Reconstructing the geographic origin of the New World jays

References

• De los Monteros AE, Cracraft J. Intergeneric relationships of the New World jays inferred from cytochrome b gene sequences. Condor. 1997;99:490–502.
   Web of Science ®Google Scholar
• Zusi RL. A feeding adaptation of the jaw articulation in New World jays (Corvidae). Auk. 1987;104:665–680.
   Web of Science ®Google Scholar
• Goodwin D. Crows of the world. Ithaca (NY): Cornell University Press; 1976.
   Google Scholar
• Madge S, Burn H. Crows and jays: A guide to the crows, jays and magpie of the world. Boston: Houghton Mifflin Company; 1994.
   Google Scholar
• Brown JL. Alternate routes to sociality in jays—with a theory for the evolution of altruism and communal breeding. Am Zool. 1974;14:63–80.10.1093/icb/14.1.63
   Google Scholar
• Brown JL. Social organization and behavior of the Mexican Jay. Condor. 1963;65:l26–l53.
   Google Scholar
• Peterson A. Phylogeny and rates of molecular evolution in the jays of the genus Aphelocoma (Corvidae). Auk. 1992;109:134–148.
   Web of Science ®Google Scholar
• Sibley CG, Ahlquist J. The phylogeny and classification of the Australo-Papuan Passerine birds. Emu. 1985;85:1–14.10.1071/MU9850001
   Web of Science ®Google Scholar
• Ericson PG, Christidis L, Cooper A, et al. A Gondwanan origin of passerine birds supported by DNA sequences of the endemic New Zealand wrens. Proc R Soc Lond B. 2002;269:235–241.10.1098/rspb.2001.1877
   PubMed Web of Science ®Google Scholar
• Ericson PG, Johansson US. Phylogeny of Passerida (Aves: Passeriformes) based on nuclear and mitochondrial sequence data. Mol Phylogenet Evol. 2003;29:126–138.10.1016/S1055-7903(03)00067-8
   PubMed Web of Science ®Google Scholar
• Ericson PG, Jansén AL, Johansson US, et al. Inter-generic relationships of the crows, jays, magpies and allied groups (Aves: Corvidae) based on nucleotide sequence data. J Avian Biol. 2005;36:222–234.10.1111/jav.2005.36.issue-3
   Web of Science ®Google Scholar
• Jønsson KA, Fabre P-H, Kennedy JD, et al. A supermatrix phylogeny of corvoid passerine birds (Aves: Corvides). Mol Phylogenet Evol. 2016;94:87–94.10.1016/j.ympev.2015.08.020
   PubMed Web of Science ®Google Scholar
• Craig A, Feare C, Hoyo Jd, et al. Handbook of the birds of the world. Vol. 14: Bush-shrikes to Old World sparrows. Barcelona: Lynx Edicions; 2009.
   Google Scholar
• Bonaccorso E, Peterson AT. A multilocus phylogeny of New World jay genera. Mol Phylogenet Evol. 2007;42:467–476.10.1016/j.ympev.2006.06.025
   PubMed Web of Science ®Google Scholar
• Benz BW, Robbins MB, Peterson AT. Evolutionary history of woodpeckers and allies (Aves: Picidae): placing key taxa on the phylogenetic tree. Mol Phylogenet Evol. 2006;40:389–399.10.1016/j.ympev.2006.02.021
   PubMed Web of Science ®Google Scholar
• Saunders MA, Edwards SV. Dynamics and phylogenetic implications of MtDNA control region sequences in New World Jays (Aves: Corvidae). J Mol Evol. 2000;51:97–109.10.1007/s002390010070
   PubMed Web of Science ®Google Scholar
• Cicero C, Johnson NK. Higher-level phylogeny of New World vireos (Aves: Vireonidae) based on sequences of multiple mitochondrial DNA genes. Mol Phylogen Evol. 2001;20:27–40.10.1006/mpev.2001.0944
   PubMed Web of Science ®Google Scholar
• Kennedy JD, Weir JT, Hooper DM, et al. Ecological limits on diversification of the Himalayan core Corvoidea. Evolution. 2012;66:2599–2613.10.1111/evo.2012.66.issue-8
   PubMed Web of Science ®Google Scholar
• Jønsson KA, Fabre P-H, Irestedt M. Brains, tools, innovation and biogeography in crows and ravens. BMC Evol Biol. 2012;12:72.
   PubMed Web of Science ®Google Scholar
• Feldman CR, Omland KE. Phylogenetics of the common raven complex (Corvus: Corvidae) and the utility of ND4, COI and intron 7 of the beta-fibrinogen gene in avian molecular systematics. Zool Scr. 2005;34:145–156.10.1111/zsc.2005.34.issue-2
   Web of Science ®Google Scholar
• Andersen MJ, Hosner PA, Filardi CE, et al. Phylogeny of the monarch flycatchers reveals extensive paraphyly and novel relationships within a major Australo-Pacific radiation. Mol Phylogen Evol. 2015;83:118–136.10.1016/j.ympev.2014.11.010
   PubMed Web of Science ®Google Scholar
• Cracraft J, Feinstein J. What is not a bird of paradise? Molecular and morphological evidence places Macgregoria in the Meliphagidae and the Cnemophilinae near the base of the corvoid tree. Proc R Soc Lond B. 2000;267:233–241.10.1098/rspb.2000.0992
   PubMed Web of Science ®Google Scholar
• Kryukov A, Spiridonova L, Nakamura S, et al. Comparative phylogeography of two crow species: jungle crow Corvus macrorhynchos and carrion crow Corvus corone. Zool Sci. 2012;29:484–492.10.2108/zsj.29.484
   PubMed Web of Science ®Google Scholar
• Slager DL, Battey C, Bryson RW, et al. A multilocus phylogeny of a major New World avian radiation: the Vireonidae. Mol Phylogen Evol. 2014;80:95–104.10.1016/j.ympev.2014.07.021
   PubMed Web of Science ®Google Scholar
• Helm-Bychowski K, Cracraft J. Recovering phylogenetic signal from DNA sequences: Relationships within the corvine assemblage (class Aves) as inferred from complete sequences of the mitochondrial DNA cytochrome-b gene. Mol Biol Evol. 1993;10:1196–1214.
   PubMed Web of Science ®Google Scholar
• Bonaccorso E, Peterson AT, Navarro-Sigüenza AG, et al. Molecular systematics and evolution of the Cyanocorax jays. Mol Phylogen Evol. 2010;54:897–909.10.1016/j.ympev.2009.11.014
   PubMed Web of Science ®Google Scholar
• Price TD, Hooper DM, Buchanan CD, et al. Niche filling slows the diversification of Himalayan songbirds. Nature. 2014;509:222–225.10.1038/nature13272
   PubMed Web of Science ®Google Scholar
• Bonaccorso E. Historical biogeography and speciation in the Neotropical highlands: molecular phylogenetics of the jay genus Cyanolyca. Mol Phylogen Evol. 2009;50:618–632.10.1016/j.ympev.2008.12.012
   PubMed Web of Science ®Google Scholar
• Kryukov A, Iwasa M, Kakizawa R, et al. Synchronic east-west divergence in azure-winged magpies (Cyanopica cyanus) and magpies (Pica pica)*. J Zool System Evol Res. 2004;42:342–351.10.1111/jzs.2004.42.issue-4
   Web of Science ®Google Scholar
• Zhang R, Song G, Qu Y, et al. Comparative phylogeography of two widespread magpies: importance of habitat preference and breeding behavior on genetic structure in China. Mol Phylogen Evol. 2012;65:562–572.10.1016/j.ympev.2012.07.011
   PubMed Web of Science ®Google Scholar
• Cibois A, Pasquet E. Molecular analysis of the phylogeny of 11 genera of the Corvidae. Ibis. 1999;141:297–306.
   Web of Science ®Google Scholar
• Morinha F, Clemente C, Cabral JA, et al. Next-generation sequencing and comparative analysis of Pyrrhocorax pyrrhocorax and Pyrrhocorax graculus (Passeriformes: Corvidae) mitochondrial genomes. Mitochondrial DNA Part A. 2016;27:2278–2281.
   PubMed Web of Science ®Google Scholar
• Gonzalez J, Wink M, Garcia-del-Rey E, et al. Evidence from DNA nucleotide sequences and ISSR profiles indicates paraphyly in subspecies of the Southern Grey Shrike (Lanius meridionalis). J Ornithol. 2008;149:495–506.10.1007/s10336-008-0293-y
   Web of Science ®Google Scholar
• Fuchs J, Crowe TM, Bowie RC. Phylogeography of the fiscal shrike (Lanius collaris): a novel pattern of genetic structure across the arid zones and savannas of Africa. J Biogeogr. 2011;38:2210–2222.10.1111/jbi.2011.38.issue-11
   Web of Science ®Google Scholar
• Primmer C, Borge T, Lindell J, et al. Single-nucleotide polymorphism characterization in species with limited available sequence information: high nucleotide diversity revealed in the avian genome. Mol Ecol. 2002;11:603–612.10.1046/j.0962-1083.2001.01452.x
   PubMed Web of Science ®Google Scholar
• Reddy S. Systematics and biogeography of the shrike-babblers (Pteruthius): species limits, molecular phylogenetics, and diversification patterns across southern Asia. Mol Phylogen Evol. 2008;47:54–72.10.1016/j.ympev.2008.01.014
   PubMed Web of Science ®Google Scholar
• Sorenson MD, Ast JC, Dimcheff DE, et al. Primers for a PCR-based approach to mitochondrial genome sequencing in birds and other vertebrates. Mol Phylogen Evol. 1999;12:105–114.10.1006/mpev.1998.0602
   PubMed Web of Science ®Google Scholar
• Chesser RT. Molecular systematics of the rhinocryptid genus Pteroptochos. Condor. 1999;101:439–446.
   Web of Science ®Google Scholar
• Prychitko TM, Moore WS. The utility of DNA sequences of an intron from the β-fibrinogen gene in phylogenetic analysis of woodpeckers (Aves: Picidae). Mol Phylogen Evol. 1997;8:193–204.10.1006/mpev.1997.0420
   PubMed Web of Science ®Google Scholar
• Fjeldsa J, Zuccon D, Irestedt M, et al. Sapayoa aenigma: a New World representative of Old World suboscines. Proc R Soc Lond B. 2003;270:S238–S241.10.1098/rsbl.2003.0075
   PubMed Web of Science ®Google Scholar
• Slade R, Moritz C, Heideman A, et al. Rapid assessment of single-copy nuclear DNA variation in diverse species. Mol Ecol. 1993;2:359–373.10.1111/j.1365-294X.1993.tb00029.x
   PubMed Web of Science ®Google Scholar
• Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004;32:1792–1797.10.1093/nar/gkh340
   PubMed Web of Science ®Google Scholar
• Nylander J. MrModeltest v2. Program distributed by the author. Uppsala: Evolutionary Biology Centre, Uppsala University; 2004.
   Google Scholar
• Gutell RR, Jansen RK. Genetic algorithm approaches for the phylogenetic analysis of large biological sequence datasets under the maximum likelihood criterion; 2006.
   Google Scholar
• Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution. 1985;39:783–791.
   PubMed Web of Science ®Google Scholar
• Paup DS. Phylogenetic analysis using parsimony (* and other methods). Sunderland, MA: Sinauer Associates; 2003.
   Google Scholar
• Hillis DM, Bull JJ. An empirical test of bootstrapping as a method for assessing confidence in phylogenetic analysis. Syst Biol. 1993;42:182–192.10.1093/sysbio/42.2.182
   Web of Science ®Google Scholar
• Wilcox TP, Zwickl DJ, Heath TA, et al. Phylogenetic relationships of the dwarf boas and a comparison of Bayesian and bootstrap measures of phylogenetic support. Mol Phylogen Evol. 2002;25:361–371.10.1016/S1055-7903(02)00244-0
   PubMed Web of Science ®Google Scholar
• Altekar G, Dwarkadas S, Huelsenbeck JP, et al. Parallel metropolis coupled Markov chain Monte Carlo for Bayesian phylogenetic inference. Bioinformatics. 2004;20:407–415.10.1093/bioinformatics/btg427
   PubMed Web of Science ®Google Scholar
• Ronquist F, Huelsenbeck JP. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics. 2003;19:1572–1574.10.1093/bioinformatics/btg180
   PubMed Web of Science ®Google Scholar
• Ronquist F, Teslenko M, van der Mark P, et al. MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst Biol. 2012;61:539–542.10.1093/sysbio/sys029
   PubMed Web of Science ®Google Scholar
• Rambaut A, Suchard M, Xie D, et al. Tracer v1. 6; 2014. Available from: http://beast.bio.ed.ac.uk/Tracer
   Google Scholar
• Ree RH, Moore BR, Webb CO, et al. A likelihood framework for inferring the evolution of geographic range on phylogenetic trees. Evolution. 2005;59:2299–2311.10.1111/evo.2005.59.issue-11
   PubMed Web of Science ®Google Scholar
• Ree RH, Smith SA. Maximum likelihood inference of geographic range evolution by dispersal, local extinction, and cladogenesis. Syst Biol. 2008;57:4–14.10.1080/10635150701883881
   PubMed Web of Science ®Google Scholar
• Yu Y, Harris A, He X. S-DIVA (Statistical Dispersal-Vicariance Analysis): a tool for inferring biogeographic histories. Mol Phylogen Evol. 2010;56:848–850.10.1016/j.ympev.2010.04.011
   PubMed Web of Science ®Google Scholar
• Yu Y, Harris AJ, Blair C, et al. RASP (Reconstruct Ancestral State in Phylogenies): a tool for historical biogeography. Mol Phylogen Evol. 2015;87:46–49.10.1016/j.ympev.2015.03.008
   PubMed Web of Science ®Google Scholar
• Ronquist F. Dispersal-vicariance analysis: a new approach to the quantification of historical biogeography. Syst Biol. 1997;46:195–203.10.1093/sysbio/46.1.195
   Web of Science ®Google Scholar
• Nylander JA, Olsson U, Alström P, et al. Accounting for phylogenetic uncertainty in biogeography: A Bayesian approach to dispersal-vicariance analysis of the thrushes (Aves: Turdus). Syst Biol. 2008;57:257–268.10.1080/10635150802044003
   PubMed Web of Science ®Google Scholar
• Smith SA. Lagrange C++ Manual; 2010.
   Google Scholar
• Ronquist F. Bayesian inference of character evolution. Trends Ecol Evol. 2004;19:475–481.10.1016/j.tree.2004.07.002
   PubMed Web of Science ®Google Scholar
• eBird. eBird: an online database of bird distribution and abundance. eBird; 2015. Available from: http://www.ebird.org
   Google Scholar
• Drummond AJ, Suchard MA, Xie D, et al. Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol Biol Evol. 2012;29:1969–1973.10.1093/molbev/mss075
   PubMed Web of Science ®Google Scholar
• Parham JF, Donoghue PC, Bell CJ, et al. Best practices for justifying fossil calibrations. Syst Biol. 2011;61:346–359.
   PubMed Web of Science ®Google Scholar
• Hosner PA, Nyári ÁS, Moyle RG. Water barriers and intra-island isolation contribute to diversification in the insular Aethopyga sunbirds (Aves: Nectariniidae). J Biogeogr. 2013;40:1094–1106.10.1111/jbi.12074
   Web of Science ®Google Scholar
• Andersen MJ, Shult HT, Cibois A, et al. Rapid diversification and secondary sympatry in Australo-Pacific kingfishers (Aves: Alcedinidae: Todiramphus). R Soc Open Sci. 2015;2:140375.10.1098/rsos.140375
   PubMed Web of Science ®Google Scholar
• Lerner HR, Meyer M, James HF, et al. Multilocus resolution of phylogeny and timescale in the extant adaptive radiation of Hawaiian honeycreepers. Curr Biol. 2011;21:1838–1844.10.1016/j.cub.2011.09.039
   PubMed Web of Science ®Google Scholar
• Fox DL. Growth increments in Gomphotherium tusks and implications for late Miocene climate change in North America. Palaeogeogr Palaeoclimatol Palaeoecol. 2000;156:327–348.10.1016/S0031-0182(99)00148-0
   Web of Science ®Google Scholar
• Kohn MJ, Fremd TJ. Miocene tectonics and climate forcing of biodiversity, western United States. Geology. 2008;36:783–786.10.1130/G24928A.1
   Web of Science ®Google Scholar
• Sanmartín I, Enghoff H, Ronquist F. Patterns of animal dispersal, vicariance and diversification in the Holarctic. Biol J Linnean Soc. 2001;73:345–390.10.1111/j.1095-8312.2001.tb01368.x
   Web of Science ®Google Scholar
• Moyle RG, Oliveros CH, Andersen MJ, et al. Tectonic collision and uplift of Wallacea triggered the global songbird radiation. Nat Comm. 2016;7:12709.10.1038/ncomms12709
   PubMed Web of Science ®Google Scholar
• ODea A, Lessios HA, Coates AG, et al. Formation of the Isthmus of Panama. Sci Adv. 2016;2:e1600883.10.1126/sciadv.1600883
   PubMed Web of Science ®Google Scholar