A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing (original) (raw)
References
Jarvis, E. D. et al. Whole-genome analyses resolve early branches in the tree of life of modern birds. Science346, 1320–1331 (2014) ADSCASPubMedPubMed Central Google Scholar
Gill, F. B. Ornithology 2nd edn (W. H. Freeman and Co., 1995) Google Scholar
Hackett, S. J. et al. A phylogenomic study of birds reveals their evolutionary history. Science320, 1763–1768 (2008) ADSCASPubMed Google Scholar
Ericson, P. G. P. et al. Diversification of Neoaves: integration of molecular sequence data and fossils. Biol. Lett.2, 543–547 (2006) PubMedPubMed Central Google Scholar
McCormack, J. E. et al. A phylogeny of birds based on over 1,500 loci collected by target enrichment and high-throughput sequencing. PLoS ONE8, e54848 (2013) ADSCASPubMedPubMed Central Google Scholar
Mayr, G. Paleogene Fossil Birds (Springer, 2009) Google Scholar
Mayr, G. Metaves, Mirandornithes, Strisores and other novelties — a critical review of the higher-level phylogeny of neornithine birds. J. Zoological Syst. Evol. Res.49, 58–76 (2011) Google Scholar
Graybeal, A. Is it better to add taxa or characters to a difficult phylogenetic problem? Syst. Biol.47, 9–17 (1998) CASPubMed Google Scholar
Heath, T. A., Hedtke, S. M. & Hillis, D. M. Taxon sampling and the accuracy of phylogenetic analyses. Journal of Systematics and Evolution46, 239–257 (2008) Google Scholar
Townsend, J. P. & Lopez-Giraldez, F. Optimal selection of gene and ingroup taxon sampling for resolving phylogenetic relationships. Syst. Biol.59, 446–457 (2010) CASPubMed Google Scholar
Lemmon, A. R., Emme, S. A. & Lemmon, E. M. Anchored hybrid enrichment for massively high-throughput phylogenomics. Syst. Biol.61, 727–744 (2012) CASPubMed Google Scholar
Lanfear, R., Calcott, B., Ho, S. Y. & Guindon, S. PartitionFinder: combined selection of partitioning schemes and substitution models for phylogenetic analyses. Mol. Biol. Evol.29, 1695–1701 (2012) CASPubMed Google Scholar
Berv, J. S. & Prum, R. O. A comprehensive multilocus phylogeny of the neotropical cotingas (Cotingidae, Aves) with a comparative evolutionary analysis of breeding system and plumage dimorphism and a revised phylogenetic classification. Mol. Phylogenet. Evol.81, 120–136 (2014) PubMed Google Scholar
Townsend, J. P. Profiling phylogenetic informativeness. Syst. Biol.56, 222–231 (2007) CASPubMed Google Scholar
Townsend, J. P., Su, Z. & Tekle, Y. I. Phylogenetic signal and noise: predicting the power of a data set to resolve phylogeny. Syst. Biol.61, 835–849 (2012) CASPubMed Google Scholar
Aberer, A. J., Kobert, K. & Stamatakis, A. ExaBayes: massively parallel Bayesian tree inference for the whole-genome era. Mol. Biol. Evol.31, 2553–2556 (2014) CASPubMedPubMed Central Google Scholar
Stamatakis, A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics30, 1312–1313 (2014) CASPubMedPubMed Central Google Scholar
Liu, L., Yu, L., Pearl, D. K. & Edwards, S. V. Estimating species phylogenies using coalescence times among sequences. Syst. Biol.58, 468–477 (2009) CASPubMed Google Scholar
Liu, L. & Yu, L. Estimating species trees from unrooted gene trees. Syst. Biol.60, 661–667 (2011) PubMed Google Scholar
Mirarab, S. et al. ASTRAL: genome-scale coalescent-based species tree estimation. Bioinformatics30, i541–i548 (2014) CASPubMedPubMed Central Google Scholar
Tonini, J., Moore, A., Stern, D., Shcheglovitova, M. & Ortí, G. Concatenation and species tree methods exhibit statistically indistinguishable accuracy under a range of simulated conditions. PLOS Currents Tree of Life1http://dx.doi.org/10.1371/currents.tol.34260cc27551a527b124ec5f6334b6be (2015)
Mirarab, S., Bayzid, M. S. & Warnow, T. Evaluating summary methods for multi-locus species tree estimation in the presence of incomplete lineage sorting. Syst. Biol.http://dx.doi.org/10.1093/sysbio/syu063 (2014)
Barker, F. K., Cibois, A., Schikler, P., Felsenstein, J. & Cracraft, J. Phylogeny and diversification of the largest avian radiation. Proc. Natl Acad. Sci. USA101, 11040–11045 (2004) ADSCASPubMedPubMed Central Google Scholar
Parham, J. F. et al. Best practices for justifying fossil calibrations. Syst. Biol.61, 346–359 (2012) PubMed Google Scholar
Longrich, N. R., Tokaryk, T. & Field, D. J. Mass extinction of birds at the Cretaceous–Paleogene (K–Pg) boundary. Proc. Natl Acad. Sci. USA108, 15253–15257 (2011) ADSCASPubMedPubMed Central Google Scholar
Feduccia, A. The Origin and Evolution of Birds 2nd edn (Yale Univ. Press, 1999) Google Scholar
Jetz, W., Thomas, G. H., Joy, J. B., Hartmann, K. & Mooers, A. O. The global diversity of birds in space and time. Nature491, 444–448 (2012) ADSCASPubMed Google Scholar
Goldsmith, T. H. Hummingbirds see near ultraviolet light. Science207, 786–788 (1980) ADSCASPubMed Google Scholar
del Hoyo, J., Elliott, A., Sargatal, J., Christie, D. A. & de Juana, E. Handbook of the Birds of the World Alive (Lynx Edicions, 2015) Google Scholar
Katoh, K. & Standley, D. M. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol. Biol. Evol.30, 772–780 (2013) CASPubMedPubMed Central Google Scholar
Meyer, M. & Kircher M Illumina sequencing library preparation for highly multiplexed target capture and sequencing. Cold Spring Harb Protoc.http://dx.doi.org/10.1101/pdb.prot5448 (2010)
Rokyta, D. R., Lemmon, A. R., Margres, M. J. & Arnow, K. The venom-gland transcriptome of the eastern diamondback rattlesnake (Crotalus adamanteus). BMC Genomics13, 312 (2012) CASPubMedPubMed Central Google Scholar
Misof, B. et al. Phylogenomics resolves the timing and pattern of insect evolution. Science346, 763–767 (2014) ADSCASPubMed Google Scholar
Dornburg, A., Santini, F. & Alfaro, M. E. The influence of model averaging on clade posteriors: an example using the triggerfishes (Family Balistidae). Syst. Biol.57, 905–919 (2008) CASPubMed Google Scholar
Robinson, D. F. & Foulds, L. R. in Combinatorial Mathematics VI in Lecture Notes in Mathematics, Vol. 748 (eds Horadam A. F. & Wallis W. D. ) Ch. 12 119–126 (Springer, 1979) Google Scholar
Bogdanowicz, D., Giaro, K. & Wróbel, B. TreeCmp: comparison of trees in polynomial time. Evol. Bioinform.8, 475–487 (2012) Google Scholar
Nye, T. M. W. Trees of Trees: an approach to comparing multiple alternative phylogenies. Syst. Biol.57, 785–794 (2008) PubMed Google Scholar
Schliep, K. P. phangorn: phylogenetic analysis in R. Bioinformatics27, 592–593 (2011) CASPubMed Google Scholar
Weyenberg, G., Huggins, P. M., Schardl, C. L., Howe, D. K. & Yoshida, R. KDETREES: non-parametric estimation of phylogenetic tree distributions. Bioinformatics30, 2280–2287 (2014) CASPubMedPubMed Central Google Scholar
Drummond, A. J., Suchard, M. A., Xie, D. & Rambaut, A. Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol. Biol. Evol.29, 1969–1973 (2012) ArticleCASPubMedPubMed Central Google Scholar
Rannala, B. & Yang, Z. Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci. Genetics164, 1645–1656 (2003) CASPubMedPubMed Central Google Scholar
Shaw, T. I., Ruan, Z., Glenn, T. C. & Liu, L. STRAW: species tree analysis web server. Nucleic Acids Res.41, W238–W241 (2013) PubMedPubMed Central Google Scholar
Liu, L., Yu, L. & Edwards, S. A maximum pseudo-likelihood approach for estimating species trees under the coalescent model. BMC Evol. Biol.10, 302 (2010) PubMedPubMed Central Google Scholar
Saitou, N. & Nei, M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol.4, 406–425 (1987) CASPubMed Google Scholar
Mirarab, S., Bayzid, M. S., Boussau, B. & Warnow, T. Statistical binning enables an accurate coalescent-based estimation of the avian tree. Science346, (2014)
Mirarab, S., Bayzid, M. S. & Warnow, T. Evaluating summary methods for multilocus species tree estimation in the presence of incomplete lineage sorting. Syst. Biol. (2014)
Bayzid, M. S. & Warnow, T. Naive binning improves phylogenomic analyses. Bioinformatics29, 2277–2284 (2013) CASPubMed Google Scholar
DeGiorgio, M. & Degnan, J. H. Fast and consistent estimation of species trees using supermatrix rooted triples. Mol. Biol. Evol.27, 552–569 (2010) CASPubMed Google Scholar
Kimball, R. T., Wang, N., Heimer-McGinn, V., Ferguson, C. & Braun, E. L. Identifying localized biases in large datasets: a case study using the avian tree of life. Mol. Phylogenet. Evol.69, 1021–1032 (2013) PubMed Google Scholar
McCormack, J. E. et al. A phylogeny of birds based on over 1,500 loci collected by target enrichment and high-throughput sequencing. PLoS ONE8, e54848 (2013) ADSCASPubMedPubMed Central Google Scholar
Springer, M. S. & Gatesy, J. Land plant origins and coalescence confusion. Trends Plant Sci.19, 267–269 (2014) CASPubMed Google Scholar
Tonini J, Moore A, Stearn D, Shcheglovitova M & Ortí, G. Concatenation and species tree methods exhibit statistically indistinguishable accuracy under a range of simulated conditions. PLOS Currents Tree of Life1, (2015)
Pond, S. L. K. & Muse, S. V. in Statistical Methods in Molecular Evolution (ed. Nielsen, R. ) 125–181 (Springer, 2005) Google Scholar
López-Giráldez, F. & Townsend, J. P. PhyDesign: an online application for profiling phylogenetic informativeness. BMC Evol. Biol.11, 152 (2011) PubMedPubMed Central Google Scholar
Sanderson, M. A nonparametric approach to estimating divergence times in the absence of rate constancy. Mol. Biol. Evol.14, 1218 (1997) CAS Google Scholar
Simmons, M. P., Carr, T. G. & O’Neill, K. Relative character-state space, amount of potential phylogenetic information, and heterogeneity of nucleotide and amino acid characters. Mol. Phylogenet. Evol.32, 913–926 (2004) CASPubMed Google Scholar
Townsend, J. P. & Leuenberger, C. Taxon sampling and the optimal rates of evolution for phylogenetic inference. Syst. Biol.60, 358–365 (2011) PubMed Google Scholar
Klopfstein, S., Kropf, C. & Quicke, D. L. J. An evaluation of phylogenetic informativeness profiles and the molecular phylogeny of Diplazontinae (Hymenoptera, Ichneumonidae). Syst. Biol.59, 226–241 (2010) CASPubMed Google Scholar
Drummond, A. J. & Bouckaret, R. R. Bayesian Evolutionary Analysis With BEAST (Cambridge Univ. Press, 2015) MATH Google Scholar
Hsiang, A. Y. et al. The origin of snakes: revealing the ecology, behavior, and evolutionary history of early snakes using genomics, phenomics, and the fossil record. BMC Evol. Biol.15, 87 (2015) PubMedPubMed Central Google Scholar
Phillips, M. J., Gibb, G. C., Crimp, E. A. & Penny, D. Tinamous and moa flock together: mitochondrial genome sequence analysis reveals independent losses of flight among ratites. Syst. Biol.59, 90–107 (2010) PubMed Google Scholar
Pereira, S. L. & Baker, A. J. A mitogenomic timescale for birds detects variable phylogenetic rates of molecular evolution and refutes the standard molecular clock. Mol. Biol. Evol.23, 1731–1740 (2006) CASPubMed Google Scholar
Drummond, A. J., Ho, S. Y. W., Phillips, M. J. & Rambaut, A. Relaxed phylogenetics and dating with confidence. PLoS Biol.4, e88 (2006) PubMedPubMed Central Google Scholar
Dornburg, A., et al. Relaxed clocks and inferences of heterogeneous patterns of nucleotide substitution and divergence time estimates across whales and dolphins (Mammalia: Cetacea). Mol. Biol. Evol.29, 721–736 (2012) CASPubMed Google Scholar
Yang, Z. & Rannala, B. Bayesian estimation of species divergence times under a molecular clock using multiple fossil calibrations with soft bounds. Mol. Biol. Evol.23, 212–226 (2006) CASPubMed Google Scholar
Ho, S. Y. W. Calibrating molecular estimates of substitution rates and divergence times in birds. J. Avian Biol.38, 409–414 (2007) Google Scholar
Heled, J. & Drummond, A. J. Calibrated tree priors for relaxed phylogenetics and divergence time estimation. Syst. Biol.61, 138–149 (2012) PubMed Google Scholar
Benton, M. J. & Donoghue, P. C. J. Paleontological evidence to date the tree of life. Mol. Biol. Evol.24, 26 (2007) CASPubMed Google Scholar
Clarke, J. A. Morphology, phylogenetic taxonomy, and systematics of Ichthyornis and Apatornis (Avialae: Ornithurae). Bull. Am. Mus. Nat. Hist.286, 1–179 (2004) Google Scholar
Field, D. J., LeBlanc, A., Gau, A. & Behlke, A. D. B. Pelagic neonatal fossils support viviparity and precocial life history of Cretaceous mosasaurs. Palaeontology58, 401–407 (2015) Google Scholar
Mayr, G. The age of the crown group of passerine birds and its evolutionary significance — molecular calibrations versus the fossil record. Syst. Biodivers.11, 7–13 (2013) Google Scholar
Jetz, W. et al. Global distribution and conservation of evolutionary distinctness in birds. Curr. Biol.24, 919–930 (2014) CASPubMed Google Scholar
Hedges, S. B., Parker, P. H., Sibley, C. G. & Kumar, S. Continental breakup and the ordinal diversification of birds and mammals. Nature381, 226–229 (1996) ADSCASPubMed Google Scholar
Benton, M. J. Early origins of modern birds and mammals: molecules vs. morphology. Bioessays21, 1043–1051 (1999) CASPubMed Google Scholar
Hope, S. in Mesozoic Birds: Above the Heads of Dinosaurs (eds Chiappe L. M. & Witmer L. M. ) 339–388 (Univ. of California Press, 2002) Google Scholar
Longrich, N. R., Tokaryk, T. & Field, D. J. Mass extinction of birds at the Cretaceous–Paleogene (K–Pg) boundary. Proc. Natl Acad. Sci. USA108, 15253–15257 (2011) ADSCASPubMedPubMed Central Google Scholar
Baker, A. J., Pereira, S. L. & Paton, T. A. Phylogenetic relationships and divergence times of Charadriiformes genera: multigene evidence for the Cretaceous origin of at least 14 clades of shorebirds. Biol. Lett.3, 205–209 (2007) PubMedPubMed Central Google Scholar
dos Reis, M. et al. Phylogenomic datasets provide both precision and accuracy in estimating the timescale of placental mammal phylogeny. Proc. R. Soc. B279, 3491–3500 (2012) PubMedPubMed Central Google Scholar
Dornburg, A., Townsend, J. P., Friedman, M. & Near, T. J. Phylogenetic informativeness reconciles ray-finned fish molecular divergence times. BMC Evol. Biol.14, 169 (2014) PubMedPubMed Central Google Scholar
Brandley, M. C. et al. Accommodating heterogenous rates of evolution in molecular divergence dating methods: an example using intercontinental dispersal of Plestiodon (Eumeces) lizards. Syst. Biol.60, 3–15 (2011) CASPubMed Google Scholar
Phillips, M. J. Branch-length estimation bias misleads molecular dating for a vertebrate mitochondrial phylogeny. Gene441, 132–140 (2009) CASPubMed Google Scholar