductive isolation between the geographically terminal forms, in this case E. e. eschscholtzii and E. e. klauberi. Previous studies have documented infrequent hybridization at the end of the ring. Here, we report the first fine-scale genetic analysis of a hybrid zone between the terminal forms in southern California using individual-based Bayesian analyses of multilocus genetic data to estimate levels and direction of hybridization and maximum-likelihood analysis of linkage disequilibrium and cline shape to make inferences about migration and selection in the hybrid zone. Results The center of the hybrid zone has a high proportion of hybrids, about half of which were classified as F1s. Clines are narrow with respect to dispersal, and there are significant deviations from Hardy-Weinberg equilibrium as well as nonrandom associations (linkage disequilibria) between alleles characteristic of each parental type. There is cytonuclear discordance, both in terms of introgression and the geographic position of mitochondrial versus nuclear clines. Genetic disequilibrium is concentrated on the eschscholtzii side of the zone. Nearly all hybrids possess klauberi mtDNA, indicating that most hybrids are formed from female klauberi mating with male eschscholtzii or male hybrids (but not vice versa). Conclusions Our results are consistent with a tension zone trapped at an ecotone, with gene combinations characteristic of klauberi showing up on the eschscholtzii side of the zone due to asymmetric hybridization. We suggest that the observed asymmetry is best explained by increased discriminatory power of eschscholtzii females, or asymmetric postzygotic isolation. The relatively high frequency of hybrids, particularly F1s, contrasts with other contacts between the terminal forms, and with other contacts between other divergent Ensatina lineages, highlighting the diverse outcomes of secondary contact within a single species complex.
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Affiliation(s)
- Thomas J Devitt
- Museum of Vertebrate Zoology and Department of Integrative Biology, 3101 Valley Life Sciences Building, University of California, Berkeley, CA 94720-3160, USA.
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Bímová BV, Macholán M, Baird SJE, Munclinger P, Dufková P, Laukaitis CM, Karn RC, Luzynski K, Tucker PK, Piálek J. Reinforcement selection acting on the European house mouse hybrid zone. Mol Ecol 2011; 20:2403-24. [PMID: 21521395 DOI: 10.1111/j.1365-294x.2011.05106.x] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Behavioural isolation may lead to complete speciation when partial postzygotic isolation acts in the presence of divergent-specific mate-recognition systems. These conditions exist where Mus musculus musculus and M. m. domesticus come into contact and hybridize. We studied two mate-recognition signal systems, based on urinary and salivary proteins, across a Central European portion of the mouse hybrid zone. Introgression of the genomic regions responsible for these signals: the major urinary proteins (MUPs) and androgen binding proteins (ABPs), respectively, was compared to introgression at loci assumed to be nearly neutral and those under selection against hybridization. The preference of individuals taken from across the zone regarding these signals was measured in Y mazes, and we develop a model for the analysis of the transition of such traits under reinforcement selection. The strongest assortative preferences were found in males for urine and females for ABP. Clinal analyses confirm nearly neutral introgression of an Abp locus and two loci closely linked to the Abp gene cluster, whereas two markers flanking the Mup gene region reveal unexpected introgression. Geographic change in the preference traits matches our reinforcement selection model significantly better than standard cline models. Our study confirms that behavioural barriers are important components of reproductive isolation between the house mouse subspecies.
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Affiliation(s)
- Barbora Vošlajerová Bímová
- Department of Population Biology, Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Brno, Czech Republic
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Evidence for population fragmentation within a subterranean aquatic habitat in the Western Australian desert. Heredity (Edinb) 2011; 107:215-30. [PMID: 21343944 DOI: 10.1038/hdy.2011.6] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
The evolution of subterranean animals following multiple colonisation events from the surface has been well documented, but few studies have investigated the potential for species diversification within cavernicolous habitats. Isolated calcrete (carbonate) aquifers in central Western Australia have been shown to contain diverse assemblages of aquatic subterranean invertebrate species (stygofauna) and to offer a unique model system for exploring the mechanisms of speciation in subterranean ecosystems. In this paper, we investigated the hypothesis that microallopatric speciation processes (fragmentation and isolation by distance (IBD)) occur within calcretes using a comparative phylogeographic study of three stygobiontic diving beetle species, one amphipod species and a lineage of isopods. Specimens were sequenced for the mitochondrial cytochrome c oxidase 1 gene from three main sites: Quandong Well, Shady Well (SW) and Mt. Windarra (MW), spanning a 15 km region of the Laverton Downs Calcrete. Phylogenetic and haplotype network analyses revealed that each species possessed a single divergent clade of haplotypes that were present only at the southern MW site, despite the existence of other haplotypes at MW that were shared with SW. IBD between MW and SW was evident, but the common phylogeographic pattern most likely resulted from fragmentation, possibly by a salt lake adjacent to MW. These findings suggest that microallopatric speciation within calcretes may be a significant diversifying force, although the proportion of stygofauna species that may have resulted from in situ speciation in this system remains to be determined.
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Macholán M, Baird SJE, Dufková P, Munclinger P, Bímová BV, Piálek J. ASSESSING MULTILOCUS INTROGRESSION PATTERNS: A CASE STUDY ON THE MOUSE X CHROMOSOME IN CENTRAL EUROPE. Evolution 2011; 65:1428-46. [DOI: 10.1111/j.1558-5646.2011.01228.x] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Miloš Macholán
- Laboratory of Mammalian Evolutionary Genetics, Institute of Animal Physiology and Genetics, Academy of Sciences of the Czech Republic, Brno, Czech Republic
- E‐mail:
| | | | - Petra Dufková
- Department of Population Biology, Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Brno, Czech Republic
- Department of Genetics, Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Pavel Munclinger
- Biodiversity Research Group, Department of Zoology, Faculty of Science, Charles University in Prague, Czech Republic
| | - Barbora Vošlajerová Bímová
- Laboratory of Mammalian Evolutionary Genetics, Institute of Animal Physiology and Genetics, Academy of Sciences of the Czech Republic, Brno, Czech Republic
- Department of Population Biology, Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Brno, Czech Republic
| | - Jaroslav Piálek
- Department of Population Biology, Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Brno, Czech Republic
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Dufková P, Macholán M, Piálek J. Inference of selection and stochastic effects in the house mouse hybrid zone. Evolution 2011; 65:993-1010. [PMID: 21463294 DOI: 10.1111/j.1558-5646.2011.01222.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
We explored the transition of 13 X-linked markers across two separate portions of the house mouse hybrid zone, asking whether such a comparison can distinguish the effects of selection from random factors. A heuristic search in the likelihood landscape revealed more complex likelihood profiles for data sampled in two-dimensional (2D) space relative to data sampled along a linear transect. Randomized resampling of localities analyzed for individual loci showed that deletion of sites away from the zone center can decrease cline width estimates whereas deletion of sites close to the center can significantly increase the width estimates. Deleting localities for all loci resulted in wider clines if the number of samples from the center was limited. The results suggest that, given the great variation in width estimates resulting from inclusion/exclusion of sampling sites, the geographic sampling design is important in hybrid zone studies and that our inferences should take into account measures of uncertainty such as support intervals. The comparison of the two transects indicates cline widths are narrower for loci in the central part of the X chromosome, suggesting selection is stronger in this region and genetic incompatibilities may have at least partly common architecture in the house mouse hybrid zone.
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Affiliation(s)
- Petra Dufková
- Institute of Vertebrate Biology, Academy of Science of the Czech Republic, Brno, Czech Republic.
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Melville J, Ritchie EG, Chapple SNJ, Glor RE, Schulte JA. Evolutionary origins and diversification of dragon lizards in Australia's tropical savannas. Mol Phylogenet Evol 2010; 58:257-70. [PMID: 21145401 DOI: 10.1016/j.ympev.2010.11.025] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2010] [Revised: 11/16/2010] [Accepted: 11/28/2010] [Indexed: 10/18/2022]
Abstract
Australia's monsoonal tropics are dominated by the largest and least modified savanna woodlands in the world, and they are globally significant for their high biodiversity and regional endemism. Despite this, there have been very few molecular studies of the evolutionary origins and diversification of vertebrates in this region. The semi-arboreal dragon lizards of Lophognathus and Amphibolurus are widely distributed in the savanna and dry sclerophyll woodlands of Australasia, including the monsoon tropics. We sequenced a ~1400 bp region of mitochondrial DNA and a ~1400 bp nuclear gene (RAG1) to investigate the phylogenetic relationships and phylogeographic structuring of all seven species of Lophognathus and Amphibolurus. Our analyses show that there is a higher level of species and generic diversity in the monsoon tropics than previously thought, and a full morphological review and taxonomic revision of these genera is required. Relaxed molecular clock analyses indicate that species across both genera originated in the late Miocene and early Pliocene, with significant phylogeographic structure within species. We did not find any evidence that the monsoon tropics species were a monophyletic group that had diversified within the region; instead Amphibolurus and Lophognathus represent at least three independent evolutionary colonizations of the monsoon tropics. It is probable that the origins and phylogeographic patterns of the northern Lophognathus species have evolved under the climatic influence of the Australian monsoon, rather than being either an ancient Gondwanan lineage that pre-dates the monsoon or the result of a more recent dispersal event across Wallace's Line.
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Affiliation(s)
- J Melville
- Department of Sciences, Museum Victoria, Melbourne, VIC 3000, Australia.
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Austin CC, Rittmeyer EN, Richards SJ, Zug GR. Phylogeny, historical biogeography and body size evolution in Pacific Island Crocodile skinks Tribolonotus (Squamata; Scincidae). Mol Phylogenet Evol 2010; 57:227-36. [DOI: 10.1016/j.ympev.2010.06.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2009] [Revised: 05/17/2010] [Accepted: 06/08/2010] [Indexed: 10/19/2022]
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PAYSEUR BRETA. Using differential introgression in hybrid zones to identify genomic regions involved in speciation. Mol Ecol Resour 2010; 10:806-20. [DOI: 10.1111/j.1755-0998.2010.02883.x] [Citation(s) in RCA: 164] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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CAMARGO ARLEY, SINERVO BARRY, SITES JACKW. Lizards as model organisms for linking phylogeographic and speciation studies. Mol Ecol 2010; 19:3250-70. [DOI: 10.1111/j.1365-294x.2010.04722.x] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Inference of population history by coupling exploratory and model-driven phylogeographic analyses. Int J Mol Sci 2010; 11:1190-227. [PMID: 20480016 PMCID: PMC2871112 DOI: 10.3390/ijms11041190] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2010] [Revised: 03/18/2010] [Accepted: 03/19/2010] [Indexed: 11/16/2022] Open
Abstract
Understanding the nature, timing and geographic context of historical events and population processes that shaped the spatial distribution of genetic diversity is critical for addressing questions relating to speciation, selection, and applied conservation management. Cladistic analysis of gene trees has been central to phylogeography, but when coupled with approaches that make use of different components of the information carried by DNA sequences and their frequencies, the strength and resolution of these inferences can be improved. However, assessing concordance of inferences drawn using different analytical methods or genetic datasets, and integrating their outcomes, can be challenging. Here we overview the strengths and limitations of different types of genetic data, analysis methods, and approaches to historical inference. We then turn our attention to the potentially synergistic interactions among widely-used and emerging phylogeographic analyses, and discuss some of the ways that spatial and temporal concordance among inferences can be assessed. We close this review with a brief summary and outlook on future research directions.
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YURI TAMAKI, JERNIGAN ROBERTW, BRUMFIELD ROBBT, BHAGABATI NIRMALK, BRAUN MICHAELJ. The effect of marker choice on estimated levels of introgression across an avian (Pipridae:Manacus) hybrid zone. Mol Ecol 2009; 18:4888-903. [DOI: 10.1111/j.1365-294x.2009.04381.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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50
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GOODMAN BA. Nowhere to run: the role of habitat openness and refuge use in defining patterns of morphological and performance evolution in tropical lizards. J Evol Biol 2009; 22:1535-44. [DOI: 10.1111/j.1420-9101.2009.01766.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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