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Volumn 33, Issue 4, 2016, Pages 1110-1125

Avoiding missing data biases in phylogenomic inference: An empirical study in the landfowl (Aves: Galliformes)

Author keywords

Bias; Coalescent; Coturnix; Gallus; Meleagris; Ultraconserved elements

Indexed keywords

CONTROLLED STUDY; EMPIRICISM; GALLIFORMES; JUNGLE FOWL; MAXIMUM LIKELIHOOD METHOD; PHYLOGENY; PREVALENCE; TAXON; ANIMAL; BIOLOGICAL MODEL; DNA SEQUENCE; GENETICS; GENOME; HIGH THROUGHPUT SEQUENCING; MOLECULAR EVOLUTION; PROCEDURES; STATISTICAL BIAS;

EID: 84964904973     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msv347     Document Type: Article
Times cited : (183)

References (121)
  • 1
    • 84871832204 scopus 로고    scopus 로고
    • Pruning rogue taxa improves phylogenetic accuracy: An efficient algorithm and webservice
    • Aberer AJ, Krompass D, Stamatakis A. 2013. Pruning rogue taxa improves phylogenetic accuracy: An efficient algorithm and webservice. Syst Biol. 62:162-166.
    • (2013) Syst Biol , vol.62 , pp. 162-166
    • Aberer, A.J.1    Krompass, D.2    Stamatakis, A.3
  • 3
    • 84894596325 scopus 로고    scopus 로고
    • Conserved genes, sampling error, and phylogenomic inference
    • Betancur-R R, Naylor GJP, Ortí G. 2014. Conserved genes, sampling error, and phylogenomic inference. Syst Biol. 63:257-262.
    • (2014) Syst Biol , vol.63 , pp. 257-262
    • Betancur-R, R.1    Naylor, G.J.P.2    Ortí, G.3
  • 4
    • 84855169251 scopus 로고    scopus 로고
    • BirdLife International. Available from
    • BirdLife International. 2012. IUCN Red List for birds. Available from: http://www.iucnredlist.org/.
    • (2012) IUCN Red List for Birds
  • 5
    • 77953133200 scopus 로고    scopus 로고
    • Comparative molecular evolution and phylogenetic utility of 30-UTRs and introns in Galliformes
    • Bonilla AJ, Braun EL, Kimball RT. 2010. Comparative molecular evolution and phylogenetic utility of 30-UTRs and introns in Galliformes. Mol Phylogent Evol. 56:536-542.
    • (2010) Mol Phylogent Evol , vol.56 , pp. 536-542
    • Bonilla, A.J.1    Braun, E.L.2    Kimball, R.T.3
  • 6
    • 0034914770 scopus 로고    scopus 로고
    • Polytomies, the power of phylogenetic inference, and the stochastic nature of molecular evolution: A comment on Walsh et al
    • 1999
    • 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.
    • (2001) Evolution , vol.55 , pp. 1261-1263
    • Braun, E.L.1    Kimball, R.T.2
  • 7
    • 84920887826 scopus 로고    scopus 로고
    • Building the avian tree of life using a large-scale, sparse supermatrix
    • Burleigh JG, Kimball RT, Braun EL. 2015. Building the avian tree of life using a large-scale, sparse supermatrix. Mol Phylogent Evol. 84:53-63.
    • (2015) Mol Phylogent Evol , vol.84 , pp. 53-63
    • Burleigh, J.G.1    Kimball, R.T.2    Braun, E.L.3
  • 8
    • 84917697072 scopus 로고    scopus 로고
    • Quartet inference from SNP data under the coalescent model
    • Chifman J, Kubatko L. 2014. Quartet inference from SNP data under the coalescent model. Bioinformatics 30:3317-3324.
    • (2014) Bioinformatics , vol.30 , pp. 3317-3324
    • Chifman, J.1    Kubatko, L.2
  • 9
    • 84865382153 scopus 로고    scopus 로고
    • More than 1000 ultraconserved elements provide evidence that turtles are the sister group of archosaurs
    • 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.
    • (2012) Biol Lett , vol.8 , pp. 783-786
    • Crawford, N.G.1    Faircloth, B.C.2    McCormack, J.E.3    Brumfield, R.T.4    Winker, K.5    Glenn, T.C.6
  • 11
    • 13844250623 scopus 로고    scopus 로고
    • Clann: Investigating phylogenetic information through supertree analyses
    • Creevey CJ, McInerney JO. 2005. Clann: investigating phylogenetic information through supertree analyses. Bioinformatics 21:390-392.
    • (2005) Bioinformatics , vol.21 , pp. 390-392
    • Creevey, C.J.1    McInerney, J.O.2
  • 12
    • 33845472296 scopus 로고    scopus 로고
    • Phylogenetics, biogeography and classification of, and character evolution in, gamebirds (Aves: Galliformes): Effects of character exclusion, data partitioning and missing data
    • Crowe T, Bowie R, Bloomer P, Mandiwana T, Hedderson T, Randi E, Pereira S, Wakeling J. 2006. Phylogenetics, biogeography and classification of, and character evolution in, gamebirds (Aves: Galliformes): Effects of character exclusion, data partitioning and missing data. Cladistics 22:495-532.
    • (2006) Cladistics , vol.22 , pp. 495-532
    • Crowe, T.1    Bowie, R.2    Bloomer, P.3    Mandiwana, T.4    Hedderson, T.5    Randi, E.6    Pereira, S.7    Wakeling, J.8
  • 14
    • 77249139678 scopus 로고    scopus 로고
    • Fast and consistent estimation of species trees using supermatrix rooted triples
    • DeGiorgio M, Degnan JH. 2010. Fast and consistent estimation of species trees using supermatrix rooted triples. Mol Biol Evol. 27:552-569.
    • (2010) Mol Biol Evol , vol.27 , pp. 552-569
    • DeGiorgio, M.1    Degnan, J.H.2
  • 15
    • 84899669558 scopus 로고    scopus 로고
    • An empirical evaluation of two-stage species tree inference strategies using a multilocus dataset from North American pines
    • DeGiorgio M, Syring J, Eckert AJ, Liston A, Cronn R, Neale DB, Rosenberg NA. 2014. An empirical evaluation of two-stage species tree inference strategies using a multilocus dataset from North American pines. BMC Evol Biol. 14:1-10.
    • (2014) BMC Evol Biol , vol.14 , pp. 1-10
    • DeGiorgio, M.1    Syring, J.2    Eckert, A.J.3    Liston, A.4    Cronn, R.5    Neale, D.B.6    Rosenberg, N.A.7
  • 16
    • 84881634032 scopus 로고    scopus 로고
    • Anomalous unrooted gene trees
    • Degnan JH. 2013. Anomalous unrooted gene trees. Syst Biol. 62:574-590.
    • (2013) Syst Biol , vol.62 , pp. 574-590
    • Degnan, J.H.1
  • 17
    • 33646928341 scopus 로고    scopus 로고
    • Discordance of species trees with their most likely gene trees
    • Degnan JH, Rosenberg NA. 2006. Discordance of species trees with their most likely gene trees. PLoS Genet. 2:e68.
    • (2006) PLoS Genet , vol.2 , pp. e68
    • Degnan, J.H.1    Rosenberg, N.A.2
  • 18
    • 65649131928 scopus 로고    scopus 로고
    • Gene tree discordance, phylogenetic inference and the multispecies coalescent
    • Degnan JH, Rosenberg NA. 2009. Gene tree discordance, phylogenetic inference and the multispecies coalescent. Trends Ecol Evol. 24:332-340.
    • (2009) Trends Ecol Evol , vol.24 , pp. 332-340
    • Degnan, J.H.1    Rosenberg, N.A.2
  • 19
    • 84879012317 scopus 로고    scopus 로고
    • Phylogeography of Silver Pheasant (Lophura nycthemera L.) across China: Aggregate effects of refugia, introgression and riverine barriers
    • Dong L, Heckel G, Liang W, Zhang Y. 2013. Phylogeography of Silver Pheasant (Lophura nycthemera L.) across China: Aggregate effects of refugia, introgression and riverine barriers. Mol Ecol. 22:3376-3390.
    • (2013) Mol Ecol , vol.22 , pp. 3376-3390
    • Dong, L.1    Heckel, G.2    Liang, W.3    Zhang, Y.4
  • 20
    • 58249100073 scopus 로고    scopus 로고
    • Is a new and general theory of molecular systematics emerging
    • Edwards SV. 2009. Is a new and general theory of molecular systematics emerging? Evolution 63:1-19.
    • (2009) Evolution , vol.63 , pp. 1-19
    • Edwards, S.V.1
  • 21
    • 34347256397 scopus 로고    scopus 로고
    • High-resolution species trees without concatenation
    • Edwards SV, Liu L, Pearl D. 2007. High-resolution species trees without concatenation. Proc Natl Acad Sci U S A 104:5936-5941.
    • (2007) Proc Natl Acad Sci U S a , vol.104 , pp. 5936-5941
    • Edwards, S.V.1    Liu, L.2    Pearl, D.3
  • 22
    • 84960093575 scopus 로고    scopus 로고
    • PHYLUCE is a software package for the analysis of conserved genomic loci
    • Faircloth BC. 2015. PHYLUCE is a software package for the analysis of conserved genomic loci. Bioinformatics.
    • (2015) Bioinformatics
    • Faircloth, B.C.1
  • 23
    • 84865046802 scopus 로고    scopus 로고
    • Not all sequence tags are created equal: Designing and validating sequence identification tags robust to indels
    • Faircloth BC, Glenn TC. 2012. Not all sequence tags are created equal: designing and validating sequence identification tags robust to indels. PLoS One. 8:e42543.
    • (2012) PLoS One , vol.8 , pp. e42543
    • Faircloth, B.C.1    Glenn, T.C.2
  • 25
    • 84879162598 scopus 로고    scopus 로고
    • A phylogenomic perspective on the radiation of ray-finned fishes based upon targeted sequencing of ultraconserved elements
    • UCEs
    • Faircloth BC, Sorenson L, Santini F, Alfaro ME. 2013. A phylogenomic perspective on the radiation of ray-finned fishes based upon targeted sequencing of ultraconserved elements (UCEs). PLoS One 8:e65923.
    • (2013) PLoS One , vol.8 , pp. e65923
    • Faircloth, B.C.1    Sorenson, L.2    Santini, F.3    Alfaro, M.E.4
  • 26
    • 84908162664 scopus 로고    scopus 로고
    • Phylogenetic analysis at deep timescales: Unreliable gene trees, bypassed hidden support, and the coalescence/concatalescence conundrum
    • Gatesy J, Springer MS. 2014. Phylogenetic analysis at deep timescales: unreliable gene trees, bypassed hidden support, and the coalescence/concatalescence conundrum. Mol Phylogent Evol. 80:231-266.
    • (2014) Mol Phylogent Evol , vol.80 , pp. 231-266
    • Gatesy, J.1    Springer, M.S.2
  • 29
    • 84928142994 scopus 로고    scopus 로고
    • Identifying unstable taxa: Efficient implementation of triplet-based measures of stability, and comparison with Phyutility and RogueNaRok
    • Goloboff PA, Szumik CA. 2015. Identifying unstable taxa: Efficient implementation of triplet-based measures of stability, and comparison with Phyutility and RogueNaRok. Mol Phylogent Evol. 88:93-104.
    • (2015) Mol Phylogent Evol , vol.88 , pp. 93-104
    • Goloboff, P.A.1    Szumik, C.A.2
  • 34
    • 84897978137 scopus 로고    scopus 로고
    • A draft de novo genome assembly for the Northern Bobwhite (Colinus virginianus) reveals evidence for a rapid decline in effective population size beginning in the Late Pleistocene
    • Halley YA, Dowd SE, Decker JE, Seabury PM, Bhattarai E, Johnson CD, Rollins D, Tizard IR, Brightsmith DJ, Peterson MJ, et al. 2014. A draft de novo genome assembly for the Northern Bobwhite (Colinus virginianus) reveals evidence for a rapid decline in effective population size beginning in the Late Pleistocene. PLoS One 9:e90240.
    • (2014) PLoS One , vol.9 , pp. e90240
    • Halley, Y.A.1    Dowd, S.E.2    Decker, J.E.3    Seabury, P.M.4    Bhattarai, E.5    Johnson, C.D.6    Rollins, D.7    Tizard, I.R.8    Brightsmith, D.J.9    Peterson, M.J.10
  • 36
    • 77249086587 scopus 로고    scopus 로고
    • Bayesian inference of species trees from multilocus data
    • Heled J, Drummond AJ. 2010. Bayesian inference of species trees from multilocus data. Mol Biol Evol. 27:570-580.
    • (2010) Mol Biol Evol , vol.27 , pp. 570-580
    • Heled, J.1    Drummond, A.J.2
  • 37
    • 84904422912 scopus 로고    scopus 로고
    • The mysterious Spotted Green Pigeon and its relation to the Dodo and its kindred
    • Heupink TH, van Grouw H, Lambert DM. 2014. The mysterious Spotted Green Pigeon and its relation to the Dodo and its kindred. BMC Evol Biol. 14:1-6.
    • (2014) BMC Evol Biol , vol.14 , pp. 1-6
    • Heupink, T.H.1    Van Grouw, H.2    Lambert, D.M.3
  • 38
    • 22844442543 scopus 로고    scopus 로고
    • Analysis and visualization of tree space
    • Hillis DM, Heath TA, St. John. 2005. Analysis and visualization of tree space. Syst Biol. 54:471-482.
    • (2005) Syst Biol , vol.54 , pp. 471-482
    • Hillis, D.M.1    Heath, T.A.2    John3
  • 39
    • 84921665305 scopus 로고    scopus 로고
    • The avian embryo as a model system for skeletal myogenesis
    • Hirst CE, Marcelle C. 2015. The avian embryo as a model system for skeletal myogenesis. Results Probl Cell Differ. 56:99-122.
    • (2015) Results Probl Cell Differ , vol.56 , pp. 99-122
    • Hirst, C.E.1    Marcelle, C.2
  • 40
    • 84928358919 scopus 로고    scopus 로고
    • Unforeseen consequences of excluding missing data from next-generation sequences: Simulation study of RAD sequences
    • Huang H, Knowles LL. 2014. Unforeseen consequences of excluding missing data from next-generation sequences: simulation study of RAD sequences. Syst Biol.
    • (2014) Syst Biol.
    • Huang, H.1    Knowles, L.L.2
  • 41
    • 10644283823 scopus 로고    scopus 로고
    • Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution
    • International Chicken Genome Sequencing Consortium
    • International Chicken Genome Sequencing Consortium 2004. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 432:695-716.
    • (2004) Nature , vol.432 , pp. 695-716
  • 42
    • 84917708482 scopus 로고    scopus 로고
    • Whole-genome analyses resolve early branches in the tree of life of modern birds
    • Jarvis ED, Mirarab S, Aberer AJ, Li B, Houde P, Li C. 2014. Whole-genome analyses resolve early branches in the tree of life of modern birds. Science 346:1320-1331.
    • (2014) Science , vol.346 , pp. 1320-1331
    • Jarvis, E.D.1    Mirarab, S.2    Aberer, A.J.3    Li, B.4    Houde, P.5    Li, C.6
  • 43
    • 84964876635 scopus 로고
    • A summary of intergeneric New World Quail hybrids, and a new intergeneric hybrid combination
    • Johnsgard PA. 1970. A summary of intergeneric New World Quail hybrids, and a new intergeneric hybrid combination. Condor 72:85-88.
    • (1970) Condor , vol.72 , pp. 85-88
    • Johnsgard, P.A.1
  • 45
    • 0037100671 scopus 로고    scopus 로고
    • MAFFT: A novel method for rapid multiple sequence alignment based on fast Fourier transform
    • Katoh K, Misawa K, Kuma K, Miyata T. 2002. MAFFT: A novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 30:3059-3066.
    • (2002) Nucleic Acids Res , vol.30 , pp. 3059-3066
    • Katoh, K.1    Misawa, K.2    Kuma, K.3    Miyata, T.4
  • 46
    • 84875619226 scopus 로고    scopus 로고
    • MAFFT Multiple sequence alignment software version 7: Improvements in performance and usability
    • Katoh K, Standley DM. 2013. MAFFT Multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 30:772-780.
    • (2013) Mol Biol Evol , vol.30 , pp. 772-780
    • Katoh, K.1    Standley, D.M.2
  • 48
    • 63049111772 scopus 로고    scopus 로고
    • A multigene phylogeny of Galliformes supports a single origin of erectile ability in non-feathered facial traits
    • Kimball RT, Braun EL. 2008. A multigene phylogeny of Galliformes supports a single origin of erectile ability in non-feathered facial traits. J Avian Biol. 39:438-445.
    • (2008) J Avian Biol , vol.39 , pp. 438-445
    • Kimball, R.T.1    Braun, E.L.2
  • 49
    • 84899076119 scopus 로고    scopus 로고
    • Does more sequence data improve estimates of galliform phylogeny? Analyses of a rapid radiation using a complete data matrix
    • Kimball RT, Braun EL. 2014. Does more sequence data improve estimates of galliform phylogeny? Analyses of a rapid radiation using a complete data matrix. PeerJ 2:e361.
    • (2014) PeerJ , vol.2 , pp. e361
    • Kimball, R.T.1    Braun, E.L.2
  • 50
    • 0034896322 scopus 로고    scopus 로고
    • A molecular phylogeny of the peacock-pheasants (Galliformes: Polyplectron spp.) indicates loss and reduction of ornamental traits and display behaviours
    • Kimball RT, Braun EL, Ligon JD, Lucchini V, Randi E. 2008. A molecular phylogeny of the peacock-pheasants (Galliformes: Polyplectron spp.) indicates loss and reduction of ornamental traits and display behaviours. Biol J Linnean Soc. 73:187-198.
    • (2008) Biol J Linnean Soc , vol.73 , pp. 187-198
    • Kimball, R.T.1    Braun, E.L.2    Ligon, J.D.3    Lucchini, V.4    Randi, E.5
  • 51
    • 84875100390 scopus 로고    scopus 로고
    • A macroevolutionary perspective on multiple sexual traits in the Phasianidae
    • Galliformes
    • Kimball RT, Mary CMS, Braun EL. 2011. A macroevolutionary perspective on multiple sexual traits in the Phasianidae (Galliformes). Int J Evol Biol. 2011:1-16.
    • (2011) Int J Evol Biol , vol.2011 , pp. 1-16
    • Kimball, R.T.1    Mary, C.M.S.2    Braun, E.L.3
  • 52
    • 84884592480 scopus 로고    scopus 로고
    • Identifying localized biases in large datasets: A case study using the avian tree of life
    • 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 Phylogent Evol. 69:1021-1032.
    • (2013) Mol Phylogent Evol , vol.69 , pp. 1021-1032
    • Kimball, R.T.1    Wang, N.2    Heimer-McGinn, V.3    Ferguson, C.4    Braun, E.L.5
  • 53
    • 79952098463 scopus 로고    scopus 로고
    • Next generation sequencing of ancient DNA: Requirements, strategies and perspectives
    • Knapp M, Hofreiter M. 2010. Next generation sequencing of ancient DNA: Requirements, strategies and perspectives. Genes 1:227-243.
    • (2010) Genes , vol.1 , pp. 227-243
    • Knapp, M.1    Hofreiter, M.2
  • 54
    • 33847302458 scopus 로고    scopus 로고
    • Inconsistency of phylogenetic estimates from concatenated data under coalescence
    • Kubatko LS, Degnan JH. 2007. Inconsistency of phylogenetic estimates from concatenated data under coalescence. Syst Biol. 56:17-24.
    • (2007) Syst Biol , vol.56 , pp. 17-24
    • Kubatko, L.S.1    Degnan, J.H.2
  • 56
    • 84861380450 scopus 로고    scopus 로고
    • PartitionFinder: Combined selection of partitioning schemes and substitution models for phylogenetic analyses
    • Lanfear R, Calcott B, Ho SYW, Guindon S. 2012. PartitionFinder: combined selection of partitioning schemes and substitution models for phylogenetic analyses. Mol Biol Evol. 29:1695-1701.
    • (2012) Mol Biol Evol , vol.29 , pp. 1695-1701
    • Lanfear, R.1    Calcott, B.2    Ho, S.Y.W.3    Guindon, S.4
  • 57
    • 84872148526 scopus 로고    scopus 로고
    • How studies on the avian embryo have opened new avenues in the understanding of development: A view about the neural and hematopoietic systems
    • Le Douarin NM, Dieterlen-Lièvre F. 2012. How studies on the avian embryo have opened new avenues in the understanding of development: A view about the neural and hematopoietic systems. Dev Growth Differ. 55:1-14.
    • (2012) Dev Growth Differ , vol.55 , pp. 1-14
    • Le, D.N.M.1    Dieterlen-Lièvre, F.2
  • 58
    • 79951561454 scopus 로고    scopus 로고
    • The accuracy of species tree estimation under simulation: A comparison of methods
    • Leaché AD, Rannala B. 2011. The accuracy of species tree estimation under simulation: A comparison of methods. Syst Biol. 60:126-137.
    • (2011) Syst Biol , vol.60 , pp. 126-137
    • Leaché, A.D.1    Rannala, B.2
  • 59
    • 84865266483 scopus 로고    scopus 로고
    • Anchored hybrid enrichment for massively high- Throughput phylogenomics
    • Lemmon AR, Emme SA, Lemmon EM. 2012. Anchored hybrid enrichment for massively high- Throughput phylogenomics. Syst Biol. 61:727-744.
    • (2012) Syst Biol , vol.61 , pp. 727-744
    • Lemmon, A.R.1    Emme, S.A.2    Lemmon, E.M.3
  • 60
    • 84888626247 scopus 로고    scopus 로고
    • High- Throughput genomic data in systematics and phylogenetics
    • Lemmon EM, Lemmon AR. 2013. High- Throughput genomic data in systematics and phylogenetics. Ann Rev Ecol Syst. 44:99-121.
    • (2013) Ann Rev Ecol Syst , vol.44 , pp. 99-121
    • Lemmon, E.M.1    Lemmon, A.R.2
  • 61
    • 70349417912 scopus 로고    scopus 로고
    • Phylogenetic analysis in the anomaly zone
    • Liu L, Edwards SV. 2009. Phylogenetic analysis in the anomaly zone. Syst Biol. 58:452-460.
    • (2009) Syst Biol , vol.58 , pp. 452-460
    • Liu, L.1    Edwards, S.V.2
  • 63
    • 79957648061 scopus 로고    scopus 로고
    • PhyDesign: An online application for profiling phylogenetic informativeness
    • López-Giráldez F, Townsend JP. 2011. PhyDesign: An online application for profiling phylogenetic informativeness. BMC Evol Biol. 11:152.
    • (2011) BMC Evol Biol , vol.11 , pp. 152
    • López-Giráldez, F.1    Townsend, J.P.2
  • 64
    • 84964874139 scopus 로고    scopus 로고
    • Gene trees in species trees. Syst Biol. 46:523-536
    • Gene trees in species trees.
    • (1997)
    • Maddison, W.1
  • 66
    • 80053540892 scopus 로고    scopus 로고
    • Efficient cross-species capture hybridization and next-generation sequencing ofmitochondrial genomes from noninvasively sampled museum specimens
    • Mason VC, Li G, Helgen KM, Murphy WJ. 2011. Efficient cross-species capture hybridization and next-generation sequencing ofmitochondrial genomes from noninvasively sampled museum specimens. Genome Res. 21:1695-1704.
    • (2011) Genome Res , vol.21 , pp. 1695-1704
    • Mason, V.C.1    Li, G.2    Helgen, K.M.3    Murphy, W.J.4
  • 68
    • 84872873481 scopus 로고    scopus 로고
    • Next-generation phylogenetics takes root
    • McCormack JE, Faircloth BC. 2013. Next-generation phylogenetics takes root. Mol Ecol. 22:19-21.
    • (2013) Mol Ecol , vol.22 , pp. 19-21
    • McCormack, J.E.1    Faircloth, B.C.2
  • 69
    • 84859530730 scopus 로고    scopus 로고
    • Ultraconserved elements are novel phylogenomic markers that resolve placental mammal phylogeny when combined with species- Tree analysis
    • 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.
    • (2012) Genome Res , vol.22 , pp. 746-754
    • McCormack, J.E.1    Faircloth, B.C.2    Crawford, N.G.3    Gowaty, P.A.4    Brumfield, R.T.5    Glenn, T.C.6
  • 70
    • 84873860010 scopus 로고    scopus 로고
    • A phylogeny of birds based on over 1, 500 loci collected by target enrichment and high- Throughput sequencing
    • 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.
    • (2013) PLoS One , vol.8 , pp. e54848
    • McCormack, J.E.1    Harvey, M.G.2    Faircloth, B.C.3    Crawford, N.G.4    Glenn, T.C.5    Brumfield, R.T.6
  • 71
    • 85027910845 scopus 로고    scopus 로고
    • Sequence capture of ultraconserved elements from bird museum specimens
    • McCormack JE, Tsai WLE, Faircloth BC. 2015. Sequence capture of ultraconserved elements from bird museum specimens. Mol Ecol Res.
    • (2015) Mol Ecol Res
    • McCormack, J.E.1    Tsai, W.L.E.2    Faircloth, B.C.3
  • 73
    • 84917708481 scopus 로고    scopus 로고
    • Statistical binning enables an accurate coalescent-based estimation of the avian tree
    • Mirarab S, Bayzid MS, Boussau B, Warnow T. 2014. Statistical binning enables an accurate coalescent-based estimation of the avian tree. Science 346:1250463-1250463.
    • (2014) Science , vol.346 , pp. 1250463
    • Mirarab, S.1    Bayzid, M.S.2    Boussau, B.3    Warnow, T.4
  • 74
    • 84921316279 scopus 로고    scopus 로고
    • Evaluating summary methods for multilocus species tree estimation in the presence of incomplete lineage sorting
    • Mirarab S, Bayzid MS, Warnow T. 2014. Evaluating summary methods for multilocus species tree estimation in the presence of incomplete lineage sorting. Syst Biol.
    • (2014) Syst Biol
    • Mirarab, S.1    Bayzid, M.S.2    Warnow, T.3
  • 76
    • 84931034856 scopus 로고    scopus 로고
    • ASTRAL-II: Coalescent -based species tree estimation with many hundreds of taxa and thousands of genes
    • Mirarab S, Warnow T. 2015. ASTRAL-II: Coalescent -based species tree estimation with many hundreds of taxa and thousands of genes. Bioinformatics 31:i44-i52.
    • (2015) Bioinformatics , vol.31 , pp. i44-i52
    • Mirarab, S.1    Warnow, T.2
  • 79
    • 60549089187 scopus 로고    scopus 로고
    • Explosive Pleistocene diversification and hemispheric expansion of a "great speciator
    • Moyle RG, Filardi CE, Smith CE, Diamond J. 2009. Explosive Pleistocene diversification and hemispheric expansion of a "great speciator". Proc Natl Acad Sci U S A 106:1863-1868.
    • (2009) Proc Natl Acad Sci U S a , vol.106 , pp. 1863-1868
    • Moyle, R.G.1    Filardi, C.E.2    Smith, C.E.3    Diamond, J.4
  • 80
    • 84909979829 scopus 로고    scopus 로고
    • Phylogeny and biogeography of Ficedula flycatchers (Aves: Muscicapidae): Novel results from fresh source material
    • Moyle RG, Hosner PA, Jones AW, Outlaw DC. 2015. Phylogeny and biogeography of Ficedula flycatchers (Aves: Muscicapidae): novel results from fresh source material. Mol Phylogent Evol 82:87-94.
    • (2015) Mol Phylogent Evol , vol.82 , pp. 87-94
    • Moyle, R.G.1    Hosner, P.A.2    Jones, A.W.3    Outlaw, D.C.4
  • 81
    • 84873149873 scopus 로고    scopus 로고
    • A reconsideration of Gallicolumba (Aves: Columbidae) relationships using fresh source material reveals pseudogenes, chimeras, and a novel phylogenetic hypothesis
    • Moyle RG, Jones RM, Andersen MJ. 2013. A reconsideration of Gallicolumba (Aves: Columbidae) relationships using fresh source material reveals pseudogenes, chimeras, and a novel phylogenetic hypothesis. Mol Phylogent Evol. 66:1060-1066.
    • (2013) Mol Phylogent Evol , vol.66 , pp. 1060-1066
    • Moyle, R.G.1    Jones, R.M.2    Andersen, M.J.3
  • 82
    • 0031036343 scopus 로고    scopus 로고
    • Skin from feet of museum specimens as a non-destructive source of DNA for avian genotyping
    • Mundy NI, Unitt P, Woodruff DS. 1997. Skin from feet of museum specimens as a non-destructive source of DNA for avian genotyping. Auk 114:126-129.
    • (1997) Auk , vol.114 , pp. 126-129
    • Mundy, N.I.1    Unitt, P.2    Woodruff, D.S.3
  • 83
    • 79961074078 scopus 로고    scopus 로고
    • Dynamic evolution of base composition: Causes and consequences in avian phylogenomics
    • Nabholz B, Kunstner A, Wang R, Jarvis ED, Ellegren H. 2011. Dynamic evolution of base composition: causes and consequences in avian phylogenomics. Mol Biol Evol. 28:2197-2210.
    • (2011) Mol Biol Evol , vol.28 , pp. 2197-2210
    • Nabholz, B.1    Kunstner, A.2    Wang, R.3    Jarvis, E.D.4    Ellegren, H.5
  • 84
    • 84893812106 scopus 로고    scopus 로고
    • Error in phylogenetic estimation for bushes in the tree of life
    • Patel S, Kimball RT, Braun EL. 2013. Error in phylogenetic estimation for bushes in the tree of life. J Phylogent Evol Biol. 1:110.
    • (2013) J Phylogent Evol Biol , vol.1 , pp. 110
    • Patel, S.1    Kimball, R.T.2    Braun, E.L.3
  • 85
    • 4143122089 scopus 로고    scopus 로고
    • Phylogenomics of eukaryotes: Impact of missing data on large alignments
    • Philippe H. 2004. Phylogenomics of eukaryotes: impact of missing data on large alignments. Mol Biol Evol. 21:1740-1752.
    • (2004) Mol Biol Evol , vol.21 , pp. 1740-1752
    • Philippe, H.1
  • 87
    • 85009825966 scopus 로고    scopus 로고
    • New information on the snow partridge Lerwa lerwa (Hodgson 1833) and its systematic position
    • Potapov LR. 2000. New information on the snow partridge Lerwa lerwa (Hodgson 1833) and its systematic position. Bull Br Orn Club. 120:112-120.
    • (2000) Bull Br Orn Club , vol.120 , pp. 112-120
    • Potapov, L.R.1
  • 89
    • 52949152371 scopus 로고    scopus 로고
    • Phylogenetic inference using whole genomes
    • Rannala B, Yang Z. 2008. Phylogenetic inference using whole genomes. Annu Rev Genomics Hum Genet. 9:217-231.
    • (2008) Annu Rev Genomics Hum Genet , vol.9 , pp. 217-231
    • Rannala, B.1    Yang, Z.2
  • 91
    • 84921289760 scopus 로고    scopus 로고
    • Likelihood-based tree reconstruction on a concatenation of aligned sequence data sets can be statistically inconsistent
    • Roch S, Steel M. 2014. Likelihood-based tree reconstruction on a concatenation of aligned sequence data sets can be statistically inconsistent. Theor Popul Biol. 100:56-62.
    • (2014) Theor Popul Biol , vol.100 , pp. 56-62
    • Roch, S.1    Steel, M.2
  • 92
    • 84931054390 scopus 로고    scopus 로고
    • On the robustness to gene tree estimation error (or lack thereof) of coalescent-based species tree methods
    • Roch S, Warnow T. 2015. On the robustness to gene tree estimation error (or lack thereof) of coalescent-based species tree methods. Syst Biol. 64:663-676.
    • (2015) Syst Biol , vol.64 , pp. 663-676
    • Roch, S.1    Warnow, T.2
  • 93
    • 84890335523 scopus 로고    scopus 로고
    • Discordance of species trees with their most likely gene trees: A unifying principle
    • Rosenberg NA. 2013. Discordance of species trees with their most likely gene trees: A unifying principle. Mol Biol Evol. 30:2709-2713.
    • (2013) Mol Biol Evol , vol.30 , pp. 2709-2713
    • Rosenberg, N.A.1
  • 95
    • 84871842306 scopus 로고    scopus 로고
    • Impact of missing data on phylogenies inferred from empirical phylogenomic data sets
    • Roure B, Baurain D, Philippe H. 2012. Impact of missing data on phylogenies inferred from empirical phylogenomic data sets. Mol Biol Evol. 30:197-214.
    • (2012) Mol Biol Evol , vol.30 , pp. 197-214
    • Roure, B.1    Baurain, D.2    Philippe, H.3
  • 96
    • 84859516080 scopus 로고    scopus 로고
    • Inferring phylogenies from RAD sequence data
    • Rubin BER, Ree RH, Moreau CS. 2012. Inferring phylogenies from RAD sequence data. PLoS One 7:e33394.
    • (2012) PLoS One , vol.7 , pp. e33394
    • Rubin, B.E.R.1    Ree, R.H.2    Moreau, C.S.3
  • 97
    • 84878113118 scopus 로고    scopus 로고
    • Inferring ancient divergences requires genes with strong phylogenetic signals
    • Salichos L, Rokas A. 2013. Inferring ancient divergences requires genes with strong phylogenetic signals. Nature 497:327-331.
    • (2013) Nature , vol.497 , pp. 327-331
    • Salichos, L.1    Rokas, A.2
  • 98
    • 77952490857 scopus 로고    scopus 로고
    • Phylogenomics with incomplete taxon coverage: The limits to inference
    • Sanderson MJ, McMahon MM, Steel M. 2010. Phylogenomics with incomplete taxon coverage: The limits to inference. BMC Evol Biol. 10:155.
    • (2010) BMC Evol Biol , vol.10 , pp. 155
    • Sanderson, M.J.1    McMahon, M.M.2    Steel, M.3
  • 99
    • 34547129072 scopus 로고    scopus 로고
    • Single base errors in PCR products from avian museum specimens and their effect on estimates of historical genetic diversity
    • Sefc KM, Payne RB, Sorenson MD. 2007. Single base errors in PCR products from avian museum specimens and their effect on estimates of historical genetic diversity. Conserv Genet. 8:879-884.
    • (2007) Conserv Genet , vol.8 , pp. 879-884
    • Sefc, K.M.1    Payne, R.B.2    Sorenson, M.D.3
  • 100
    • 84908164854 scopus 로고    scopus 로고
    • A confounding effect of missing data on character conflict in maximum likelihood and Bayesian MCMC phylogenetic analyses
    • Simmons MP. 2014. A confounding effect of missing data on character conflict in maximum likelihood and Bayesian MCMC phylogenetic analyses. Mol Phylogent Evol. 80:267-280.
    • (2014) Mol Phylogent Evol , vol.80 , pp. 267-280
    • Simmons, M.P.1
  • 101
    • 84891531569 scopus 로고    scopus 로고
    • Target capture and massively parallel sequencing of ultraconserved elements for comparative studies at shallow evolutionary time scales
    • 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.
    • (2014) Syst Biol , vol.63 , pp. 83-95
    • Smith, B.T.1    Harvey, M.G.2    Faircloth, B.C.3    Glenn, T.C.4    Brumfield, R.T.5
  • 102
    • 84871841236 scopus 로고    scopus 로고
    • Ratite nonmonophyly: Independent evidence from 40 novel loci
    • Smith JV, Braun EL, Kimball RT. 2013. Ratite nonmonophyly: independent evidence from 40 novel loci. Syst Biol. 62:35-49.
    • (2013) Syst Biol , vol.62 , pp. 35-49
    • Smith, J.V.1    Braun, E.L.2    Kimball, R.T.3
  • 103
    • 78149235569 scopus 로고    scopus 로고
    • Quartets MaxCut: A divide and conquer quartets algorithm
    • Snir S, Rao S. 2010. Quartets MaxCut: A divide and conquer quartets algorithm. IEEE/ACM Trans Comput Biol Bioinform. 7:704-718.
    • (2010) IEEE/ACM Trans Comput Biol Bioinform , vol.7 , pp. 704-718
    • Snir, S.1    Rao, S.2
  • 104
    • 83655184666 scopus 로고    scopus 로고
    • Quartet MaxCut: A fast algorithm for amalgamating quartet trees
    • Snir S, Rao S. 2012. Quartet MaxCut: A fast algorithm for amalgamating quartet trees. Mol Phylogent Evol. 62:1-8.
    • (2012) Mol Phylogent Evol , vol.62 , pp. 1-8
    • Snir, S.1    Rao, S.2
  • 106
    • 84899553363 scopus 로고    scopus 로고
    • RAxML version 8: A tool for phylogenetic analysis and post- Analysis of large phylogenies
    • Stamatakis A. 2014. RAxML version 8: A tool for phylogenetic analysis and post- Analysis of large phylogenies. Bioinformatics 30:1312-1313.
    • (2014) Bioinformatics , vol.30 , pp. 1312-1313
    • Stamatakis, A.1
  • 107
    • 50249100595 scopus 로고    scopus 로고
    • A rapid bootstrap algorithm for the RAxML web servers
    • Stamatakis A, Hoover P, Rougemont J. 2008. A rapid bootstrap algorithm for the RAxML web servers. Syst Biol. 57:758-771.
    • (2008) Syst Biol , vol.57 , pp. 758-771
    • Stamatakis, A.1    Hoover, P.2    Rougemont, J.3
  • 108
    • 84960362109 scopus 로고    scopus 로고
    • How should genes and taxa be sampled for phylogenomic analyses with missing data? An empirical study in iguanian lizards
    • Streicher JW, Schulte JA, Wiens JJ. 2016. How should genes and taxa be sampled for phylogenomic analyses with missing data? An empirical study in iguanian lizards. Syst Biol. 65:128-145.
    • (2016) Syst Biol , vol.65 , pp. 128-145
    • Streicher, J.W.1    Schulte, J.A.2    Wiens, J.J.3
  • 111
    • 72049129449 scopus 로고    scopus 로고
    • Sparse supermatrices for phylogenetic inference: Taxonomy, alignment, rogue taxa, and the phylogeny of living turtles
    • Thomson RC, Shaffer HB. 2010. Sparse supermatrices for phylogenetic inference: Taxonomy, alignment, rogue taxa, and the phylogeny of living turtles. Syst Biol. 59:42-58.
    • (2010) Syst Biol , vol.59 , pp. 42-58
    • Thomson, R.C.1    Shaffer, H.B.2
  • 112
    • 84956878549 scopus 로고    scopus 로고
    • Concatenation and species tree methods exhibit statistically indistinguishable accuracy under a range of simulated conditions
    • Tonini J, Moore A, Stern DL, Shcheglovitova M, Orti G. 2015. Concatenation and species tree methods exhibit statistically indistinguishable accuracy under a range of simulated conditions. PLoS Curr 7.
    • (2015) PLoS Curr , vol.7
    • Tonini, J.1    Moore, A.2    Stern, D.L.3    Shcheglovitova, M.4    Orti, G.5
  • 113
    • 34447279942 scopus 로고    scopus 로고
    • Profiling phylogenetic informativeness
    • Townsend JP. 2007. Profiling phylogenetic informativeness. Syst.Biol. 56:222-231.
    • (2007) Syst.Biol , vol.56 , pp. 222-231
    • Townsend, J.P.1
  • 114
    • 84944723546 scopus 로고    scopus 로고
    • ASTRID: Accurate species TRees from internode distances
    • Vachaspati P, Warnow T. 2015. ASTRID: Accurate Species TRees from Internode Distances. BMC Genomics 16:S3.
    • (2015) BMC Genomics , vol.16 , pp. S3
    • Vachaspati, P.1    Warnow, T.2
  • 115
    • 84872480881 scopus 로고    scopus 로고
    • Genome-wide RAD sequence data provide unprecedented resolution of species boundaries and relationships in the Lake Victoria cichlid adaptive radiation
    • Wagner CE, Keller I, Wittwer S, Selz OM, Mwaiko S, Greuter L, Sivasundar A, Seehausen O. 2013. Genome-wide RAD sequence data provide unprecedented resolution of species boundaries and relationships in the Lake Victoria cichlid adaptive radiation. Mol Ecol. 22:787-798.
    • (2013) Mol Ecol , vol.22 , pp. 787-798
    • Wagner, C.E.1    Keller, I.2    Wittwer, S.3    Selz, O.M.4    Mwaiko, S.5    Greuter, L.6    Sivasundar, A.7    Seehausen, O.8
  • 116
    • 84878569337 scopus 로고    scopus 로고
    • Assessing phylogenetic relationships among Galliformes: A multigene phylogeny with expanded taxon sampling in Phasianidae
    • Wang N, Kimball RT, Braun EL, Liang B, Zhang Z. 2013. Assessing phylogenetic relationships among Galliformes: A multigene phylogeny with expanded taxon sampling in Phasianidae. PLoS One 8:e64312.
    • (2013) PLoS One , vol.8 , pp. e64312
    • Wang, N.1    Kimball, R.T.2    Braun, E.L.3    Liang, B.4    Zhang, Z.5
  • 117
    • 84958559378 scopus 로고    scopus 로고
    • Concatenation analyses in the presence of incomplete lineage sorting
    • Warnow T. 2015. Concatenation analyses in the presence of incomplete lineage sorting. PLoS Curr. 22:7.
    • (2015) PLoS Curr , vol.22 , pp. 7
    • Warnow, T.1
  • 118
  • 119
    • 80052006478 scopus 로고    scopus 로고
    • Missing data in phylogenetic analysis: Reconciling results from simulations and empirical data
    • Wiens JJ, Morrill MC. 2011. Missing data in phylogenetic analysis: Reconciling results from simulations and empirical data. Syst Biol. 60:719-731.
    • (2011) Syst Biol , vol.60 , pp. 719-731
    • Wiens, J.J.1    Morrill, M.C.2
  • 120
    • 84865026977 scopus 로고    scopus 로고
    • Highly incomplete taxa can rescue phylogenetic analyses from the negative impacts of limited taxon sampling
    • Wiens JJ, Tiu J. 2012. Highly incomplete taxa can rescue phylogenetic analyses from the negative impacts of limited taxon sampling. PLoS One 7:e42925.
    • (2012) PLoS One , vol.7 , pp. e42925
    • Wiens, J.J.1    Tiu, J.2
  • 121
    • 77953127071 scopus 로고    scopus 로고
    • The Monticola rock- Thrushes: Phylogeny and biogeography revisited
    • Zuccon D, Ericson PGP. 2010. The Monticola rock- Thrushes: phylogeny and biogeography revisited. Mol Phylogent Evol. 55:901-910. 1125.
    • (2010) Mol Phylogent Evol , vol.55 , Issue.1125 , pp. 901-910
    • Zuccon, D.1    Ericson, P.G.P.2


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