Evolutionary and ecological drivers of local adaptation and speciation in a North American avian species complex.

التفاصيل البيبلوغرافية
العنوان:	Evolutionary and ecological drivers of local adaptation and speciation in a North American avian species complex.
المؤلفون:	Brown JI; Department of Biological Sciences, University of Texas at El Paso, El Paso, Texas, USA., Harrigan RJ; Center for Tropical Research, University of California, Los Angeles, Los Angeles, California, USA., Lavretsky P; Department of Biological Sciences, University of Texas at El Paso, El Paso, Texas, USA.
المصدر:	Molecular ecology [Mol Ecol] 2022 May; Vol. 31 (9), pp. 2578-2593. Date of Electronic Publication: 2022 Mar 18.
نوع المنشور:	Journal Article; Research Support, Non-U.S. Gov't
اللغة:	English
بيانات الدورية:	Publisher: Blackwell Scientific Publications Country of Publication: England NLM ID: 9214478 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1365-294X (Electronic) Linking ISSN: 09621083 NLM ISO Abbreviation: Mol Ecol Subsets: MEDLINE
أسماء مطبوعة:	Original Publication: Oxford, UK : Blackwell Scientific Publications, c1992-
مواضيع طبية MeSH:	Birds* , Genetic Speciation*, Adaptation, Physiological ; Animals ; Ducks/genetics ; Gene Flow/genetics ; North America
مستخلص:	Throughout the speciation process, genomic divergence can be differentially impacted by selective pressures, as well as gene flow and genetic drift. Disentangling the effects of these evolutionary mechanisms remains challenging, especially for nonmodel organisms. Accounting for complex evolutionary histories and contemporary population structure often requires sufficient sample sizes, for which the expense of full genomes remains prohibitive. Here, we demonstrate the utility of partial-genome sequence data for range-wide samples to shed light into the divergence process of two closely related ducks, the Mexican duck (Anas diazi) and mallard (A. platyrhynchos). We determine the role of selective and neutral processes during speciation of Mexican ducks by integrating evolutionary and demographic modelling with genotype-environment and genotype-phenotype association testing. First, evolutionary models and demographic analyses support the hypothesis that Mexican ducks originally diverged ~300,000 years ago in climate refugia arising during a glacial period in southwest North America, and that subsequent environmental selective pressures played a key role in divergence. Mexican ducks then showed cyclical demographic patterns that probably reflected repeated range expansions and contractions, along with bouts of gene flow with mallards during glacial cycles. Finally, we provide evidence that sexual selection acted on several phenotypic traits as a co-evolutionary process, facilitating the development of reproductive barriers that initially arose due to strong ecological selection. More broadly, this work reveals that the genomic and phenotypic patterns observed across species complexes are the result of myriad factors that contribute in dynamic ways to the evolutionary trajectories of a lineage. (© 2022 John Wiley & Sons Ltd.)
References:	Allendorf, F. W. (1986). Genetic drift and the loss of alleles vs heterozygosity. Zoo Biology, 5, 181-190. Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990). Basic local alignment search tool. Journal of Molecular Biology, 215(3), 403-410. https://doi.org/10.1016/S0022-2836(05)80360-2. Baldassarre, G. A. (2014). Ducks, geese, and swans of North America. Johns Hopkins University Press. Batchelor, C. L., Margold, M., Krapp, M., Murton, D. K., Dalton, A. S., Gibbard, P. L., Stokes, C. R., Murton, J. B., & Manica, A. (2019). The configuration of Northern Hemisphere ice sheets through the Quaternary. Nature Communications, 10(1), 1-10. https://doi.org/10.1038/s41467-019-11601-2. Bay, R. A., Harrigan, R. J., Underwood, V. L., Gibbs, H. L., Smith, T. B., & Ruegg, K. (2018). Genomic signals of selection predict climate-driven population declines in a migratory bird. Science, 359(6371), 83-86. https://doi.org/10.1126/science.aan4380. Bemmels, J. B., Title, P. O., Ortego, J., & Knowles, L. L. (2016). Tests of species-specific models reveal the importance of drought in postglacial range shifts of a Mediterranean-climate tree: Insights from integrative distributional, demographic and coalescent modelling and ABC model selection. Molecular Ecology, 25(19), 4889-4906. https://doi.org/10.1111/mec.13804. Berger, B., Crucifix, M., Hodell, D. A., Mangili, C., McManus, J. F., Otto-Bliesner, B., & Vazquez Riveiros, N. (2016). Interglacials of the last 800,000 years. Reviews of Geophysics, 54(1), 162-219. https://doi.org/10.1002/2015RG000482. Betancourt, J. L. (2004). Arid lands paleobiogeography: The rodent midden record in the Americas. In M. V. Lomolino, & L. R. Heaney (Eds.), Frontiers of biogeography: New directions in the geography of nature. Sinauer Associates Inc. Blischak, P. D., Barker, M. S., & Gutenkunst, R. N. (2020). Inferring the demographi history of inbred species from genome-wide SNP frequency data. Molecular Biology and Evolution, 37(7), 2124-2136. https://doi.org/10.1093/molbev/msaa042. Butlin, R. K., & Smadja, C. M. (2018). Coupling, reinforcement, and speciation. The American Naturalist, 191(2), 155-172. https://doi.org/10.1086/695136. Byers, K. J. R. P., Xu, S., & Schlüter, P. M. (2017). Molecular mechanisms of adaptation and speciation: Why do we need an integrative approach? Molecular Ecology, 26(1), 277-290. https://doi.org/10.1111/mec.13678. Capblancq, T., Fitzpatrick, M. C., Bay, R. A., Exposito-Alonso, M., & Keller, S. R. (2020). Genomic prediction of (Mal)Adaptation across current and future climatic landscapes. Annual Review of Ecology, Evolution, and Systematics, 51(1), 245-269. https://doi.org/10.1146/annurev-ecolsys-020720-042553. Castiglia, P. J., & Fawcett, P. J. (2006). Large Holocene lakes and climate change in the Chihuahuan Desert. Geology, 34(2), 113-116. https://doi.org/10.1130/G22036.1. Chen, N., Juric, I., Cosgrove, E. J., Bowman, R., Fitzpatrick, J. W., Schoech, S. J., Clark, A. G., & Coop, G. (2019). Allele frequency dynamics in a pedigreed natural population. Proceedings of the National Academy of Sciences of the United States of America, 116(6), 2158-2164. https://doi.org/10.1073/pnas.1813852116. Coffman, A. J., Hsieh, P. H., Gravel, S., & Gutenkunst, R. N. (2016). Computationally efficient composite likelihood statistics for demographic inference. Molecular Biology and Evolution, 33(2), 591-593. https://doi.org/10.1093/molbev/msv255. Cooney, C. R., Tobias, J. A., Weir, J. T., Botero, C. A., & Seddon, N. (2017). Sexual selection, speciation and constraints on geographical range overlap in birds. Ecology Letters, 20(7), 863-871. https://doi.org/10.1111/ele.12780. 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(13), 3133-3157. https://doi.org/10.1111/mec.12796. Cumming, G. S., & Ndlovu, M. (2015). Satellite telemetry of Afrotropical ducks: Methodological details and assessment of success rates. African Zoology, 46(2), 425-434. https://doi.org/10.1080/15627020.2011.11407654. DaCosta, J. M., & Sorenson, M. D. (2014). Amplification biases and consistent recovery of loci in a double-digest RAD-seq protocol. PLoS One, 9(9), e106713. https://doi.org/10.1371/journal.pone.0106713. Dixon, P. (2003). VEGAN, a package of R functions for community ecology. Journal of Vegetation Science, 14(6), 927-930. https://doi.org/10.1111/j.1654-1103.2003.tb02228.x. Douglas, M. E., Douglas, M. R., Schuett, G. W., & Porras, L. W. (2006). Evolution of rattlesnakes (Viperidae; Crotalus) in the warm deserts of western North America shaped by Neogene vicariance and Quaternary climate change. Molecular Ecology, 15(11), 3353-3374. https://doi.org/10.1111/j.1365-294X.2006.03007.x. Drilling, N., Williams, S. O. III, Titman, R. D., & McKinney, F. (2020). Mexican Duck (Anas diazi). In P. G. Rodewald, & B. K. Keeney (Eds.), Birds of the world. Cornell Lab of Ornithology. https://doi.org/10.2173/bow.mexduc.01. Edgar, R. C. (2010). Search and clustering orders of magnitude faster than BLAST. Bioinformatics, 26(19), 2460-2461. https://doi.org/10.1093/bioinformatics/btq461. Eliason, C. M., & Shawkey, M. D. (2012). A photonic heterostructure produces diverse iridescent colours in duck wing patches. Journal of the Royal Society Interface, 9(74), 2279-2289. https://doi.org/10.1098/rsif.2012.0118. Ellegren, H. (2014). Genome sequencing and population genomics in non-model organisms. Trends in Ecology and Evolution, 29(1), 51-63. https://doi.org/10.1016/j.tree.2013.09.008. Ellis, N., Smith, S. J., & Roland Pitcher, C. (2012). Gradient forests: Calculating importance gradients on physical predictors. Ecology, 93(1), 156-168. https://doi.org/10.1890/11-0252.1. Feder, J. L., Egan, S. P., & Nosil, P. (2012). The genomics of speciation-with-gene-flow. Trends in Genetics, 28(7), 342-350. https://doi.org/10.1016/j.tig.2012.03.009. Fitzpatrick, M. C., & Keller, S. R. (2015). Ecological genomics meets community-level modelling of biodiversity: Mapping the genomic landscape of current and future environmental adaptation. Ecology Letters, 18(1), 1-16. https://doi.org/10.1111/ele.12376. Gasca-Pineda, J., Cassaigne, I., Alonso, R. A., & Eguiarte, L. E. (2013). Effective population size, genetic variation, and their relevance for conservation: The bighorn sheep in Tiburon Island and comparisons with managed artiodactyls. PLoS One, 8(10), e78120. https://doi.org/10.1371/journal.pone.0078120. Gavin, D. G., Fitzpatrick, M. C., Gugger, P. F., Heath, K. D., Rodríguez-Sánchez, F., Dobrowski, S. Z., Hampe, A., Hu, F. S., Ashcroft, M. B., Bartlein, P. J., Blois, J. L., Carstens, B. C., Davis, E. B., Lafontaine, G., Edwards, M. E., Fernandez, M., Henne, P. D., Herring, E. M., Holden, Z. A., … Williams, J. W. (2014). Climate refugia: Joint inference from fossil records, species distribution models and phylogeography. New Phytologist, 204, 37-54. https://doi.org/10.1111/nph.12929. Gougherty, A. V., Keller, S. R., & Fitzpatrick, M. C. (2021). Maladaptation, migration and extirpation fuel climate change risk in a forest tree species. Nature Climate Change, 11(2), 166-171. https://doi.org/10.1038/s41558-020-00968-6. Gutenkunst, R. N., Hernandez, R. D., Williamson, S. H., & Bustamante, C. D. (2009). Inferring the joint demographic history of multiple populations from multidimensional SNP frequency data. PLoS Genetics, 5(10), e1000695. https://doi.org/10.1371/journal.pgen.1000695. Gutenkunst, R. N., Hernandez, R. D., Williamson, S. H., & Bustamante, C. D. (2010). Diffusion approximations for demographic inference: ∂a∂i. Nature Precedings, 5, 1. https://doi.org/10.1038/npre.2010.4594.1. Harvey, M. G., Singhal, S., & Rabosky, D. L. (2019). Beyond reproductive isolation: Demographic controls on the speciation process. Annual Review of Ecology, Evolution, and Systematics, 50(1), 75-95. https://doi.org/10.1146/annurev-ecolsys-110218-024701. Hernández, F., Brown, J. I., Kaminski, M., & Lavretsky, P. (2021). Species genomics reveals rare hybridization, robust species trees, and large demographic changes in the evolutionary histories of four dove species. Animals, 11(9), 2677. Hewitt, G. M. (1996). Some genetic consequences of ice ages, and their role in divergence and speciation. Biological Journal of the Linnean Society, 58(3), 247-276. https://doi.org/10.1111/j.1095-8312.1996.tb01434.x. Hewitt, G. M. (1999). Post-glacial re-colonization of European biota. Biological Journal of the Linnean Society, 68(1-2), 87-112. https://doi.org/10.1111/j.1095-8312.1999.tb01160.x. Hewitt, G. M. (2000). The genetic legacy of the quaternary ice ages. Nature, 405(6789), 907-913. https://doi.org/10.1038/35016000. Hijmans, R. J., Cameron, S. E., Parra, J. L., Jones, P. G., & Jarvis, A. (2005). Very high resolution interpolated climate surfaces for global land areas. International Journal of Climatology, 25(15), 1965-1978. https://doi.org/10.1002/joc.1276. Hill, G. E. (1994). Geographic variation in male ornamentation and female mate preference in the house finch: A comparative test of models of sexual selection. Behavioral Ecology, 5(1), 64-73. https://doi.org/10.1093/beheco/5.1.64. Huang, B. H., Huang, C. W., Huang, C. L., & Liao, P. C. (2017). Continuation of the genetic divergence of ecological speciation by spatial environmental heterogeneity in island endemic plants. Scientific Reports, 7(1), 1-13. https://doi.org/10.1038/s41598-017-05900-1. Huang, Y., Li, Y., Burt, D. W., Chen, H., Zhang, Y., Qian, W., Kim, H., Gan, S., Zhao, Y., Li, J., Yi, K., Feng, H., Zhu, P., Li, B. O., Liu, Q., Fairley, S., Magor, K. E., Du, Z., Hu, X., … Li, N. (2013). The duck genome and transcriptome provide insight into an avian influenza virus reservoir species. Nature Genetics, 45(7), 776-783. https://doi.org/10.1038/ng.2657. Hubbard, J. P. (1977). The biological and taxonomic status of the Mexican Duck. New Mexico Department of Game and Fish Bulletin, No. 16, pp. 1-56. Irwin, D. E., Milá, B., Toews, D. P. L., Brelsford, A., Kenyon, H. L., Porter, A. N., Grossen, C., Delmore, K. E., Alcaide, M., & Irwin, J. H. (2018). A comparison of genomic islands of differentiation across three young avian species pairs. Molecular Ecology, 27(23), 4839-4855. https://doi.org/10.1111/mec.14858. Jaeger, J. R., Riddle, B. R., & Bradford, D. F. (2005). Cryptic Neogene vicariance and Quaternary dispersal of the red-spotted toad (Bufo punctatus): Insights on the evolution of North American warm desert biotas. Molecular Ecology, 14(10), 3033-3048. https://doi.org/10.1111/j.1365-294X.2005.02645.x. Johnson, N. K., & Cicero, C. (2004). New mitochondrial DNA data affirm the importance of pleistocene speciation in North American birds. Evolution, 58(5), 1122-1130. https://doi.org/10.1111/j.0014-3820.2004.tb00445.x. Jombart, T. (2008). adegenet: A R package for the multivariate analysis of genetic markers. Bioinformatics, 24(11), 1403-1405. https://doi.org/10.1093/bioinformatics/btn129. Kautt, A. F., Kratochwil, C. F., Nater, A., Machado-Schiaffino, G., Olave, M., Henning, F., Torres-Dowdall, J., Härer, A., Hulsey, C. D., Franchini, P., Pippel, M., Myers, E. W., & Meyer, A. (2020). Contrasting signatures of genomic divergence during sympatric speciation. Nature, 588(7836), 106-111. https://doi.org/10.1038/s41586-020-2845-0. Kearns, A. M., Joseph, L., Toon, A., & Cook, L. G. (2014). Australia’s arid-adapted butcherbirds experienced range expansions during Pleistocene glacial maxima. Nature Communications, 5(1), 1-11. https://doi.org/10.1038/ncomms4994. Kraus, R. H. S., Kerstens, H. H. D., Van Hooft, P., Crooijmans, R. P. M. A., Van Der Poel, J. J., Elmberg, J., Vignal, A., Huang, Y., Li, N., Prins, H. H. T., & Groenen, M. A. M. (2011). Genome wide SNP discovery, analysis and evaluation in mallard (Anas platyrhynchos). BMC Genomics, 12(1), 150. https://doi.org/10.1186/1471-2164-12-150. Kulikova, I. V., Drovetski, S. V., Gibson, D. D., Harrigan, R. J., Rohwer, S., Sorenson, M. D., Winker, K., Zhuravlev, Y. N., & McCracken, K. G. (2005). Phylogeography of the mallard (Anas platyrhynchos): Hybridization, dispersal, and lineage sorting contribute to complex geographic structure. The Auk, 122(3), 949-965. https://doi.org/10.1093/auk/122.3.949. Lavretsky, P., Dacosta, J. M., Hernández-Baños, B. E., Engilis, A., Sorenson, M. D., & Peters, J. L. (2015). Speciation genomics and a role for the Z chromosome in the early stages of divergence between Mexican ducks and mallards. Molecular Ecology, 24(21), 5364-5378. https://doi.org/10.1111/mec.13402. Lavretsky, P., DaCosta, J. M., Sorenson, M. D., McCracken, K. G., & Peters, J. L. (2019). ddRAD-seq data reveal significant genome-wide population structure and divergent genomic regions that distinguish the mallard and close relatives in North America. Molecular Ecology, 28(10), 2594-2609. https://doi.org/10.1111/mec.15091. Lavretsky, P., Hernández-Baños, B. E., & Peters, J. L. (2014). Rapid radiation and hybridization contribute to weak differentiation and hinder phylogenetic inferences in the New World Mallard complex (Anas spp.). The Auk, 131, 524-538. https://doi.org/10.1642/AUK-13-164.1. Lavretsky, P., Janzen, T., & McCracken, K. G. (2019). Identifying hybrids & the genomics of hybridization: Mallards & American black ducks of Eastern North America. Ecology and Evolution, 9(6), 3470-3490. https://doi.org/10.1002/ece3.4981. Lavretsky, P., McCracken, K. G., & Peters, J. L. (2014). Phylogenetics of a recent radiation in the mallards and allies (Aves: Anas): Inferences from a genomic transect and the multispecies coalescent. Molecular Phylogenetics and Evolution, 70(1), 402-411. https://doi.org/10.1016/j.ympev.2013.08.008. Lavretsky, P., McInerney, N. R., Mohl, J. E., Brown, J. I., James, H. F., McCracken, K. G., & Fleischer, R. C. (2020). Assessing changes in genomic divergence following a century of human-mediated secondary contact among wild and captive-bred ducks. Molecular Ecology, 29(3), 578-595. https://doi.org/10.1111/mec.15343. Lavretsky, P., Wilson, R. E., Talbot, S. L., & Sonsthagen, S. A. (2021). Phylogenomics reveals ancient and contemporary gene flow contributing to the evolutionary history of sea ducks (Tribe Mergini). Molecular Phylogenetics and Evolution, 161, 107164. https://doi.org/10.1016/j.ympev.2021.107164. Layton, K. K. S., Snelgrove, P. V. R., Dempson, J. B., Kess, T., Lehnert, S. J., Bentzen, P., Duffy, S. J., Messmer, A. M., Stanley, R. R. E., DiBacco, C., Salisbury, S. J., Ruzzante, D. E., Nugent, C. M., Ferguson, M. M., Leong, J. S., Koop, B. F., & Bradbury, I. R. (2021). Genomic evidence of past and future climate-linked loss in a migratory Arctic fish. Nature Climate Change, 11(2), 158-165. https://doi.org/10.1038/s41558-020-00959-7. Le Corre, V., & Kremer, A. (2012). The genetic differentiation at quantitative trait loci under local adaptation. Molecular Ecology, 21(7), 1548-1566. https://doi.org/10.1111/j.1365-294X.2012.05479.x. Lecomte, N., Gauthier, G., & Giroux, J.-F. (2009). A link between water availability and nesting success mediated by predator-prey interactions in the Arctic. Ecology, 90(2), 465-475. https://doi.org/10.1890/08-0215.1. Legendre, P., & Gallagher, E. D. (2001). Ecologically meaningful transformations for ordination of species data. Oecologia, 129(2), 271-280. https://doi.org/10.1007/s004420100716. Lenormand, T. (2012). From local adaptation to speciation: Specialization and reinforcement. International Journal of Ecology, 2012, 1-11. https://doi.org/10.1155/2012/508458. Licciardi, J. M., Clark, P. U., Brook, E. J., Elmore, D., & Sharma, P. (2004). Variable responses of western U.S. glaciers during the last deglaciation. Geology, 32(1), 81-84. https://doi.org/10.1130/G19868.1. Lim, E. P., Hendon, H. H., Hope, P., Chung, C., Delage, F., & McPhaden, M. J. (2019). Continuation of tropical Pacific Ocean temperature trend may weaken extreme El Niño and its linkage to the Southern Annular Mode. Scientific Reports, 9(1), 1-15. https://doi.org/10.1038/s41598-019-53371-3. Lockwood, J. G. (2001). Abrupt and sudden climatic transitions and fluctuations: A review. International Journal of Climatology, 21(9), 1153-1179. https://doi.org/10.1002/joc.630. Lonsinger, R. C., Adams, J. R., & Waits, L. P. (2018). Evaluating effective population size and genetic diversity of a declining kit fox population using contemporary and historical specimens. Ecology and Evolution, 8(23), 12011-12021. https://doi.org/10.1002/ece3.4660. Marchetti, K. (1993). Dark habitats and bright birds illustrate the role of the environment in species divergence. Nature, 362(6416), 149-152. https://doi.org/10.1038/362149a0. Martin, R. A., & Pfennig, D. W. (2009). Disruptive selection in natural populations: The roles of ecological specialization and resource competition. The American Naturalist, 174(2), 268-281. https://doi.org/10.1086/600090. McEvoy, J. F., Ribot, R. F. H., Wingfield, J. C., & Bennett, A. T. D. (2017). Heavy rainfall triggers increased nocturnal flight in desert populations of the Pacific black duck (Anas superciliosa). Scientific Reports, 7(1), 1-9. https://doi.org/10.1038/s41598-017-17859-0. Meester, L. D., Stoks, R., & Brans, K. I. (2018). Genetic adaptation as a biological buffer against climate change: Potential and limitations. Integrative Zoology, 13(4), 372-391. https://doi.org/10.1111/1749-4877.12298. Meier, J. I., Marques, D. A., Wagner, C. E., Excoffier, L., & Seehausen, O. (2018). Genomics of parallel ecological speciation in Lake Victoria Cichlids. Molecular Biology and Evolution, 35(6), 1489-1506. https://doi.org/10.1093/molbev/msy051. Mellink, E. (2000). Breeding of brown boobies in the Gulf of California: Seasonality and apparent effects of El Nino. Waterbirds, 23(3), 494-499. https://doi.org/10.2307/1522189. Mellink, E., Luévano, J., & Riojas-López, M. E. (2018). Half a century of changes in waterbird populations in a semiarid wetland system. Wetlands Ecology and Management, 26(6), 1047-1060. https://doi.org/10.1007/s11273-018-9630-y. Metcalfe, S., Say, A., Black, S., McCulloch, R., & O’Hara, S. (2002). Wet conditions during the last glaciation in the Chihuahuan Desert, Alta Babicora Basin, Mexico. Quaternary Research, 57(1), 91-101. https://doi.org/10.1006/qres.2001.2292. Miller, C. R., & Waits, L. P. (2003). The history of effective population size and genetic diversity in the Yellowstone grizzly (Ursus arctos): Implications for conservation. Proceedings of the National Academy of Sciences of the United States of America, 100(7), 4334-4339. https://doi.org/10.1073/pnas.0735531100. Momigliano, P., Florin, A.-B., & Merilä, J. (2021). Biases in demographic modelling affect our understanding of recent divergence. Molecular Biology and Evolution, 38(7), 2967-2985. https://doi.org/10.1093/molbev/msab047. Moodley, Y., Westbury, M. V., Russo, I.-R., Gopalakrishnan, S., Rakotoarivelo, A., Olsen, R.-A., Prost, S., Tunstall, T., Ryder, O. A., Dalén, L., & Bruford, M. W. (2020). Interspecific gene flow and the evolution of specialization in black and white rhinoceros. Molecular Biology and Evolution, 37(11), 3105-3117. https://doi.org/10.1093/molbev/msaa148. Nevo, E. (2011). Evolution under environmental stress at macro- and microscales. Genome Biology and Evolution, 3(1), 1039-1052. https://doi.org/10.1093/gbe/evr052. Omland, K. E. (1996). Female mallard mating preferences for multiple male ornaments: I. Natural variation. Behavioral Ecology and Sociobiology, 39(6), 353-360. https://doi.org/10.1007/s002650050300. Omland, K. E. (1997). Examining two standard assumptions of ancestral reconstructions: Repeated loss of dichromatism in dabbling ducks (Anatini). Evolution, 51(5), 1636-1646. https://doi.org/10.1111/j.1558-5646.1997.tb01486.x. Otto-Bliesner, B. L., Marshall, S. J., Overpeck, J. T., Miller, G. H., & Hu, A. (2006). Simulating arctic climate warmth and icefield retreat in the last interglaciation. Science, 311(5768), 1751-1753. https://doi.org/10.1126/science.1120808. Payne, P., Polechová, J., & Payne, P. (2020). Sympatric ecological divergence with coevolution of niche preference: Sympatric divergence with niche choice. Philosophical Transactions of the Royal Society B, 375(1806), 1-11. https://doi.org/10.1098/rstb.2019.0749. Perez-Arteaga, A., Gaston, K. J., & Kershaw, M. (2002). Population trends and priority conservation sites for Mexican Duck Anas diazi. Bird Conservation International, 12(1), 35-52. https://doi.org/10.1017/S0959270902002034. Peters, J. L., Roberts, T. E., Winker, K., & McCracken, K. G. (2012). Heterogeneity in genetic diversity among non-coding loci fails to fit neutral coalescent models of population history. PLoS One, 7(2), e31972. https://doi.org/10.1371/journal.pone.0031972. Peters, J. L., Winker, K., Millam, K. C., Lavretsky, P., Kulikova, I., Wilson, R. E., & McCracken, K. G. (2014). Mito-nuclear discord in six congeneric lineages of Holarctic ducks (genus Anas). Molecular Ecology, 23(12), 2961-2974. https://doi.org/10.1111/mec.12799. Pfeifer, B., Wittelsbürger, U., Ramos-Onsins, S. E., & Lercher, M. J. (2014). PopGenome: An efficient Swiss army knife for population genomic analyses in R. Molecular Biology and Evolution, 31(7), 1929-1936. https://doi.org/10.1093/molbev/msu136. Price, T. D. (1998). Sexual selection and natural selection in bird speciation. Philosophical Transactions of the Royal Society B, 353(1366), 251-260. https://doi.org/10.1098/rstb.1998.0207. Price, T. D., & Bouvier, M. M. (2002). The evolution of F1 postzygotic incompatabilities in birds. Evolution, 56(10), 2083-2089. https://doi.org/10.1111/j.0014-3820.2002.tb00133.x. Provan, J., & Bennett, K. D. (2008). Phylogeographic insights into cryptic glacial refugia. Trends in Ecology & Evolution, 23(10), 564-571. https://doi.org/10.1016/j.tree.2008.06.010. Purcell, S., Neale, B., Todd-Brown, K., Thomas, L., Ferreira, M. A. R., Bender, D., Maller, J., Sklar, P., de Bakker, P. I. W., Daly, M. J., & Sham, P. C. (2007). PLINK: A tool set for whole-genome association and population-based linkage analyses. The American Journal of Human Genetics, 81(3), 559-575. https://doi.org/10.1086/519795. Razgour, O., Forester, B., Taggart, J. B., Bekaert, M., Juste, J., Ibáñez, C., Puechmaille, S. J., Novella-Fernandez, R., Alberdi, A., & Manel, S. (2019). Considering adaptive genetic variation in climate change vulnerability assessment reduces species range loss projections. Proceedings of the National Academy of Sciences of the United States of America, 116(21), 10418-10423. https://doi.org/10.1073/pnas.1820663116. Reynolds, R. E., Blohm, R. J., Nichols, J. D., & Hines, J. E. (1995). Spring-summer survival rates of yearling versus adult mallard females. The Journal of Wildlife Management, 59(4), 696. https://doi.org/10.2307/3801945. Rhoné, B., Defrance, D., Berthouly-Salazar, C., Mariac, C., Cubry, P., Couderc, M., Dequincey, A., Assoumanne, A., Kane, N. A., Sultan, B., Barnaud, A., & Vigouroux, Y. (2020). Pearl millet genomic vulnerability to climate change in West Africa highlights the need for regional collaboration. Nature Communications, 11(1), 1-9. https://doi.org/10.1038/s41467-020-19066-4. Roshier, D. A., Klomp, N. I., & Asmus, M. (2006). Movements of a nomadic waterfowl, Grey Teal Anas gracilis, across inland Australia-Results from satellite telemetry spanning fifteen months. Ardea, 94(3), 461-475. Ruegg, K., Bay, R. A., Anderson, E. C., Saracco, J. F., Harrigan, R. J., Whitfield, M., Paxton, E. H., & Smith, T. B. (2018). Ecological genomics predicts climate vulnerability in an endangered southwestern songbird. Ecology Letters, 21(7), 1085-1096. https://doi.org/10.1111/ele.12977. Rundle, H. D., & Nosil, P. (2005). Ecological speciation. Ecology Letters, 8(3), 336-352. https://doi.org/10.1111/j.1461-0248.2004.00715.x. Rundle, H. D., & Rowe, L. (2018). The contribution of sexual selection to ecological and mutation-order speciation. Evolution, 72(11), 2571-2575. https://doi.org/10.1111/evo.13599. Saether, B.-E., Lande, R., Engen, S., Weimerskirch, H., Lillegård, M., Altwegg, R., Becker, P. H., Bregnballe, T., Brommer, J. E., McCleery, R. H., Merilä, J., Nyholm, E., Rendell, W., Robertson, R. R., Tryjanowski, P., & Visser, M. E. (2005). Generation time and temporal scaling of bird population dynamics. Nature, 436(7047), 99-102. https://doi.org/10.1038/nature03666. Saintilan, N., Rogers, K., Kelleway, J. J., Ens, E., & Sloane, D. R. (2019). Climate change impacts on the coastal Wetlands of Australia. Wetlands, 39(6), 1145-1154. https://doi.org/10.1007/s13157-018-1016-7. Sarabia, C., VonHoldt, B., Larrasoaña, J. C., Uríos, V., & Leonard, J. A. (2020). Pleistocene climate fluctuations drove demographic history of African golden wolves (Canis lupaster). Molecular Ecology. 30(23), 6101-6120. https://doi.org/10.1111/mec.15784. Sato, Y., Ogden, R., Kishida, T., Nakajima, N., Maeda, T., & Inoue-Murayama, M. (2020). Population history of the golden eagle inferred from whole-genome sequencing of three of its subspecies. Biological Journal of the Linnean Society, 130(4), 826-838. https://doi.org/10.1093/biolinnean/blaa068. Savolainen, O., Lascoux, M., & Merilä, J. (2013). Ecological genomics of local adaptation. Nature Reviews Genetics, 14(11), 807-820. https://doi.org/10.1038/nrg3522. Scott, N. J., & Reynolds, R. P. (1984). Phenotypic variation of the Mexican Duck (Anas platyrhynchos diazi) in Mexico. The Condor, 86, 266-274. https://doi.org/10.2307/1366994. Seddon, N., Botero, C. A., Tobias, J. A., Dunn, P. O., MacGregor, H. E. A., Rubenstein, D. R., Uy, J. A. C., Weir, J. T., Whittingham, L. A., & Safran, R. J. (2013). Sexual selection accelerates signal evolution during speciation in birds. Proceedings of the Royal Society B, 280(1766), 20131065. https://doi.org/10.1098/rspb.2013.1065. Seehausen, O., Butlin, R. K., Keller, I., Wagner, C. E., Boughman, J. W., Hohenlohe, P. A., Peichel, C. L., Saetre, G.-P., Bank, C., Brännström, Å., Brelsford, A., Clarkson, C. S., Eroukhmanoff, F., Feder, J. L., Fischer, M. C., Foote, A. D., Franchini, P., Jiggins, C. D., Jones, F. C., … Widmer, A. (2014). Genomics and the origin of species. Nature Reviews Genetics, 15(3), 176-192. https://doi.org/10.1038/nrg3644. Sillero, N. (2011). What does ecological modelling model? A proposed classification of ecological niche models based on their underlying methods. Ecological Modelling, 222(8), 1343-1346. https://doi.org/10.1016/j.ecolmodel.2011.01.018. Smith, A. B., Godsoe, W., Rodríguez-Sánchez, F., Wang, H. H., & Warren, D. (2019). Niche estimation above and below the species level. Trends in Ecology & Evolution, 34, 260-273. https://doi.org/10.1016/j.tree.2018.10.012. Stewart, J. R., Lister, A. M., Barnes, I., & Dalén, L. (2010). Refugia revisited: Individualistic responses of species in space and time. Proceedings of the Royal Society B, 277(1682), 661-671. https://doi.org/10.1098/rspb.2009.1272. Stuart-Fox, D. M., & Ord, T. J. (2004). Sexual selection, natural selection and the evolution of dimorphic coloration and ornamentation in agamid lizards. Proceedings of the Royal Society B, 271(1554), 2249-2255. https://doi.org/10.1098/rspb.2004.2802. Talbot, B., Chen, T.-W., Zimmerman, S., Joost, S., Eckert, A. J., Crow, T. M., Semizer-Cuming, D., Seshadri, C., & Manel, S. (2017). Combining genotype, phenotype, and environment to infer potential candidate genes. Journal of Heredity, 108(2), 207-216. https://doi.org/10.1093/jhered/esw077. Theodoridis, S., Fordham, D. A., Brown, S. C., Li, S., Rahbek, C., & Nogues-Bravo, D. (2020). Evolutionary history and past climate change shape the distribution of genetic diversity in terrestrial mammals. Nature Communications, 11(1), 1-11. https://doi.org/10.1038/s41467-020-16449-5. Thompson, R. S., & Anderson, K. H. (2000). Biomes of western North America at 18,000, 6000 and 0 14C yr bp reconstructed from pollen and packrat midden data. Journal of Biogeography, 27(3), 555-584. https://doi.org/10.1046/j.1365-2699.2000.00427.x. Tigano, A., & Friesen, V. L. (2016). Genomics of local adaptation with gene flow. Molecular Ecology, 25, 2144-2164. https://doi.org/10.1111/mec.13606. Tobias, J. A., Ottenburghs, J., & Pigot, A. L. (2020). Avian diversity: Speciation, macroevolution, and ecological function. Annual Review of Ecology, Evolution, and Systematics, 51(1), 533-560. https://doi.org/10.1146/annurev-ecolsys-110218-025023. Tobler, M., Kelley, J. L., Plath, M., & Riesch, R. (2018). Extreme environments and the origins of biodiversity: Adaptation and speciation in sulphide spring fishes. Molecular Ecology, 27(4), 843-859. https://doi.org/10.1111/mec.14497. Turner, T. L., Hahn, M. W., & Nuzhdin, S. V. (2005). Genomic islands of speciation in Anopheles gambiae. PLoS Biology, 3(9), e285. https://doi.org/10.1371/journal.pbio.0030285. Wang, J., Street, N. R., Park, E., Liu, J., & Ingvarsson, P. K. (2020). Evidence for widespread selection in shaping the genomic landscape during speciation of Populus. Molecular Ecology, 29(6), 1120-1136. https://doi.org/10.1111/mec.15388. Wang, T., O’Neill, G. A., & Aitken, S. N. (2010). Integrating environmental and genetic effects to predict responses of tree populations to climate. Ecological Applications, 20(1), 153-163. https://doi.org/10.1890/08-2257.1. Weir, J. T., & Schluter, D. (2004). Ice sheets promote speciation in boreal birds. Proceedings of the Royal Society B, 271(1551), 1881-1887. https://doi.org/10.1098/rspb.2004.2803. Willi, Y., Van Buskirk, J., & Hoffmann, A. A. (2006). Limits to the adaptive potential of small populations. Annual Review of Ecology, Evolution, and Systematics, 37(1), 433-458. https://doi.org/10.1146/annurev.ecolsys.37.091305.110145. Wingfield, J. C., Ramos-Fernandez, G., Nuñez-De La Mora, A., & Drummond, H. (1999). The effects of an “El Nino” southern oscillation event on reproduction in male and female blue-footed boobies, Sula nebouxii. General and Comparative Endocrinology, 114(2), 163-172. https://doi.org/10.1006/gcen.1998.7243. Wolf, J. B. W., & Ellegren, H. (2017). Making sense of genomic islands of differentiation in light of speciation. Nature Reviews Genetics, 18(2), 87-100. https://doi.org/10.1038/nrg.2016.133. Yamasaki, Y. Y., Kakioka, R., Takahashi, H., Toyoda, A., Nagano, A. J., Machida, Y., & Kitano, J. (2020). Genome-wide patterns of divergence and introgression after secondary contact between Pungitius sticklebacks. Philosophical Transactions of the Royal Society B, 375(1806), 1-11. https://doi.org/10.1098/rstb.2019.0548. Yannic, G., Pellissier, L., Ortego, J., Lecomte, N., Couturier, S., Cuyler, C., Dussault, C., Hundertmark, K. J., Irvine, R. J., Jenkins, D. A., Kolpashikov, L., Mager, K., Musiani, M., Parker, K. L., Røed, K. H., Sipko, T., Þórisson, S. G., Weckworth, B. V., Guisan, A., … Côté, S. D. (2014). Genetic diversity in caribou linked to past and future climate change. Nature Climate Change, 4(2), 132-137. https://doi.org/10.1038/nclimate2074. Yeaman, S. (2015). Local adaptation by alleles of small effect. The American Naturalist, 186(S1), S74-S89. https://doi.org/10.1086/682405.
فهرسة مساهمة:	Keywords: Anas; Mexican duck; adaption; ddRAD-seq; evolution; mallard; speciation
سلسلة جزيئية:	RefSeq SS263068950; SS263191362; SAMN25245926; SAMN25247720
تواريخ الأحداث:	Date Created: 20220309 Date Completed: 20220427 Latest Revision: 20220629
رمز التحديث:	20240628
DOI:	10.1111/mec.16423
PMID:	35263000
قاعدة البيانات:	MEDLINE

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تدمد:	1365-294X
DOI:	10.1111/mec.16423