51
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Shipilina D, Serbyn M, Ivanitskii V, Marova I, Backström N. Patterns of genetic, phenotypic, and acoustic variation across a chiffchaff ( Phylloscopus collybita abietinus/tristis) hybrid zone. Ecol Evol 2017; 7:2169-2180. [PMID: 28405281 PMCID: PMC5383471 DOI: 10.1002/ece3.2782] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Revised: 12/30/2016] [Accepted: 01/05/2017] [Indexed: 12/21/2022] Open
Abstract
Characterizing patterns of evolution of genetic and phenotypic divergence between incipient species is essential to understand how evolution of reproductive isolation proceeds. Hybrid zones are excellent for studying such processes, as they provide opportunities to assess trait variation in individuals with mixed genetic background and to quantify gene flow across different genomic regions. Here, we combine plumage, song, mtDNA and whole‐genome sequence data and analyze variation across a sympatric zone between the European and the Siberian chiffchaff (Phylloscopus collybita abietinus/tristis) to study how gene exchange between the lineages affects trait variation. Our results show that chiffchaff within the sympatric region show more extensive trait variation than allopatric birds, with a large proportion of individuals exhibiting intermediate phenotypic characters. The genomic differentiation between the subspecies is lower in sympatry than in allopatry and sympatric birds have a mix of genetic ancestry indicating extensive ongoing and past gene flow. Patterns of phenotypic and genetic variation also vary between regions within the hybrid zone, potentially reflecting differences in population densities, age of secondary contact, or differences in mate recognition or mate preference. The genomic data support the presence of two distinct genetic clades corresponding to allopatric abietinus and tristis and that genetic admixture is the force underlying trait variation in the sympatric region—the previously described subspecies (“fulvescens”) from the region is therefore not likely a distinct taxon. In addition, we conclude that subspecies identification based on appearance is uncertain as an individual with an apparently distinct phenotype can have a considerable proportion of the genome composed of mixed alleles, or even a major part of the genome introgressed from the other subspecies. Our results provide insights into the dynamics of admixture across subspecies boundaries and have implications for understanding speciation processes and for the identification of specific chiffchaff individuals based on phenotypic characters.
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Affiliation(s)
- Daria Shipilina
- Department of Vertebrate Zoology Lomonosov Moscow State University Moscow Russia
| | - Maksym Serbyn
- Department of Physics University of California Berkeley CA USA
| | - Vladimir Ivanitskii
- Department of Vertebrate Zoology Lomonosov Moscow State University Moscow Russia
| | - Irina Marova
- Department of Vertebrate Zoology Lomonosov Moscow State University Moscow Russia
| | - Niclas Backström
- Department of Evolutionary Biology Evolutionary Biology Centre (EBC) Uppsala University Uppsala Sweden
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52
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Anderson BM, Thiele KR, Krauss SL, Barrett MD. Genotyping-by-Sequencing in a Species Complex of Australian Hummock Grasses (Triodia): Methodological Insights and Phylogenetic Resolution. PLoS One 2017; 12:e0171053. [PMID: 28135342 PMCID: PMC5279811 DOI: 10.1371/journal.pone.0171053] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 01/13/2017] [Indexed: 12/16/2022] Open
Abstract
Next-generation sequencing is becoming increasingly accessible to researchers asking biosystematic questions, but current best practice in both choosing a specific approach and effectively analysing the resulting data set is still being explored. We present a case study for the use of genotyping-by-sequencing (GBS) to resolve relationships in a species complex of Australian arid and semi-arid grasses (Triodia R.Br.), highlighting our solutions to methodological challenges in the use of GBS data. We merged overlapping paired-end reads then optimised locus assembly in the program PyRAD to generate GBS data sets for phylogenetic and distance-based analyses. In addition to traditional concatenation analyses in RAxML, we also demonstrate the novel use of summary species tree analyses (taking gene trees as input) with GBS loci. We found that while species tree analyses were relatively robust to variation in PyRAD assembly parameters, our RAxML analyses resulted in well-supported but conflicting topologies under different assembly settings. Despite this conflict, multiple clades in the complex were consistently supported as distinct across analyses. Our GBS data assembly and analyses improve the resolution of taxa and phylogenetic relationships in the Triodia basedowii complex compared to our previous study based on Sanger sequencing of nuclear (ITS/ETS) and chloroplast (rps16-trnK spacer) markers. The genomic results also partly support previous evidence for hybridization between species in the complex. Our methodological insights for analysing GBS data will assist researchers using similar data to resolve phylogenetic relationships within species complexes.
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Affiliation(s)
- Benjamin M. Anderson
- School of Plant Biology, The University of Western Australia, Crawley, Western Australia, Australia
- Kings Park and Botanic Garden, Botanic Gardens and Parks Authority, Kings Park, Western Australia, Australia
| | - Kevin R. Thiele
- School of Plant Biology, The University of Western Australia, Crawley, Western Australia, Australia
- Western Australian Herbarium, Department of Parks and Wildlife, Kensington, Western Australia, Australia
| | - Siegfried L. Krauss
- School of Plant Biology, The University of Western Australia, Crawley, Western Australia, Australia
- Kings Park and Botanic Garden, Botanic Gardens and Parks Authority, Kings Park, Western Australia, Australia
| | - Matthew D. Barrett
- School of Plant Biology, The University of Western Australia, Crawley, Western Australia, Australia
- Kings Park and Botanic Garden, Botanic Gardens and Parks Authority, Kings Park, Western Australia, Australia
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53
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Vijay N. Digest: Why are there no ring species?*. Evolution 2017; 71:501-502. [DOI: 10.1111/evo.13162] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 12/16/2016] [Indexed: 11/30/2022]
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54
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de Brito Martins A, de Aguiar MAM. Barriers to gene flow and ring species formation. Evolution 2016; 71:442-448. [PMID: 27861800 DOI: 10.1111/evo.13121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 10/20/2016] [Indexed: 11/30/2022]
Abstract
Ring species are groups of organisms that dispersed along a ring-shaped region in such a way that the two ends of the population that meet after many generations are reproductively isolated. They provide a rare opportunity to understand the role of spatial structuring in speciation. Here, we simulate the evolution of ring species assuming that individuals become sexually isolated if the genetic distance between them is above a certain threshold. The model incorporates two forms of dispersal limitation: exogenous geographic barriers that limit the population range and endogenous barriers that result in genetic structuring within the population range. As expected, species' properties that reduce gene flow within the population range facilitate the evolution of reproductive isolation and ring species formation. However, if populations are confined to narrow ranges by geographic barriers, ring species formation increases when local mating is less spatially restricted. Ring species are most likely to form if a population expands while confined to a quasi-unidimensional range but preserving high mobility in the direction of the range expansion. These conditions are unlikely to be met or persist in real populations and may explain why ring species are rare.
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Affiliation(s)
- Ayana de Brito Martins
- Depto. de Física da Matéria Condensada, Inst. de Física "Gleb Wataghin", Universidade Estadual de Campinas, Campinas, SP, Brazil.,Depto. de Ecologia, Inst. de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil.,Department of Fish Ecology and Evolution, Center for Ecology, Evolution and Biogeochemistry, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, ZH, Switzerland
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55
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Calderón L, Campagna L, Wilke T, Lormee H, Eraud C, Dunn JC, Rocha G, Zehtindjiev P, Bakaloudis DE, Metzger B, Cecere JG, Marx M, Quillfeldt P. Genomic evidence of demographic fluctuations and lack of genetic structure across flyways in a long distance migrant, the European turtle dove. BMC Evol Biol 2016; 16:237. [PMID: 27821052 PMCID: PMC5100323 DOI: 10.1186/s12862-016-0817-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 10/28/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Understanding how past climatic oscillations have affected organismic evolution will help predict the impact that current climate change has on living organisms. The European turtle dove, Streptopelia turtur, is a warm-temperature adapted species and a long distance migrant that uses multiple flyways to move between Europe and Africa. Despite being abundant, it is categorized as vulnerable because of a long-term demographic decline. We studied the demographic history and population genetic structure of the European turtle dove using genomic data and mitochondrial DNA sequences from individuals sampled across Europe, and performing paleoclimatic niche modelling simulations. RESULTS Overall our data suggest that this species is panmictic across Europe, and is not genetically structured across flyways. We found the genetic signatures of demographic fluctuations, inferring an effective population size (Ne) expansion that occurred between the late Pleistocene and early Holocene, followed by a decrease in the Ne that started between the mid Holocene and the present. Our niche modelling analyses suggest that the variations in the Ne are coincident with recent changes in the availability of suitable habitat. CONCLUSIONS We argue that the European turtle dove is prone to undergo demographic fluctuations, a trait that makes it sensitive to anthropogenic impacts, especially when its numbers are decreasing. Also, considering the lack of genetic structure, we suggest all populations across Europe are equally relevant for conservation.
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Affiliation(s)
- Luciano Calderón
- Department of Animal Ecology & Systematics, Justus Liebig University Giessen, Heinrich-Buff-Ring 82, Giessen, 35392, Germany.
| | - Leonardo Campagna
- Fuller Evolutionary Biology Program, Cornell Lab of Ornithology, 159 Sapsucker Woods Road, Ithaca, NY, 14850, USA
- Department of Ecology and Evolutionary Biology, Cornell University, 215 Tower Road, Ithaca, NY, 14853, USA
| | - Thomas Wilke
- Department of Animal Ecology & Systematics, Justus Liebig University Giessen, Heinrich-Buff-Ring 82, Giessen, 35392, Germany
| | - Hervé Lormee
- Unité Avifaune Migratrice, Office National de la Chasse et de la Faune Sauvage, Villiers en Bois, Chizé, 79360, France
| | - Cyril Eraud
- Unité Avifaune Migratrice, Office National de la Chasse et de la Faune Sauvage, Villiers en Bois, Chizé, 79360, France
| | - Jenny C Dunn
- School of Life Sciences, University of Lincoln, Joseph Banks Laboratories, Lincoln, LN6 7TS, UK
| | - Gregorio Rocha
- Department of Agro-forestry Engineering, University of Extremadura, Avda. Virgen del Puerto 2, Plasencia, Cáceres, 10600, Spain
| | - Pavel Zehtindjiev
- Bulgarian Academy of Sciences, Institute of Biodiversity and Ecosystem Research, 2 Gagarin Street, Sofia, 1113, Bulgaria
| | - Dimitrios E Bakaloudis
- Aristotle University of Thessaloniki, School of Forestry and Natural Environment, PO Box 241, Thessaloniki, 541 24, Greece
| | | | - Jacopo G Cecere
- Instituto Superiore per la Protezione e la Ricerca Ambientale, Via Ca' Fornacetta 9, Ozzano Dell'Emilia, (BO), 40064, Italy
| | - Melanie Marx
- Department of Animal Ecology & Systematics, Justus Liebig University Giessen, Heinrich-Buff-Ring 82, Giessen, 35392, Germany
| | - Petra Quillfeldt
- Department of Animal Ecology & Systematics, Justus Liebig University Giessen, Heinrich-Buff-Ring 82, Giessen, 35392, Germany
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56
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Kenyon HL, Alcaide M, Toews DPL, Irwin DE. Cultural isolation is greater than genetic isolation across an avian hybrid zone. J Evol Biol 2016; 30:81-95. [DOI: 10.1111/jeb.12989] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Revised: 10/05/2016] [Accepted: 10/06/2016] [Indexed: 11/30/2022]
Affiliation(s)
- H. L. Kenyon
- Department of Zoology and Biodiversity Research Centre; University of British Columbia; Vancouver BC Canada
| | - M. Alcaide
- Department of Zoology and Biodiversity Research Centre; University of British Columbia; Vancouver BC Canada
- Department of Evolutionary Ecology; Estación Biologica de Doñana (CSIC); Sevilla Spain
| | - D. P. L. Toews
- Department of Zoology and Biodiversity Research Centre; University of British Columbia; Vancouver BC Canada
| | - D. E. Irwin
- Department of Zoology and Biodiversity Research Centre; University of British Columbia; Vancouver BC Canada
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57
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Parchman TL, Buerkle CA, Soria‐Carrasco V, Benkman CW. Genome divergence and diversification within a geographic mosaic of coevolution. Mol Ecol 2016; 25:5705-5718. [DOI: 10.1111/mec.13825] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 08/10/2016] [Accepted: 08/18/2016] [Indexed: 12/24/2022]
Affiliation(s)
| | - C. Alex Buerkle
- Department of Botany University of Wyoming Laramie WY 82071 USA
| | - Víctor Soria‐Carrasco
- Department of Animal and Plant Sciences University of Sheffield Sheffield S10 2TN UK
| | - Craig W. Benkman
- Department of Zoology and Physiology University of Wyoming Laramie WY 82071 USA
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58
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Irwin DE, Alcaide M, Delmore KE, Irwin JH, Owens GL. Recurrent selection explains parallel evolution of genomic regions of high relative but low absolute differentiation in a ring species. Mol Ecol 2016; 25:4488-507. [PMID: 27484941 DOI: 10.1111/mec.13792] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Revised: 07/21/2016] [Accepted: 07/25/2016] [Indexed: 12/13/2022]
Abstract
Recent technological developments allow investigation of the repeatability of evolution at the genomic level. Such investigation is particularly powerful when applied to a ring species, in which spatial variation represents changes during the evolution of two species from one. We examined genomic variation among three subspecies of the greenish warbler ring species, using genotypes at 13 013 950 nucleotide sites along a new greenish warbler consensus genome assembly. Genomic regions of low within-group variation are remarkably consistent between the three populations. These regions show high relative differentiation but low absolute differentiation between populations. Comparisons with outgroup species show the locations of these peaks of relative differentiation are not well explained by phylogenetically conserved variation in recombination rates or selection. These patterns are consistent with a model in which selection in an ancestral form has reduced variation at some parts of the genome, and those same regions experience recurrent selection that subsequently reduces variation within each subspecies. The degree of heterogeneity in nucleotide diversity is greater than explained by models of background selection, but is consistent with selective sweeps. Given the evidence that greenish warblers have had both population differentiation for a long period of time and periods of gene flow between those populations, we propose that some genomic regions underwent selective sweeps over a broad geographic area followed by within-population selection-induced reductions in variation. An important implication of this 'sweep-before-differentiation' model is that genomic regions of high relative differentiation may have moved among populations more recently than other genomic regions.
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Affiliation(s)
- Darren E Irwin
- Department of Zoology and Biodiversity Research Center, University of British Columbia, 6270 University Blvd., Vancouver, BC, V6T 1Z4, Canada.
| | - Miguel Alcaide
- Department of Zoology and Biodiversity Research Center, University of British Columbia, 6270 University Blvd., Vancouver, BC, V6T 1Z4, Canada
| | - Kira E Delmore
- Department of Zoology and Biodiversity Research Center, University of British Columbia, 6270 University Blvd., Vancouver, BC, V6T 1Z4, Canada
| | - Jessica H Irwin
- Department of Zoology and Biodiversity Research Center, University of British Columbia, 6270 University Blvd., Vancouver, BC, V6T 1Z4, Canada
| | - Gregory L Owens
- Department of Zoology and Biodiversity Research Center, University of British Columbia, 6270 University Blvd., Vancouver, BC, V6T 1Z4, Canada
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59
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Grossen C, Seneviratne SS, Croll D, Irwin DE. Strong reproductive isolation and narrow genomic tracts of differentiation among three woodpecker species in secondary contact. Mol Ecol 2016; 25:4247-66. [DOI: 10.1111/mec.13751] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2015] [Revised: 06/25/2016] [Accepted: 06/27/2016] [Indexed: 12/29/2022]
Affiliation(s)
- Christine Grossen
- Department of Zoology and Biodiversity Research Centre; University of British Columbia; 6270 University Blvd. Vancouver BC V6T 1Z4 Canada
- Institute of Evolutionary Biology and Environmental Studies; University of Zürich; Winterthurerstrasse 190 CH-8057 Zürich Switzerland
| | - Sampath S. Seneviratne
- Department of Zoology and Biodiversity Research Centre; University of British Columbia; 6270 University Blvd. Vancouver BC V6T 1Z4 Canada
- Avian Evolution Node; Department of Zoology; University of Colombo; PO Box 1490 Colombo 03 Sri Lanka
| | - Daniel Croll
- Integrative Biology; ETH Zürich; Universitätstrasse 2 CH-8092 Zürich Switzerland
| | - Darren E. Irwin
- Department of Zoology and Biodiversity Research Centre; University of British Columbia; 6270 University Blvd. Vancouver BC V6T 1Z4 Canada
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60
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Dufresnes C, Litvinchuk SN, Leuenberger J, Ghali K, Zinenko O, Stöck M, Perrin N. Evolutionary melting pots: a biodiversity hotspot shaped by ring diversifications around the Black Sea in the Eastern tree frog (Hyla orientalis). Mol Ecol 2016; 25:4285-300. [PMID: 27220555 DOI: 10.1111/mec.13706] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Revised: 04/26/2016] [Accepted: 05/11/2016] [Indexed: 11/30/2022]
Abstract
Hotspots of intraspecific genetic diversity, which are of primary importance for the conservation of species, have been associated with glacial refugia, that is areas where species survived the Quaternary climatic oscillations. However, the proximate mechanisms generating these hotspots remain an open issue. Hotspots may reflect the long-term persistence of large refugial populations; alternatively, they may result from allopatric differentiation between small and isolated populations, that later admixed. Here, we test these two scenarios in a widely distributed species of tree frog, Hyla orientalis, which inhabits Asia Minor and southeastern Europe. We apply a fine-scale phylogeographic survey, combining fast-evolving mitochondrial and nuclear markers, with a dense sampling throughout the range, as well as ecological niche modelling, to understand what shaped the genetic variation of this species. We documented an important diversity centre around the Black Sea, composed of multiple allopatric and/or parapatric diversifications, likely driven by a combination of Pleistocene climatic fluctuations and complex regional topography. Remarkably, this diversification forms a ring around the Black Sea, from the Caucasus through Anatolia and eastern Europe, with terminal forms coming into contact and partially admixing in Crimea. Our results support the view that glacial refugia generate rather than host genetic diversity and can also function as evolutionary melting pots of biodiversity. Moreover, we report a new case of ring diversification, triggered by a large, yet cohesive dispersal barrier, a very rare situation in nature. Finally, we emphasize the Black Sea region as an important centre of intraspecific diversity in the Palearctic with implications for conservation.
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Affiliation(s)
- Christophe Dufresnes
- Department of Ecology & Evolution, University of Lausanne, Biophore Building, Lausanne, 1015, Switzerland
| | - Spartak N Litvinchuk
- Institute of Cytology, Russian Academy of Sciences, Tikhoretsky pr. 4, St. Petersburg, 194064, Russia
| | - Julien Leuenberger
- Department of Ecology & Evolution, University of Lausanne, Biophore Building, Lausanne, 1015, Switzerland
| | - Karim Ghali
- Department of Ecology & Evolution, University of Lausanne, Biophore Building, Lausanne, 1015, Switzerland
| | - Oleksandr Zinenko
- The Museum of Nature, V. N. Karazin Kharkiv National University, Trinkler st. 8, Kharkiv, 61058, Ukraine
| | - Matthias Stöck
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301, Berlin, D-12587, Germany
| | - Nicolas Perrin
- Department of Ecology & Evolution, University of Lausanne, Biophore Building, Lausanne, 1015, Switzerland
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61
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Kautt AF, Machado-Schiaffino G, Meyer A. Multispecies Outcomes of Sympatric Speciation after Admixture with the Source Population in Two Radiations of Nicaraguan Crater Lake Cichlids. PLoS Genet 2016; 12:e1006157. [PMID: 27362536 PMCID: PMC4928843 DOI: 10.1371/journal.pgen.1006157] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 06/09/2016] [Indexed: 12/19/2022] Open
Abstract
The formation of species in the absence of geographic barriers (i.e. sympatric speciation) remains one of the most controversial topics in evolutionary biology. While theoretical models have shown that this most extreme case of primary divergence-with-gene-flow is possible, only a handful of accepted empirical examples exist. And even for the most convincing examples uncertainties remain; complex histories of isolation and secondary contact can make species falsely appear to have originated by sympatric speciation. This alternative scenario is notoriously difficult to rule out. Midas cichlids inhabiting small and remote crater lakes in Nicaragua are traditionally considered to be one of the best examples of sympatric speciation and lend themselves to test the different evolutionary scenarios that could lead to apparent sympatric speciation since the system is relatively small and the source populations known. Here we reconstruct the evolutionary history of two small-scale radiations of Midas cichlids inhabiting crater lakes Apoyo and Xiloá through a comprehensive genomic data set. We find no signs of differential admixture of any of the sympatric species in the respective radiations. Together with coalescent simulations of different demographic models our results support a scenario of speciation that was initiated in sympatry and does not result from secondary contact of already partly diverged populations. Furthermore, several species seem to have diverged simultaneously, making Midas cichlids an empirical example of multispecies outcomes of sympatric speciation. Importantly, however, the demographic models strongly support an admixture event from the source population into both crater lakes shortly before the onset of the radiations within the lakes. This opens the possibility that the formation of reproductive barriers involved in sympatric speciation was facilitated by genetic variants that evolved in a period of isolation between the initial founding population and the secondary migrants that came from the same source population. Thus, the exact mechanisms by which these species arose might be different from what had been thought before.
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Affiliation(s)
- Andreas F. Kautt
- Department of Biology, University of Konstanz, Konstanz, Baden-Württemberg, Germany
| | | | - Axel Meyer
- Department of Biology, University of Konstanz, Konstanz, Baden-Württemberg, Germany
- * E-mail:
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62
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Payseur BA, Rieseberg LH. A genomic perspective on hybridization and speciation. Mol Ecol 2016; 25:2337-60. [PMID: 26836441 PMCID: PMC4915564 DOI: 10.1111/mec.13557] [Citation(s) in RCA: 292] [Impact Index Per Article: 36.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Revised: 01/18/2016] [Accepted: 01/25/2016] [Indexed: 12/13/2022]
Abstract
Hybridization among diverging lineages is common in nature. Genomic data provide a special opportunity to characterize the history of hybridization and the genetic basis of speciation. We review existing methods and empirical studies to identify recent advances in the genomics of hybridization, as well as issues that need to be addressed. Notable progress has been made in the development of methods for detecting hybridization and inferring individual ancestries. However, few approaches reconstruct the magnitude and timing of gene flow, estimate the fitness of hybrids or incorporate knowledge of recombination rate. Empirical studies indicate that the genomic consequences of hybridization are complex, including a highly heterogeneous landscape of differentiation. Inferred characteristics of hybridization differ substantially among species groups. Loci showing unusual patterns - which may contribute to reproductive barriers - are usually scattered throughout the genome, with potential enrichment in sex chromosomes and regions of reduced recombination. We caution against the growing trend of interpreting genomic variation in summary statistics across genomes as evidence of differential gene flow. We argue that converting genomic patterns into useful inferences about hybridization will ultimately require models and methods that directly incorporate key ingredients of speciation, including the dynamic nature of gene flow, selection acting in hybrid populations and recombination rate variation.
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Affiliation(s)
- Bret A. Payseur
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Loren H. Rieseberg
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
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63
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Olsson U, Rguibi-Idrissi H, Copete JL, Arroyo Matos JL, Provost P, Amezian M, Alström P, Jiguet F. Mitochondrial phylogeny of the Eurasian/African reed warbler complex (Acrocephalus, Aves). Disagreement between morphological and molecular evidence and cryptic divergence: A case for resurrecting Calamoherpe ambigua Brehm 1857. Mol Phylogenet Evol 2016; 102:30-44. [PMID: 27233439 DOI: 10.1016/j.ympev.2016.05.026] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Revised: 04/06/2016] [Accepted: 05/20/2016] [Indexed: 10/21/2022]
Abstract
A tree based on the mitochondrial cyt b gene for 278 samples from throughout the range of the Eurasian Reed Warbler Acrocephalus scirpaceus - African Reed Warbler A. baeticatus complex shows well-supported geographically structured divergence for eight distinct lineages. The phylogenetic structuring together with the clarification of priority, provided by sequence data from seven type specimens, suggests that both taxonomy and distribution boundaries are in need of revision. The Iberian and Moroccan populations form a well-supported clade, and we propose that these are treated as taxonomically distinct, under the name ambiguus (Brehm, 1857). We propose that the names scirpaceus, fuscus, avicenniae, ambiguus, minor, cinnamomeus, hallae and baeticatus are used for the well supported clades in the complex, which we recommend to treat as one polytypic species, A. scirpaceus, pending studies of gene flow and assortative mating in the contact zones.
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Affiliation(s)
- Urban Olsson
- University of Gothenburg, Department of Biology and Environmental Sciences, Systematics and Biodiversity, Box 463, SE-405 30 Göteborg, Sweden
| | - Hamid Rguibi-Idrissi
- Equipe de Recherche «Valorisation des Ressources Naturelles et Biodiversité», Faculty of Sciences, University Chouaib Doukkali, El Jadida, Morocco
| | | | - José Luis Arroyo Matos
- Natural Processes Monitoring Team, Doñana Biological Station - CSIC, C/Americo Vespucio s/n, E-41092 Seville, Spain
| | | | - Mohamed Amezian
- Abdelmalek Essaadi University, Faculty of Sciences, Department of Biology, M'Hannech II, 93030 Tétouan, Morocco
| | - Per Alström
- Department of Animal Ecology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18 D, SE-752 36 Uppsala, Sweden; Swedish Species Information Centre, Swedish University of Agricultural Sciences, Box 7007, SE-750 07 Uppsala, Sweden
| | - Frédéric Jiguet
- CESCO, UMR7204 Sorbonne Universités-MNHN-CNRS-UPMC, Centre de Recherches sur la Biologie des Populations d'Oiseaux, CP 135, 43 Rue Buffon, 75005 Paris, France.
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64
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Pereira RJ, Wake DB. Ring species as demonstrations of the continuum of species formation. Mol Ecol 2016; 24:5312-4. [PMID: 26509692 DOI: 10.1111/mec.13412] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 10/02/2015] [Indexed: 11/28/2022]
Abstract
In the mid-20th century, Ernst Mayr (1942) and Theodosius Dobzhansky (1958) championed the significance of 'circular overlaps' or 'ring species' as the perfect demonstration of the gradual nature of species formation. As an ancestral species expands its range, wrapping around a geographic barrier, derived taxa within the ring display interactions typical of populations, such as genetic and morphological intergradation, while overlapping taxa at the terminus of the ring behave largely as sympatric, reproductively isolated species. Are ring species extremely rare or are they just difficult to detect? What conditions favour their formation? Modelling studies have attempted to address these knowledge gaps by estimating the biological parameters that result in stable ring species (Martins et al. 2013), and determining the necessary topographic parameters of the barriers encircled (Monahan et al. 2012). However, any generalization is undermined by a major limitation: only a handful of ring species are known to exist in nature. In addition, many of them have been broken into multiple species presumed to be evolving independently, usually obscuring the evolutionary dynamics that generate diversity. A paper in this issue of Molecular Ecology by Fuchs et al. (2015), focused on the entire genealogy of a bulbul (Alophoixus) species complex, offers key insights into the evolutionary processes underlying diversification of this Indo-Malayan bird. Their findings fulfil most of the criteria that can be expected for ring species (Fig. ): an ancestor has colonized the mainland from Sundaland, expanded along the forested habitat wrapping around Thailand's lowlands, adjacent taxa intergrade around the ring distribution, and terminal taxa overlap at the ring closure. Although it remains unclear whether ring divergence has resulted in restrictive gene flow relative to that observed around the ring, their results suggest that circular overlaps might be more common in nature than currently recognized in the literature. Most importantly, this work shows that the continuum of species formation that Mayr and Dobzhansky praised in circular overlaps is found in biological systems currently described as 'rings of species', in addition to the idealized 'ring species'.
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Affiliation(s)
- Ricardo J Pereira
- Faculty of Science, Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen, Denmark
| | - David B Wake
- Museum of Vertebrate Zoology, University of California, 3101 Valley Life Sciences Building, Berkeley, CA, 94720, USA
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Bradburd GS, Ralph PL, Coop GM. A Spatial Framework for Understanding Population Structure and Admixture. PLoS Genet 2016; 12:e1005703. [PMID: 26771578 PMCID: PMC4714911 DOI: 10.1371/journal.pgen.1005703] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Accepted: 11/05/2015] [Indexed: 01/26/2023] Open
Abstract
Geographic patterns of genetic variation within modern populations, produced by complex histories of migration, can be difficult to infer and visually summarize. A general consequence of geographically limited dispersal is that samples from nearby locations tend to be more closely related than samples from distant locations, and so genetic covariance often recapitulates geographic proximity. We use genome-wide polymorphism data to build "geogenetic maps," which, when applied to stationary populations, produces a map of the geographic positions of the populations, but with distances distorted to reflect historical rates of gene flow. In the underlying model, allele frequency covariance is a decreasing function of geogenetic distance, and nonlocal gene flow such as admixture can be identified as anomalously strong covariance over long distances. This admixture is explicitly co-estimated and depicted as arrows, from the source of admixture to the recipient, on the geogenetic map. We demonstrate the utility of this method on a circum-Tibetan sampling of the greenish warbler (Phylloscopus trochiloides), in which we find evidence for gene flow between the adjacent, terminal populations of the ring species. We also analyze a global sampling of human populations, for which we largely recover the geography of the sampling, with support for significant histories of admixture in many samples. This new tool for understanding and visualizing patterns of population structure is implemented in a Bayesian framework in the program SpaceMix.
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Affiliation(s)
- Gideon S. Bradburd
- Center for Population Biology, Department of Evolution and Ecology, University of California, Davis, California, United States of America
| | - Peter L. Ralph
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, California, United States of America
| | - Graham M. Coop
- Center for Population Biology, Department of Evolution and Ecology, University of California, Davis, California, United States of America
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Burri R, Antoniazza S, Gaigher A, Ducrest AL, Simon C, Fumagalli L, Goudet J, Roulin A. The genetic basis of color-related local adaptation in a ring-like colonization around the Mediterranean. Evolution 2015; 70:140-53. [DOI: 10.1111/evo.12824] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Revised: 10/08/2015] [Accepted: 11/09/2015] [Indexed: 01/18/2023]
Affiliation(s)
- Reto Burri
- Department of Evolutionary Biology, Evolutionary Biology Centre; Uppsala University; Norbyvägen 18D SE-75236 Uppsala Sweden
| | - Sylvain Antoniazza
- Department of Ecology and Evolution; University of Lausanne; Biophore CH-1015 Lausanne Switzerland
- Swiss Ornithological Institute; Seerose 1 CH-6204 Sempach Switzerland
| | - Arnaud Gaigher
- Laboratory for Conservation Biology, Department of Ecology and Evolution; University of Lausanne; Biophore CH-1015 Lausanne Switzerland
| | - Anne-Lyse Ducrest
- Department of Ecology and Evolution; University of Lausanne; Biophore CH-1015 Lausanne Switzerland
| | - Céline Simon
- Department of Ecology and Evolution; University of Lausanne; Biophore CH-1015 Lausanne Switzerland
| | - Luca Fumagalli
- Laboratory for Conservation Biology, Department of Ecology and Evolution; University of Lausanne; Biophore CH-1015 Lausanne Switzerland
| | - Jérôme Goudet
- Department of Ecology and Evolution; University of Lausanne; Biophore CH-1015 Lausanne Switzerland
| | - Alexandre Roulin
- Department of Ecology and Evolution; University of Lausanne; Biophore CH-1015 Lausanne Switzerland
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Edwards SV, Shultz AJ, Campbell-Staton SC. Next-generation sequencing and the expanding domain of phylogeography. FOLIA ZOOLOGICA 2015. [DOI: 10.25225/fozo.v64.i3.a2.2015] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Scott V. Edwards
- Department of Organismic and Evolutionary Biology, and Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, U.S.A.
| | - Allison J. Shultz
- Department of Organismic and Evolutionary Biology, and Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, U.S.A.
| | - Shane C. Campbell-Staton
- Department of Organismic and Evolutionary Biology, and Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, U.S.A.
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Smyth JF, Patten MA, Pruett CL. The evolutionary ecology of a species ring: a test of alternative models. FOLIA ZOOLOGICA 2015. [DOI: 10.25225/fozo.v64.i3.a5.2015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Jason F. Smyth
- Florida Institute of Technology, Department of Biological Sciences, Melbourne, FL 32901, U.S.A.
| | - Michael A. Patten
- University of Oklahoma, Oklahoma Biological Survey and Department of Biology, Norman, OK 73019, U.S.A.
| | - Christin L. Pruett
- Florida Institute of Technology, Department of Biological Sciences, Melbourne, FL 32901, U.S.A.
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Eweleit L, Reinhold K, Sauer J. Speciation Progress: A Case Study on the Bushcricket Poecilimon veluchianus. PLoS One 2015; 10:e0139494. [PMID: 26436732 PMCID: PMC4593647 DOI: 10.1371/journal.pone.0139494] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Accepted: 09/13/2015] [Indexed: 12/26/2022] Open
Abstract
Different mechanisms such as selection or genetic drift permitted e.g. by geographical isolation can lead to differentiation of populations and could cause subsequent speciation. The two subspecies of Poecilimon veluchianus, a bushcricket endemic to central Greece, show a parapatric distribution and are partially reproductively isolated. Therefore, P. veluchianus is suitable to investigate an ongoing speciation process. We based our analysis on sequences of the internal transcribed spacer (ITS) and the mitochondrial control region (CR). The population genetic analysis based on the nuclear marker ITS revealed a barrier to gene flow within the range of Poecilimon veluchianus, which corresponds well to the described subspecies. In contrast to the results based on the nuclear ITS marker, the mitochondrial CR marker does not clearly support the separation into two subspecies with restricted gene flow and a clear contact zone. Furthermore, we could identify isolation by distance (IBD) as one important mechanism responsible for the observed genetic structure (based on the ITS marker). The population genetic analysis based on the nuclear marker ITS also suggests the existence of hybrids in the wild. Furthermore, the simultaneous lack of strong prezygotic barriers and the presence of postzygotic mating barriers, observed in previous laboratory experiments, suggest that a secondary contact after an allopatric phase is more likely than parapatric speciation.
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Affiliation(s)
- Lucienne Eweleit
- Department of Evolutionary Biology, Bielefeld University, Bielefeld, Germany
| | - Klaus Reinhold
- Department of Evolutionary Biology, Bielefeld University, Bielefeld, Germany
| | - Jan Sauer
- Department of Chemical Ecology, Bielefeld University, Bielefeld, Germany
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Genetic responses to seasonal variation in altitudinal stress: whole-genome resequencing of great tit in eastern Himalayas. Sci Rep 2015; 5:14256. [PMID: 26404527 PMCID: PMC4585896 DOI: 10.1038/srep14256] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 08/21/2015] [Indexed: 01/29/2023] Open
Abstract
Species that undertake altitudinal migrations are exposed to a considerable seasonal variation in oxygen levels and temperature. How they cope with this was studied in a population of great tit (Parus major) that breeds at high elevations and winters at lower elevations in the eastern Himalayas. Comparison of population genomics of high altitudinal great tits and those living in lowlands revealed an accelerated genetic selection for carbohydrate energy metabolism (amino sugar, nucleotide sugar metabolism and insulin signaling pathways) and hypoxia response (PI3K-akt, mTOR and MAPK signaling pathways) in the high altitudinal population. The PI3K-akt, mTOR and MAPK pathways modulate the hypoxia-inducible factors, HIF-1α and VEGF protein expression thus indirectly regulate hypoxia induced angiogenesis, erythropoiesis and vasodilatation. The strategies observed in high altitudinal great tits differ from those described in a closely related species on the Tibetan Plateau, the sedentary ground tit (Parus humilis). This species has enhanced selection in lipid-specific metabolic pathways and hypoxia-inducible factor pathway (HIF-1). Comparative population genomics also revealed selection for larger body size in high altitudinal great tits.
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Hidalgo-Galiana A, Monge M, Biron DG, Canals F, Ribera I, Cieslak A. Protein expression parallels thermal tolerance and ecologic changes in the diversification of a diving beetle species complex. Heredity (Edinb) 2015; 116:114-23. [PMID: 26328758 DOI: 10.1038/hdy.2015.80] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Revised: 07/26/2015] [Accepted: 07/29/2015] [Indexed: 11/09/2022] Open
Abstract
Physiological changes associated with evolutionary and ecological processes such as diversification, range expansion or speciation are still incompletely understood, especially for non-model species. Here we study differences in protein expression in response to temperature in a western Mediterranean diving beetle species complex, using two-dimensional differential gel electrophoresis with one Moroccan and one Iberian population each of Agabus ramblae and Agabus brunneus. We identified proteins with significant expression differences after thermal treatments comparing them with a reference EST library generated from one of the species of the complex (A. ramblae). The colonisation during the Middle Pleistocene of the Iberian peninsula by A. ramblae, where maximum temperatures and seasonality are lower than in the ancestral north African range, was associated with changes in the response to 27 °C in proteins related to energy metabolism. The subsequent speciation of A. brunneus from within populations of Iberian A. ramblae was associated with changes in the expression of several stress-related proteins (mostly chaperons) when exposed to 4 °C. These changes are in agreement with the known tolerance to lower temperatures of A. brunneus, which occupies a larger geographical area with a wider range of climatic conditions. In both cases, protein expression changes paralleled the evolution of thermal tolerance and the climatic conditions experienced by the species. However, although the colonisation of the Iberian peninsula did not result in morphological change, the speciation process of A. brunneus within Iberia involved genetic isolation and substantial differences in male genitalia and body size and shape.
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Affiliation(s)
- A Hidalgo-Galiana
- Animal Biodiversity and Evolution, Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - M Monge
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - D G Biron
- Laboratoire 'Microorganismes: Génome et Environnement', UMR CNRS 6023, Equipe Interactions hôtes-parasites, Université Blaise Pascal, Aubière Cedex, France
| | - F Canals
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - I Ribera
- Animal Biodiversity and Evolution, Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - A Cieslak
- Animal Biodiversity and Evolution, Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
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Fuchs J, Ericson PG, Bonillo C, Couloux A, Pasquet E. The complex phylogeography of the Indo-MalayanAlophoixusbulbuls with the description of a putative new ring species complex. Mol Ecol 2015. [DOI: 10.1111/mec.13337] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jérôme Fuchs
- Département Systématique et Evolution; UMR7205 Institut de Systématique, Evolution, Biodiversité CNRS MNHN UPMC EPHE, Sorbonne Universités, Muséum National d'Histoire Naturelle; CP 51, 57 rue Cuvier F-75231 Paris Cedex 05 France
- UMS MNHN/CNRS 2700 Outils et Méthodes de la Systématique Intégrative (OMSI), Muséum National d'Histoire Naturelle; 57 rue Cuvier F-75231 Paris Cedex 05 France
| | - Per G.P. Ericson
- Department of Zoology; Swedish Museum of Natural History; P.O. Box 50007 SE-10405 Stockholm Sweden
| | - Céline Bonillo
- UMS MNHN/CNRS 2700 Outils et Méthodes de la Systématique Intégrative (OMSI), Muséum National d'Histoire Naturelle; 57 rue Cuvier F-75231 Paris Cedex 05 France
| | - Arnaud Couloux
- Genoscope; Centre National de Séquençage; 2, rue Gaston Crémieux, CP5706 91057 Evry Cedex France
| | - Eric Pasquet
- Département Systématique et Evolution; UMR7205 Institut de Systématique, Evolution, Biodiversité CNRS MNHN UPMC EPHE, Sorbonne Universités, Muséum National d'Histoire Naturelle; CP 51, 57 rue Cuvier F-75231 Paris Cedex 05 France
- UMS MNHN/CNRS 2700 Outils et Méthodes de la Systématique Intégrative (OMSI), Muséum National d'Histoire Naturelle; 57 rue Cuvier F-75231 Paris Cedex 05 France
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Beck EA, Thompson AC, Sharbrough J, Brud E, Llopart A. Gene flow between Drosophila yakuba and Drosophila santomea in subunit V of cytochrome c oxidase: A potential case of cytonuclear cointrogression. Evolution 2015; 69:1973-86. [PMID: 26155926 PMCID: PMC5042076 DOI: 10.1111/evo.12718] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2014] [Revised: 06/13/2015] [Accepted: 06/16/2015] [Indexed: 12/11/2022]
Abstract
Introgression is the effective exchange of genetic information between species through natural hybridization. Previous genetic analyses of the Drosophila yakuba—D. santomea hybrid zone showed that the mitochondrial genome of D. yakuba had introgressed into D. santomea and completely replaced its native form. Since mitochondrial proteins work intimately with nuclear‐encoded proteins in the oxidative phosphorylation (OXPHOS) pathway, we hypothesized that some nuclear genes in OXPHOS cointrogressed along with the mitochondrial genome. We analyzed nucleotide variation in the 12 nuclear genes that form cytochrome c oxidase (COX) in 33 Drosophila lines. COX is an OXPHOS enzyme composed of both nuclear‐ and mitochondrial‐encoded proteins and shows evidence of cytonuclear coadaptation in some species. Using maximum‐likelihood methods, we detected significant gene flow from D. yakuba to D. santomea for the entire COX complex. Interestingly, the signal of introgression is concentrated in the three nuclear genes composing subunit V, which shows population migration rates significantly greater than the background level of introgression in these species. The detection of introgression in three proteins that work together, interact directly with the mitochondrial‐encoded core, and are critical for early COX assembly suggests this could be a case of cytonuclear cointrogression.
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Affiliation(s)
- Emily A Beck
- Interdisciplinary Graduate Program in Genetics, The University of Iowa, Iowa City, Iowa, 52242
| | - Aaron C Thompson
- The Department of Biology, The University of Iowa, Iowa City, IA, 52242
| | - Joel Sharbrough
- The Department of Biology, The University of Iowa, Iowa City, IA, 52242
| | - Evgeny Brud
- The Department of Biology, The University of Iowa, Iowa City, IA, 52242
| | - Ana Llopart
- Interdisciplinary Graduate Program in Genetics, The University of Iowa, Iowa City, Iowa, 52242. .,The Department of Biology, The University of Iowa, Iowa City, IA, 52242.
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Martin CH, Cutler JS, Friel JP, Dening Touokong C, Coop G, Wainwright PC. Complex histories of repeated gene flow in Cameroon crater lake cichlids cast doubt on one of the clearest examples of sympatric speciation. Evolution 2015; 69:1406-1422. [PMID: 25929355 DOI: 10.1111/evo.12674] [Citation(s) in RCA: 106] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 04/20/2015] [Indexed: 12/19/2022]
Abstract
One of the most celebrated examples of sympatric speciation in nature are monophyletic radiations of cichlid fishes endemic to Cameroon crater lakes. However, phylogenetic inference of monophyly may not detect complex colonization histories involving some allopatric isolation, such as double invasions obscured by genome-wide gene flow. Population genomic approaches are better suited to test hypotheses of sympatric speciation in these cases. Here, we use comprehensive sampling from all four sympatric crater lake cichlid radiations in Cameroon and outgroups across Africa combined with next-generation sequencing to genotype tens of thousands of SNPs. We find considerable evidence of gene flow between all four radiations and neighboring riverine populations after initial colonization. In a few cases, some sympatric species are more closely related to outgroups than others, consistent with secondary gene flow facilitating their speciation. Our results do not rule out sympatric speciation in Cameroon cichlids, but rather reveal a complex history of speciation with gene flow, including allopatric and sympatric phases, resulting in both reproductively isolated species and incipient species complexes. The best remaining non-cichlid examples of sympatric speciation all involve assortative mating within microhabitats. We speculate that this feature may be necessary to complete the process of sympatric speciation in nature.
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Affiliation(s)
- Christopher H Martin
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina
| | - Joseph S Cutler
- Department of Conservation Biology, University of California, Santa Cruz, California
| | - John P Friel
- Alabama Museum of Natural History, University of Alabama, Tuscaloosa, Alabama
| | | | - Graham Coop
- Center for Population Biology and Department of Evolution & Ecology, University of California, Davis, California
| | - Peter C Wainwright
- Center for Population Biology and Department of Evolution & Ecology, University of California, Davis, California
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76
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Genotyping-By-Sequencing for Plant Genetic Diversity Analysis: A Lab Guide for SNP Genotyping. DIVERSITY-BASEL 2014. [DOI: 10.3390/d6040665] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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77
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Phylogenetic analysis of beak and feather disease virus across a host ring-species complex. Proc Natl Acad Sci U S A 2014; 111:14153-8. [PMID: 25225394 DOI: 10.1073/pnas.1403255111] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Pathogens have been hypothesized to play a major role in host diversity and speciation. Susceptibility of hybrid hosts to pathogens is thought to be a common phenomenon that could promote host population divergence and subsequently speciation. However, few studies have tested for pathogen infection across animal hybrid zones while testing for codivergence of the pathogens in the hybridizing host complex. Over 8 y, we studied natural infection by a rapidly evolving single-strand DNA virus, beak and feather diseases virus (BFDV), which infects parrots, exploiting a host-ring species complex (Platycercus elegans) in Australia. We found that host subspecies and their hybrids varied strikingly in both BFDV prevalence and load: both hybrid and phenotypically intermediate subspecies had lower prevalence and load compared with parental subspecies, while controlling for host age, sex, longitude and latitude, as well as temporal effects. We sequenced viral isolates throughout the range, which revealed patterns of genomic variation analogous to Mayr's ring-species hypothesis, to our knowledge for the first time in any host-pathogen system. Viral phylogeny, geographic location, intraspecific host density, and parrot community diversity and composition did not explain the differences in BFDV prevalence or load between subpopulations. Overall, our analyses suggest that functional host responses to infection, or force of infection, differ between subspecies and hybrids. Our findings highlight the role of host hybridization and clines in altering host-pathogen interactions, dynamics that can have important implications for models of speciation with gene flow, and offer insights into how pathogens may adapt to diverging host populations.
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