Speciation, gene flow, and seasonal migration in Catharus thrushes (Aves:Turdidae)

Afgan, 2016, The Galaxy platform for accessible, reproducible and collaborative biomedical analyses, Nucleic Acids Res., 44, 3, 10.1093/nar/gkw343 Akaike, 1974, A new look at the statistical model identification, IEEE Trans. Automat. Cont., 19, 716, 10.1109/TAC.1974.1100705 American Ornithologists’ Union, 1957 American Ornithologists’ Union, 1995, Fortieth supplement to the American Ornithologists’ Union check-list of North American birds, The Auk, 112, 819 American Ornithologists’ Union, 1998 Arnold, 2016 Bay, 2017, Genomic islands of divergence or opportunities for introgression?, Proc. Royal Soc. B, 284, 20162414, 10.1098/rspb.2016.2414 Bejerano, 2004, Ultraconserved elements in the human genome, Science, 304, 1321, 10.1126/science.1098119 Belliure, 2000, Dispersal distances predict subspecies richness in birds, J. Evol. Biol., 13, 480, 10.1046/j.1420-9101.2000.00178.x Blackmon, H., Adams, A.A., 2015. EvobiR: tools for comparative analyses and teaching evolutionary biology. https://doi.org/10.5281/zenodo.30938. Bouckaert, R.R., Heled, J., 2014. DensiTree 2: seeing trees through the forest. bioRxiv. https://doi.org/10.1101/012401. Bouckaert, 2014, BEAST 2: a software platform for Bayesian evolutionary analysis, PLoS Comput. Biol., 10, e1003537, 10.1371/journal.pcbi.1003537 Bryant, 2012, Inferring species trees directly from biallelic genetic markers: bypassing gene trees in a full coalescent analysis, Mol. Biol. Evol., 29, 1917, 10.1093/molbev/mss086 Burnham, 2002 Charlesworth, 2016, Population genetics from 1966 to 2016, Heredity, 118, 2, 10.1038/hdy.2016.55 Clement, 2000 Coyne, 2004 Danecek, 2011, The variant call format and VCFtools, Bioinformatics, 27, 2156, 10.1093/bioinformatics/btr330 Delmore, 2015, Genomic analysis of a migratory divide reveals candidate genes for migration and implicates selective sweeps in generating islands of differentiation, Mol. Ecol., 24, 1873, 10.1111/mec.13150 Delmore, 2016, The genetics of seasonal migration and plumage color, Curr. Biol., 26, 2167, 10.1016/j.cub.2016.06.015 de Queiroz, 2007, Species concepts and species delimitation, Syst. Biol., 56, 879, 10.1080/10635150701701083 Derti, 2006, Mammalian ultraconserved elements are strongly depleted among segmental duplications and copy number variants, Nature Genet., 38, 1216, 10.1038/ng1888 Drovetski, 2018, Multi-locus reassessment of a striking discord between mtDNA gene trees and taxonomy across two congeneric species complexes, Mol. Phylogenet. Evol., 120, 43, 10.1016/j.ympev.2017.11.023 Durand, 2011, Testing for ancient admixture between closely related populations, Mol. Biol. Evol., 28, 2239, 10.1093/molbev/msr048 Edgar, 2004, MUSCLE: multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Res., 32, 1792, 10.1093/nar/gkh340 Evans, 1994, Nocturnal flight call of Bicknell’s Thrush, Wilson Bull., 106, 55 Ewing, 2015, The consequences of not accounting for background selection in demographic inference, Mol. Ecol., 25, 135, 10.1111/mec.13390 Faircloth, B.C., 2013. Illumiprocessor: a trimmomatic wrapper for parallel adapter and quality trimming. https://doi.org/10.6079/J9ILL. Faircloth, 2016, PHYLUCE is a software package for the analysis of conserved genomic loci, Bioinformatics, 32, 786, 10.1093/bioinformatics/btv646 Faircloth, 2012, Ultraconserved elements anchor thousands of genetic markers spanning multiple evolutionary timescales, Syst. Biol., 61, 717, 10.1093/sysbio/sys004 Feder, 2012, The genomics of speciation-with-gene-flow, Trends Genet., 28, 342, 10.1016/j.tig.2012.03.009 Felsenstein, 2005, Accuracy of coalescent likelihood estimates: Do we need more sites, more sequences, or more loci?, Mol. Biol. Evol., 23, 691, 10.1093/molbev/msj079 Ferreira, 2018, Evidence for mtDNA capture in the jacamar Galbula leucogastra/chalcothorax species-complex and insights on the evolution of white-sand ecosystems in the Amazon basin, Mol. Phylogenet. Evol., 129, 149, 10.1016/j.ympev.2018.07.007 Fitzgerald, 2017, Taxonomy and distribution of the imperiled Newfoundland Gray-cheeked Thrush, Catharus minimus minimus, Avian Conserv. Ecol., 12, 10, 10.5751/ACE-00976-120110 Fontaine, 2015, Extensive introgression in a malaria vector species complex revealed by phylogenomics, Science, 347, 1258524, 10.1126/science.1258524 Gagnaire, 2013, The genetic architecture of reproductive isolation during speciation-with-gene-flow in lake whitefish species pairs assessed by RAD sequencing, Evolution, 67, 2483, 10.1111/evo.12075 Glenn, 2019, Adapterama I: Universal stubs and primers for thousands of dual-indexed Illumina libraries (iTru & iNext), PeerJ, 10.7717/peerj.7755 Grabherr, 2011, Full-length transcriptome assembly from RNA-seq data without a reference genome, Nat. Biotechnol., 29, 644, 10.1038/nbt.1883 Green, 2010, A draft sequence of the Neandertal genome, Science, 328, 710, 10.1126/science.1188021 Gutenkunst, 2009, Inferring the joint demographic history of multiple populations from multidimensional SNP frequency data, PLOS Genet., 5, e1000695, 10.1371/journal.pgen.1000695 Harris, 2018, Discordance between genomic divergence and phenotypic variation in a rapidly evolving avian genus (Motacilla), Mol. Phylogenet. Evol., 120, 183, 10.1016/j.ympev.2017.11.020 Harvey, 2016, Sequence capture versus restriction site associated DNA sequencing for shallow systematics, Syst. Biol., 65, 910, 10.1093/sysbio/syw036 Heckscher, 2017, Veery (Catharus fuscescens), version 3.0 Hines, 2011, Wing patterning gene redefines the mimetic history of Heliconius butterflies, Proc. Natl. Acad. Sci., 108, 19666, 10.1073/pnas.1110096108 Huson, 2005, Application of phylogenetic networks in evolutionary studies, Mol. Biol. Evol., 23, 254, 10.1093/molbev/msj030 Katoh, 2013, MAFFT multiple sequence alignment software version 7: improvements in performance and usability, Mol. Biol. Evol., 30, 772, 10.1093/molbev/mst010 Katzman, 2007, Human genome ultraconserved elements are ultraselected, Science, 317, 915, 10.1126/science.1142430 Kumar, 2017, The evolutionary history of bears is characterized by gene flow across species, Sci. Rep., 7, 46487, 10.1038/srep46487 Leaché, 2014, The influence of gene flow on species tree estimation: a simulation study, Syst. Biol., 63, 17, 10.1093/sysbio/syt049 Li, H., 2013. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv:1303.3997v1. Li, 2009, Fast and accurate short read alignment with Burrows-Wheeler transform, Bioinformatics, 25, 1754, 10.1093/bioinformatics/btp324 Li, 2009, The sequence alignment/map (SAM) format and SAMtools, Bioinformatics, 25, 2078, 10.1093/bioinformatics/btp352 Lowther, 2001, Gray-cheeked Thrush (Catharus minimus), version 2.0 Lugo Ramos, 2017, Candidate genes for migration do not distinguish migratory and non-migratory birds, J. Comp. Physiol. A, 203, 383, 10.1007/s00359-017-1184-6 Maddisson, 1997, Gene trees in species trees, Syst. Biol., 46, 523, 10.1093/sysbio/46.3.523 Mallet, 2015, How reticulated are species?, BioEssays, 38, 140, 10.1002/bies.201500149 Marshall, 2001, The Gray-cheeked Thrush, Catharus minimus, and its New England subspecies, Bicknell’s Thrush, Catharus minimus bicknelli, Nuttall Ornithological Club, 28, 1 Martin, 2013, Genome-wide evidence for speciation with gene flow in Heliconius butterflies, Genome Res., 23, 1817, 10.1101/gr.159426.113 Martinsen, 2018, Documentation of a hybrid Bicknell’s Thrush (Catharus bicknelli) × Veery (C. fuscescens) using vocalization and genetic data, Wilson J. Ornithol., 130, 70, 10.1676/16-061.1 Mayr, 2004, 80 years of watching the evolutionary scenery, Science, 305, 46, 10.1126/science.1100561 McCormack, 2012, Ultraconserved elements are novel phylogenomic markers that resolve placental mammal phylogeny when combined with species tree analysis, Genome Res., 22, 746, 10.1101/gr.125864.111 McCormack, 2013, A phylogeny of birds based on over 1,500 loci collected by target enrichment and high-throughput sequencing, PLoS One, 8, e54848, 10.1371/journal.pone.0054848 McKenna, 2010, The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data, Genome Res., 20, 1297, 10.1101/gr.107524.110 Mirarab, 2014, ASTRAL: genome-scale coalescent-based species tree estimation, Bioinformatics, 30, 541, 10.1093/bioinformatics/btu462 Montgomery, 1896, Extensive migration in birds as a check upon the production of geographical varieties, Am. Nat., 458, 10.1086/276410 Nazareno, 2017, Minimum sample sizes for population genomics: an empirical study from an Amazonian plant species, Mol. Ecol. Res., 17, 1136, 10.1111/1755-0998.12654 Nosil, 2012 Nuttall, 1840 Ouellet, 1993, Bicknell’s Thrush: taxonomic status and distribution, Wilson Bull., 105, 545 Outlaw, 2003, Evolution of long-distance migration in and historical biogeography of Catharus thrushes: a molecular phylogenetic approach, Auk, 120, 299, 10.1093/auk/120.2.299 Price, 2008 Rambaut, A., Suchard, M.A., Xie, D., Drummond, A.J., 2014. Tracer v1.6. Available from http://beast.bio.ed.ac.uk/Tracer. Ruegg, 2014, A role for migration-linked genes and genomic islands in divergence of a songbird, Mol. Ecol., 23, 4757, 10.1111/mec.12842 Rundle, 2005, Ecological speciation, Ecol. Lett., 8, 336, 10.1111/j.1461-0248.2004.00715.x Sayyari, 2016, Fast coalescent-based computation of local branch support from quartet frequencies, Mol. Biol. Evol., 33, 1654, 10.1093/molbev/msw079 Schluter, 1996, Ecological speciation in postglacial fishes, Philos. Trans. R. Soc. Lond. B, 351, 807, 10.1098/rstb.1996.0075 Schluter, 2001, Ecology and the origin of species, Trends Ecol. Evol., 16, 372, 10.1016/S0169-5347(01)02198-X Shipham, 2017, A genomic approach reinforces a hypothesis of mitochondrial capture in eastern Australian rosellas, The Auk, 134, 181, 10.1642/AUK-16-31.1 Simons, 2006, Transposon-free regions in mammalian genomes, Genome Res., 16, 164, 10.1101/gr.4624306 Smith, 2014, Target capture and massively parallel sequencing of ultraconserved elements (UCEs) for comparative studies at shallow evolutionary time scales, Syst. Biol., 63, 83, 10.1093/sysbio/syt061 Stamatakis, 2014, RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies, Bioinformatics, 30, 1312, 10.1093/bioinformatics/btu033 Sukumaran, 2017, Multispecies coalescent delimits structure, not species, Proc. Natl. Acad. Sci., 114, 1607, 10.1073/pnas.1607921114 Topp, 2013, How migratory thrushes conquered northern North America: a comparative phylogeography approach, PeerJ, 1, e206, 10.7717/peerj.206 Townsend, 2015, Bicknell's Thrush (Catharus bicknelli), version 2.0 Voelker, 2013, Gene trees, species trees and Earth history combine to shed light on the evolution of migration in a model avian system, Mol. Ecol., 22, 3333, 10.1111/mec.12305 Wallace, 1939, Bicknell’s Thrush, its taxonomy, distribution, and life history, Proc. Boston Soc. Nat. Hist., 41, 211 Whitaker, 2018, Gray-cheeked Thrush (Catharus minimus), version 2.0 White, 2017, Ultraconserved elements resolve the phylogeny of potoos (Aves: Nyctibiidae), J. Avian Biol., 48, 872, 10.1111/jav.01313 Winker, 2000, Migration and speciation, Nature, 404, 36, 10.1038/35003651 Winker, 2010, On the origin of species through heteropatric differentiation: a review and a model of speciation in migratory animals, Ornithol. Monogr., 69, 1, 10.1525/om.2010.69.1.1 Winker, 2018, Ultraconserved elements (UCEs) illuminate the population genomics of a recent, high-latitude avian speciation event, PeerJ, 6, e5735, 10.7717/peerj.5735 Winker, 2019, Speciation despite gene flow in two owls (Aegolius ssp.): Evidence from 2517 ultraconserved element loci, The Auk, 136, 10.1093/auk/ukz012 Winker, 2013, Heteropatric speciation in a duck, Anas crecca, Mol. Ecol., 22, 5922, 10.1111/mec.12525 Winker, 2006, Seasonal migration, speciation, and morphological convergence in the genus Catharus (Turdidae), The Auk, 123, 1052 Winker, 1988, The relationship between Hylocichla and Catharus (Turdinae), The Auk, 105, 392, 10.2307/4087513 Xi, 2015, Genes with minimal phylogenetic information are problematic for coalescent analyses when gene tree estimation is biased, Mol. Phylogenet. Evol., 92, 63, 10.1016/j.ympev.2015.06.009 Zarza, 2016, Hidden histories of gene flow in highland birds revealed with genomic markers, Mol. Ecol., 25, 5144, 10.1111/mec.13813 Zhang, 2000, A greedy algorithm for aligning DNA sequences, J. Comput. Biol., 7, 203, 10.1089/10665270050081478 Zheng, 2011, Exploring patterns and extent of bias in estimating divergence time from mitochondrial DNA sequence data in a particular lineage: a case study of salamanders (order Caudata), Mol. Biol. Evol., 9, 2521, 10.1093/molbev/msr072 Zheng, 2018, Gene flow analysis method, the D-statistic, is robust in a wide parameter space, BMC Bioinform., 19, 1, 10.1186/s12859-017-2002-4