-
1
-
-
53849128215
-
-
Brumfield R.T., Liu L., Lum D.E., Edwards S.V. 2008. Comparison of species tree methods for reconstructing the phylogeny of bearded manakins (Aves: Pipridae, Manacus) from multilocus sequence data. Syst. Biol. 57:719-731.
-
(2008)
Comparison of Species Tree Methods for Reconstructing the Phylogeny of Bearded Manakins (Aves: Pipridae, Manacus) from Multilocus Sequence Data. Syst. Biol
, vol.57
, pp. 719-731
-
-
Brumfield, R.T.1
Liu, L.2
Lum, D.E.3
Edwards, S.V.4
-
2
-
-
35948952881
-
Gene sampling strategies for multi-locus population estimates of genetic diversity (theta)
-
Carling M.D., Brumfield R.T. 2007. Gene sampling strategies for multi-locus population estimates of genetic diversity (theta). PLoS ONE. 2:e160.
-
(2007)
PLoS ONE
, vol.2
-
-
Carling, M.D.1
Brumfield, R.T.2
-
3
-
-
40849120246
-
Integrating phylogenetic and population genetic analyses of multiple loci to test species divergence hypotheses in Passerina buntings
-
Carling M.D., Brumfield R.T. 2008. Integrating phylogenetic and population genetic analyses of multiple loci to test species divergence hypotheses in Passerina buntings. Genetics. 178:363-377.
-
(2008)
Genetics
, vol.178
, pp. 363-377
-
-
Carling, M.D.1
Brumfield, R.T.2
-
4
-
-
34249700809
-
Estimating species phylogeny from gene-tree probabilities despite incomplete lineage sorting: An example from Melanoplus grasshoppers
-
Carstens B.C., Knowles L.L. 2007. Estimating species phylogeny from gene-tree probabilities despite incomplete lineage sorting: an example from Melanoplus grasshoppers. Syst. Biol. 56:400-411.
-
(2007)
Syst. Biol
, vol.56
, pp. 400-411
-
-
Carstens, B.C.1
Knowles, L.L.2
-
5
-
-
67449167484
-
Properties of consensus methods for inferring species trees from gene trees
-
Degnan J.H., DeGiorigio M., Bryant D., Rosenberg N.A. 2009. Properties of consensus methods for inferring species trees from gene trees. Syst. Biol. 58:35-64.
-
(2009)
Syst. Biol
, vol.58
, pp. 35-64
-
-
Degnan, J.H.1
Degiorigio, M.2
Bryant, D.3
Rosenberg, N.A.4
-
6
-
-
33646928341
-
Discordance of species trees with their most likely gene trees
-
Degnan J.H., Rosenberg N.A. 2006. Discordance of species trees with their most likely gene trees. PLoS Genet. 2:e68.
-
(2006)
PLoS Genet
, vol.2
-
-
Degnan, J.H.1
Rosenberg, N.A.2
-
7
-
-
13244292527
-
Gene tree distributions under the coa-lescent process
-
Degnan J.H., Salter L.A. 2005. Gene tree distributions under the coa-lescent process. Evolution. 59:24-37.
-
(2005)
Evolution
, vol.59
, pp. 24-37
-
-
Degnan, J.H.1
Salter, L.A.2
-
8
-
-
0029078029
-
Biological Basis of Germline Mutation: Comparisons of Spontaneous Germline Mutation Rates among Drosophila, Mouse, and Human
-
Drost J.B., Lee W.R. 1995. Biological basis of germline mutation: comparisons of spontaneous germline mutation rates among drosophila, mouse, and human. Environ. Mol. Mutagen. 25(Suppl 26):48-64.
-
(1995)
Environ. Mol. Mutagen
, vol.25
, Issue.SUPPL. 26
, pp. 48-64
-
-
Drost, J.B.1
Lee, W.R.2
-
11
-
-
0001935493
-
Gene genealogies and the coalescent process
-
Futuyma D., Antonovics J., editors New York: Oxford University Press
-
Hudson R.R. 1990. Gene genealogies and the coalescent process. In: Futuyma D., Antonovics J., editors. Oxford surveys in evolutionary biology. Vol.7. New York: Oxford University Press. p. 1-44.
-
(1990)
Oxford Surveys in Evolutionary Biology
, vol.7
, pp. 1-44
-
-
Hudson, R.R.1
-
12
-
-
0036184745
-
Generating samples under a Wright-Fisher neutral model of genetic variation
-
Hudson R.R. 2002. Generating samples under a Wright-Fisher neutral model of genetic variation. Bioinformatics. 18:337-338.
-
(2002)
Bioinformatics
, vol.18
, pp. 337-338
-
-
Hudson, R.R.1
-
13
-
-
0029821511
-
Do phylogenetic methods produce trees with biased shapes?
-
Huelsenbeck J.P., Kirkpatrick M. 1996. Do phylogenetic methods produce trees with biased shapes? Evolution. 50:1418-1424.
-
(1996)
Evolution
, vol.50
, pp. 1418-1424
-
-
Huelsenbeck, J.P.1
Kirkpatrick, M.2
-
14
-
-
25644452054
-
Speciational history of Australian grass finches (Poephila) inferred from thirty gene trees
-
Jennings W.B., Edwards S.V. 2005. Speciational history of Australian grass finches (Poephila) inferred from thirty gene trees. Evolution. 59:2033-2047.
-
(2005)
Evolution
, vol.59
, pp. 2033-2047
-
-
Jennings, W.B.1
Edwards, S.V.2
-
16
-
-
34247500920
-
Estimating a geographically explicit model of population divergence
-
Knowles L.L., Carstens B.C. 2007. Estimating a geographically explicit model of population divergence. Evolution. 61:477-493.
-
(2007)
Evolution
, vol.61
, pp. 477-493
-
-
Knowles, L.L.1
Carstens, B.C.2
-
17
-
-
45849088450
-
Resolving species phylogenies of recent evolutionary radiations
-
Knowles L.L., Chan Y.-H. 2008. Resolving species phylogenies of recent evolutionary radiations. Ann. Mo. Bot. Gard. 95:224-231.
-
(2008)
Ann. Mo. Bot. Gard
, vol.95
, pp. 224-231
-
-
Knowles, L.L.1
Chan, Y.-H.2
-
18
-
-
63549118031
-
STEM: Species tree estimation using maximum likelihood for gene trees under coalescence
-
Kubatko L.S., Carstens B.C., Knowles L.L. 2009. STEM: species tree estimation using maximum likelihood for gene trees under coalescence. Bioinformatics. 25:971-973.
-
(2009)
Bioinformatics
, vol.25
, pp. 971-973
-
-
Kubatko, L.S.1
Carstens, B.C.2
Knowles, L.L.3
-
19
-
-
33847302458
-
Inconsistency of phylogenetic estimates from concatenated data under coalescence
-
Kubatko L.S., Degnan J.H. 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
-
20
-
-
34548575126
-
Species trees from gene trees: Reconstructing Bayesian posterior distributions of a species phylogeny using estimated gene tree distributions
-
Liu L., Pearl D.K. 2007. Species trees from gene trees: reconstructing Bayesian posterior distributions of a species phylogeny using estimated gene tree distributions. Syst. Biol. 56:504-514.
-
(2007)
Syst. Biol
, vol.56
, pp. 504-514
-
-
Liu, L.1
Pearl, D.K.2
-
21
-
-
0031504952
-
Gene trees in species trees
-
Maddison W.P. 1997. Gene trees in species trees. Syst. Biol. 46:523-536.
-
(1997)
Syst. Biol
, vol.46
, pp. 523-536
-
-
Maddison, W.P.1
-
22
-
-
33644606488
-
Inferring phylogeny despite incomplete lineage sorting
-
Maddison W.P., Knowles L.L. 2006. Inferring phylogeny despite incomplete lineage sorting. Syst. Biol. 55:21-30.
-
(2006)
Syst. Biol
, vol.55
, pp. 21-30
-
-
Maddison, W.P.1
Knowles, L.L.2
-
23
-
-
70450265498
-
Maximum-likelihood estimates of species trees: How accuracy of phylogenetic inference depends upon the divergence history and sampling design
-
in press
-
McCormack J.E., Huang H., Knowles L.L. 2009. Maximum-likelihood estimates of species trees: how accuracy of phylogenetic inference depends upon the divergence history and sampling design. Syst. Biol (in press).
-
(2009)
Syst. Biol
-
-
McCormack, J.E.1
Huang, H.2
Knowles, L.L.3
-
24
-
-
0023822631
-
Relationships between gene trees and species trees
-
Pamilo P., Nei M. 1988. Relationships between gene trees and species trees. Mol. Biol. Evol. 5:568-583.
-
(1988)
Mol. Biol. Evol
, vol.5
, pp. 568-583
-
-
Pamilo, P.1
Nei, M.2
-
25
-
-
0030928378
-
Seq-gen: An application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees
-
Rambaut A., Grassly N.C. 1997. Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Comput. Appl. Biosci. 13:235-238. (Pubitemid 27249927)
-
(1997)
Computer Applications in the Biosciences
, vol.13
, Issue.3
, pp. 235-238
-
-
Rambaut, A.1
Grassly, N.C.2
-
26
-
-
47749153850
-
Does choice in model selection affect maximum likelihood analysis?
-
Ripplinger J., Sullivan J. 2008. Does choice in model selection affect maximum likelihood analysis? Syst. Biol. 57:76-85.
-
(2008)
Syst Biol
, vol.57
, pp. 76-85
-
-
Ripplinger, J.1
Sullivan, J.2
-
27
-
-
47749087905
-
Discordance of species trees with their most likely gene trees: The case of five taxa
-
Rosenberg N.A., Tao R. 2008. Discordance of species trees with their most likely gene trees: the case of five taxa. Syst. Biol. 57:131-140.
-
(2008)
Syst. Biol
, vol.57
, pp. 131-140
-
-
Rosenberg, N.A.1
Tao, R.2
-
28
-
-
0023375195
-
The neighbor-joining method: A new method for reconstructing phylogenetic trees
-
Saitou N., Nei M. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4:406-425.
-
(1987)
Mol. Biol. Evol
, vol.4
, pp. 406-425
-
-
Saitou, N.1
Nei, M.2
-
29
-
-
46849087728
-
Phylogenetic signal in the eukaryotic tree of life
-
Sanderson M.J. 2008. Phylogenetic signal in the eukaryotic tree of life. Science. 321:121-123.
-
(2008)
Science
, vol.321
, pp. 121-123
-
-
Sanderson, M.J.1
-
31
-
-
0024713112
-
Gene genealogy in three related populations: Consistency probability between gene and population trees
-
Takahata N. 1989. Gene genealogy in three related populations: consistency probability between gene and population trees. Genetics. 122:957-966.
-
(1989)
Genetics
, vol.122
, pp. 957-966
-
-
Takahata, N.1
-
32
-
-
0022390691
-
Gene genealogy and variance of interpopu-lational nucleotide differences
-
Takahata N., Nei M. 1985. Gene genealogy and variance of interpopu-lational nucleotide differences. Genetics. 110:325-344.
-
(1985)
Genetics
, vol.110
, pp. 325-344
-
-
Takahata, N.1
Nei, M.2
-
33
-
-
34248679898
-
Phylogenetic incon-gruence in the Drosophila melanogaster species group
-
Wong A., Jensen J.D., Pool J.E., Aquadro C.F. 2007. Phylogenetic incon-gruence in the Drosophila melanogaster species group. Mol. Phylo-genet. Evol. 43:1138-1150.
-
(2007)
Mol. Phylo-genet. Evol
, vol.43
, pp. 1138-1150
-
-
Wong, A.1
Jensen, J.D.2
Pool, J.E.3
Aquadro, C.F.4
-
34
-
-
34548534411
-
Evolutionary analysis for functional divergence of the toll-like receptor gene family and altered functional constraints
-
Zhou H., Gu J., Lamont S.J., Gu X. 2007. Evolutionary analysis for functional divergence of the toll-like receptor gene family and altered functional constraints. J. Mol. Evol. 65:119-123.
-
(2007)
J. Mol. Evol
, vol.65
, pp. 119-123
-
-
Zhou, H.1
Gu, J.2
Lamont, S.J.3
Gu, X.4
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