TY - JOUR AU - Campbell, R. C. AU - Poelstra, J. W. AU - Yoder, A. D. PY - 2018 DA - 2018// TI - What is speciation genomics? The roles of ecology, gene flow, and genomic architecture in the formation of species JO - Biol J Linnean Soc VL - 124 ID - Campbell2018 ER - TY - BOOK AU - Mayr, E. PY - 1963 DA - 1963// TI - Animal species and evolution PB - Harvard University Press CY - Cambridge, Mass ID - Mayr1963 ER - TY - JOUR AU - Mallet, J. PY - 2005 DA - 2005// TI - Hybridization as an invasion of the genome JO - Trends Ecol Evol VL - 20 ID - Mallet2005 ER - TY - JOUR AU - Ottenburghs, J. AU - Megens, H. J. AU - Kraus, R. H. S. AU - Hooft, P. AU - Wieren, S. E. AU - Crooijmans, R. P. M. A. PY - 2017 DA - 2017// TI - A history of hybrids? Genomic patterns of introgression in the True Geese JO - BMC Evol Biol VL - 17 ID - Ottenburghs2017 ER - TY - JOUR AU - Rutherford, S. AU - Rossetto, M. AU - Bragg, J. G. AU - McPherson, H. AU - Benson, D. AU - Bonser, S. P. PY - 2018 DA - 2018// TI - Speciation in the presence of gene flow: population genomics of closely related and diverging Eucalyptus species JO - Heredity VL - 121 ID - Rutherford2018 ER - TY - JOUR AU - Wang, X. AU - Que, P. AU - Heckel, G. AU - Hu, J. AU - Zhang, X. AU - Chiang, C. -. Y. PY - 2019 DA - 2019// TI - Genetic, phenotypic and ecological differentiation suggests incipient speciation in two Charadrius plovers along the Chinese coast JO - BMC Evol Biol VL - 19 ID - Wang2019 ER - TY - JOUR AU - Servedio, M. R. AU - Hermisson, J. PY - 2020 DA - 2020// TI - The evolution of partial reproductive isolation as an adaptive optimum JO - Evolution VL - 74 ID - Servedio2020 ER - TY - STD TI - Ottenburghs J. Ghost introgression: spooky gene flow in the distant past. Bioessays. 2020;42. https://doi.org/10.1002/bies.202000012. ID - ref8 ER - TY - JOUR AU - Ravinet, M. AU - Faria, R. AU - Butlin, R. K. AU - Galindo, J. AU - Bierne, N. AU - Rafajlović, M. PY - 2017 DA - 2017// TI - Interpreting the genomic landscape of speciation: a road map for finding barriers to gene flow JO - J Evol Biol VL - 30 ID - Ravinet2017 ER - TY - JOUR AU - Martin, S. H. AU - Davey, J. W. AU - Salazar, C. AU - Jiggins, C. D. PY - 2019 DA - 2019// TI - Recombination rate variation shapes barriers to introgression across butterfly genomes JO - PLoS Biol VL - 17 ID - Martin2019 ER - TY - JOUR AU - Ellison, C. K. AU - Wiley, C. AU - Shaw, K. L. PY - 2011 DA - 2011// TI - The genetics of speciation: genes of small effect underlie secual isolation in the Hawaiian cricket Laupala JO - J Evol Biol VL - 24 ID - Ellison2011 ER - TY - JOUR AU - Ottenburghs, J. AU - Kraus, R. H. S. AU - Hooft, P. AU - Wieren, S. E. AU - Ydenberg, R. C. AU - Prins, H. H. T. PY - 2017 DA - 2017// TI - Avian introgression in the genomic era JO - Avian Res VL - 8 ID - Ottenburghs2017 ER - TY - JOUR AU - Wright, S. PY - 1949 DA - 1949// TI - The genetical structure of populations JO - Ann Eugenics VL - 15 ID - Wright1949 ER - TY - JOUR AU - Lewontin, R. C. AU - Krakauer, J. PY - 1973 DA - 1973// TI - Distribution of gene frequency as a test of the theory of the selective neutrality of polymorphisms JO - Genetics VL - 74 ID - Lewontin1973 ER - TY - JOUR AU - Martin, S. H. AU - Dasmahapatra, K. K. AU - Nadeau, N. J. AU - Salazar, C. AU - Walters, J. R. AU - Simpson, F. PY - 2013 DA - 2013// TI - Genome-wide evidence for speciation with gene flow in Heliconius butterflies JO - Genome Res VL - 23 ID - Martin2013 ER - TY - JOUR AU - Gosset, C. C. AU - Bierne, N. PY - 2013 DA - 2013// TI - Differential introgression from a sister species explains high FST outlier loci within a mussel species JO - J Evol Biol VL - 26 ID - Gosset2013 ER - TY - JOUR AU - Toews, D. P. L. AU - Taylor, S. A. AU - Vallender, R. AU - Brelsford, A. AU - Butcher, B. G. AU - Messer, P. W. PY - 2016 DA - 2016// TI - Plumage genes and little Else distinguish the genomes of hybridizing warblers JO - Curr Biol VL - 26 ID - Toews2016 ER - TY - JOUR AU - Irwin, D. E. PY - 2018 DA - 2018// TI - Sex chromosomes and speciation in birds and other ZW systems JO - Mol Ecol VL - 27 ID - Irwin2018 ER - TY - JOUR AU - Burri, R. AU - Nater, A. AU - Kawakami, T. AU - Mugal, C. F. AU - Olason, P. I. AU - Smeds, L. PY - 2015 DA - 2015// TI - Linked selection and recombination rate variation drive the evolution of the genomic landscape of differentiation across the speciation continuum of Ficedula flycatchers JO - Genome Res VL - 25 UR - https://doi.org/10.1101/gr.196485.115 DO - 10.1101/gr.196485.115 ID - Burri2015 ER - TY - JOUR AU - Wu, C. -. I. PY - 2001 DA - 2001// TI - Genes and speciation JO - J Evol Biol VL - 14 ID - Wu2001 ER - TY - JOUR AU - Turner, T. L. AU - Hahn, M. W. AU - Nuzhdin, S. V. PY - 2005 DA - 2005// TI - Genomic Islands of speciation in Anopheles gambiae JO - PLoS Biol VL - 3 ID - Turner2005 ER - TY - JOUR AU - Noor, M. A. F. AU - Bennett, S. M. PY - 2009 DA - 2009// TI - Islands of speciation or mirages in the desert? Examining the role of restricted recombination in maintaining species JO - Heredity. VL - 103 ID - Noor2009 ER - TY - JOUR AU - Cruickshank, T. E. AU - Hahn, M. W. PY - 2014 DA - 2014// TI - Reanalysis suggests that genomic islands of speciation are due to reduced diversity, not reduced gene flow JO - Mol Ecol VL - 23 ID - Cruickshank2014 ER - TY - JOUR AU - Wolf, J. B. W. AU - Ellegren, H. PY - 2017 DA - 2017// TI - Making sense of genomic islands of differentiation in light of speciation JO - Nat Rev Genet VL - 18 ID - Wolf2017 ER - TY - JOUR AU - Nielsen, R. AU - Mountain, J. L. AU - Huelsenbeck, J. P. AU - Slatkin, M. PY - 1998 DA - 1998// TI - Maximum-likelihood estimation of population divergence times and population phylogeny in models without mutation JO - Evolution VL - 52 ID - Nielsen1998 ER - TY - JOUR AU - Miller, K. M. W. AU - Bracewell, R. R. AU - Eison, M. B. AU - Bachtrog, D. PY - 2017 DA - 2017// TI - Patterns of genome-wide diversity and population structure in the Drosophila athabasca species complex JO - Molec Biol Evol VL - 43 ID - Miller2017 ER - TY - JOUR AU - Dutoit, L. AU - Vijay, N. AU - Mugal, C. F. AU - Bossu, C. M. AU - Burri, R. AU - Wolf, J. AU - Ellegren, H. PY - 2017 DA - 2017// TI - Covariation in levels of nucleotide diversity in homologous regions of the avian genome long after completion of lineage sorting JO - Proc Royal Soc B VL - 284 ID - Dutoit2017 ER - TY - JOUR AU - Burri, R. PY - 2017 DA - 2017// TI - Interpreting differentiation landscapes in the light of long-term linked selection: differentiation and long-term linked selection JO - Evol Lett VL - 1 ID - Burri2017 ER - TY - JOUR AU - Jackson, B. C. AU - Campos, J. L. AU - Zeng, K. PY - 2015 DA - 2015// TI - The effects of purifying selection on patterns of genetic differentiation between Drosophila melanogaster populations JO - Heredity VL - 114 ID - Jackson2015 ER - TY - JOUR AU - Wang, J. AU - Street, N. R. AU - Scofield, D. G. AU - Ingvarsson, P. K. PY - 2016 DA - 2016// TI - Variation in linked selection and recombination drive genomic divergence during allopatric speciation of European and American aspens JO - Mol Biol Evol VL - 33 ID - Wang2016 ER - TY - JOUR AU - Delmore, K. E. AU - Lugo Ramos, J. S. AU - Doren, B. M. AU - Lundberg, M. AU - Bensch, S. AU - Irwin, D. E. PY - 2018 DA - 2018// TI - Comparative analysis examining patterns of genomic differentiation across multiple episodes of population divergence in birds JO - Evol Lett VL - 2 ID - Delmore2018 ER - TY - JOUR AU - Talla, V. AU - Johansson, A. AU - Dincă, V. AU - Vila, R. AU - Friberg, M. AU - Wiklund, C. PY - 2019 DA - 2019// TI - Lack of gene flow: narrow and dispersed differentiation islands in a triplet of Leptidea butterfly species JO - Mol Ecol VL - 28 ID - Talla2019 ER - TY - JOUR AU - Mandeville, E. G. AU - Walters, A. W. AU - Nordberg, B. J. AU - Higgins, K. H. AU - Burckhardt, J. C. AU - Wagner, C. E. PY - 2019 DA - 2019// TI - Variable hybridization outcomes in trout are predicted by historical fish stocking and environmental context JO - Mol Ecol VL - 28 ID - Mandeville2019 ER - TY - JOUR AU - Papadopulos, A. S. T. AU - Igea, J. AU - Dunning, L. T. AU - Osborne, O. G. AU - Quan, X. AU - Pellicer, J. PY - 2019 DA - 2019// TI - Ecological speciation in sympatric palms: 3. Genetic map reveals genomic islands underlying species divergence in Howea JO - Evolution VL - 73 ID - Papadopulos2019 ER - TY - JOUR AU - Uyeda, J. C. AU - Hansen, T. F. AU - Arnold, S. J. AU - Pienaar, J. PY - 2011 DA - 2011// TI - The million-year wait for macroevolutionary bursts JO - Proc Natl Acad Sci VL - 108 ID - Uyeda2011 ER - TY - JOUR AU - Supple, M. A. AU - Papa, R. AU - Hines, H. M. AU - McMillan, W. O. AU - Counterman, B. A. PY - 2015 DA - 2015// TI - Divergence with gene flow across a speciation continuum of Heliconius butterflies JO - BMC Evol Biol VL - 15 ID - Supple2015 ER - TY - JOUR AU - Irwin, D. E. AU - Alcaide, M. AU - Delmore, K. E. AU - Irwin, J. H. AU - Owens, G. L. PY - 2016 DA - 2016// TI - Recurrent selection explains parallel evolution of genomic regions of high relative but low absolute differentiation in a ring species JO - Mol Ecol VL - 25 ID - Irwin2016 ER - TY - JOUR AU - Christie, K. AU - Strauss, S. Y. PY - 2018 DA - 2018// TI - Along the speciation continuum: quantifying intrinsic and extrinsic isolating barriers across five million years of evolutionary divergence in California jewelflowers: reproductive isolation and genetic distance JO - Evolution VL - 72 ID - Christie2018 ER - TY - JOUR AU - Dufresnes, C. AU - Mazepa, G. AU - Jablonski, D. AU - Oliveira, R. C. AU - Wenseleers, T. AU - Shabanov, D. A. PY - 2019 DA - 2019// TI - Fifteen shades of green: the evolution of Bufotes toads revisited JO - Molec Phylogenet Evol VL - 141 ID - Dufresnes2019 ER - TY - JOUR AU - Zieliński, P. AU - Dudek, K. AU - Arntzen, J. W. AU - Palomar, G. AU - Niedzicka, M. AU - Fijarczyk, A. PY - 2019 DA - 2019// TI - Differential introgression across newt hybrid zones: evidence from replicated transects JO - Mol Ecol VL - 28 ID - Zieliński2019 ER - TY - JOUR AU - Coyne, J. A. PY - 1992 DA - 1992// TI - Genetics and speciation JO - Nature. VL - 355 ID - Coyne1992 ER - TY - JOUR AU - Presgraves, D. C. PY - 2018 DA - 2018// TI - Evaluating genomic signatures of “the large X-effect” during complex speciation JO - Mol Ecol VL - 27 ID - Presgraves2018 ER - TY - JOUR AU - Burt, D. W. PY - 2002 DA - 2002// TI - Origin and evolution of avian microchromosomes JO - Cytogenet Genome Res VL - 96 ID - Burt2002 ER - TY - STD TI - Rodionov AV. Micro versus macro: a review of structure and functions of avian micro- and macrochromosomes. Russ J Genet. 1996:32517–27. ID - ref44 ER - TY - JOUR AU - Smith, J. M. AU - Haigh, J. PY - 1974 DA - 1974// TI - The hitch-hiking effect of a favourable gene JO - Genet Res VL - 23 ID - Smith1974 ER - TY - JOUR AU - Charlesworth, D. AU - Morgon, M. T. AU - Charlesworth, D. PY - 1993 DA - 1993// TI - The effect of deleterious mutations on neutral molecular variation JO - Genetics VL - 134 ID - Charlesworth1993 ER - TY - JOUR AU - Kim, Y. AU - Stephan, W. PY - 2000 DA - 2000// TI - Joint effects of genetic hitchhiking and background selection on neutral variation JO - Genetics VL - 155 ID - Kim2000 ER - TY - JOUR AU - Huynh, L. Y. AU - Maney, D. L. AU - Thomas, J. W. PY - 2010 DA - 2010// TI - Contrasting population genetic patterns within the white-throated sparrow genome (Zonotrichia albicollis) JO - BMC Genet VL - 11 ID - Huynh2010 ER - TY - JOUR AU - Ellegren, H. PY - 2013 DA - 2013// TI - The evolutionary genomics of birds JO - Annu Rev Ecol Evol Syst VL - 44 ID - Ellegren2013 ER - TY - JOUR AU - Manthey, J. D. AU - Robbins, M. B. AU - Moyle, R. G. PY - 2016 DA - 2016// TI - A genomic investigation of the putative contact zone between divergent Brown creeper (Certhia americana) lineages: chromosomal patterns of genetic differentiation JO - Genome. VL - 59 ID - Manthey2016 ER - TY - JOUR AU - McGuire, J. A. AU - Witt, C. C. AU - Remsen, J. V. AU - Corl, A. AU - Rabosky, D. L. AU - Altshuler, D. L. PY - 2014 DA - 2014// TI - Molecular Phylogenetics and the diversification of hummingbirds JO - Curr Biol VL - 24 ID - McGuire2014 ER - TY - JOUR AU - Abrahamczyk, S. AU - Renner, S. PY - 2015 DA - 2015// TI - The temporal build-up of hummingbird/plant mutualisms in North America and temperate South America JO - BMC Evol Biol VL - 15 ID - Abrahamczyk2015 ER - TY - JOUR AU - Licona-Vera, Y. AU - Ornelas, J. F. PY - 2017 DA - 2017// TI - The conquering of North America: dated phylogenetic and biogeographic inference of migratory behavior in bee hummingbirds JO - BMC Evol Biol VL - 17 ID - Licona-Vera2017 ER - TY - JOUR AU - Judd, E. R. AU - Butler, C. J. AU - Batchelder, N. PY - 2011 DA - 2011// TI - Hybridization between black-chinned (Archilochus alexandri) and ruby-throated (A. colubris) hummingbirds in Oklahoma. Bulletin of the OK Ornith JO - Soc. VL - 44 ID - Judd2011 ER - TY - JOUR AU - Myers, B. M. AU - Rankin, D. T. AU - Burns, K. J. AU - Clark, C. J. PY - 2019 DA - 2019// TI - Behavioral and morphological evidence of an Allen’s × Rufous hummingbird (Selasphorus sasin × S. rufus) hybrid zone in southern Oregon and northern California JO - Auk VL - 136 ID - Myers2019 ER - TY - STD TI - Wells S, Bradley RA, Baptista LF. Hybridization in Calypte hummingbirds. Auk. 1978;95:537–49. ID - ref56 ER - TY - BOOK AU - McCarthy, E. M. PY - 2006 DA - 2006// TI - Handbook of avian hybrids of the world PB - Oxford University Press CY - New York, NY ID - McCarthy2006 ER - TY - STD TI - Battey CJ. Evidence of linked selection on the Z chromosome of hybridizing hummingbirds. Evolution. 2019;74:725–39. ID - ref58 ER - TY - JOUR AU - Elgvin, T. O. AU - Trier, C. N. AU - Torresen, O. K. AU - Hagen, I. J. AU - Lien, S. AU - Nederbragt, A. J. PY - 2017 DA - 2017// TI - The genomic mosaicism of hybrid speciation JO - Sci Adv VL - 3 ID - Elgvin2017 ER - TY - JOUR AU - Hillier, L. AU - Miller, W. AU - Birney, E. PY - 2004 DA - 2004// TI - Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution JO - Nature VL - 432 ID - Hillier2004 ER - TY - JOUR AU - Norris, L. C. AU - Main, B. J. AU - Lee, Y. AU - Collier, T. C. AU - Fofana, A. AU - Cornel, A. J. AU - Lanzaro, G. C. PY - 2015 DA - 2015// TI - Adaptive introgression in an African malaria mosquito coincident with the increased usage of insecticide-treated bed nets JO - PNAS VL - 112 ID - Norris2015 ER - TY - JOUR AU - Doren, B. M. AU - Campagna, L. AU - Helm, B. AU - Illera, J. C. AU - Lovette, I. J. AU - Liedvogel, M. PY - 2017 DA - 2017// TI - Correlated patterns of genetic diversity and differentiation across an avian family JO - Mol Ecol VL - 26 ID - Doren2017 ER - TY - JOUR AU - Vijay, N. AU - Weissensteiner, M. AU - Burri, R. AU - Kawakami, T. AU - Ellegren, H. AU - Wolf, J. B. W. PY - 2017 DA - 2017// TI - Genomewide patterns of variation in genetic diversity are shared among populations, species and higher-order taxa JO - Mol Ecol VL - 26 ID - Vijay2017 ER - TY - STD TI - Clark CJ, Russell SM. Anna's Hummingbird (Calypte anna), version 1.0. In Birds of the World (A. F. Poole, Editor). Cornell Lab of Ornithology, Ithaca, NY, USA. 2020. https://doi.org/10.2173/bow.annhum.01. ID - ref64 ER - TY - STD TI - Baltosser WH, Scott PE. Costa's Hummingbird (Calypte costae), version 1.0. In Birds of the World (A. F. Poole and F. B. Gill, Editors). Cornell Lab of Ornithology, Ithaca, NY, USA. 2020. https://doi.org/10.2173/bow.coshum.01. ID - ref65 ER - TY - STD TI - Baltosser WH, Russell SM. Black-chinned Hummingbird (Archilochus alexandri), version 1.0. In Birds of the World (A. F. Poole and F. B. Gill, Editors). Cornell Lab of Ornithology, Ithaca, NY, USA. 2020. https://doi.org/10.2173/bow.bkchum.01. ID - ref66 ER - TY - STD TI - Weidensaul S, Robinson TR, Sargent RR, Sargent MB, Zenzal TJ. Ruby-throated Hummingbird (Archilochus colubris), version 1.0. In Birds of the World (P. G. Rodewald, Editor). Cornell Lab of Ornithology, Ithaca, NY, USA. 2020. https://doi.org/10.2173/bow.rthhum.01. ID - ref67 ER - TY - STD TI - Healy S, Calder WA. Rufous Hummingbird (Selasphorus rufus), version 1.0. In Birds of the World (A. F. Poole, Editor). Cornell Lab of Ornithology, Ithaca, NY, USA. 2020. https://doi.org/10.2173/bow.rufhum.01. ID - ref68 ER - TY - STD TI - Clark CJ, Mitchell DE. Allen's Hummingbird (Selasphorus sasin), version 1.0. In Birds of the World (A. F. Poole, Editor). Cornell Lab of Ornithology, Ithaca, NY, USA. 2020. https://doi.org/10.2173/bow.allhum.01. ID - ref69 ER - TY - JOUR AU - Zimmerman, D. A. PY - 1973 DA - 1973// TI - Range expansion of Anna's hummingbird JO - Am Birds VL - 27 ID - Zimmerman1973 ER - TY - JOUR AU - Clark, C. J. PY - 2018 DA - 2018// TI - EBird records show substantial growth of the Allen's hummingbird (Selasphorus sasin sedentarius) population in urban Southern California JO - Condor VL - 119 ID - Clark2018 ER - TY - JOUR AU - Baym, M. AU - Kryazhimskiy, S. AU - Lieberman, T. D. AU - Chung, H. AU - Desai, M. M. AU - Kishony, R. PY - 2015 DA - 2015// TI - Inexpensive multiplexed library preparation for megabase-sized genomes JO - PLoS One VL - 10 ID - Baym2015 ER - TY - STD TI - Li H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. 2013; arXiv:13033997. ID - ref73 ER - TY - STD TI - Rhie A, McCarthy SA, Fedrigo O, Damas J, Formenti G, Koren S. Towards complete and error-free genome assemblies of all vertebrate species. 2020. bioRxiv:2020.05.22.110833. ID - ref74 ER - TY - STD TI - Vertebrate Genomes Project. Genome Ark: Calypte anna. Individual 1 Alternate Assembly. 2018. https://vgp.github.io/genomeark/Calypte_anna/. Accessed Oct 2018. UR - https://vgp.github.io/genomeark/Calypte_anna/ ID - ref75 ER - TY - JOUR AU - Li, H. PY - 2011 DA - 2011// TI - A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data JO - Bioinformatics. VL - 27 ID - Li2011 ER - TY - JOUR AU - Danecek, P. AU - Auton, A. AU - Abecasis, G. AU - Albers, C. A. AU - Banks, E. AU - DePristo, M. A. PY - 2011 DA - 2011// TI - And 1000 genomes project analysis group. The variant call format and VCFtools JO - Bioinformatics VL - 27 ID - Danecek2011 ER - TY - JOUR AU - Weir, B. S. AU - Cockerham, C. C. PY - 1984 DA - 1984// TI - Estimating F-statistics for the analysis of population-structure JO - Evolution VL - 38 ID - Weir1984 ER - TY - JOUR AU - Quinlan, A. R. AU - Hall, I. M. PY - 2010 DA - 2010// TI - 2010. BEDTools: a flexible suite of utilities for comparing genomic features JO - Bioinformatics VL - 26 ID - Quinlan2010 ER -