Phylogeny, migration and life history: filling the gaps in the origin and biogeography of the Turdus thrushes

ABA (2016) The ABA checklist version 7.9.0. American Birding Association, Delaware City. http://listing.aba.org/aba-checklist/. Accessed 17 Aug 2016 Alerstam T, Hedenström A, Akesson S (2003) Long-distance migration: evolution and determinants. Oikos 103:247–260 Arnaiz-Villena A, Guillén J, Ruiz-del-Valle V, Lowy E, Zamora J, Varela P, Stefani D, Allende LM (2001) Phylogeography of crossbills, bullfinches, grosbeaks, and rosefinches. CMLS Cell Mol Life Sci 58:1–8 Arnaiz-Villena A, Ruiz-del-Valle V, Gomez-Prieto P, Rey D, Enriquez-de-Salamanca M, Marco J, Muniz E, Martin-Villa M, Areces C (2014) Carduelini new sistematics: Crimson-winged Finch (Rhodopechys sanguineus) is included in “arid-zone” Carduelini finches by mitochondrial DNA phylogeny. Open Ornithol J 7:55–62 Barke R, Lamb S (2006) Late Cenozoic uplift of the Eastern Cordillera, Bolivian Andes. Earth Planet Sci Lett 249:350–367 Barker FK, Burns KJ, Klicka J, Lanyon SM, Lovette IJ (2015) New insights into New World biogeography: an integrated view from the phylogeny of blackbirds, cardinals, sparrows, tanagers, warblers, and allies. Auk 132:333–348 Bartoń K (2015) MuMIn: multi-model inference. R package version 1.13.4. https://cran.r-project.org/web/packages/. Accessed 23 Nov 2016 Barve S, Mason NA (2015) Interspecific competition affects evolutionary links between cavity nesting, migration and clutch size in Old World flycatchers (Muscicapdae). Ibis 157:299–311 Bates JM, Zink RM (1994) Evolution into the Andes: molecular evidence for species relationships in the genus Leptopogon. Auk 111:507–515 Bell CP (1996) The relationship between geographic variation in clutch size and migration pattern in the Yellow Wagtail. Bird Study 43:333–341 Belthoff JR, Gauthreaux SA (1991) Partial migration and differential winter distribution of House Finches in the eastern United States. Condor 93:374–382 Benkman CW (2003) Divergent selection drives the adaptive radiation of crossbills. Evolution 57:1176–1181 BirdLife International (2015a) The BirdLife checklist of the birds of the world: version 8. http://datazone.birdlife.org/home. Accessed 29 Oct 2015 BirdLife International (2015b) IUCN Red List for birds. http://datazone.birdlife.org/home. Accessed 29 Oct 2015 Bloch NI, Morrow JM, Chang BSW, Price TD (2015) SWS2 visual pigment evolution as a test of historically contingent patterns of plumage color evolution in warblers. Evolution 69:341–356 Bobe R, Behrensmeyer AK (2004) The expansion of grassland ecosystems in Africa in relation to mammalian evolution and the origin of the genus Homo. Palaeogeogr Palaeoclimatol Palaeoecol 207:399–420 Boyce AJ, Martin TE (2017) Contrasting latitudinal patterns of life history divergence in two genera of New World thrushes (Turdinae). J Avian Biol 48:581–590 Brumfield RT, Edwards SV (2007) Evolution into and out of the Andes: a Bayesian analysis of historical diversification in Thamnophilus antshrikes. Evolution 61:346–367 Castresana J (2000) Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 17:540–552 Charif D, Lobry JR (2007) SeqinR 1.0-2: a contributed package to the R project for statistical computing devoted to biological sequences retrieval and analysis. Structural approaches to sequence evolution. Springer, Berlin, Heidelberg, pp 207–232 Clement P, Hathway R (2010) Thrushes. Bloomsbury, London Clot A, Chaline J, Heintz E, Jammot D, Mourer-Chauviré C, Rage JC (1976) Montoussé 5 (Hautes-Pyrénées), un nouveau remplissage de fissure à faune de vertébrés du Pléistocène inférieur. Geobios 9:511–514 Cooney CR, Seddon N, Tobias JA (2016) Widespread correlations between climatic niche evolution and species diversification in birds. J Anim Ecol 85:869–878 Crochet PA, Joynt G (2015) AERC list of Western Palearctic birds. http://www.aerc.eu/tac.html. Accessed 19 Aug 2016 del Hoyo J, Elliot A, Christie DA (2005) Handbook of the birds of the world (Volume 10): cuckoo-shrikes to thrushes. Lynx, Barcelona del Hoyo J, Elliott A, Sargatal J, Christie DA, de Juana E (2016) Handbook of the birds of the world alive. Lynx, Barcelona deMenocal PB (2004) African climate change and faunal evolution during the Pliocene–Pleistocene. Earth Planet Sci Lett 220:3–24 Drovetski SV, Zink RM, Rohwer S, Fadeev IV, Nesterov EV, Karagodin I, Koblik EA, Red’kin YA (2004) Complex biogeographic history of a Holarctic passerine. Proc R Soc Lond B Biol Sci 271:545–551 Drovetski SV, Zink RM, Ericson PGP, Fadeev IV (2010) A multilocus study of Pine Grosbeak phylogeography supports the pattern of greater intercontinental divergence in Holarctic boreal forest birds than in birds inhabiting other high-latitude habitats. J Biogeogr 37:696–706 Drovetski SV, Semenov G, Drovetskaya SS, Fadeev IV, Red’kin YA YA, Voelker G (2013) Geographic mode of speciation in a mountain specialist avian family endemic to the Palearctic. Ecol Evol 3:1518–1528 Drummond AJ, Rambaut A (2007) BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol 7:214 Drummond AJ, Ho SY, Phillips MJ, Rambaut A (2006) Relaxed phylogenetics and dating with confidence. PLoS Biol 4:e88 Emslie SD (1998) Avian community, climate, and sea-level changes in the Plio-Pleistocene of the Florida Peninsula. Ornithol Monogr 50:1–113 Faaborg J, Holmes RT, Anders AD, Bildstein KL, Dugger KM, Gauthreaux SA, Heglund P, Hobson KA, Jahn AE, Johnson DH, Latta SC, Levey DJ, Marra PP, Merkord CL, Nol E, Rothstein SI, Sherry TW, Sillett TS, Thompson FR, Warnock N (2010) Recent advances in understanding migration systems of New World land birds. Ecol Monogr 80:3–48 Fjeldså J (2013) The global diversification of songbirds (Oscines) and the build-up of the Sino-Himalayan diversity hotspot. Chin Birds 4:132–143 Fuchs J, Johnson JA, Mindell DP (2015) Rapid diversification of falcons (Aves: Falconidae) due to expansion of open habitats in the Late Miocene. Mol Phylogenet Evol 82:166–182 Gill F, Donsker D (2018) IOC world bird list (version 8.2). https://doi.org/10.14344/IOC.ML.8.2; https://www.worldbirdnames.org/ Gómez C, Tenorio EA, Montoya P, Cadena CD (2016) Niche-tracking migrants and niche-switching residents: evolution of climatic niches in New World warblers (Parulidae). Proc R Soc Lond B Biol Sci 283:20152458 Gregory-Wodzicki KM (2000) Uplift history of the Central and Northern Andes: a review. GSA Bull 112:1097–1105 Hadarics T (2016) New species in the Hungarian avifauna in 2015. Ornis Hung 24:78–83 Harrison CJO (1987) Pleistocene and prehistoric birds of south-west Britain. Proc Univ Bristol Spelaeol Soc 18:81–104 Hedges SB (1996) Historical biogeography of West Indian vertebrates. Annu Rev Ecol Syst 27:163–196 Hernández Fernández M, Vrba ES (2006) Plio-Pleistocene climatic change in the Turkana Basin (East Africa): evidence from large mammal faunas. J Hum Evol 50:595–626 Hooghiemstra H, Van de Hammen T (2004) Quaternary Ice-Age dynamics in the Colombian Andes: developing an understanding of our legacy. Philos Trans R Soc Lond B 359:173–181 Jahn AE, Cueto VR (2012) The potential for comparative research across New World bird migration systems. J Ornithol 153:199–205 Jánossy D (1991) Late Miocene bird remains from Polgárdi (W-Hungary). Aquila 98:13–35 Jetz W, Thomas GH, Joy JB, Hartmann K, Mooers AO (2012) The global diversity of birds in space and time. Nature 491:444–448 Johansson US, Nylinder S, Ohlson JI, Tietze DT (2018) Reconstruction of the late Miocene biogeographical history of tits and chickadees (Aves: Passeriformes: Paridae): a comparison between discrete area analyses and probabilistic diffusion approach. J Biogeogr 45:14–25 Jonsson KA, Holt BG (2015) Islands contribute disproportionately high amounts of evolutionary diversity in passerine birds. Nat Commun 6:8538 Kamilar JM, Cooper N (2013) Phylogenetic signal in primate behaviour, ecology and life history. Philos Trans R Soc B 368:20120341 Katoh K, Kuma KI, Toh H, Miyata T (2005) MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res 33:511–518 Kennedy JD, Price TD, Fjeldså J, Rahbek C (2016) Historical limits on species co-occurrence determine variation in clade richness among New World passerine birds. J Biogeogr 44:736–747 Ketterson ED, Nolan V (1982) The role of migration and winter mortality in the life history of a temperate-zone migrant, the Dark-eyed Junco, as determined from demographic analyses of winter populations. Auk 99:243–259 Klicka J, Voelker G, Spellman GM (2005) A molecular phylogenetic analysis of the “true thrushes” (Aves: Turdinae). Mol Phylogenet Evol 34:486–500 Landis MJ, Matzke NJ, Moore BR, Huelsenbeck JP (2013) Bayesian analysis of biogeography when the number of areas is large. Syst Biol 62:789–804 Liedvogel M, Delmore K (2018) (Micro) evolutionary changes and the evolutionary potential of bird migration. In: Tietze DT (ed) Bird species. Springer, Cham, pp 109–127 Martin TE (1995) Avian life history evolution in relation to nest sites, nest predation, and food. Ecol Monogr 65:101–127 Matzke NJ (2013) Probabilistic historical biogeography: new models for founder-event speciation, imperfect detection, and fossils allow improved accuracy and model-testing. Ph.D. thesis, Department of Integrative Biology and Designated Emphasis in Computational and Genomic Biology, University of California, Berkeley Matzke NJ (2016) Stochastic mapping under biogeographical models. PhyloWiki BioGeoBEARS. http://phylo.wikidot.com/. Accessed 15 Jan 2018 Mazerolle DF, Hobson KA, Wassenaar LI (2005) Stable isotope and band-encounter analyses delineate migratory patterns and catchment areas of White-throated Sparrows at a migration monitoring station. Oecologia 144:541–549 Moyle RG, Hosner PA, Jones AW, Outlaw DC (2015) Phylogeny and biogeography of Ficedula flycatchers (Aves: Muscicapidae): novel results from fresh source material. Mol Phylogenet Evol 82:87–94 Moyle RG, Oliveros CH, Andersen MJ, Hosner PA, Benz BW, Manthey JD, Travers SL, Brown RM, Faircloth BC (2016) Tectonic collision and uplift of Wallacea triggered the global songbird radiation. Nat Commun 7:12790 Myers JP (1981) A test of three hypotheses for latitudinal segregation of the sexes in wintering birds. Can J Zool 59:1527–1534 Nagy J (2017) Phylogeny and evolution of the European Goldfinch (Carduelis carduelis) and its allies–a review of the “bird of the year”. Ornis Hung 25:1–10 Nagy J, Tökölyi J (2014) Phylogeny, historical biogeography and the evolution of migration in accipitrid birds of prey (Aves: Accipitriformes). Ornis Hung 22:15–35 Nagy J, Zs Végvári, Varga Z (2017) Life history traits, bio-climate and migratory systems of accipitrid birds of prey (Aves: Accipitriformes). Biol J Linn Soc 121:63–71 Newton I (2008) The migration ecology of birds. Academic Press, London Nguembock B, Fjeldså J, Couloux A, Pasquet E (2009) Molecular phylogeny of Carduelinae (Aves, Passeriformes, Fringillidae) proves polyphyletic origin of the genera Serinus and Carduelis and suggests redefined generic limits. Mol Phylogenet Evol 51:169–181 Núñez-Zapata J, Peterson AT, Navarro-Sigüenza AG (2016) Pleistocene diversification and speciation of White-throated Thrush (Turdus assimilis; Aves: Turdidae). J Ornithol 157:1073–1085 Nylander JAA, Olsson U, Alström P, Sanmartin I (2008) Accounting for phylogenetic uncertainty in biogeography: a Bayesian approach to dispersal-vicariance analysis of the thrushes (Aves: Turdus). Syst Biol 57:257–268 Oatley G, Simmons RE, Fuchs J (2015) A molecular phylogeny of the harriers (Circus, Accipitridae) indicate the role of long-distance dispersal and migration in diversification. Mol Phylogenet Evol 85:150–160 Olsson U, Alström P (2013) Molecular evidence suggests that the enigmatic Sulawesi endemic Geomalia heinrichi belongs in the genus Zoothera (Turdidae, Aves). Chin Birds 4:155–160 Outlaw DC, Voelker G, Mila B, Girman DJ (2003) Evolution of long-distance migration in and historical biogeography of Catharus thrushes: a molecular phylogenetic approach. Auk 120:299–310 Päckert M, Sun Y, Strutzenberger P, Valchuk O, Tietze DT, Martens J (2015) Phylogenetic relationships of endemic bunting species (Aves, Passeriformes, Emberizidae, Emberiza koslowi) from the eastern Qinghai-Tibet Plateau. Vertebr Zool 65:135–150 Pagel M (1997) Inferring evolutionary processes from phylogenies. Zool Scr 26:331–348 Pagel M (1999) Inferring the historical patterns of biological evolution. Nature 401:877 Pagel M, Meade A, Barker D (2004) Bayesian estimation of ancestral character states on phylogenies. Syst Biol 53:673–684 Paradis E, Claude J, Strimmer K (2004) APE: analyses of phylogenetics and evolution in R language. Bioinformatics 20:289–290 Parchman TL, Benkman CW, Britch SC (2006) Patterns of genetic variation in the adaptive radiation of New World crossbills (Aves: Loxia). Mol Ecol 15:1873–1887 Payevsky VA (2014) Phylogeny and classification of passerine birds, Passeriformes. Biol Bull Rev 4:143–156 Pinheiro J, Bates D, DebRoy S, Sarkar D, R Development Core Team (2015) nlme: linear and nonlinear mixed effects models. R package version 3.1-121. https://cran.r-project.org/web/packages/. Accessed 13 Jan 2018 Price TD (2010) The roles of time and ecology in the continental radiation of the Old World leaf warblers (Phylloscopus and Seicercus). Philos Trans R Soc Lond B 365:1749–1762 Pulido F (2007) The genetics and evolution of avian migration. AIBS Bull 57:165–174 Qu Y, Song G, Gao B, Quan Q, Ericson PGP, Lei F (2014) The influence of geological events on the endemism of East Asian birds studied through comparative phylogeography. J Biogeogr 42:179–192 R Development Core Team (2016) R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna. https://www.r-project.org/. Accessed 13 Mar 2016 Rainio MJ, Kanerva M, Wahlberg N, Nikinmaa M, Eeva T (2012) Variation of basal EROD activities in ten passerine bird species—relationships with diet and migration status. PLoS One 7:e33926 Rambaut A, Drummond AJ (2016) TreeAnnotator version 1.8.3. University of Edinburgh, Edinburgh. http://beast.community/programs. Accessed 4 Nov 2016 Rambaut A, Drummond AJ, Xie D, Baele G, Suchard MA (2018) Posterior summarisation in Bayesian phylogenetics using Tracer 1.7. Syst Biol 67:901–904 Rappole JH, Ramos MA, Winker K (1989) Wintering Wood Thrush movements and mortality in Southern Veracruz. Auk 106:402–410 Ravelo AC, Andreasen DK, Lyle M, Lyle AO, Wara MW (2004) Regional climate shifts caused by gradual global cooling in the Pliocene epoch. Nature 429:263–267 Reddy S, Kimball RT, Pandey A, Hosner PA, Braun MJ, Hackett SJ, Han K, Harshman J, Huddleston CJ, Kingston S, Marks BD, Miglia KJ, Moore WS, Sheldon FH, Witt CC, Yuri T, Braun EL (2017) Why do phylogenomic data sets yield conflicting trees? Data type influences the avian tree of life more than taxon sampling. Syst Biol 66:857–879 Ree RH, Sanmartín I (2018) Conceptual and statistical problems with the DEC+J model of founder-event speciation and its comparison with DEC via model selection. J Biogeogr 45:741–749 Ree RH, Smith SA (2008) Maximum likelihood inference of geographic range evolution by dispersal, local extinction, and cladogenesis. Syst Biol 57:4–14 Ree RH, Moore BR, Webb CO, Donoghue MJ (2005) A likelihood framework for inferring the evolution of geographic range on phylogenetic trees. Evolution 59:2299–2311 Revell LJ (2012) phytools: an R package for phylogenetic comparative biology (and other things). Methods Ecol Evol 3:217–223 Ricklefs R, Bermingham E (2008) The West Indies as a laboratory of biogeography and evolution. Philos Trans R Soc Lond B 363:2393–2413 Rodewald P (2016) The birds of North America online. Cornell Laboratory of Ornithology, Ithaca Rolland J, Jiguet F, Jonsson KA, Condamine FL, Morlon H (2014) Settling down of seasonal migrants promotes bird diversification. Proc R Soc B 281:20140473 Ronquist F (1997) Dispersal-vicariance analysis: a new approach to the quantification of historical biogeography. Syst Biol 46:195–203 Salisbury CL, Seddon N, Cooney CR, Tobias JA (2012) The latitudinal gradient in dispersal constraints: ecological specialisation drives diversification in tropical birds. Ecol Lett 15:847–855 Schliep KP (2011) phangorn: phylogenetic analysis in R. Bioinformatics 27:592–593 Selvatti AP, Gonzaga LP, de Moraes Russo CA (2015) A Paleogene origin for crown passerines and the diversification of the Oscines in the New World. Mol Phylogenet Evol 88:1–15 Smith RB, Meehan TD, Wolf BO (2003) Assessing migration patterns of Sharp-shinned Hawks Accipiter striatus using stable-isotope and band encounter analysis. J Avian Biol 34:387–392 Sol D, Stirling DG, Lefebvre L (2005) Behavioural drive or behavioural inhibition in evolution: subspecific diversification in Holarctic passerines. Evolution 59:2669–2677 Stamatakis A (2006) RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22:2688–2690 Telleria JL, Blázquez M, De La Hera I, Pérez-Tris J (2013) Migratory and resident Blackcaps Sylvia atricapilla wintering in southern Spain show no resource partitioning. Ibis 155:750–761 Thompson JN (2016) Coevolution, local adaptation and ecological speciation. Mol Ecol 25:5608–5610 Voelker G, Outlaw RK (2008) Establishing a perimeter position: speciation around the Indian Ocean Basin. J Evol Biol 21:1779–1788 Voelker G, Rohwer S, Bowie RCK, Outlaw DC (2007) Molecular systematics of a speciose, cosmopolitan songbird genus: defining the limits of, and relationships among, the Turdus thrushes. Mol Phylogenet Evol 42:422–434 Voelker G, Rohwer S, Outlaw DC, Bowie RCK (2009) Repeated trans-Atlantic dispersal catalysed a global songbird radiation. Glob Ecol Biogeogr 18:41–49 Voelker G, Bowie RCK, Klicka J (2013) Gene trees, species trees and Earth history combine to shed light on the evolution of migration in a model avian system. Mol Ecol 22:3333–3344 Wang N, Kimball RT, Braun EL, Liang B, Zhang Z (2016) Ancestral range reconstruction of Galliformes: the effects of topology and taxon sampling. J Biogeogr 44:122–135 Winger BM, Lovette IJ, Winker DW (2012) Ancestry and evolution of seasonal migration in the Parulidae. Proc R Soc B 279:610–618 Winger BM, Barker FK, Ree RH (2014) Temperate origins of long-distance seasonal migration in New World songbirds. Proc Natl Acad Sci 111:12115–12120 Winker K, Pruett CL (2006) Seasonal migration, speciation, and morphological convergence in the genus Catharus (Turdidae). Auk 123:1052–1068 Zachos J, Pagani M, Sloan S, Thomas E, Billups K (2001) Trends, rhythms, and aberrations in global climate 65 Ma to present. Science 292:686–693 Zink RM, Rohwer S, Andreev AV, Dittmann DL (1995) Trans-Beringia comparisons of mitochondrial DNA differentiation in birds. Condor 97:639–649 Zink RM, Rohwer S, Drovetski S, Blackwell-Rago RC, Farrell SL (2002) Holarctic phylogeography and species limits of Three-toed Woodpeckers. Condor 104:167–170