-
1
-
-
0025183708
-
Basic local alignment search tool
-
Altshul S.F., Gish W., Miller W., Myers E.W., Lipman D.J. Basic local alignment search tool. J. Mol. Biol. 1990, 215:403-410.
-
(1990)
J. Mol. Biol.
, vol.215
, pp. 403-410
-
-
Altshul, S.F.1
Gish, W.2
Miller, W.3
Myers, E.W.4
Lipman, D.J.5
-
2
-
-
84903745828
-
Genomic support for a Moa-Tinamou clade and adaptive morphological convergence in flightless ratites
-
Baker A.J., Haddrath O., McPherson J.D., Cloutier A. Genomic support for a Moa-Tinamou clade and adaptive morphological convergence in flightless ratites. Mol. Biol. Evol. 2014, 31:1686-1696.
-
(2014)
Mol. Biol. Evol.
, vol.31
, pp. 1686-1696
-
-
Baker, A.J.1
Haddrath, O.2
McPherson, J.D.3
Cloutier, A.4
-
3
-
-
34548499987
-
Phylogenetic relationships and divergence times of Charadriiformes genera: multigene evidence for the Cretaceous origin of at least 14 clades of shorebirds
-
Baker A.J., Pereira S.L., Paton T.P. Phylogenetic relationships and divergence times of Charadriiformes genera: multigene evidence for the Cretaceous origin of at least 14 clades of shorebirds. Biol. Lett. 2007, 3:205-209.
-
(2007)
Biol. Lett.
, vol.3
, pp. 205-209
-
-
Baker, A.J.1
Pereira, S.L.2
Paton, T.P.3
-
4
-
-
0842347322
-
A phylogenetic hypothesis for passerine birds: taxonomic and biogeographic implications of an analysis of nuclear DNA sequence data
-
Barker F.K., Barrowclough G.F., Groth J.G. A phylogenetic hypothesis for passerine birds: taxonomic and biogeographic implications of an analysis of nuclear DNA sequence data. Proc. Biol. Sci. 2002, 269:295-308.
-
(2002)
Proc. Biol. Sci.
, vol.269
, pp. 295-308
-
-
Barker, F.K.1
Barrowclough, G.F.2
Groth, J.G.3
-
5
-
-
3342978151
-
Phylogeny and diversification of the largest avian radiation
-
Barker F.K., Cibois A., Schikler P., Feinstein J., Cracraft J. Phylogeny and diversification of the largest avian radiation. Proc. Natl. Acad. Sci. USA 2004, 101:11040-11045.
-
(2004)
Proc. Natl. Acad. Sci. USA
, vol.101
, pp. 11040-11045
-
-
Barker, F.K.1
Cibois, A.2
Schikler, P.3
Feinstein, J.4
Cracraft, J.5
-
6
-
-
58149185141
-
GenBank
-
Benson D.A., Karsch-Mizrachi I., Lipman D.J., Ostell J., Sayers E.W. GenBank. Nucleic Acids Res. 2009, 37:D26-D31.
-
(2009)
Nucleic Acids Res.
, vol.37
, pp. D26-D31
-
-
Benson, D.A.1
Karsch-Mizrachi, I.2
Lipman, D.J.3
Ostell, J.4
Sayers, E.W.5
-
8
-
-
0036931408
-
The (super)tree of life: procedures, problems and prospects
-
Bininda-Emonds O.R.P., Gittleman J.L., Steel M.A. The (super)tree of life: procedures, problems and prospects. Annu. Rev. Ecol. Syst. 2002, 33:265-289.
-
(2002)
Annu. Rev. Ecol. Syst.
, vol.33
, pp. 265-289
-
-
Bininda-Emonds, O.R.P.1
Gittleman, J.L.2
Steel, M.A.3
-
9
-
-
34047108602
-
The delayed rise of present-day mammals
-
Bininda-Emonds O.R.P., Cardillo M., Jones K.E., MacPhee R.D., Beck R.M., Grenyer R., Price S.A., Vos R.A., Gittleman J.L., Purvis A. The delayed rise of present-day mammals. Nature 2007, 446:507-512.
-
(2007)
Nature
, vol.446
, pp. 507-512
-
-
Bininda-Emonds, O.R.P.1
Cardillo, M.2
Jones, K.E.3
MacPhee, R.D.4
Beck, R.M.5
Grenyer, R.6
Price, S.A.7
Vos, R.A.8
Gittleman, J.L.9
Purvis, A.10
-
11
-
-
0036700155
-
Examining Basal avian divergences with mitochondrial sequences: model complexity, taxon sampling, and sequence length
-
Braun E.L., Kimball R.T. Examining Basal avian divergences with mitochondrial sequences: model complexity, taxon sampling, and sequence length. Syst. Biol. 2002, 51:614-625.
-
(2002)
Syst. Biol.
, vol.51
, pp. 614-625
-
-
Braun, E.L.1
Kimball, R.T.2
-
12
-
-
80053315278
-
Homoplastic microinversions and the avian tree of life
-
Braun E.L., Kimball R.T., Han K.-L., Iuhasz-Velez N.R., Bonilla A.J., Chojnowski J.L., Smith J.V., Bowie R.C.K., Braun M.J., Hackett S.J., Harshman J., Huddleston C.J., Marks B.D., Miglia K.J., Moore W.S., Reddy S., Sheldon F.H., Witt C.C., Yuri T. Homoplastic microinversions and the avian tree of life. BMC Evol. Biol. 2011, 11:141.
-
(2011)
BMC Evol. Biol.
, vol.11
, pp. 141
-
-
Braun, E.L.1
Kimball, R.T.2
Han, K.-L.3
Iuhasz-Velez, N.R.4
Bonilla, A.J.5
Chojnowski, J.L.6
Smith, J.V.7
Bowie, R.C.K.8
Braun, M.J.9
Hackett, S.J.10
Harshman, J.11
Huddleston, C.J.12
Marks, B.D.13
Miglia, K.J.14
Moore, W.S.15
Reddy, S.16
Sheldon, F.H.17
Witt, C.C.18
Yuri, T.19
-
13
-
-
4544357678
-
A species-level phylogenetic supertree of marsupials
-
Cardillo M., Bininda-Emonds O.R.P., Boakes E., Purvis A. A species-level phylogenetic supertree of marsupials. J. Zool. 2006, 264:11-31.
-
(2006)
J. Zool.
, vol.264
, pp. 11-31
-
-
Cardillo, M.1
Bininda-Emonds, O.R.P.2
Boakes, E.3
Purvis, A.4
-
14
-
-
66349134056
-
The merging of community ecology and phylogenetic biology
-
Cavender-Bares J., Kozak K.H., Fine P.V.A., Kembel S.W. The merging of community ecology and phylogenetic biology. Ecol. Lett. 2009, 12:1-23.
-
(2009)
Ecol. Lett.
, vol.12
, pp. 1-23
-
-
Cavender-Bares, J.1
Kozak, K.H.2
Fine, P.V.A.3
Kembel, S.W.4
-
15
-
-
40649089624
-
Introns outperform exons in analyses of basal avian phylogeny using clathrin heavy chain genes
-
Chojnowski J.L., Kimball R.T., Braun E.L. Introns outperform exons in analyses of basal avian phylogeny using clathrin heavy chain genes. Gene 2008, 410:89-96.
-
(2008)
Gene
, vol.410
, pp. 89-96
-
-
Chojnowski, J.L.1
Kimball, R.T.2
Braun, E.L.3
-
16
-
-
79955696806
-
-
Clements, J.F., Schulenberg, T.S., Iliff, M.J., Sullivan, B.L., Wood, C.L., Roberson, D., 2011. The Clements checklist of birds of the world: Version 6.6. http://www.birds.cornell.edu/clementschecklist/downloadable-clements-checklist.
-
(2011)
The Clements checklist of birds of the world: Version 6.6.
-
-
Clements, J.F.1
Schulenberg, T.S.2
Iliff, M.J.3
Sullivan, B.L.4
Wood, C.L.5
Roberson, D.6
-
17
-
-
84866467089
-
Phylogenetic affinities of evolutionarily enigmatic African galliforms: the Stone Partridge Ptilopachus petrosus and Nahan's Francolin Francolinus nahani, and support for their sister relationship with New World quails
-
Cohen C., Wakeling J.L., Mandiwana-Neudani T.G., Sande E., Dranzoa C., Crowe T.M., Bowie R.C.K. Phylogenetic affinities of evolutionarily enigmatic African galliforms: the Stone Partridge Ptilopachus petrosus and Nahan's Francolin Francolinus nahani, and support for their sister relationship with New World quails. Ibis 2012, 154:768-780.
-
(2012)
Ibis
, vol.154
, pp. 768-780
-
-
Cohen, C.1
Wakeling, J.L.2
Mandiwana-Neudani, T.G.3
Sande, E.4
Dranzoa, C.5
Crowe, T.M.6
Bowie, R.C.K.7
-
18
-
-
84920896410
-
Reweaving the Tapestry: a supertree of birds
-
Davis K.E., Page R.D.M. Reweaving the Tapestry: a supertree of birds. PLoS Curr. Tree Life 2014, 10.1371/currents.tol.c1af68dda7c999ed9f1e4b2d2df7a08e.
-
(2014)
PLoS Curr. Tree Life
-
-
Davis, K.E.1
Page, R.D.M.2
-
19
-
-
17744394753
-
Phylogenomics and the reconstruction of the tree of life
-
Delsuc F., Brinkmann H., Philippe H. Phylogenomics and the reconstruction of the tree of life. Nat. Rev. Genet. 2005, 6:361-375.
-
(2005)
Nat. Rev. Genet.
, vol.6
, pp. 361-375
-
-
Delsuc, F.1
Brinkmann, H.2
Philippe, H.3
-
20
-
-
84888130684
-
Darwinian shortfalls in biodiversity conservation
-
Diniz-Filho J.A.F., Loyola R.D., Raia P., Mooers A.O., Bini L.M. Darwinian shortfalls in biodiversity conservation. Trends Ecol. Evol. 2013, 28:689-695.
-
(2013)
Trends Ecol. Evol.
, vol.28
, pp. 689-695
-
-
Diniz-Filho, J.A.F.1
Loyola, R.D.2
Raia, P.3
Mooers, A.O.4
Bini, L.M.5
-
21
-
-
8444222732
-
Prospects for building the tree of life from large sequence databases
-
Driskell A.C., Ané C., Burleigh J.G., McMahon M.M., O'Meara B.C., Sanderson M.J. Prospects for building the tree of life from large sequence databases. Science 2004, 306:1172-1174.
-
(2004)
Science
, vol.306
, pp. 1172-1174
-
-
Driskell, A.C.1
Ané, C.2
Burleigh, J.G.3
McMahon, M.M.4
O'Meara, B.C.5
Sanderson, M.J.6
-
22
-
-
84896336566
-
Patterns of research effort in birds
-
Ducatez S., Lefebvre L. Patterns of research effort in birds. PLoS ONE 2014, 9:e89955.
-
(2014)
PLoS ONE
, vol.9
, pp. e89955
-
-
Ducatez, S.1
Lefebvre, L.2
-
23
-
-
84879775736
-
Congruification: support for time scaling large phylogenetic trees
-
Eastman J.M., Harmon L.J., Tank D.C. Congruification: support for time scaling large phylogenetic trees. Methods Ecol. Evol. 2013, 4:688-691.
-
(2013)
Methods Ecol. Evol.
, vol.4
, pp. 688-691
-
-
Eastman, J.M.1
Harmon, L.J.2
Tank, D.C.3
-
24
-
-
3042666256
-
MUSCLE: multiple sequence alignment with high accuracy and high throughput
-
Edgar R.C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucl. Acids Res. 2004, 32:1792-1797.
-
(2004)
Nucl. Acids Res.
, vol.32
, pp. 1792-1797
-
-
Edgar, R.C.1
-
26
-
-
58249100073
-
Is a new and general theory of molecular systematics emerging?
-
Edwards S.V. Is a new and general theory of molecular systematics emerging?. Evolution 2009, 63:1-19.
-
(2009)
Evolution
, vol.63
, pp. 1-19
-
-
Edwards, S.V.1
-
27
-
-
53649083413
-
Phylogenetic analysis of community assembly and structure over space and time
-
Emerson B.C., Gillespie R.G. Phylogenetic analysis of community assembly and structure over space and time. Trends Evol. Ecol. 2008, 23:619-630.
-
(2008)
Trends Evol. Ecol.
, vol.23
, pp. 619-630
-
-
Emerson, B.C.1
Gillespie, R.G.2
-
28
-
-
33845585115
-
Diversification of Neoaves: integration of molecular sequence data and fossils
-
Ericson P.G., Anderson C.L., Britton T., Elzanowski A., Johansson U.S., Källersjö M., Ohlson J.I., Parsons T.J., Zuccon D., Mayr G. Diversification of Neoaves: integration of molecular sequence data and fossils. Biol. Lett. 2006, 2:543-547.
-
(2006)
Biol. Lett.
, vol.2
, pp. 543-547
-
-
Ericson, P.G.1
Anderson, C.L.2
Britton, T.3
Elzanowski, A.4
Johansson, U.S.5
Källersjö, M.6
Ohlson, J.I.7
Parsons, T.J.8
Zuccon, D.9
Mayr, G.10
-
29
-
-
84926372294
-
Dating the diversification of the major lineages of Passeriformes (Aves)
-
Ericson P.G.P., Klopfstein S., Irestedt M., Nguyen J.M., Nylander J.A.A. Dating the diversification of the major lineages of Passeriformes (Aves). BMC Evol. Biol. 2014, 14:8.
-
(2014)
BMC Evol. Biol.
, vol.14
, pp. 8
-
-
Ericson, P.G.P.1
Klopfstein, S.2
Irestedt, M.3
Nguyen, J.M.4
Nylander, J.A.A.5
-
30
-
-
84856562355
-
The NCBI Taxonomy database
-
Federhen S. The NCBI Taxonomy database. Nucl. Acids Res. 2012, 40:D136-D143.
-
(2012)
Nucl. Acids Res.
, vol.40
, pp. D136-D143
-
-
Federhen, S.1
-
31
-
-
0000461280
-
Confidence limits on phylogenies: an approach using the bootstrap
-
Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985, 39:783-791.
-
(1985)
Evolution
, vol.39
, pp. 783-791
-
-
Felsenstein, J.1
-
32
-
-
33847171828
-
Preserving the evolutionary potential of floras in biodiversity hotspots
-
Forest F., Grenyer R., Rouget M., Davies T.J., Cowling R.M., Faith D.P., Balmford A., Manning J.C., Proches S., van der Bank M., Reeves G., Hedderson T.A.J., Savolainen V. Preserving the evolutionary potential of floras in biodiversity hotspots. Nature 2007, 445:757-760.
-
(2007)
Nature
, vol.445
, pp. 757-760
-
-
Forest, F.1
Grenyer, R.2
Rouget, M.3
Davies, T.J.4
Cowling, R.M.5
Faith, D.P.6
Balmford, A.7
Manning, J.C.8
Proches, S.9
van der Bank, M.10
Reeves, G.11
Hedderson, T.A.J.12
Savolainen, V.13
-
33
-
-
0038785934
-
Combined support for wholesale taxic atavism in gavialine crocodylians
-
Erratum in: Syst. Biol. 52, 734
-
Gatesy J., Amato G., Norell M., DeSalle R., Hayashi C. Combined support for wholesale taxic atavism in gavialine crocodylians. Syst. Biol. 2003, 52:403-422. Erratum in: Syst. Biol. 52, 734.
-
(2003)
Syst. Biol.
, vol.52
, pp. 403-422
-
-
Gatesy, J.1
Amato, G.2
Norell, M.3
DeSalle, R.4
Hayashi, C.5
-
34
-
-
2442449251
-
Inconsistencies in arguments for the supertree approach: supermatrices versus supertrees of Crocodylia
-
Gatesy J., Baker R.H., Hayashi C. Inconsistencies in arguments for the supertree approach: supermatrices versus supertrees of Crocodylia. Syst. Biol. 2004, 53:342-355.
-
(2004)
Syst. Biol.
, vol.53
, pp. 342-355
-
-
Gatesy, J.1
Baker, R.H.2
Hayashi, C.3
-
35
-
-
84920896409
-
-
(Eds.), IOC World Bird Names (v 3.2).
-
Gill, F., Donsker, D. (Eds.), 2012. IOC World Bird Names (v 3.2). http://www.worldbirdnames.org.
-
(2012)
-
-
Gill, F.1
Donsker, D.2
-
36
-
-
2442620190
-
Using complete phylogenies in comparative biology
-
Kluwer Academic Publishers, Netherlands, O.R.P. Bininda-Emonds (Ed.)
-
Gittleman J.L., Jones K.E., Price S.A. Using complete phylogenies in comparative biology. Phylogenetic Supertrees: Combining Information to Reveal the Tree of Life 2004, 439-460. Kluwer Academic Publishers, Netherlands. O.R.P. Bininda-Emonds (Ed.).
-
(2004)
Phylogenetic Supertrees: Combining Information to Reveal the Tree of Life
, pp. 439-460
-
-
Gittleman, J.L.1
Jones, K.E.2
Price, S.A.3
-
37
-
-
66649120526
-
Phylogenetic analysis of 73 060 taxa corroborates major eukaryotic groups
-
Goloboff P.A., Catalano S.A., Mirande J.M., Szumik C.A., Arias J.S., Källersjö M., Farris J.S. Phylogenetic analysis of 73 060 taxa corroborates major eukaryotic groups. Cladistics 2009, 25:211-230.
-
(2009)
Cladistics
, vol.25
, pp. 211-230
-
-
Goloboff, P.A.1
Catalano, S.A.2
Mirande, J.M.3
Szumik, C.A.4
Arias, J.S.5
Källersjö, M.6
Farris, J.S.7
-
38
-
-
46449135061
-
A phylogenomic study of birds reveals their evolutionary history
-
Hackett S.J., Kimball R.T., Reddy S., Bowie R.C.K., Braun E.L., Braun M.J., Chojnowski J.L., Cox W.A., Han K.-L., Harshman J., Huddleston C.J., Marks B.D., Miglia K.J., Moore W.S., Sheldon F.H., Steadman D.W., Witt C.C., Yuri T. A phylogenomic study of birds reveals their evolutionary history. Science 2008, 320:1763-1768.
-
(2008)
Science
, vol.320
, pp. 1763-1768
-
-
Hackett, S.J.1
Kimball, R.T.2
Reddy, S.3
Bowie, R.C.K.4
Braun, E.L.5
Braun, M.J.6
Chojnowski, J.L.7
Cox, W.A.8
Han, K.-L.9
Harshman, J.10
Huddleston, C.J.11
Marks, B.D.12
Miglia, K.J.13
Moore, W.S.14
Sheldon, F.H.15
Steadman, D.W.16
Witt, C.C.17
Yuri, T.18
-
39
-
-
84867569468
-
Multiple nuclear genes and retroposons support vicariance and dispersal of the palaeognaths, and an Early Cretaceous origin of modern birds
-
Haddrath O., Baker A.J. Multiple nuclear genes and retroposons support vicariance and dispersal of the palaeognaths, and an Early Cretaceous origin of modern birds. Proc. Roy. Soc. B 2012, 279:4617-4625.
-
(2012)
Proc. Roy. Soc. B
, vol.279
, pp. 4617-4625
-
-
Haddrath, O.1
Baker, A.J.2
-
40
-
-
79955390248
-
Are transposable element insertions homoplasy free? An examination using the avian tree of life
-
Han K.-L., Braun E.L., Kimball R.T., Reddy S., Bowie R.C.K., Braun M.J., Chojnowski J.L., Hackett S.J., Harshman J., Huddleston C.J., Marks B.D., Miglia K.J., Moore W.S., Sheldon F.H., Steadman D.W., Witt C.C., Yuri T. Are transposable element insertions homoplasy free? An examination using the avian tree of life. Syst. Biol. 2011, 60:375-386.
-
(2011)
Syst. Biol.
, vol.60
, pp. 375-386
-
-
Han, K.-L.1
Braun, E.L.2
Kimball, R.T.3
Reddy, S.4
Bowie, R.C.K.5
Braun, M.J.6
Chojnowski, J.L.7
Hackett, S.J.8
Harshman, J.9
Huddleston, C.J.10
Marks, B.D.11
Miglia, K.J.12
Moore, W.S.13
Sheldon, F.H.14
Steadman, D.W.15
Witt, C.C.16
Yuri, T.17
-
41
-
-
51649095653
-
Phylogenomic evidence for multiple losses of flight in ratite birds
-
Harshman J., Braun E.L., Braun M.J., Huddleston C.J., Bowie R.C.K., Chojnowski J.L., Hackett S.J., Han K.L., Kimball R.T., Marks B.D., Miglia K.J., Moore W.S., Reddy S., Sheldon F.H., Steadman D.W., Steppan S.J., Witt C.C., Yuri T. Phylogenomic evidence for multiple losses of flight in ratite birds. Proc. Natl. Acad. Sci. USA 2008, 105:13462-13467.
-
(2008)
Proc. Natl. Acad. Sci. USA
, vol.105
, pp. 13462-13467
-
-
Harshman, J.1
Braun, E.L.2
Braun, M.J.3
Huddleston, C.J.4
Bowie, R.C.K.5
Chojnowski, J.L.6
Hackett, S.J.7
Han, K.L.8
Kimball, R.T.9
Marks, B.D.10
Miglia, K.J.11
Moore, W.S.12
Reddy, S.13
Sheldon, F.H.14
Steadman, D.W.15
Steppan, S.J.16
Witt, C.C.17
Yuri, T.18
-
43
-
-
84871922008
-
An update of Wallace's zoogeographic regions of the world
-
Holt B.G., Lessard J.P., Borregaard M.K., Fritz S.A., Araújo M.B., Dimitrov D., Fabre P.H., Graham C.H., Graves G.R., Jønsson K.A., Nogués-Bravo D., Wang Z., Whittaker R.J., Fjeldså J., Rahbek C. An update of Wallace's zoogeographic regions of the world. Science 2013, 339:74-78.
-
(2013)
Science
, vol.339
, pp. 74-78
-
-
Holt, B.G.1
Lessard, J.P.2
Borregaard, M.K.3
Fritz, S.A.4
Araújo, M.B.5
Dimitrov, D.6
Fabre, P.H.7
Graham, C.H.8
Graves, G.R.9
Jønsson, K.A.10
Nogués-Bravo, D.11
Wang, Z.12
Whittaker, R.J.13
Fjeldså, J.14
Rahbek, C.15
-
44
-
-
33645850710
-
Phylogenomics: the beginning of incongruence?
-
Jeffroy O., Brinkmann H., Delsuc F., Philippe H. Phylogenomics: the beginning of incongruence?. Trends Genet. 2006, 22:225-231.
-
(2006)
Trends Genet.
, vol.22
, pp. 225-231
-
-
Jeffroy, O.1
Brinkmann, H.2
Delsuc, F.3
Philippe, H.4
-
45
-
-
84869088692
-
The global diversity of birds in space and time
-
Jetz W., Thomas G.H., Joy J.B., Hartmann K., Mooers A.O. The global diversity of birds in space and time. Nature 2012, 491:444-448.
-
(2012)
Nature
, vol.491
, pp. 444-448
-
-
Jetz, W.1
Thomas, G.H.2
Joy, J.B.3
Hartmann, K.4
Mooers, A.O.5
-
46
-
-
84899923627
-
Global distribution and conservation of evolutionary distinctness in birds
-
Jetz W., Thomas G.H., Joy J.B., Redding D.W., Hartmann K., Mooers A.O. Global distribution and conservation of evolutionary distinctness in birds. Curr. Biol. 2014, 24:919-930.
-
(2014)
Curr. Biol.
, vol.24
, pp. 919-930
-
-
Jetz, W.1
Thomas, G.H.2
Joy, J.B.3
Redding, D.W.4
Hartmann, K.5
Mooers, A.O.6
-
47
-
-
84855841862
-
New morphological evidence supports congruent phylogenies and Gondwana vicariance for palaeognathous birds
-
Johnston P. New morphological evidence supports congruent phylogenies and Gondwana vicariance for palaeognathous birds. Zool. J. Linn. Soc. 2011, 163:959-982.
-
(2011)
Zool. J. Linn. Soc.
, vol.163
, pp. 959-982
-
-
Johnston, P.1
-
48
-
-
84899076119
-
Does more sequence data improve estimates of galliform phylogeny? Analyses of a rapid radiation using a complete data matrix
-
Kimball R.T., Braun E.L. Does more sequence data improve estimates of galliform phylogeny? Analyses of a rapid radiation using a complete data matrix. PeerJ 2014, 2:e361.
-
(2014)
PeerJ
, vol.2
, pp. e361
-
-
Kimball, R.T.1
Braun, E.L.2
-
49
-
-
13744252890
-
MAFFT version 5: improvement in accuracy of multiple sequence alignment
-
Katoh K., Kuma K.-I., Toh H., Miyata T. MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucl. Acids Res. 2005, 33:511-518.
-
(2005)
Nucl. Acids Res.
, vol.33
, pp. 511-518
-
-
Katoh, K.1
Kuma, K.-I.2
Toh, H.3
Miyata, T.4
-
50
-
-
84884592480
-
Identifying localized biases in large datasets: a case study using the avian tree of life
-
Kimball R.T., Wang N., Heimer-McGinn V., Ferguson C., Braun E.L. Identifying localized biases in large datasets: a case study using the avian tree of life. Mol. Phylogenet. Evol. 2013, 69:1021-1032.
-
(2013)
Mol. Phylogenet. Evol.
, vol.69
, pp. 1021-1032
-
-
Kimball, R.T.1
Wang, N.2
Heimer-McGinn, V.3
Ferguson, C.4
Braun, E.L.5
-
51
-
-
7244221755
-
Performance of maximum parsimony and likelihood phylogenetics when evolution is heterogeneous
-
Kolaczkowski B., Thornton J.W. Performance of maximum parsimony and likelihood phylogenetics when evolution is heterogeneous. Nature 2004, 431:980-984.
-
(2004)
Nature
, vol.431
, pp. 980-984
-
-
Kolaczkowski, B.1
Thornton, J.W.2
-
52
-
-
84880747419
-
Comment on "An update of Wallace's zoogeographic regions of the world"
-
Kreft H., Jetz W. Comment on "An update of Wallace's zoogeographic regions of the world". Science 2013, 341:343.
-
(2013)
Science
, vol.341
, pp. 343
-
-
Kreft, H.1
Jetz, W.2
-
54
-
-
0025905252
-
The order of sequence alignment can bias the selection of tree topology
-
Lake J.A. The order of sequence alignment can bias the selection of tree topology. Mol. Biol. Evol. 1991, 8:378-385.
-
(1991)
Mol. Biol. Evol.
, vol.8
, pp. 378-385
-
-
Lake, J.A.1
-
55
-
-
67449163699
-
The effect of ambiguous data on phylogenetic estimates obtained by maximum likelihood and Bayesian inference
-
Lemmon A.R., Brown J.M., Stanger-Hall K., Lemmon E.R. The effect of ambiguous data on phylogenetic estimates obtained by maximum likelihood and Bayesian inference. Syst. Biol. 2009, 58:130-145.
-
(2009)
Syst. Biol.
, vol.58
, pp. 130-145
-
-
Lemmon, A.R.1
Brown, J.M.2
Stanger-Hall, K.3
Lemmon, E.R.4
-
56
-
-
0035793857
-
Molecular and morphological supertrees for eutherian (placental) mammals
-
Liu F.G., Miyamoto M.M., Freire N.P., Ong P.Q., Tennant M.R., Young T.S., Gugel K.F. Molecular and morphological supertrees for eutherian (placental) mammals. Science 2001, 291:1786-1789.
-
(2001)
Science
, vol.291
, pp. 1786-1789
-
-
Liu, F.G.1
Miyamoto, M.M.2
Freire, N.P.3
Ong, P.Q.4
Tennant, M.R.5
Young, T.S.6
Gugel, K.F.7
-
57
-
-
80053194704
-
Multiple sequence alignment: a major challenge to large-scale phylogenetics
-
PMC2989897
-
Liu K., Linder C.R., Warnow T. Multiple sequence alignment: a major challenge to large-scale phylogenetics. PLoS Curr. Tree Life 2010, PMC2989897.
-
(2010)
PLoS Curr. Tree Life
-
-
Liu, K.1
Linder, C.R.2
Warnow, T.3
-
58
-
-
0031504952
-
Gene trees in species trees
-
Maddison W.P. Gene trees in species trees. Syst. Biol. 1997, 46:523-536.
-
(1997)
Syst. Biol.
, vol.46
, pp. 523-536
-
-
Maddison, W.P.1
-
59
-
-
84861358284
-
Retroposon insertion patterns of neoavian birds: strong evidence for an extensive incomplete lineage sorting era
-
Matzke A., Churakov G., Berkes P., Arms E.M., Kelsey D., Brosius J., Kriegs J.O., Schmitz J. Retroposon insertion patterns of neoavian birds: strong evidence for an extensive incomplete lineage sorting era. Mol. Biol. Evol. 2012, 29:1497-1501.
-
(2012)
Mol. Biol. Evol.
, vol.29
, pp. 1497-1501
-
-
Matzke, A.1
Churakov, G.2
Berkes, P.3
Arms, E.M.4
Kelsey, D.5
Brosius, J.6
Kriegs, J.O.7
Schmitz, J.8
-
60
-
-
84873860010
-
A phylogeny of birds based on over 1,500 loci collected by target enrichment and high-throughput sequencing
-
McCormack J.E., Harvey M.G., Faircloth B.C., Crawford N.G., Glenn T.C., Brumfield R.T. A phylogeny of birds based on over 1,500 loci collected by target enrichment and high-throughput sequencing. PLoS ONE 2013, 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
-
61
-
-
84873084821
-
Applications of next-generation sequencing to phylogeography and phylogenetics
-
McCormack J.E., Hird S.M., Zellmer A.J., Carstens B.C., Brumfield R.T. Applications of next-generation sequencing to phylogeography and phylogenetics. Mol. Phylogenet. Evol. 2013, 66:526-538.
-
(2013)
Mol. Phylogenet. Evol.
, vol.66
, pp. 526-538
-
-
McCormack, J.E.1
Hird, S.M.2
Zellmer, A.J.3
Carstens, B.C.4
Brumfield, R.T.5
-
62
-
-
84904409979
-
Incongruence among different mitochondrial regions: A case study using complete mitogenomes
-
Meicklejohn K.A., Danielson M.J., Braun E.L., Faircloth B.C., Glenn T.C., Kimball R.T. Incongruence among different mitochondrial regions: A case study using complete mitogenomes. Mol. Phylogenet. Evol. 2014, 10.1016/j.ympev.2014.06.003.
-
(2014)
Mol. Phylogenet. Evol.
-
-
Meicklejohn, K.A.1
Danielson, M.J.2
Braun, E.L.3
Faircloth, B.C.4
Glenn, T.C.5
Kimball, R.T.6
-
63
-
-
84862858217
-
Phylogeny and biogeography of the core Babblers (Aves: Timaliidae)
-
Moyle R.G., Andersen M.J., Oliveros C.H., Steinheimer F.D., Reddy S. Phylogeny and biogeography of the core Babblers (Aves: Timaliidae). Syst. Biol. 2012, 61:631-651.
-
(2012)
Syst. Biol.
, vol.61
, pp. 631-651
-
-
Moyle, R.G.1
Andersen, M.J.2
Oliveros, C.H.3
Steinheimer, F.D.4
Reddy, S.5
-
64
-
-
33744993430
-
Multiple sequence alignment accuracy and phylogenetic inference
-
Ogden T.H., Rosenberg M.S. Multiple sequence alignment accuracy and phylogenetic inference. Syst. Biol. 2006, 55:314-328.
-
(2006)
Syst. Biol.
, vol.55
, pp. 314-328
-
-
Ogden, T.H.1
Rosenberg, M.S.2
-
65
-
-
84878665325
-
Microevolutionary processes generate phylogenomic discordance at ancient divergences
-
Oliver J.C. Microevolutionary processes generate phylogenomic discordance at ancient divergences. Evolution 2013, 67:1823-1830.
-
(2013)
Evolution
, vol.67
, pp. 1823-1830
-
-
Oliver, J.C.1
-
66
-
-
41749120055
-
Density-dependent cladogenesis in birds
-
Phillimore A.B., Price T.D. Density-dependent cladogenesis in birds. PLoS Biol. 2008, 6:e71.
-
(2008)
PLoS Biol.
, vol.6
, pp. e71
-
-
Phillimore, A.B.1
Price, T.D.2
-
67
-
-
72049124323
-
Tinamous and moa flock together: mitochondrial genome sequence analysis reveals independent losses of flight among ratites
-
Phillips M.J., Gibb G.C., Crimp E.A., Penny D. Tinamous and moa flock together: mitochondrial genome sequence analysis reveals independent losses of flight among ratites. Syst. Biol. 2010, 59:90-107.
-
(2010)
Syst. Biol.
, vol.59
, pp. 90-107
-
-
Phillips, M.J.1
Gibb, G.C.2
Crimp, E.A.3
Penny, D.4
-
68
-
-
1642401431
-
Birds in a bush: five genes indicate explosive evolution of avian orders
-
Poe S., Chubb A.L. Birds in a bush: five genes indicate explosive evolution of avian orders. Evolution 2004, 58:404-415.
-
(2004)
Evolution
, vol.58
, pp. 404-415
-
-
Poe, S.1
Chubb, A.L.2
-
69
-
-
84870236542
-
Empirical evaluation of partitioning schemes for phylogenetic analyses of mitogenomic data: an avian case study
-
Powell A.F., Barker F.K., Lanyon S.M. Empirical evaluation of partitioning schemes for phylogenetic analyses of mitogenomic data: an avian case study. Mol. Phylogenet. Evol. 2013, 66:69-79.
-
(2013)
Mol. Phylogenet. Evol.
, vol.66
, pp. 69-79
-
-
Powell, A.F.1
Barker, F.K.2
Lanyon, S.M.3
-
70
-
-
84876805079
-
A phylogeny and revised classification of Squamata, including 4161 species of lizards and snakes
-
Pyron R.A., Burbrink F.T., Wiens J.J. A phylogeny and revised classification of Squamata, including 4161 species of lizards and snakes. BMC Evol. Biol. 2013, 13:93.
-
(2013)
BMC Evol. Biol.
, vol.13
, pp. 93
-
-
Pyron, R.A.1
Burbrink, F.T.2
Wiens, J.J.3
-
71
-
-
84884341444
-
Rates of speciation and morphological evolution are correlated across the largest vertebrate radiation
-
Rabosky D.L., Santini F., Eastman J., Smith S.A., Sidlauskas B., Chang J., Alfaro M.E. Rates of speciation and morphological evolution are correlated across the largest vertebrate radiation. Nat. Commun. 2013, 4:1958.
-
(2013)
Nat. Commun.
, vol.4
, pp. 1958
-
-
Rabosky, D.L.1
Santini, F.2
Eastman, J.3
Smith, S.A.4
Sidlauskas, B.5
Chang, J.6
Alfaro, M.E.7
-
72
-
-
36249028141
-
Estimating diversification rates from phylogenetic information
-
Ricklefs R.E. Estimating diversification rates from phylogenetic information. Trends Evol. Ecol. 2007, 22:601-610.
-
(2007)
Trends Evol. Ecol.
, vol.22
, pp. 601-610
-
-
Ricklefs, R.E.1
-
73
-
-
84871842306
-
Impact of missing data on phylogenies inferred from empirical phylogenomic data sets
-
Roure B., Baurain D., Philippe H. Impact of missing data on phylogenies inferred from empirical phylogenomic data sets. Mol. Biol. Evol. 2013, 30:197-214.
-
(2013)
Mol. Biol. Evol.
, vol.30
, pp. 197-214
-
-
Roure, B.1
Baurain, D.2
Philippe, H.3
-
74
-
-
46849087728
-
Phylogenetic signal in the eukaryotic tree of life
-
Sanderson M.J. Phylogenetic signal in the eukaryotic tree of life. Science 2008, 321:121-123.
-
(2008)
Science
, vol.321
, pp. 121-123
-
-
Sanderson, M.J.1
-
75
-
-
0032030505
-
Phylogenetic supertrees: assembling the trees of life
-
Sanderson M.J., Purvis A., Henze C. Phylogenetic supertrees: assembling the trees of life. Trends Ecol. Evol. 1998, 13:105-109.
-
(1998)
Trends Ecol. Evol.
, vol.13
, pp. 105-109
-
-
Sanderson, M.J.1
Purvis, A.2
Henze, C.3
-
76
-
-
77952490857
-
Phylogenomics with incomplete taxon coverage: the limits to inference
-
Sanderson M.J., McMahon M.M., Steel M. Phylogenomics with incomplete taxon coverage: the limits to inference. BMC Evol. Biol. 2010, 10:155.
-
(2010)
BMC Evol. Biol.
, vol.10
, pp. 155
-
-
Sanderson, M.J.1
McMahon, M.M.2
Steel, M.3
-
78
-
-
77956227788
-
Multilocus phylogenetic analysis of Old World chats and flycatchers reveals extensive paraphyly at family, subfamily and genus level (Aves: Muscicapidae)
-
Sangster G., Alström P., Forsmark E., Olsson U. Multilocus phylogenetic analysis of Old World chats and flycatchers reveals extensive paraphyly at family, subfamily and genus level (Aves: Muscicapidae). Mol. Phylogenet. Evol. 2010, 57:380-392.
-
(2010)
Mol. Phylogenet. Evol.
, vol.57
, pp. 380-392
-
-
Sangster, G.1
Alström, P.2
Forsmark, E.3
Olsson, U.4
-
79
-
-
84880157756
-
An artifact caused by undersampling optimal trees in supermatrix analyses of locally sampled characters
-
Simmons M.P., Goloboff P.A. An artifact caused by undersampling optimal trees in supermatrix analyses of locally sampled characters. Mol. Phylogenet. Evol. 2013, 69:265-275.
-
(2013)
Mol. Phylogenet. Evol.
, vol.69
, pp. 265-275
-
-
Simmons, M.P.1
Goloboff, P.A.2
-
80
-
-
84871841236
-
Ratite non-monophyly: independent evidence from 40 novel loci
-
Smith J.V., Braun E.L., Kimball R.T. Ratite non-monophyly: independent evidence from 40 novel loci. Syst. Biol. 2013, 62:35-49.
-
(2013)
Syst. Biol.
, vol.62
, pp. 35-49
-
-
Smith, J.V.1
Braun, E.L.2
Kimball, R.T.3
-
81
-
-
60849123934
-
Mega-phylogeny approach for comparative biology: an alternative to supertree and supermatrix approaches
-
Smith S.A., Beaulieu J.M., Donoghue M.J. Mega-phylogeny approach for comparative biology: an alternative to supertree and supermatrix approaches. BMC Evol. Biol. 2009, 9:37.
-
(2009)
BMC Evol. Biol.
, vol.9
, pp. 37
-
-
Smith, S.A.1
Beaulieu, J.M.2
Donoghue, M.J.3
-
82
-
-
84884681647
-
Analyzing and synthesizing phylogenies using tree alignment graphs
-
Smith S.A., Brown J.W., Hinchliff C.E. Analyzing and synthesizing phylogenies using tree alignment graphs. PLoS Comput. Biol. 2013, 9:e1003223.
-
(2013)
PLoS Comput. Biol.
, vol.9
, pp. e1003223
-
-
Smith, S.A.1
Brown, J.W.2
Hinchliff, C.E.3
-
83
-
-
84877284835
-
Phylogenetic relationships and character evolution analysis of Saxifragales using a supermatrix approach
-
Soltis D.E., Mort M.E., Latvis M., Mavrodiev E.V., O'Meara B.C., Soltis P.S., Burleigh J.G., de Casa R.R. Phylogenetic relationships and character evolution analysis of Saxifragales using a supermatrix approach. Am. J. Bot. 2013, 100:916-929.
-
(2013)
Am. J. Bot.
, vol.100
, pp. 916-929
-
-
Soltis, D.E.1
Mort, M.E.2
Latvis, M.3
Mavrodiev, E.V.4
O'Meara, B.C.5
Soltis, P.S.6
Burleigh, J.G.7
de Casa, R.R.8
-
84
-
-
33750403801
-
RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
-
Stamatakis A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 2006, 22:2688-2690.
-
(2006)
Bioinformatics
, vol.22
, pp. 2688-2690
-
-
Stamatakis, A.1
-
85
-
-
80052392767
-
Mesozoic retroposons reveal parrots as the closest living relatives of passerine birds
-
Suh A., Paus M., Kiefmann M., Churakov G., Franziska A.F., Brosius J., Kriegs J.O., Schmitz J. Mesozoic retroposons reveal parrots as the closest living relatives of passerine birds. Nat. Commun. 2011, 2:443.
-
(2011)
Nat. Commun.
, vol.2
, pp. 443
-
-
Suh, A.1
Paus, M.2
Kiefmann, M.3
Churakov, G.4
Franziska, A.F.5
Brosius, J.6
Kriegs, J.O.7
Schmitz, J.8
-
86
-
-
84887168027
-
PASTIS: an R package to facilitate phylogenetic assembly with soft taxonomic inferences
-
Thomas G.H., Hartmann K., Jetz W., Joy J.B., Mimoto A., Mooers A.O. PASTIS: an R package to facilitate phylogenetic assembly with soft taxonomic inferences. Methods Ecol. Evol. 2013, 4:1011-1017.
-
(2013)
Methods Ecol. Evol.
, vol.4
, pp. 1011-1017
-
-
Thomas, G.H.1
Hartmann, K.2
Jetz, W.3
Joy, J.B.4
Mimoto, A.5
Mooers, A.O.6
-
87
-
-
72049129449
-
Sparse supermatrices for phylogenetic inference: taxonomy, alignment, rogue taxa, and the phylogeny of living turtles
-
Thomson R.C., Shaffer H.B. Sparse supermatrices for phylogenetic inference: taxonomy, alignment, rogue taxa, and the phylogeny of living turtles. Syst. Biol. 2010, 59:42-58.
-
(2010)
Syst. Biol.
, vol.59
, pp. 42-58
-
-
Thomson, R.C.1
Shaffer, H.B.2
-
88
-
-
84870949217
-
Disparity in the timing of vertebrate diversification events between the northern and southern hemispheres
-
Tingley R., Dubey S. Disparity in the timing of vertebrate diversification events between the northern and southern hemispheres. BMC Evol. Biol. 2012, 12:244.
-
(2012)
BMC Evol. Biol.
, vol.12
, pp. 244
-
-
Tingley, R.1
Dubey, S.2
-
89
-
-
77954866541
-
Adding time-calibrated branch lengths to the Asteraceae supertree
-
Torices E. Adding time-calibrated branch lengths to the Asteraceae supertree. J. Syst. Evol. 2010, 48:271-278.
-
(2010)
J. Syst. Evol.
, vol.48
, pp. 271-278
-
-
Torices, E.1
-
90
-
-
58849095783
-
Emerging patterns in the comparative analysis of phylogenetic community structure
-
Vamosi S.M., Heard B., Vamosi J.C., Webb C.O. Emerging patterns in the comparative analysis of phylogenetic community structure. Mol. Ecol. 2009, 18:572-592.
-
(2009)
Mol. Ecol.
, vol.18
, pp. 572-592
-
-
Vamosi, S.M.1
Heard, B.2
Vamosi, J.C.3
Webb, C.O.4
-
91
-
-
0141795524
-
Taxonomic misidentification in public DNA databases
-
Vilgalys R. Taxonomic misidentification in public DNA databases. New Phytol. 2003, 160:4-5.
-
(2003)
New Phytol.
, vol.160
, pp. 4-5
-
-
Vilgalys, R.1
-
92
-
-
84855873417
-
Testing hypotheses about the sister group of the Passeriformes using an independent 30 locus dataset
-
Wang N., Braun E.L., Kimball R.T. Testing hypotheses about the sister group of the Passeriformes using an independent 30 locus dataset. Mol. Biol. Evol. 2012, 29:737-750.
-
(2012)
Mol. Biol. Evol.
, vol.29
, pp. 737-750
-
-
Wang, N.1
Braun, E.L.2
Kimball, R.T.3
-
93
-
-
84878569337
-
Assessing phylogenetic relationships among Galliformes: a multigene phylogeny with expanded taxon sampling in Phasianidae
-
Wang N., Kimball R.T., Braun E.L., Liang B., Zhang Z. Assessing phylogenetic relationships among Galliformes: a multigene phylogeny with expanded taxon sampling in Phasianidae. PLoS ONE 2013, 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
-
94
-
-
14844350168
-
Phylomatic: tree assembly for applied phylogenetics
-
Webb C.O., Donoghue M.J. Phylomatic: tree assembly for applied phylogenetics. Mol. Ecol. Notes 2004, 5:181-183.
-
(2004)
Mol. Ecol. Notes
, vol.5
, pp. 181-183
-
-
Webb, C.O.1
Donoghue, M.J.2
-
95
-
-
84934434878
-
Inferring trees
-
Whelan S. Inferring trees. Methods Mol. Biol. 2008, 452:287-309.
-
(2008)
Methods Mol. Biol.
, vol.452
, pp. 287-309
-
-
Whelan, S.1
-
96
-
-
84862814389
-
Molecular phylogenetics: principles and practice
-
Yang Z., Rannala B. Molecular phylogenetics: principles and practice. Nat. Rev. Genet. 2012, 13:303-314.
-
(2012)
Nat. Rev. Genet.
, vol.13
, pp. 303-314
-
-
Yang, Z.1
Rannala, B.2
-
97
-
-
84884350638
-
Parsimony and model-based analyses of indels in avian nuclear genes reveal congruent and incongruent phylogenetic signals
-
Yuri T., Kimball R.T., Harshman J., Bowie R.C.K., Braun M.J., Chojnowski J.L., Han K.-L., Hackett S.J., Huddleston C.J., Moore W.S., Reddy S., Sheldon F.H., Steadman D.W., Witt C.C., Braun E.L. Parsimony and model-based analyses of indels in avian nuclear genes reveal congruent and incongruent phylogenetic signals. Biology 2013, 2:419-444.
-
(2013)
Biology
, vol.2
, pp. 419-444
-
-
Yuri, T.1
Kimball, R.T.2
Harshman, J.3
Bowie, R.C.K.4
Braun, M.J.5
Chojnowski, J.L.6
Han, K.-L.7
Hackett, S.J.8
Huddleston, C.J.9
Moore, W.S.10
Reddy, S.11
Sheldon, F.H.12
Steadman, D.W.13
Witt, C.C.14
Braun, E.L.15
-
98
-
-
84888192712
-
-
Proc. Int. Conf. Bioinform., Comput. Biol., Biomed. Inform. ACM.
-
Zhbannikov, I.Y., Brown, J.W., Foster, J.A., 2013. decisivatoR: an R infrastructure package that addresses the problem of phylogenetic decisiveness. In: Proc. Int. Conf. Bioinform., Comput. Biol., Biomed. Inform. ACM.
-
(2013)
decisivatoR: an R infrastructure package that addresses the problem of phylogenetic decisiveness
-
-
Zhbannikov, I.Y.1
Brown, J.W.2
Foster, J.A.3
|