publication . Article . 2017

Insight into the roles of selection in speciation from genomic patterns of divergence and introgression in secondary contact in venomous rattlesnakes

Schield, Drew R.; Adams, Richard H.; Card, Daren C.; Perry, Blair W.; Pasquesi, Giulia M.; Jezkova, Tereza; Portik, Daniel M.; Andrew, Audra L.; Spencer, Carol L.; Sanchez, Elda E.; ...
Open Access
  • Published: 01 Apr 2017 Journal: Ecology and Evolution, volume 7, pages 3,951-3,966 (issn: 2045-7758, Copyright policy)
  • Publisher: Wiley
Abstract
Abstract Investigating secondary contact of historically isolated lineages can provide insight into how selection and drift influence genomic divergence and admixture. Here, we studied the genomic landscape of divergence and introgression following secondary contact between lineages of the Western Diamondback Rattlesnake (Crotalus atrox) to determine whether genomic regions under selection in allopatry also contribute to reproductive isolation during introgression. We used thousands of nuclear loci to study genomic differentiation between two lineages that have experienced recent secondary contact following isolation, and incorporated sampling from a zone of sec...
Subjects
free text keywords: Speciation, media_common.quotation_subject, media_common, Introgression, VIPeR, Evolutionary biology, Gene flow, Biology, Divergence, Original Research, adaptation, genomic clines, hybridization, RADseq
90 references, page 1 of 6

Adams, R. H., Schield, D. R., Card, D. C., Blackmon, H., & Castoe, T. A. (2016). GppFst: Genomic posterior predictive simulations of FST and dXY for identifying outlier loci from population genomic data. Bioinformatics, btw795.28011784 [PubMed]

Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990). Basic local alignment search tool. Journal of Molecular Biology, 215, 403–410.2231712 [OpenAIRE] [PubMed]

Boughman, J. W. (2001). Divergent sexual selection enhances reproductive isolation in sticklebacks. Nature, 411, 944–948.11418857 [PubMed]

Bryant, D., Bouckaert, R., Felsenstein, J., Rosenberg, N. A., & RoyChoudhury, A. (2012). Inferring species trees directly from biallelic genetic markers: Bypassing gene trees in a full coalescent analysis. Molecular Biology and Evolution, 29, 1917–1932.22422763 [OpenAIRE] [PubMed]

Burnham, K. P., & Anderson, D. R. (2003). Model selection and multimodel inference: A practical informat ion‐theoretic approach. New York, NY: Springer Science & Business Media.

Burton, R. S., Ellison, C. K., & Harrison, J. S. (2006). The sorry state of F2 hybrids: Consequences of rapid mitochondrial DNA evolution in allopatric populations. The American Naturalist, 168, S14–S24.

Campbell, J. A., & Lamar, W. W. (2004). The venomous reptiles of the western hemisphere. Ithaca, NY, USA: Cornell University Press.

Caro, S. P., Charmantier, A., Lambrechts, M. M., Blondel, J., Balthazart, J., & Williams, T. D. (2009). Local adaptation of timing of reproduction: Females are in the driver's seat. Functional Ecology, 23, 172–179.

Caseys, C., Stölting, K. N., Barbará, T., González‐Martínez, S. C., & Lexer, C. (2015). Patterns of genetic diversity and differentiation in resistance gene clusters of two hybridizing European Populus species. Tree Genetics & Genomes, 11, 81.

Castoe, T. A., Spencer, C. L., & Parkinson, C. L. (2007). Phylogeographic structure and historical demography of the western diamondback rattlesnake (Crotalus atrox): A perspective on North American desert biogeography. Molecular Phylogenetics and Evolution, 42, 193–212.16934495 [PubMed]

Catchen, J., Hohenlohe, P. A., Bassham, S., Amores, A., & Cresko, W. A. (2013). Stacks: An analysis tool set for population genomics. Molecular Ecology, 22, 3124–3140.23701397 [OpenAIRE] [PubMed]

Coyne, J. A., & Orr, H. A. (2004). Speciation. Sunderland, MA: Sinauer Associates.

Cruickshank, T. E., & Hahn, M. W. (2014). Reanalysis suggests that genomic islands of speciation are due to reduced diversity, not reduced gene flow. Molecular Ecology, 23, 3133–3157.24845075 [OpenAIRE] [PubMed]

Danecek, P., Aut on, A., Abecasis, G., Albers, C. A., Banks, E., De Pristo, M. A., … Sherry, S. T. (2011). The variant call format and VCFtools. Bioinformatics, 27, 2156–2158.21653522 [OpenAIRE] [PubMed]

Dobzhansky, T. H. (1936). Studies on hybrid sterility. II. Localization of sterility factors in Drosophila pseudoobscura hybrids. Genetics, 21, 113.17246786 [OpenAIRE] [PubMed]

90 references, page 1 of 6
Abstract
Abstract Investigating secondary contact of historically isolated lineages can provide insight into how selection and drift influence genomic divergence and admixture. Here, we studied the genomic landscape of divergence and introgression following secondary contact between lineages of the Western Diamondback Rattlesnake (Crotalus atrox) to determine whether genomic regions under selection in allopatry also contribute to reproductive isolation during introgression. We used thousands of nuclear loci to study genomic differentiation between two lineages that have experienced recent secondary contact following isolation, and incorporated sampling from a zone of sec...
Subjects
free text keywords: Speciation, media_common.quotation_subject, media_common, Introgression, VIPeR, Evolutionary biology, Gene flow, Biology, Divergence, Original Research, adaptation, genomic clines, hybridization, RADseq
90 references, page 1 of 6

Adams, R. H., Schield, D. R., Card, D. C., Blackmon, H., & Castoe, T. A. (2016). GppFst: Genomic posterior predictive simulations of FST and dXY for identifying outlier loci from population genomic data. Bioinformatics, btw795.28011784 [PubMed]

Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990). Basic local alignment search tool. Journal of Molecular Biology, 215, 403–410.2231712 [OpenAIRE] [PubMed]

Boughman, J. W. (2001). Divergent sexual selection enhances reproductive isolation in sticklebacks. Nature, 411, 944–948.11418857 [PubMed]

Bryant, D., Bouckaert, R., Felsenstein, J., Rosenberg, N. A., & RoyChoudhury, A. (2012). Inferring species trees directly from biallelic genetic markers: Bypassing gene trees in a full coalescent analysis. Molecular Biology and Evolution, 29, 1917–1932.22422763 [OpenAIRE] [PubMed]

Burnham, K. P., & Anderson, D. R. (2003). Model selection and multimodel inference: A practical informat ion‐theoretic approach. New York, NY: Springer Science & Business Media.

Burton, R. S., Ellison, C. K., & Harrison, J. S. (2006). The sorry state of F2 hybrids: Consequences of rapid mitochondrial DNA evolution in allopatric populations. The American Naturalist, 168, S14–S24.

Campbell, J. A., & Lamar, W. W. (2004). The venomous reptiles of the western hemisphere. Ithaca, NY, USA: Cornell University Press.

Caro, S. P., Charmantier, A., Lambrechts, M. M., Blondel, J., Balthazart, J., & Williams, T. D. (2009). Local adaptation of timing of reproduction: Females are in the driver's seat. Functional Ecology, 23, 172–179.

Caseys, C., Stölting, K. N., Barbará, T., González‐Martínez, S. C., & Lexer, C. (2015). Patterns of genetic diversity and differentiation in resistance gene clusters of two hybridizing European Populus species. Tree Genetics & Genomes, 11, 81.

Castoe, T. A., Spencer, C. L., & Parkinson, C. L. (2007). Phylogeographic structure and historical demography of the western diamondback rattlesnake (Crotalus atrox): A perspective on North American desert biogeography. Molecular Phylogenetics and Evolution, 42, 193–212.16934495 [PubMed]

Catchen, J., Hohenlohe, P. A., Bassham, S., Amores, A., & Cresko, W. A. (2013). Stacks: An analysis tool set for population genomics. Molecular Ecology, 22, 3124–3140.23701397 [OpenAIRE] [PubMed]

Coyne, J. A., & Orr, H. A. (2004). Speciation. Sunderland, MA: Sinauer Associates.

Cruickshank, T. E., & Hahn, M. W. (2014). Reanalysis suggests that genomic islands of speciation are due to reduced diversity, not reduced gene flow. Molecular Ecology, 23, 3133–3157.24845075 [OpenAIRE] [PubMed]

Danecek, P., Aut on, A., Abecasis, G., Albers, C. A., Banks, E., De Pristo, M. A., … Sherry, S. T. (2011). The variant call format and VCFtools. Bioinformatics, 27, 2156–2158.21653522 [OpenAIRE] [PubMed]

Dobzhansky, T. H. (1936). Studies on hybrid sterility. II. Localization of sterility factors in Drosophila pseudoobscura hybrids. Genetics, 21, 113.17246786 [OpenAIRE] [PubMed]

90 references, page 1 of 6
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publication . Article . 2017

Insight into the roles of selection in speciation from genomic patterns of divergence and introgression in secondary contact in venomous rattlesnakes

Schield, Drew R.; Adams, Richard H.; Card, Daren C.; Perry, Blair W.; Pasquesi, Giulia M.; Jezkova, Tereza; Portik, Daniel M.; Andrew, Audra L.; Spencer, Carol L.; Sanchez, Elda E.; ...