Abstract
Reconstructing relationships among extant birds (Neornithes) has been one of the most difficult problems in phylogenetics, and, despite intensive effort, the avian tree of life remains (at least partially) unresolved. Thus far, the most difficult problem is the relationship among the orders of Neoaves, the major clade that includes the most (~95%) named bird species. This clade appears to have undergone a rapid radiation near the end Cretaceous mass extinction (the K-Pg boundary). On the other hand, if one embraces a “glass half full” view, the fact that most orders in Neoaves can be placed into seven clades, recently designated the “magnificent seven,” could be viewed as remarkable progress. We propose that the dawning era of whole-genome phylogenetics will only resolve the remaining relationships, if we improve data quality, exploit information from other sources (i.e., rare genomic changes), and learn more about the functional and evolutionary landscape of avian genomes. Of course, it is possible that the remaining unresolved relationships are unresolvable regardless of the data available, but we suggest that the community should avoid this conclusion until more data collection has been completed and improved analyses have been conducted. We say this because there is ample evidence that estimates of avian phylogeny based on large-scale datasets may be affected by well-characterized artifacts (e.g., long-branch attraction, heterotachy, and discordance among gene trees) and by subtle “data-type effects” that reflect poor fit to empirical data for available models of sequence evolution. Even if these analytical challenges can be addressed, we need to integrate phylogenomic and fossil data. Finally, we also emphasize that, regardless of the resolution (or lack thereof) for relationships among major avian clades, we are only at the dawn of the phylogenomics of birds. Large-scale molecular data remain unavailable for the vast majority of the ~10,000 named bird species, and those named bird species probably represent an underestimate of the true number of distinct evolutionary lineages of birds (whether or not those lineages are assigned the rank of species) by as much as threefold. A true biodiversity genomics effort in birds is likely to reveal many additional examples of cases where it is very difficult to resolve relationships; the effort to resolve as many of those relationships as possible will represent a major scientific achievement and provide lessons for phylogenomic studies in other parts of the tree of life.
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References
Aberer AJ, Kobert K, Stamatakis A (2014) ExaBayes: massively parallel Bayesian tree inference for the whole-genome era. Mol Biol Evol 31:2553–2556. https://doi.org/10.1093/molbev/msu236
Agnolín FL, Egli FB, Chatterjee S, Marsà JAG, Novas FE (2017) Vegaviidae, a new clade of southern diving birds that survived the K/T boundary. Sci Nat 104:87. https://doi.org/10.1007/s00114-017-1508-y
Allentoft ME, Rawlence NJ (2012) Moa’s Ark or volant ghosts of Gondwana? Insights from nineteen years of ancient DNA research on the extinct moa (Aves: Dinornithiformes) of New Zealand. Ann Anat 194:36–51. https://doi.org/10.1016/j.aanat.2011.04.002
Andermann T et al (2018) Allele phasing greatly improves the phylogenetic utility of ultraconserved elements. Syst Biol. https://doi.org/10.1093/sysbio/syy039
Andersen MJ, McCullough JM, Mauck WM, Smith BT, Moyle RG (2017) A phylogeny of kingfishers reveals an Indomalayan origin and elevated rates of diversification on oceanic islands. J Biogeogr. https://doi.org/10.1111/jbi.13139
Ané C, Larget B, Baum DA, Smith SD, Rokas A (2007) Bayesian estimation of concordance among gene trees. Mol Biol Evol 24:412–426. https://doi.org/10.1093/molbev/msl170
Axelsson E, Webster MT, Smith NG, Burt DW, Ellegren H (2005) Comparison of the chicken and turkey genomes reveals a higher rate of nucleotide divergence on microchromosomes than macrochromosomes. Genome Res 15:120–125. https://doi.org/10.1101/gr.3021305
Baker AJ, Haddrath O, McPherson JD, Cloutier A (2014) Genomic support for a moa-tinamou clade and adaptive morphological convergence in flightless ratites. Mol Biol Evol 31:1686–1696. https://doi.org/10.1093/molbev/msu153
Barker FK, Oyler-McCance S, Tomback DF (2015) Blood from a turnip: tissue origin of low-coverage shotgun sequencing libraries affects recovery of mitogenome sequences. Mitochondrial DNA 26:384–388. https://doi.org/10.3109/19401736.2013.840588
Barrera-Guzmán AO, Aleixo A, Shawkey MD, Weir JT (2018) Hybrid speciation leads to novel male secondary sexual ornamentation of an Amazonian bird. Proc Natl Acad Sci USA 115:E218–E225. https://doi.org/10.1073/pnas.1717319115
Barrowclough GF, Zink RM (2009) Funds enough, and time: mtDNA, nuDNA and the discovery of divergence. Mol Ecol 18:2934–2936. https://doi.org/10.1111/j.1365-294X.2009.04271.x
Barrowclough GF, Cracraft J, Klicka J, Zink RM (2016) How many kinds of birds are there and why does it matter? PLoS One 11:e0166307. https://doi.org/10.1371/journal.pone.0166307
Baum BR (1992) Combining trees as a way of combining data sets for phylogenetic inference, and the desirability of combining gene trees. Taxon 41:3–10. https://doi.org/10.2307/1222480
Baum DA (2007) Concordance trees, concordance factors, and the exploration of reticulate genealogy. Taxon 56:417–426. https://doi.org/10.1002/tax.562013
Bejerano G, Pheasant M, Makunin I, Stephen S, Kent WJ, Mattick JS, Haussler D (2004) Ultraconserved elements in the human genome. Science 304:1321–1325. https://doi.org/10.1126/science.1098119
Bergsten J (2005) A review of long-branch attraction. Cladistics 21(2):163–193. https://doi.org/10.1111/j.1096-0031.2005.00059.x
Bergstrom CT, Dugatkin LA (2012) Evolution. W. W. Norton & Company, New York
Berv JS, Field DJ (2018) Genomic signature of an avian Lilliput effect across the K-Pg extinction. Syst Biol 67:1–13. https://doi.org/10.1093/sysbio/syx064
Bleidorn C (2016) Third generation sequencing: technology and its potential impact on evolutionary biodiversity research. Syst Biodivers 14:1–8. https://doi.org/10.1080/14772000.2015.1099575
Bleidorn C (2017) Rare genomic changes. In: Bleidorn C (ed) Phylogenomics. Springer, Cham, pp 195–211. https://doi.org/10.1007/978-3-319-54064-1_10
Botero-Castro F, Figuet E, Tilak MK, Nabholz B, Galtier N (2017) Avian genomes revisited: hidden genes uncovered and the rates versus traits paradox in birds. Mol Biol Evol 34:3123–3131. https://doi.org/10.1093/molbev/msx236
Bourdon E, de Ricqles A, Cubo J (2009) A new transantarctic relationship: morphological evidence for a Rheidae-Dromaiidae-Casuariidae clade (Aves, Palaeognathae, Ratitae). Zool J Linn Soc 156:641–663. https://doi.org/10.1111/j.1096-3642.2008.00509.x
Braun EL (2018) Data for: Resolving the avian tree of life from top to bottom: the promise and potential boundaries of the phylogenomic era (Version 1.0) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.1419827
Braun EL, Kimball RT (2001) Polytomies, the power of phylogenetic inference, and the stochastic nature of molecular evolution: a comment on Walsh et al. (1999). Evolution 55:1261–1263
Braun EL, Kimball RT (2002) Examining basal avian divergences with mitochondrial sequences: model complexity, taxon sampling, and sequence length. Syst Biol 51:614–625. https://doi.org/10.1080/10635150290102294
Braun EL et al (2011) Homoplastic microinversions and the avian tree of life. BMC Evol Biol 11:141. https://doi.org/10.1186/1471-2148-11-141
Bronson CL, Grubb TC, Braun MJ (2003) A test of the endogenous and exogenous selection hypotheses for the maintenance of a narrow avian hybrid zone. Evolution 57:630–637. https://doi.org/10.1111/j.0014-3820.2003.tb01554.x
Brower AVZ (2018) Statistical consistency and phylogenetic inference: a brief review. Cladistics 34: 562–567. https://doi.org/10.1111/cla.12216
Brown JW, Wang N, Smith SA (2017) The development of scientific consensus: analyzing conflict and concordance among avian phylogenies. Mol Phylogenet Evol 116:69–77. https://doi.org/10.1016/j.ympev.2017.08.002
Brusatte SL, O’Connor JK, Jarvis ED (2015) The origin and diversification of birds. Curr Biol 25:R888–R898. https://doi.org/10.1016/j.cub.2015.08.003
Bruxaux J et al (2017) Recovering the evolutionary history of crowned pigeons (Columbidae: Goura): implications for the biogeography and conservation of New Guinean lowland birds. Mol Phylogenet Evol. https://doi.org/10.1016/j.ympev.2017.11.022
Bryson RW, Faircloth BC, Tsai WLE, McCormack JE, Klicka J (2016) Target enrichment of thousands of ultraconserved elements sheds new light on early relationships within New World sparrows (Aves: Passerellidae). Auk 133:451–458. https://doi.org/10.1642/Auk-16-26.1
Burleigh JG, Kimball RT, Braun EL (2015) Building the avian tree of life using a large-scale, sparse supermatrix. Mol Phylogenet Evol 84:53–63. https://doi.org/10.1016/j.ympev.2014.12.003
Campillo LC, Oliveros CH, Sheldon FH, Moyle RG (2017) Genomic data resolve gene tree discordance in spiderhunters (Nectariniidae, Arachnothera). Mol Phylogenet Evol. https://doi.org/10.1016/j.ympev.2017.12.011
Cantor CR (1990) Orchestrating the human genome project. Science 248:49–51
Casanellas M, Fernandez-Sanchez J (2007) Performance of a new invariants method on homogeneous and nonhomogeneous quartet trees. Mol Biol Evol 24:288–293. https://doi.org/10.1093/molbev/msl153
Chaisson MJ, Raphael BJ, Pevzner PA (2006) Microinversions in mammalian evolution. Proc Natl Acad Sci USA 103:19824–19829. https://doi.org/10.1073/pnas.0603984103
Chifman J, Kubatko L (2014) Quartet inference from SNP data under the coalescent model. Bioinformatics 30:3317–3324. https://doi.org/10.1093/bioinformatics/btu530
Chojnowski JL, Kimball RT, Braun EL (2008) Introns outperform exons in analyses of basal avian phylogeny using clathrin heavy chain genes. Gene 410:89–96. https://doi.org/10.1016/j.gene.2007.11.016
Chubb AL (2004) New nuclear evidence for the oldest divergence among neognath birds: the phylogenetic utility of ZENK (i). Mol Phylogenet Evol 30:140–151. https://doi.org/10.1016/S1055-7903(03)00159-3
Claramunt S, Cracraft J (2015) A new time tree reveals Earth history’s imprint on the evolution of modern birds. Sci Adv 1:e1501005. https://doi.org/10.1126/sciadv.1501005
Clarke JA (2004) Morphology, phylogenetic taxonomy, and systematics of Ichthyornis and Apatornis (Avialae: Ornithurae). Bull Am Mus Nat Hist 286:1–179. https://doi.org/10.1206/0003-0090(2004)286<0001:MPTASO>2.0.CO;2
Clarke JA, Norell MA (2004) New avialan remains and a review of the known avifauna from the Late Cretaceous Nemegt Formation of Mongolia. Am Mus Novit 3447:1–12. https://doi.org/10.1206/0003-0082(2004)447<0001:NARAAR>2.0.CO;2
Clarke JA, Tambussi CP, Noriega JI, Erickson GM, Ketcham RA (2005) Definitive fossil evidence for the extant avian radiation in the Cretaceous. Nature 433:305–308. https://doi.org/10.1038/nature03150
Clements JF, Schulenberg TS, Iliff MJ, Roberson D, Fredericks TA, Sullivan BL, Wood CL (2017) The eBird/clements checklist of birds of the world: v2016. http://www.birds.cornell.edu/clementschecklist/download/. Accessed 31 Aug 2017
Cloutier A, Sackton TB, Grayson P, Edwards SV, Baker AJ (2018) First nuclear genome assembly of an extinct moa species, the little bush moa (Anomalopteryx didiformis). bioRxiv:262816. https://doi.org/10.1101/262816
Collins TM, Fedrigo O, Naylor GJP (2005) Choosing the best genes for the job: the case for stationary genes in genome-scale phylogenetics. Syst Biol 54:493–500. https://doi.org/10.1080/10635150590947339
Cooney CR et al (2017) Mega-evolutionary dynamics of the adaptive radiation of birds. Nature 542:344–347. https://doi.org/10.1038/nature21074
Cornetti L, Valente LM, Dunning LT, Quan X, Black RA, Hebert O, Savolainen V (2015) The genome of the “great speciator” provides insights into bird diversification. Genome Biol Evol 7:2680–2691. https://doi.org/10.1093/gbe/evv168
Coulombe-Huntington J, Majewski J (2007) Characterization of intron loss events in mammals. Genome Res 17:23–32. https://doi.org/10.1101/gr.5703406
Cox WA, Kimball RT, Braun EL (2007) Phylogenetic position of the New World quail (Odontophoridae): eight nuclear loci and three mitochondrial regions contradict morphology and the Sibley-Ahlquist tapestry. Auk 124:71–84. https://doi.org/10.1642/0004-8038(2007)124[71:Ppotnw]2.0.Co;2
Cracraft J (1973) Continental drift, palaeoclimatology, and the evolution and biogeography of birds. J Zool 169:455–545. https://doi.org/10.1111/j.1469-7998.1973.tb03122.x
Cracraft J (1974) Phylogeny and evolution of ratite birds. Ibis 116:494–521. https://doi.org/10.1111/j.1474-919X.1974.tb07648.x
Cracraft J (2001) Avian evolution, Gondwana biogeography and the Cretaceous-Tertiary mass extinction event. Proc Biol Sci 268:459–469. https://doi.org/10.1098/rspb.2000.1368
Cracraft J (2013) Avian higher-level relationships and classification: nonpasseriforms. In: Dickinson EC, Remsen JV Jr (eds) The Howard and Moore complete checklist of the birds of the world, vol 1, 4th edn. Aves Press, Eastbourne, pp xxi–xliii
Cracraft J et al (2004) Phylogenetic relationships among modern birds (Neornithes): towards an avian tree of life. In: Cracraft J, Donoghue MJ (eds) Assembling the tree of life. Oxford University Press, New York, pp 468–489
Crawford NG, Faircloth BC, McCormack JE, Brumfield RT, Winker K, Glenn TC (2012) More than 1000 ultraconserved elements provide evidence that turtles are the sister group of archosaurs. Biol Lett 8:783–786. https://doi.org/10.1098/rsbl.2012.0331
Davis KE, Page RDM (2014) Reweaving the tapestry: a supertree of birds. PLoS Curr 6. https://doi.org/10.1371/currents.tol.c1af68dda7c999ed9f1e4b2d2df7a08e
De Pietri VL, Scofield RP, Zelenkov N, Boles WE, Worthy TH (2016) The unexpected survival of an ancient lineage of anseriform birds into the Neogene of Australia: the youngest record of Presbyornithidae. R Soc Open Sci 3:150635. https://doi.org/10.1098/rsos.150635
DeGiorgio M, Degnan JH (2010) Fast and consistent estimation of species trees using supermatrix rooted triples. Mol Biol Evol 27:552–569. https://doi.org/10.1093/molbev/msp250
del Hoyo J, Elliott A, Sargatal J, Christie DA, de Juana E (eds) (2017) Handbook of the birds of the world alive. Lynx Edicions, Barcelona. http://www.hbw.com
Delsuc F, Brinkmann H, Philippe H (2005) Phylogenomics and the reconstruction of the tree of life. Nat Rev Genet 6:361–375. https://doi.org/10.1038/nrg1603
Dickinson EC, Christidis L (2014) The Howard and Moore complete checklist of the birds of the world, 4th edn, vol 2. Passerines. Aves Press, Eastbourne
Dickinson EC, Remsen JV Jr (2013) The Howard and Moore complete checklist of the birds of the world, 4th edn, vol 1. Passerines. Aves Press, Eastbourne
Dimitrieva S, Bucher P (2012) UCNEbase – a database of ultraconserved non-coding elements and genomic regulatory blocks. Nucleic Acids Res 41:D101–D109. https://doi.org/10.1093/nar/gks1092
Diniz-Filho JA, Loyola RD, Raia P, Mooers AO, Bini LM (2013) Darwinian shortfalls in biodiversity conservation. Trends Ecol Evol 28:689–695. https://doi.org/10.1016/j.tree.2013.09.003
Dufort MJ (2016) An augmented supermatrix phylogeny of the avian family Picidae reveals uncertainty deep in the family tree. Mol Phylogenet Evol 94:313–326. https://doi.org/10.1016/j.ympev.2015.08.025
Edwards SV (2009) Is a new and general theory of molecular systematics emerging? Evolution 63:1–19. https://doi.org/10.1111/J.1558-5646.2008.00549.X
Edwards SV (2016) Phylogenomic subsampling: a brief review. Zool Scr 45:63–74. https://doi.org/10.1111/zsc.12210
Edwards SV, Wilson AC (1990) Phylogenetically informative length polymorphism and sequence variability in mitochondrial DNA of Australian songbirds (Pomatostomus). Genetics 126:695–711
Edwards SV, Arctander P, Wilson AC (1991) Mitochondrial resolution of a deep branch in the genealogical tree for perching birds. Proc Biol Sci 243:99–107. https://doi.org/10.1098/rspb.1991.0017
Edwards SV et al (2016) Implementing and testing the multispecies coalescent model: a valuable paradigm for phylogenomics. Mol Phylogenet Evol 94:447–462. https://doi.org/10.1016/j.ympev.2015.10.027
Edwards SV, Cloutier A, Baker AJ (2017) Conserved nonexonic elements: a novel class of marker for phylogenomics. Syst Biol 66:1028–1044. https://doi.org/10.1093/sysbio/syx058
Eisen JA (1998) Phylogenomics: improving functional predictions for uncharacterized genes by evolutionary analysis. Genome Res 8:163–167
Eisen JA, Kaiser D, Myers RM (1997) Gastrogenomic delights: a movable feast. Nat Med 3:1076–1078
Ericson PGP (1996) The skeletal evidence for a sister-group relationship of anseriform and galliform birds: a critical evaluation. J Avian Biol 27:195–202. https://doi.org/10.2307/3677222
Ericson PGP (2012) Evolution of terrestrial birds in three continents: biogeography and parallel radiations. J Biogeogr 39:813–824. https://doi.org/10.1111/j.1365-2699.2011.02650.x
Ericson PGP et al (2006) Diversification of Neoaves: integration of molecular sequence data and fossils. Biol Lett 2:543–U541. https://doi.org/10.1098/rsbl.2006.0523
Fain MG, Houde P (2004) Parallel radiations in the primary clades of birds. Evolution 58:2558–2573. https://doi.org/10.1111/j.0014-3820.2004.tb00884.x
Faircloth BC, McCormack JE, Crawford NG, Harvey MG, Brumfield RT, Glenn TC (2012) Ultraconserved elements anchor thousands of genetic markers spanning multiple evolutionary timescales. Syst Biol 61:717–726. https://doi.org/10.1093/sysbio/sys004
Faux C, Field DJ (2017) Distinct developmental pathways underlie independent losses of flight in ratites. Biol Lett 13:20170234. https://doi.org/10.1098/rsbl.2017.0234
Feduccia A (1996) The origin and evolution of birds. Yale University Press, New Haven, CT
Felsenstein J (1978) Cases in which parsimony or compatibility methods will be positively misleading. Syst Zool 27:401–410. https://doi.org/10.2307/2412923
Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791. https://doi.org/10.1111/j.1558-5646.1985.tb00420.x
Feng Y, Zhang Y, Ying C, Wang D, Du C (2015) Nanopore-based fourth-generation DNA sequencing technology. Genomics Proteomics Bioinformatics 13:4–16. https://doi.org/10.1016/j.gpb.2015.01.009
Field DJ, Hsiang AY (2018) A North American stem turaco, and the complex biogeographic history of modern birds. BMC Evol Biol 18:102. https://doi.org/10.1186/s12862-018-1212-3
Field DJ et al (2018) Early evolution of modern birds structured by global forest collapse at the end-Cretaceous mass extinction. Curr Biol 28:1825–1831. https://doi.org/10.1016/j.cub.2018.04.062
Fountaine TM, Benton MJ, Dyke GJ, Nudds RL (2005) The quality of the fossil record of Mesozoic birds. Proc Biol Sci 272:289–294. https://doi.org/10.1098/rspb.2004.2923
Fuchs J, Pons JM, Ericson PGP, Bonillo C, Couloux A, Pasquet E (2008) Molecular support for a rapid cladogenesis of the woodpecker clade Malarpicini, with further insights into the genus Picus (Piciformes: Picinae). Mol Phylogenet Evol 48:34–46. https://doi.org/10.1016/j.ympev.2008.03.036
Fuchs J, Pons JM, Liu L, Ericson PGP, Couloux A, Pasquet E (2013) A multi-locus phylogeny suggests an ancient hybridization event between Campephilus and melanerpine woodpeckers (Aves: Picidae). Mol Phylogenet Evol 67:578–588. https://doi.org/10.1016/j.ympev.2013.02.014
Futuyma DJ (2005) Evolution. Sinauer, Sunderland, MA
Gatesy J, Springer MS (2014) Phylogenetic analysis at deep timescales: unreliable gene trees, bypassed hidden support, and the coalescence/concatalescence conundrum. Mol Phylogenet Evol 80:231–266. https://doi.org/10.1016/J.Ympev.2014.08.013
Gaut BS, Lewis PO (1995) Success of maximum likelihood phylogeny inference in the four-taxon case. Mol Biol Evol 12:152–162. https://doi.org/10.1093/oxfordjournals.molbev.a040183
Gee H (2003) Evolution: ending incongruence. Nature 425:782. https://doi.org/10.1038/425782a
Gilbert PS, Wu J, Simon MW, Sinsheimer JS, Alfaro ME (2018) Filtering nucleotide sites by phylogenetic signal to noise ratio increases confidence in the Neoaves phylogeny generated from ultraconserved elements. Mol Phylogenet Evol 126:116–128. https://doi.org/10.1016/j.ympev.2018.03.033
Gill FB (2014) Species taxonomy of birds: which null hypothesis? Auk 131:150–161. https://doi.org/10.1642/Auk-13-206.1
Gill F, Donsker D (2017) IOC World Bird List (v 7.3). http://www.worldbirdnames.org/. Accessed 31 Aug 2017
Glenn TC (2011) Field guide to next-generation DNA sequencers. Mol Ecol Resour 11:759–769. https://doi.org/10.1111/j.1755-0998.2011.03024.x
Gonzalez-Garay ML (2016) Introduction to isoform sequencing using pacific biosciences technology (Iso-Seq). In: Wu J (ed) Transcriptomics and Gene Regulation. Translational Bioinformatics, vol 9. Springer, Dordrecht, pp 141–160. https://doi.org/10.1007/1978-1094-1017-7450-1005_1006
Grant PR, Grant BR (2016) Introgressive hybridization and natural selection in Darwin’s finches. Biol J Linn Soc 117:812–822. https://doi.org/10.1111/bij.12702
Grealy A et al (2017) Eggshell palaeogenomics: Palaeognath evolutionary history revealed through ancient nuclear and mitochondrial DNA from Madagascan elephant bird (Aepyornis sp.) eggshell. Mol Phylogenet Evol 109:151–163. https://doi.org/10.1016/j.ympev.2017.01.005
Griffin DK, Larkin M, O’Connor RE (2019) Jurassic Spark: what did the genomes of dinosaurs look like? In: Kraus RHS (ed) Avian genomics in ecology and evolution – from the lab into the wild. Springer, Cham
Hackett SJ et al (2008) A phylogenomic study of birds reveals their evolutionary history. Science 320:1763–1768. https://doi.org/10.1126/Science.1157704
Haddrath O, Baker AJ (2012) Multiple nuclear genes and retroposons support vicariance and dispersal of the palaeognaths, and an Early Cretaceous origin of modern birds. Proc Biol Sci 279:4617–4625. https://doi.org/10.1098/rspb.2012.1630
Hahn MW, Nakhleh L (2016) Irrational exuberance for resolved species trees. Evolution 70:7–17. https://doi.org/10.1111/evo.12832
Han K-L et al (2011) Are transposable element insertions homoplasy free? An examination using the avian tree of life. Syst Biol 60:375–386. https://doi.org/10.1093/Sysbio/Syq100
Harshman J et al (2008) Phylogenomic evidence for multiple losses of flight in ratite birds. Proc Natl Acad Sci USA 105:13462–13467. https://doi.org/10.1073/pnas.0803242105
Harvey MG, Smith BT, Glenn TC, Faircloth BC, Brumfield RT (2016) Sequence capture versus restriction site associated DNA sequencing for shallow systematics. Syst Biol 65:910–924. https://doi.org/10.1093/sysbio/syw036
Heath TA, Hedtke SM, Hillis DM (2008) Taxon sampling and the accuracy of phylogenetic analyses. J Syst Evol 46:239–257. https://doi.org/10.3724/SP.J.1002.2008.08016
Hedges SB, Marin J, Suleski M, Paymer M, Kumar S (2015) Tree of life reveals clock-like speciation and diversification. Mol Biol Evol 32:835–845. https://doi.org/10.1093/molbev/msv037
Heled J, Drummond AJ (2010) Bayesian inference of species trees from multilocus data. Mol Biol Evol 27:570–580. https://doi.org/10.1093/molbev/msp274
Helm-Bychowski K, Cracraft J (1993) 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 10:1196–1214
Hendy MD, Penny D (1989) A framework for the quantitative study of evolutionary trees. Syst Zool 38:297–309. https://doi.org/10.2307/2992396
Hennig W (1966) Phylogenetic systematics. University of Illinois Press, Chicago, IL
Higuchi RG, Ochman H (1989) Production of single-stranded DNA templates by exonuclease digestion following the polymerase chain reaction. Nucleic Acids Res 17:5865. https://doi.org/10.1093/nar/17.14.5865
Hillis DM, Moritz C (eds) (1990) Molecular systematics. Sinauer, Sunderland, MA
Hillis DM, Huelsenbeck JP, Cunningham CW (1994) Application and accuracy of molecular phylogenies. Science 264:671–677. https://doi.org/10.1126/science.8171318
Hinchliff CE et al (2015) Synthesis of phylogeny and taxonomy into a comprehensive tree of life. Proc Natl Acad Sci USA 112:12764–12769. https://doi.org/10.1073/pnas.1423041112
Höhna S et al (2016) RevBayes: Bayesian phylogenetic inference using graphical models and an interactive model-specification language. Syst Biol 65(4):726–736. https://doi.org/10.1093/sysbio/syw021
Hope S (2002) The Mesozoic radiation of Neornithes. In: Chiappe LM, Witmer LM (eds) Mesozoic birds: above the heads of dinosaurs. University of California Press, Berkeley, CA, pp 339–388
Hosner PA, Braun EL, Kimball RT (2015a) Land connectivity changes and global cooling shaped the colonization history and diversification of New World quail (Aves: Galliformes: Odontophoridae). J Biogeogr 42:1883–1895
Hosner PA, Faircloth BC, Glenn TC, Braun EL, Kimball RT (2015b) Avoiding missing data biases in phylogenomic inference: an empirical study in the landfowl (Aves: Galliformes). Mol Biol Evol 33:1110–1125. https://doi.org/10.1093/molbev/msv347
Hosner PA, Braun EL, Kimball RT (2016) Rapid and recent diversification of curassows, guans, and chachalacas (Galliformes: Cracidae) out of Mesoamerica: phylogeny inferred from mitochondrial, intron, and ultraconserved element sequences. Mol Phylogenet Evol 102:320–330. https://doi.org/10.1016/j.ympev.2016.06.006
Hosner PA, Tobias JA, Braun EL, Kimball RT (2017) How do seemingly non-vagile clades accomplish trans-marine dispersal? Trait and dispersal evolution in the landfowl (Aves: Galliformes). Proc Biol Sci 284:20170210. https://doi.org/10.1098/rspb.2017.0210
Houde P (1986) Ostrich ancestors found in the Northern Hemisphere suggest new hypothesis of ratite origins. Nature 324:563–565. https://doi.org/10.1038/324563a0
Houde P (1988) Paleognathous birds from the early Tertiary of the Northern Hemisphere. Publ Nuttall Ornithol Club 22:1–148
Hu F, Lin Y, Tang J (2014) MLGO: phylogeny reconstruction and ancestral inference from gene-order data. BMC Bioinformatics 15:354. https://doi.org/10.1186/s12859-014-0354-6
Huelsenbeck JP (1997) Is the Felsenstein zone a fly trap? Syst Biol 46:69–74. https://doi.org/10.2307/2413636
Huelsenbeck JP, Bollback JP (2001) Empirical and hierarchical Bayesian estimation of ancestral states. Syst Biol 50:351–366. https://doi.org/10.1080/10635150119871
Hughes JM, Baker AJ (1999) Phylogenetic relationships of the enigmatic Hoatzin (Opisthocomus hoazin) resolved using mitochondrial and nuclear gene sequences. Mol Biol Evol 16:1300–1307. https://doi.org/10.1093/oxfordjournals.molbev.a026220
Hughes RA, Ellington AD (2017) Synthetic DNA synthesis and assembly: putting the synthetic in synthetic biology. Cold Spring Harb Perspect Biol 9:a023812. https://doi.org/10.1101/cshperspect.a023812
Jarvis ED et al (2014) Whole-genome analyses resolve early branches in the tree of life of modern birds. Science 346:1320–1331. https://doi.org/10.1126/Science.1253451
Jeffroy O, Brinkmann H, Delsuc F, Philippe H (2006) Phylogenomics: the beginning of incongruence? Trends Genet 22:225–231. https://doi.org/10.1016/J.Tig.2006.02.003
Jetz W, Thomas GH, Joy JB, Hartmann K, Mooers AO (2012) The global diversity of birds in space and time. Nature 491:444–448. https://doi.org/10.1038/Nature11631
Jetz W, Thomas GH, Joy JB, Redding DW, Hartmann K, Mooers AO (2014) Global distribution and conservation of evolutionary distinctness in birds. Curr Biol 24:919–930. https://doi.org/10.1016/j.cub.2014.03.011
Johnston P (2011) New morphological evidence supports congruent phylogenies and Gondwana vicariance for palaeognathous birds. Zool J Linn Soc 163:959–982. https://doi.org/10.1111/j.1096-3642.2011.00730.x
Joseph L, Buchanan KL (2015) A quantum leap in avian biology. Emu 115:1–5. https://doi.org/10.1071/MUv115n1_ED
Kapusta A, Suh A (2017) Evolution of bird genomes-a transposon’s-eye view. Ann N Y Acad Sci 1389:164–185. https://doi.org/10.1111/nyas.13295
Katsu Y, Braun EL, Guillette LJ Jr, Iguchi T (2009) From reptilian phylogenomics to reptilian genomes: analyses of c-Jun and DJ-1 proto-oncogenes. Cytogenet Genome Res 127:79–93. https://doi.org/10.1159/000297715
Kearns AM et al (2018) Genomic evidence of speciation reversal in ravens. Nat Commun 9:906. https://doi.org/10.1038/s41467-018-03294-w
Kim J (2000) Slicing hyperdimensional oranges: the geometry of phylogenetic estimation. Mol Phylogenet Evol 17:58–75. https://doi.org/10.1006/mpev.2000.0816
Kimball RT, Wang N, Heimer-McGinn V, Ferguson C, Braun EL (2013) Identifying localized biases in large datasets: a case study using the avian tree of life. Mol Phylogenet Evol 69:1021–1032. https://doi.org/10.1016/j.ympev.2013.05.029
King N, Rokas A (2017) Embracing uncertainty in reconstructing early animal evolution. Curr Biol 27:R1081–R1088. https://doi.org/10.1016/j.cub.2017.08.054
Kocher TD, Thomas WK, Meyer A, Edwards SV, Paabo S, Villablanca FX, Wilson AC (1989) Dynamics of mitochondrial DNA evolution in animals: amplification and sequencing with conserved primers. Proc Natl Acad Sci USA 86:6196–6200
Korlach J et al (2017) De novo PacBio long-read and phased avian genome assemblies correct and add to reference genes generated with intermediate and short reads. Gigascience 6:1–16. https://doi.org/10.1093/gigascience/gix085
Kraus RHS, Wink M (2015) Avian genomics: fledging into the wild! J Ornithol 156:851–865. https://doi.org/10.1007/s10336-015-1253-y
Ksepka DT (2009) Broken gears in the avian molecular clock: new phylogenetic analyses support stem galliform status for Gallinuloides wyomingensis and rallid affinities for Amitabha urbsinterdictensis. Cladistics 25:173–197. https://doi.org/10.1111/j.1096-0031.2009.00250.x
Ksepka DT, Clarke JA (2009) Affinities of Palaeospiza bella and the phylogeny and biogeography of Mousebirds (Coliiformes). Auk 126:245–259. https://doi.org/10.1525/auk.2009.07178
Ksepka DT, Stidham TA, Williamson TE (2017) Early Paleocene landbird supports rapid phylogenetic and morphological diversification of crown birds after the K-Pg mass extinction. Proc Natl Acad Sci USA 114:8047–8052. https://doi.org/10.1073/pnas.1700188114
Kubatko LS, Degnan JH (2007) Inconsistency of phylogenetic estimates from concatenated data under coalescence. Syst Biol 56:17–24. https://doi.org/10.1080/10635150601146041
Kurochkin EN, Dyke GJ, Karhu AA (2002) A new presbyornithid bird (Aves, Anseriformes) from the Late Cretaceous of Southern Mongolia. Am Mus Novit 3386:1–11. https://doi.org/10.1206/0003-0082(2002)386<0001:ANPBAA>2.0.CO;2
Lamichhaney S et al (2015) Evolution of Darwin’s finches and their beaks revealed by genome sequencing. Nature 518:371–375. https://doi.org/10.1038/nature14181
Lanfear R, Calcott B, Kainer D, Mayer C, Stamatakis A (2014) Selecting optimal partitioning schemes for phylogenomic datasets. BMC Evol Biol 14:82. https://doi.org/10.1186/1471-2148-14-82
Lavretsky P, Hernández-Baños BE, Peters JL (2014) Rapid radiation and hybridization contribute to weak differentiation and hinder phylogenetic inferences in the New World Mallard complex (Anas spp.). Auk 131:524–538. https://doi.org/10.1642/AUK-13-164.1
Le Duc D et al (2015) Kiwi genome provides insights into evolution of a nocturnal lifestyle. Genome Biol 16:147. https://doi.org/10.1186/s13059-015-0711-4
Lee MSY, Cau A, Naish D, Dyke GJ (2014) Morphological clocks in paleontology, and a mid-Cretaceous origin of crown Aves. Syst Biol 63:442–449. https://doi.org/10.1093/sysbio/syt110
Lemmon AR, Emme SA, Lemmon EM (2012) Anchored hybrid enrichment for massively high-throughput phylogenomics. Syst Biol 61:727–744. https://doi.org/10.1093/sysbio/sys049
Liang B, Wang N, Li N, Kimball RT, Braun EL (2018) Comparative genomics reveals a burst of homoplasy-free numt insertions. Mol Biol Evol 35(8):2060–2064. https://doi.org/10.1093/molbev/msy112
Liu L (2008) BEST: Bayesian estimation of species trees under the coalescent model. Bioinformatics 24:2542–2543. https://doi.org/10.1093/bioinformatics/btn484
Liu L, Yu L (2011) Estimating species trees from unrooted gene trees. Syst Biol 60:661–667. https://doi.org/10.1093/sysbio/syr027
Liu L, Yu L, Kubatko L, Pearl DK, Edwards SV (2009) Coalescent methods for estimating phylogenetic trees. Mol Phylogenet Evol 53:320–328. https://doi.org/10.1016/j.ympev.2009.05.033
Liu LA, Yu LL, Edwards SV (2010) A maximum pseudo-likelihood approach for estimating species trees under the coalescent model. BMC Evol Biol 10:302. https://doi.org/10.1186/1471-2148-10-302
Livezey BC, Zusi RL (2007a) Higher-order phylogeny of modern birds (Theropoda, Aves: Neornithes) based on comparative anatomy. II. Analysis and discussion. Zool J Linn Soc 149:1–95. https://doi.org/10.1111/j.1096-3642.2006.00293.x
Livezey BC, Zusi RL (2007b) Higher-order phylogeny of modern birds (Theropoda, Aves: Neornithes) based on comparative anatomy. I. Methods and characters. Bull Carnegie Mus Nat Hist 37:1–544
Lockhart PJ, Larkum AW, Steel M, Waddell PJ, Penny D (1996) Evolution of chlorophyll and bacteriochlorophyll: the problem of invariant sites in sequence analysis. Proc Natl Acad Sci USA 93:1930–1934. https://doi.org/10.1073/pnas.93.5.1930
Long C, Kubatko L (2017) Identifiability and reconstructibility of species phylogenies under a modified coalescent. arXiv preprint:1701.06871
Lopez P, Casane D, Philippe H (2002) Heterotachy, an important process of protein evolution. Mol Biol Evol 19:1–7. https://doi.org/10.1093/oxfordjournals.molbev.a003973
Maddison WP (1997) Gene trees in species trees. Syst Biol 46:523–536. https://doi.org/10.2307/2413694
Manthey JD, Campillo LC, Burns KJ, Moyle RG (2016) Comparison of target-capture and restriction-site associated DNA sequencing for phylogenomics: a test in cardinalid tanagers (Aves, Genus: Piranga). Syst Biol 65:640–650. https://doi.org/10.1093/sysbio/syw005
Matsen FA, Steel M (2007) Phylogenetic mixtures on a single tree can mimic a tree of another topology. Syst Biol 56:767–775. https://doi.org/10.1080/10635150701627304
Matzke A et al (2012) Retroposon insertion patterns of neoavian birds: strong evidence for an extensive incomplete lineage sorting era. Mol Biol Evol 29:1497–1501. https://doi.org/10.1093/Molbev/Msr319
Mayr G (2004a) Morphological evidence for sister group relationship between flamingos (Aves: Phoenicopteridae) and grebes (Podicipedidae). Zool J Linn Soc 140:157–169. https://doi.org/10.1111/j.1096-3642.2003.00094.x
Mayr G (2004b) Old World fossil record of modern-type hummingbirds. Science 304:861–864. https://doi.org/10.1126/science.1096856
Mayr G (2008) Avian higher-level phylogeny: well-supported clades and what we can learn from a phylogenetic analysis of 2954 morphological characters. J Zool Syst Evol Res 46:63–72. https://doi.org/10.1111/j.1439-0469.2007.00433.x
Mayr G (2009) Paleogene fossil birds. Springer, Berlin
Mayr G (2011) Metaves, Mirandornithes, Strisores and other novelties – a critical review of the higher-level phylogeny of neornithine birds. J Zool Syst Evol Res 49:58–76. https://doi.org/10.1111/j.1439-0469.2010.00586.x
Mayr G (2014) A Hoatzin fossil from the middle Miocene of Kenya documents the past occurrence of modern-type Opisthocomiformes in Africa. Auk 131:55–60. https://doi.org/10.1642/Auk-13-134.1
Mayr G, De Pietri VL (2014) Earliest and first Northern Hemispheric Hoatzin fossils substantiate Old World origin of a “Neotropic endemic”. Naturwissenschaften 101:143–148. https://doi.org/10.1007/s00114-014-1144-8
Mayr G, Alvarenga H, Mourer-Chauvire C (2011) Out of Africa: fossils shed light on the origin of the Hoatzin, an iconic Neotropic bird. Naturwissenschaften 98:961–966. https://doi.org/10.1007/s00114-011-0849-1
Mayr G, De Pietri VL, Scofield RP, Worthy TH (2018) On the taxonomic composition and phylogenetic affinities of the recently proposed clade Vegaviidae Agnolín et al., 2017 – neornithine birds from the Upper Cretaceous of the Southern Hemisphere. Cretac Res 86:178–185. https://doi.org/10.1016/j.cretres.2018.02.013
McCormack JE, Faircloth BC, Crawford NG, Gowaty PA, Brumfield RT, Glenn TC (2012) Ultraconserved elements are novel phylogenomic markers that resolve placental mammal phylogeny when combined with species-tree analysis. Genome Res 22:746–754. https://doi.org/10.1101/gr.125864.111
McCormack JE, Harvey MG, Faircloth BC, Crawford NG, Glenn TC, Brumfield RT (2013) A phylogeny of birds based on over 1,500 loci collected by target enrichment and high-throughput sequencing. PLoS One 8:e54848. https://doi.org/10.1371/journal.pone.0054848
McCormack JE, Tsai WLE, Faircloth BC (2016) Sequence capture of ultraconserved elements from bird museum specimens. Mol Ecol Resour 16:1189–1203. https://doi.org/10.1111/1755-0998.12466
Meikejohn KA, Danielson MJ, Faircloth BC, Glenn TC, Braun EL, Kimball RT (2014) Incongruence among different mitochondrial regions: a case study using complete mitogenomes. Mol Phylogenet Evol 78:314–323. https://doi.org/10.1016/j.ympev.2014.06.003
Meiklejohn KA, Faircloth BC, Glenn TC, Kimball RT, Braun EL (2016) Analysis of a rapid evolutionary radiation using ultraconserved elements: evidence for a bias in some multispecies coalescent methods. Syst Biol 65:612–627. https://doi.org/10.1093/sysbio/syw014
Mendes FK, Hahn MW (2017) Why concatenation fails near the anomaly zone. Syst Biol. https://doi.org/10.1093/sysbio/syx063
Mendoza MLZ, Nygaard S, da Fonseca RR (2014) DivA: detection of non-homologous and very divergent regions in protein sequence alignments. BMC Res Notes 7:806. https://doi.org/10.1186/1756-0500-7-806
Mindell DP (ed) (1997) Avian molecular evolution and systematics. Academic, San Diego, CA
Minh BQ, Nguyen MA, von Haeseler A (2013) Ultrafast approximation for phylogenetic bootstrap. Mol Biol Evol 30:1188–1195. https://doi.org/10.1093/molbev/mst024
Mirarab S, Warnow T (2015) ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes. Bioinformatics 31:44–52. https://doi.org/10.1093/bioinformatics/btv234
Mirarab S, Bayzid MS, Boussau B, Warnow T (2014a) Statistical binning enables an accurate coalescent-based estimation of the avian tree. Science 346:1250463. https://doi.org/10.1126/science.1250463
Mirarab S, Reaz R, Bayzid MS, Zimmermann T, Swenson MS, Warnow T (2014b) ASTRAL: genome-scale coalescent-based species tree estimation. Bioinformatics 30:i541–i548. https://doi.org/10.1093/bioinformatics/btu462
Mitchell KJ et al (2014) Ancient DNA reveals elephant birds and kiwi are sister taxa and clarifies ratite bird evolution. Science 344:898–900. https://doi.org/10.1126/science.1251981
Miyamoto MM, Cracraft J (eds) (1991) Phylogenetic analysis of DNA sequences. Oxford University Press, New York
Mossel E (2003) On the impossibility of reconstructing ancestral data and phylogenies. J Comput Biol 10:669–676. https://doi.org/10.1089/106652703322539015
Moyle RG et al (2016) Tectonic collision and uplift of Wallacea triggered the global songbird radiation. Nat Commun 7:12709. https://doi.org/10.1038/ncomms12709
Musher LJ, Cracraft J (2018) Phylogenomics and species delimitation of a complex radiation of Neotropical suboscine birds (Pachyramphus). Mol Phylogenet Evol 118:204–221. https://doi.org/10.1016/j.ympev.2017.09.013
Nadachowska-Brzyska K, Li C, Smeds L, Zhang G, Ellegren H (2015) Temporal dynamics of avian populations during Pleistocene revealed by whole-genome sequences. Curr Biol 25:1375–1380. https://doi.org/10.1016/j.cub.2015.03.047
Nater A, Burri R, Kawakami T, Smeds L, Ellegren H (2015) Resolving evolutionary relationships in closely related species with whole-genome sequencing data. Syst Biol 62:1000–1017. https://doi.org/10.1093/sysbio/syv045
Nguyen L-T, Schmidt HA, von Haeseler A, Minh BQ (2015) IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol 32:268–274. https://doi.org/10.1093/molbev/msu300
O’Connor JK, Zhou Z (2013) A redescription of Chaoyangia beishanensis (Aves) and a comprehensive phylogeny of Mesozoic birds. J Syst Palaeontol 11:889–906. https://doi.org/10.1080/14772019.2012.690455
Olson SL (1985) The fossil record of birds. Avian Biol 8:79–252
Ota R, Penny D (2003) Estimating changes in mutational mechanisms of evolution. J Mol Evol 57(Suppl 1):S233–S240. https://doi.org/10.1007/s00239-003-0032-1
Ottenburghs J (2019) Avian species concepts in the light of genomics. In: Kraus RHS (ed) Avian genomics in ecology and evolution – from the lab into the wild. Springer, Cham
Ottenburghs J, Ydenberg RC, Van Hooft P, Van Wieren SE, Prins HH (2015) The Avian Hybrids Project: gathering the scientific literature on avian hybridization. Ibis 157:892–894. https://doi.org/10.1111/ibi.12285
Ottenburghs J et al (2016a) A tree of geese: a phylogenomic perspective on the evolutionary history of True Geese. Mol Phylogenet Evol 101:303–313
Ottenburghs J, van Hooft P, van Wieren SE, Ydenberg RC, Prins HH (2016b) Birds in a bush: toward an avian phylogenetic network. Auk 133:577–582. https://doi.org/10.1642/AUK-16-53.1
Ottenburghs J et al (2017a) A history of hybrids? Genomic patterns of introgression in the True Geese. BMC Evol Biol 17:201. https://doi.org/10.1186/s12862-017-1048-2
Ottenburghs J, Kraus RHS, van Hooft P, van Wieren SE, Ydenberg RC, Prins HH (2017b) Avian introgression in the genomic era. Avian Res 8:30. https://doi.org/10.1186/s40657-017-0088-z
Pamilo P, Nei M (1988) Relationships between gene trees and species trees. Mol Biol Evol 5:568–583. https://doi.org/10.1093/oxfordjournals.molbev.a040517
Pandey A, Braun EL (2018) Why do phylogenomic analyses of early animal evolution continue to disagree? Sites in different structural environments yield different answers. biorXiv:400465. https://doi.org/10.1101/400465
Patel S, Kimball RT, Braun EL (2013) Error in phylogenetic estimation for bushes in the tree of life. J Phylogen Evol Biol 1:110. https://doi.org/10.4172/jpgeb.1000110
Pease JB, Brown JW, Walker JF, Hinchliff CE, Smith SA (2018) Quartet sampling distinguishes lack of support from conflicting support in the green plant tree of life. Am J Bot 105:385–403. https://doi.org/10.1002/ajb2.1016
Pennisi E (2018) Bigger, better bird tree of life will soon fly into view. Science. https://doi.org/10.1126/science.aat8989
Penny D, McComish BJ, Charleston MA, Hendy MD (2001) Mathematical elegance with biochemical realism: the covarion model of molecular evolution. J Mol Evol 53:711–723. https://doi.org/10.1007/s002390010258
Persons NW, Hosner PA, Meiklejohn KA, Braun EL, Kimball RT (2016) Sorting out relationships among the grouse and ptarmigan using intron, mitochondrial, and ultra-conserved element sequences. Mol Phylogenet Evol 98:123–132. https://doi.org/10.1016/j.ympev.2016.02.003
Philippe H, Brinkmann H, Lavrov DV, Littlewood DT, Manuel M, Worheide G, Baurain D (2011) Resolving difficult phylogenetic questions: why more sequences are not enough. PLoS Biol 9:e1000602. https://doi.org/10.1371/journal.pbio.1000602
Phillips MJ, Delsuc F, Penny D (2004) Genome-scale phylogeny and the detection of systematic biases. Mol Biol Evol 21:1455–1458. https://doi.org/10.1093/molbev/msh137
Phillips MJ, Gibb GC, Crimp EA, Penny D (2010) Tinamous and moa flock together: mitochondrial genome sequence analysis reveals independent losses of flight among ratites. Syst Biol 59:90–107. https://doi.org/10.1093/sysbio/syp079
Poelstra JW et al (2014) The genomic landscape underlying phenotypic integrity in the face of gene flow in crows. Science 344:1410–1414. https://doi.org/10.1126/science.1253226
Prum RO, Berv JS, Dornburg A, Field DJ, Townsend JP, Lemmon EM, Lemmon AR (2015) A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing. Nature 526:569–573. https://doi.org/10.1038/nature15697
Rabosky DL (2015) No substitute for real data: a cautionary note on the use of phylogenies from birth-death polytomy resolvers for downstream comparative analyses. Evolution 69:3207–3216. https://doi.org/10.1111/evo.12817
Ragan MA (1992) Phylogenetic inference based on matrix representation of trees. Mol Phylogenet Evol 1:53–58. https://doi.org/10.1016/1055-7903(92)90035-F
Rannala B, Yang Z (2017) Efficient Bayesian species tree inference under the multispecies coalescent. Syst Biol 66:823–842. https://doi.org/10.1093/sysbio/syw119
Raposo do Amaral F, Neves LG, Resende MF Jr, Mobili F, Miyaki CY, Pellegrino KC, Biondo C (2015) Ultraconserved elements sequencing as a low-cost source of complete mitochondrial genomes and microsatellite markers in non-model amniotes. PLoS One 10:e0138446. https://doi.org/10.1371/journal.pone.0138446
Reddy S et al (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. https://doi.org/10.1093/sysbio/syx041
Redelings BD, Holder MT (2017) A supertree pipeline for summarizing phylogenetic and taxonomic information for millions of species. PeerJ 5:e3058. https://doi.org/10.7717/peerj.3058
Reid NM, Hird SM, Brown JM, Pelletier TA, McVay JD, Satler JD, Carstens BC (2013) Poor fit to the multispecies coalescent is widely detectable in empirical data. Syst Biol 63:322–333. https://doi.org/10.1093/sysbio/syt057
Rheindt FE, Edwards SV (2011) Genetic introgression: an integral but neglected component of speciation in birds. Auk 128:620–632. https://doi.org/10.1525/auk.2011.128.4.620
Ricklefs RE (2007) Estimating diversification rates from phylogenetic information. Trends Ecol Evol 22:601–610. https://doi.org/10.1016/j.tree.2007.06.013
Rindal E, Brower AVZ (2011) Do model-based phylogenetic analyses perform better than parsimony? A test with empirical data. Cladistics 27:331–334. https://doi.org/10.1111/j.1096-0031.2010.00342.x
Roberts A, Pimentel H, Trapnell C, Pachter L (2011) Identification of novel transcripts in annotated genomes using RNA-Seq. Bioinformatics 27:2325–2329. https://doi.org/10.1093/bioinformatics/btr355
Roch S, Steel M (2015) Likelihood-based tree reconstruction on a concatenation of aligned sequence data sets can be statistically inconsistent. Theor Popul Biol 100:56–62. https://doi.org/10.1016/j.tpb.2014.12.005
Ronquist F et al (2012) MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst Biol 61:539–542. https://doi.org/10.1093/sysbio/sys029
Sackton TB et al (2018) Convergent regulatory evolution and the origin of flightlessness in palaeognathous birds. bioRxiv:262584. https://doi.org/10.1101/262584
Saiki RK et al (1988) Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science 239:487–491
Salichos L, Stamatakis A, Rokas A (2014) Novel information theory-based measures for quantifying incongruence among phylogenetic trees. Mol Biol Evol 31:1261–1271. https://doi.org/10.1093/molbev/msu061
Sanderson MJ, Kim J (2000) Parametric phylogenetics? Syst Biol 49:817–829. https://doi.org/10.1080/106351500750049860
Sayyari E, Mirarab S (2016) Fast coalescent-based computation of local branch support from quartet frequencies. Mol Biol Evol 33:1654–1668. https://doi.org/10.1093/molbev/msw079
Sayyari E, Whitfield JB, Mirarab S (2018) DiscoVista: interpretable visualizations of gene tree discordance. Mol Phylogenet Evol 122:110–115. https://doi.org/10.1016/j.ympev.2018.01.019
Seki R et al (2017) Functional roles of Aves class-specific cis-regulatory elements on macroevolution of bird-specific features. Nat Commun 8:14229. https://doi.org/10.1038/ncomms14229
Seo TK (2008) Calculating bootstrap probabilities of phylogeny using multilocus sequence data. Mol Biol Evol 25:960–971. https://doi.org/10.1093/molbev/msn043
Sheldon FH, Bledsoe AH (1993) Avian molecular systematics, 1970s to 1990s. Annu Rev Ecol Syst 24:243–278. https://doi.org/10.1146/annurev.es.24.110193.001331
Sibley CG, Ahlquist JE (1990) Phylogeny and classification of birds: a study in molecular evolution. Yale University Press, New Haven, CT
Slack KE, Delsuc F, McLenachan PA, Arnason U, Penny D (2007) Resolving the root of the avian mitogenomic tree by breaking up long branches. Mol Phylogenet Evol 42:1–13. https://doi.org/10.1016/j.ympev.2006.06.002
Slatkin M, Pollack JL (2008) Subdivision in an ancestral species creates asymmetry in gene trees. Mol Biol Evol 25:2241–2246. https://doi.org/10.1093/molbev/msn172
Smith JV, Braun EL, Kimball RT (2013) Ratite nonmonophyly: independent evidence from 40 novel loci. Syst Biol 62:35–49. https://doi.org/10.1093/Sysbio/Sys067
Smith BT, Harvey MG, Faircloth BC, Glenn TC, Brumfield RT (2014) Target capture and massively parallel sequencing of ultraconserved elements for comparative studies at shallow evolutionary time scales. Syst Biol 63:83–95. https://doi.org/10.1093/sysbio/syt061
Snir S, Rao S (2012) Quartet MaxCut: a fast algorithm for amalgamating quartet trees. Mol Phylogenet Evol 62:1–8. https://doi.org/10.1016/j.ympev.2011.06.021
Sorenson MD, Oneal E, Garcia-Moreno J, Mindell DP (2003) More taxa, more characters: the Hoatzin problem is still unresolved. Mol Biol Evol 20:1484–1498. https://doi.org/10.1093/molbev/msg157
Springer MS, Gatesy J (2016) The gene tree delusion. Mol Phylogenet Evol 94:1–33. https://doi.org/10.1016/j.ympev.2015.07.018
Springer MS, Gatesy J (2018) On the importance of homology in the age of phylogenomics. Syst Biodivers 16:210–228. https://doi.org/10.1080/14772000.2017.1401016
Stamatakis A (2014) RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30:1312–1313. https://doi.org/10.1093/Bioinformatics/Btu033
Stearns SC, Hoekstra RF (2005) Evolution: an introduction, 2nd edn. Oxford University Press, New York
Steel M (2005) Should phylogenetic models be trying to “fit an elephant”? Trends Genet 21:307–309. https://doi.org/10.1016/j.tig.2005.04.001
Steel M, Penny D (2004) Two further links between MP and ML under the Poisson model. Appl Math Lett 17:785–790. https://doi.org/10.1016/j.aml.2004.06.006
Steel M, Penny D (2005) Maximum parsimony and the phylogenetic information in multistate characters. In: Albert VA (ed) Parsimony, phylogeny, and genomics. Oxford University Press, Oxford, pp 163–178
Stoddard MC, Yong EH, Akkaynak D, Sheard C, Tobias JA, Mahadevan L (2017) Avian egg shape: form, function, and evolution. Science 356:1249–1254. https://doi.org/10.1126/science.aaj1945
Stryjewski KF, Sorenson MD (2017) Mosaic genome evolution in a recent and rapid avian radiation. Nat Ecol Evol 1:1912–1922. https://doi.org/10.1038/s41559-017-0364-7
Suh A (2015) The specific requirements for CR1 retrotransposition explain the scarcity of retrogenes in birds. J Mol Evol 81:18–20. https://doi.org/10.1007/s00239-015-9692-x
Suh A (2016) The phylogenomic forest of bird trees contains a hard polytomy at the root of Neoaves. Zool Scr 45:50–62. https://doi.org/10.1111/zsc.12213
Suh A et al (2011) Mesozoic retroposons reveal parrots as the closest living relatives of passerine birds. Nat Commun 2:443. https://doi.org/10.1038/Ncomms1448
Suh A, Smeds L, Ellegren H (2015) The dynamics of incomplete lineage sorting across the ancient adaptive radiation of neoavian birds. PLoS Biol 13:e1002224. https://doi.org/10.1371/journal.pbio.1002224
Suh A, Bachg S, Donnellan S, Joseph L, Brosius J, Kriegs JO, Schmitz J (2017) De-novo emergence of SINE retroposons during the early evolution of passerine birds. Mob DNA 8:21. https://doi.org/10.1186/s13100-017-0104-1
Sumner JG, Jarvis PD, Fernández-Sánchez J, Ferńandez-Sánchez J, Kaine BT, Woodhams MD, Holland BR (2012) Is the general time-reversible model bad for molecular phylogenetics? Syst Biol 61:1069–1074. https://doi.org/10.1093/sysbio/sys042
Sun K, Meiklejohn KA, Faircloth BC, Glenn TC, Braun EL, Kimball RT (2014) The evolution of peafowl and other taxa with ocelli (eyespots): a phylogenomic approach. Proc R Soc B 281:20140823. https://doi.org/10.1098/rspb.2014.0823
Sun Z et al (2017) Rapid and recent diversification patterns in Anseriformes birds: inferred from molecular phylogeny and diversification analyses. PLoS One 12(9):e0184529. https://doi.org/10.1371/journal.pone.0184529
Swofford DL, Waddell PJ, Huelsenbeck JP, Foster PG, Lewis PO, Rogers JS (2001) Bias in phylogenetic estimation and its relevance to the choice between parsimony and likelihood methods. Syst Biol 50:525–539. https://doi.org/10.1080/106351501750435086
Thomas GH (2015) Evolution: an avian explosion. Nature 526:516–517. https://doi.org/10.1038/nature15638
Tiley GP, Kimball RT, Braun EL, Burleigh JG (2018) Comparison of the Chinese bamboo partridge and Red Junglefowl genome sequences highlights the importance of demography in genome evolution. BMC Genomics 19:336. https://doi.org/10.1186/s12864-018-4711-0
Title PO, Rabosky DL (2017) Do macrophylogenies yield stable macroevolutionary inferences? An example from squamate reptiles. Syst Biol 66:843–856. https://doi.org/10.1093/sysbio/syw102
Toews DPL, Taylor SA, Vallender R, Brelsford A, Butcher BG, Messer PW, Lovette IJ (2016a) Plumage genes and little else distinguish the genomes of hybridizing warblers. Curr Biol 26:2313–2318. https://doi.org/10.1016/j.cub.2016.06.034
Toews DPL et al (2016b) Genomic approaches to understanding population divergence and speciation in birds. Auk 133:13–30. https://doi.org/10.1642/Auk-15-51.1
Tonini J, Moore A, Stern D, Shcheglovitova M, Ortí G (2015) Concatenation and species tree methods exhibit statistically indistinguishable accuracy under a range of simulated conditions. PLoS Curr. https://doi.org/10.1371/currents.tol.34260cc27551a527b124ec5f6334b6be
Tuttle EM et al (2016) Divergence and functional degradation of a sex chromosome-like supergene. Curr Biol 26:344–350. https://doi.org/10.1016/j.cub.2015.11.069
Urbanek A (1993) Biotic crises in the history of Upper Silurian graptoloids: a Palaeobiological model. Hist Biol 7:29–50. https://doi.org/10.1080/10292389309380442
Vachaspati P, Warnow T (2015) ASTRID: Accurate Species TRees from Internode Distances. BMC Genomics 16(Suppl 10):S3. https://doi.org/10.1186/1471-2164-16-S10-S3
Van Tuinen M, Butvill DB, Kirsch JA, Hedges SB (2001) Convergence and divergence in the evolution of aquatic birds. Proc Biol Sci 268:1345–1350. https://doi.org/10.1098/rspb.2001.1679
Wang M, Zhou Z (2017) The evolution of birds with implications from new fossil evidences. In: Maina JN (ed) The biology of the avian respiratory system. Springer, Cham, pp 1–26. https://doi.org/10.1007/978-3-319-44153-5_1
Wang N, Braun EL, Kimball RT (2012) Testing hypotheses about the sister group of the Passeriformes using an independent 30-locus data set. Mol Biol Evol 29:737–750. https://doi.org/10.1093/Molbev/Msr230
Wang N, Hosner PA, Liang B, Braun EL, Kimball RT (2017) Historical relationships of three enigmatic phasianid genera (Aves: Galliformes) inferred using phylogenomic and mitogenomic data. Mol Phylogenet Evol 109:217–225. https://doi.org/10.1016/j.ympev.2017.01.006
Wang N, Kimball RT, Braun EL, Liang B, Zhang ZW (2016) Ancestral range reconstruction of Galliformes: the effects of topology and taxon sampling. J Biogeogr 44:122–135. https://doi.org/10.1111/jbi.12782
Warnow T (2015) Concatenation analyses in the presence of incomplete lineage sorting. PLoS Curr. https://doi.org/10.1371/currents.tol.8d41ac0f13d1abedf4c4a59f5d17b1f7
Warnow T (2018) Computational phylogenetics: an introduction to designing methods for phylogeny estimation. Cambridge University Press, Cambridge
Watson JD (1990) The human genome project: past, present, and future. Science 248:44–49. https://doi.org/10.1126/science.2181665
Weber CC, Boussau B, Romiguier J, Jarvis ED, Ellegren H (2014a) Evidence for GC-biased gene conversion as a driver of between-lineage differences in avian base composition. Genome Biol 15:549. https://doi.org/10.1186/s13059-014-0549-1
Weber CC, Nabholz B, Romiguier J, Ellegren H (2014b) Kr/Kc but not dN/dS correlates positively with body mass in birds, raising implications for inferring lineage-specific selection. Genome Biol 15:542. https://doi.org/10.1186/s13059-014-0542-8
Weissensteiner MH, Suh A (2018) Repetitive DNA – the dark matter of avian genomics. In: Kraus RHS (ed) Avian genomics in ecology and evolution – from the lab into the wild. Springer, Cham
White ND, Mitter C, Braun MJ (2017) Ultraconserved elements resolve the phylogeny of potoos (Aves: Nyctibiidae). J Avian Biol 48:872–880. https://doi.org/10.1111/jav.01313
Wink M (2019) A historical perspective of avian genomics. In: Kraus RHS (ed) Avian genomics in ecology and evolution – from the lab into the wild. Springer, Cham
Workman RE, Myrka AM, Tseng E, Wong GW, Welch KC, Timp W (2017) Single molecule, full-length transcript sequencing provides insight into the extreme metabolism of ruby-throated hummingbird Archilochus colubris. Gigascience 7:1–12. https://doi.org/10.1093/gigascience/giy009
Worthy TH, Scofield RP (2012) Twenty-first century advances in knowledge of the biology of moa (Aves: Dinornithiformes): a new morphological analysis and moa diagnoses revised. New Zeal J Zool 39:87–153. https://doi.org/10.1080/03014223.2012.665060
Worthy TH, Degrange FJ, Handley WD, Lee MSY (2017) The evolution of giant flightless birds and novel phylogenetic relationships for extinct fowl (Aves, Galloanseres). R Soc Open Sci 4:170975. https://doi.org/10.1098/rsos.170975
Wright NA, Steadman DW, Witt CC (2016) Predictable evolution toward flightlessness in volant island birds. Proc Natl Acad Sci USA 113:4765–4770. https://doi.org/10.1073/pnas.1522931113
Xu B, Yang Z (2016) Challenges in species tree estimation under the multispecies coalescent model. Genetics 204:1353–1368. https://doi.org/10.1534/genetics.116.190173
Yonezawa T et al (2017) Phylogenomics and morphology of extinct paleognaths reveal the origin and evolution of the ratites. Curr Biol 27:68–77. https://doi.org/10.1016/j.cub.2016.10.029
Younger JL et al (2018) Hidden diversity of forest birds in Madagascar revealed using integrative taxonomy. Mol Phylogenet Evol 124:16–26. https://doi.org/10.1016/j.ympev.2018.02.017
Yuri T, Kimball RT, Braun EL, Braun MJ (2008) Duplication of accelerated evolution and growth hormone gene in passerine birds. Mol Biol Evol 25:352–361. https://doi.org/10.1093/molbev/msm260
Yuri T et al (2013) Parsimony and model-based analyses of indels in avian nuclear genes reveal congruent and incongruent phylogenetic signals. Biology 2:419–444. https://doi.org/10.3390/biology2010419
Zarza E, Faircloth BC, Tsai WLE, Bryson RW, Klicka J, Mccormack JE (2016) Hidden histories of gene flow in highland birds revealed with genomic markers. Mol Ecol 25:5144–5157. https://doi.org/10.1111/mec.13813
Zhang G et al (2014) Comparative genomics reveals insights into avian genome evolution and adaptation. Science 346:1311–1320. https://doi.org/10.1126/science.1251385
Zhang G, Rahbek C, Graves GR, Lei F, Jarvis ED, Gilbert MTP (2015) Genomics: bird sequencing project takes off. Nature 522:34. https://doi.org/10.1038/522034d
Zhang C, Rabiee M, Sayyari E, Mirarab S (2018) ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees. BMC Bioinformatics 19:153. https://doi.org/10.1186/s12859-018-2129-y
Zhou X, Shen X, Hittinger CT, Rokas A (2018) Evaluating fast maximum likelihood-based phylogenetic programs using empirical phylogenomic data sets. Mol Biol Evol 35:486–503. https://doi.org/10.1093/molbev/msx302
Zwickl DJ, Stein JC, Wing RA, Ware D, Sanderson MJ (2014) Disentangling methodological and biological sources of gene tree discordance on Oryza (Poaceae) chromosome 3. Syst Biol 63:645–659. https://doi.org/10.1093/sysbio/syu027
Acknowledgments
We are grateful to Robert Kraus for inviting this chapter and for his encouragement (and patience) while we were writing it. We would also like to express our gratitude to Tom Gilbert and two anonymous reviewers for insightful comments that improved the manuscript. E.L.B. acknowledges support from the US National Science Foundation grants DEB-1118823 and DEB-1655683 (the “OpenWings” project) and a seed grant from the University of Florida Biodiversity Institute; J.C. acknowledges the US National Science Foundation awards DEB-1241066 and DEB-1146423.
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Braun, E.L., Cracraft, J., Houde, P. (2019). Resolving the Avian Tree of Life from Top to Bottom: The Promise and Potential Boundaries of the Phylogenomic Era. In: Kraus, R. (eds) Avian Genomics in Ecology and Evolution. Springer, Cham. https://doi.org/10.1007/978-3-030-16477-5_6
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