-
1
-
-
0000989175
-
Gene trees and species trees: molecular systematics as one-character taxonomy
-
Doyle JJ, (1992) Gene trees and species trees: molecular systematics as one-character taxonomy. Syst Bot 17: 144-163.
-
(1992)
Syst Bot
, vol.17
, pp. 144-163
-
-
Doyle, J.J.1
-
2
-
-
0031504952
-
Gene trees in species trees
-
Maddison W, (1997) Gene trees in species trees. Syst Biol 46: 523-536.
-
(1997)
Syst Biol
, vol.46
, pp. 523-536
-
-
Maddison, W.1
-
3
-
-
58249100073
-
Is a new and general theory of molecular systematic biology emerging?
-
Edwards SV, (2009) Is a new and general theory of molecular systematic biology emerging? Evolution 63: 1-19.
-
(2009)
Evolution
, vol.63
, pp. 1-19
-
-
Edwards, S.V.1
-
4
-
-
0001336205
-
Phylogenetic inference
-
In: Hillis D, Mable B, Moritz C, editors, Sunderland, Mass., Sinauer Assoc
-
Swofford D, Olsen G, Waddell P, Hillis D, (1996) Phylogenetic inference. In: Hillis D, Mable B, Moritz C, editors. Molecular Syst Biol.s Sunderland, Mass. Sinauer Assoc pp. 407-514.
-
(1996)
Molecular Syst Biol.S
, pp. 407-514
-
-
Swofford, D.1
Olsen, G.2
Waddell, P.3
Hillis, D.4
-
5
-
-
0036515730
-
The probability of topological concordance of gene trees and species trees
-
Rosenberg NA, (2002) The probability of topological concordance of gene trees and species trees. Theor Pop Biol 61: 225-247.
-
(2002)
Theor Pop Biol
, vol.61
, pp. 225-247
-
-
Rosenberg, N.A.1
-
6
-
-
65649131928
-
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
-
8
-
-
33947219934
-
Hybrid speciation
-
Mallet J, (2007) Hybrid speciation. Nature 446: 279-283.
-
(2007)
Nature
, vol.446
, pp. 279-283
-
-
Mallet, J.1
-
10
-
-
77951579970
-
Evolutionary phylogenetic networks: models and issues
-
In: Heath L, Ramakrishnan N, editors, New York, Springer
-
Nakhleh L, (2010) Evolutionary phylogenetic networks: models and issues. In: Heath L, Ramakrishnan N, editors. The Problem Solving Handbook for Computational Biology and Bioinformatics New York Springer pp. 125-158.
-
(2010)
The Problem Solving Handbook for Computational Biology and Bioinformatics
, pp. 125-158
-
-
Nakhleh, L.1
-
11
-
-
17844367344
-
Hybridization as an invasion of the genome
-
Mallet J, (2005) Hybridization as an invasion of the genome. Trends Ecol Evol 20: 229-237.
-
(2005)
Trends Ecol Evol
, vol.20
, pp. 229-237
-
-
Mallet, J.1
-
12
-
-
17044416291
-
Reconstructing patterns of reticulate evolution in plants
-
Linder CR, Rieseberg LH, (2004) Reconstructing patterns of reticulate evolution in plants. Am J Bot 91: 1700-1708.
-
(2004)
Am J Bot
, vol.91
, pp. 1700-1708
-
-
Linder, C.R.1
Rieseberg, L.H.2
-
13
-
-
67449167484
-
Properties of consensus methods for inferring species trees from gene trees
-
Degnan JH, DeGiorgio M, Bryant D, Rosenberg NA, (2009) Properties of consensus methods for inferring species trees from gene trees. Syst Biol 58: 35-54.
-
(2009)
Syst Biol
, vol.58
, pp. 35-54
-
-
Degnan, J.H.1
DeGiorgio, M.2
Bryant, D.3
Rosenberg, N.A.4
-
14
-
-
78651298101
-
Consistency properties of species tree inference by minimizing deep coalescences
-
Than CV, Rosenberg NA, (2011) Consistency properties of species tree inference by minimizing deep coalescences. J Comput Biol 18: 1-15.
-
(2011)
J Comput Biol
, vol.18
, pp. 1-15
-
-
Than, C.V.1
Rosenberg, N.A.2
-
15
-
-
79958164317
-
Performance of matrix representation with parsimony for inferring species from gene trees
-
Wang Y, Degnan JH, (2011) Performance of matrix representation with parsimony for inferring species from gene trees. Stat Appl Genet Mol 10: 21.
-
(2011)
Stat Appl Genet Mol
, vol.10
, pp. 21
-
-
Wang, Y.1
Degnan, J.H.2
-
16
-
-
79955439952
-
Reconstructing concordance trees and testing the coalescent model from genome- wide data sets
-
In: Knowles LL, Kubatko LS, editors, Hoboken, NJ, Wiley-Blackwell
-
Ané C, (2010) Reconstructing concordance trees and testing the coalescent model from genome- wide data sets. In: Knowles LL, Kubatko LS, editors. Estimating species trees: Theoretical and practical aspects Hoboken, NJ Wiley-Blackwell pp. 35-52.
-
(2010)
Estimating Species Trees: Theoretical and Practical Aspects
, pp. 35-52
-
-
Ané, C.1
-
17
-
-
79956154434
-
Identifying the rooted species tree from the distribution of unrooted gene trees under the coalescent
-
Allman ES, Degnan JH, Rhodes JA, (2011) Identifying the rooted species tree from the distribution of unrooted gene trees under the coalescent. J Math Biol 62: 833-862.
-
(2011)
J Math Biol
, vol.62
, pp. 833-862
-
-
Allman, E.S.1
Degnan, J.H.2
Rhodes, J.A.3
-
18
-
-
80052517011
-
Determining species tree topologies from clade probabilities under the coalescent
-
Allman ES, Degnan JH, Rhodes JA, (2011) Determining species tree topologies from clade probabilities under the coalescent. J Theor Biol 289: 96-106.
-
(2011)
J Theor Biol
, vol.289
, pp. 96-106
-
-
Allman, E.S.1
Degnan, J.H.2
Rhodes, J.A.3
-
19
-
-
34447620474
-
Delimiting species without monophyletic gene trees
-
Knowles LL, Carstens BC, (2007) Delimiting species without monophyletic gene trees. Syst Biol 56: 887-895.
-
(2007)
Syst Biol
, vol.56
, pp. 887-895
-
-
Knowles, L.L.1
Carstens, B.C.2
-
20
-
-
33847302458
-
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
-
21
-
-
70349425459
-
Estimating species phylogenies using coalescence times among sequences
-
Liu L, Yu L, Pearl DK, Edwards SV, (2009) Estimating species phylogenies using coalescence times among sequences. Syst Biol 58: 468-477.
-
(2009)
Syst Biol
, vol.58
, pp. 468-477
-
-
Liu, L.1
Yu, L.2
Pearl, D.K.3
Edwards, S.V.4
-
22
-
-
77249139678
-
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
-
23
-
-
34249700809
-
Estimating species phylogeny from gene-tree probabilities despite incomplete lineage sorting: an example from Melanoplus grasshoppers
-
Carstens B, Knowles LL, (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.1
Knowles, L.L.2
-
24
-
-
84857687426
-
Coalescent-based species tree inference from gene tree topologies under incomplete lineage sorting by maximum likelihood
-
Wu Y, (2012) Coalescent-based species tree inference from gene tree topologies under incomplete lineage sorting by maximum likelihood. Evolution 66: 763-775.
-
(2012)
Evolution
, vol.66
, pp. 763-775
-
-
Wu, Y.1
-
25
-
-
33846839390
-
Bayesian estimation of concordance factors
-
Ané C, Larget B, Baum DA, Smith SD, Rokas A, (2007) Bayesian estimation of concordance factors. Mol Biol Evol 24: 412-426.
-
(2007)
Mol Biol Evol
, vol.24
, pp. 412-426
-
-
Ané, C.1
Larget, B.2
Baum, D.A.3
Smith, S.D.4
Rokas, A.5
-
26
-
-
13244292527
-
Gene tree distributions under the coalescent process
-
Degnan JH, Salter LA, (2005) Gene tree distributions under the coalescent process. Evolution 59: 24-37.
-
(2005)
Evolution
, vol.59
, pp. 24-37
-
-
Degnan, J.H.1
Salter, L.A.2
-
27
-
-
34250380386
-
Confounding factors in HGT detection: Statistical error, coalescent effects, and multiple solutions
-
Than C, Ruths D, Innan H, Nakhleh L, (2007) Confounding factors in HGT detection: Statistical error, coalescent effects, and multiple solutions. J Comput Biol 14: 517-535.
-
(2007)
J Comput Biol
, vol.14
, pp. 517-535
-
-
Than, C.1
Ruths, D.2
Innan, H.3
Nakhleh, L.4
-
28
-
-
58249136809
-
Detecting hybrid speciation in the presence of incomplete lineage sorting using gene tree incongruence: A model
-
Meng C, Kubatko LS, (2009) Detecting hybrid speciation in the presence of incomplete lineage sorting using gene tree incongruence: A model. Theor Popul Biol 75: 35-45.
-
(2009)
Theor Popul Biol
, vol.75
, pp. 35-45
-
-
Meng, C.1
Kubatko, L.S.2
-
29
-
-
70450277249
-
Identifying hybridization events in the presence of coalescence via model selection
-
Kubatko LS, (2009) Identifying hybridization events in the presence of coalescence via model selection. Syst Biol 58: 478-488.
-
(2009)
Syst Biol
, vol.58
, pp. 478-488
-
-
Kubatko, L.S.1
-
30
-
-
79951575208
-
Coalescent histories on phylogenetic networks and detection of hybridization despite incomplete lineage sorting
-
Yu Y, Than C, Degnan JH, Nakhleh L, (2011) Coalescent histories on phylogenetic networks and detection of hybridization despite incomplete lineage sorting. Syst Biol 60: 138-149.
-
(2011)
Syst Biol
, vol.60
, pp. 138-149
-
-
Yu, Y.1
Than, C.2
Degnan, J.H.3
Nakhleh, L.4
-
31
-
-
0016355478
-
A new look at the statistical model identification
-
Akaike H, (1974) A new look at the statistical model identification. IEEE Trans Automat Contr 19: 716-723.
-
(1974)
IEEE Trans Automat Contr
, vol.19
, pp. 716-723
-
-
Akaike, H.1
-
33
-
-
0000120766
-
Estimating the dimension of a model
-
Schwarz G, (1978) Estimating the dimension of a model. Ann Stat 6: 461-464.
-
(1978)
Ann Stat
, vol.6
, pp. 461-464
-
-
Schwarz, G.1
-
34
-
-
51349098340
-
PhyloNet: a software package for analyzing and reconstructing reticulate evolutionary relationships
-
Than C, Ruths D, Nakhleh L, (2008) PhyloNet: a software package for analyzing and reconstructing reticulate evolutionary relationships. BMC Bioinformatics 9: 322.
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 322
-
-
Than, C.1
Ruths, D.2
Nakhleh, L.3
-
35
-
-
0242365676
-
Genome-scale approaches to resolving incongruence in molecular phylogenies
-
Rokas A, Williams BL, King N, Carroll SB, (2003) Genome-scale approaches to resolving incongruence in molecular phylogenies. Nature 425: 798-804.
-
(2003)
Nature
, vol.425
, pp. 798-804
-
-
Rokas, A.1
Williams, B.L.2
King, N.3
Carroll, S.B.4
-
36
-
-
70349658769
-
Species tree inference by minimizing deep coalescences
-
doi:10.1371/journal.pcbi.1000501
-
Than C, Nakhleh L, (2009) Species tree inference by minimizing deep coalescences. PLoS Comput Biol 5: e1000501 doi:10.1371/journal.pcbi.1000501.
-
(2009)
PLoS Comput Biol
, vol.5
-
-
Than, C.1
Nakhleh, L.2
-
37
-
-
0034849408
-
MRBAYES: Bayesian inference of phylogenetic trees
-
Huelsenbeck JP, Ronquist F, (2001) MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17: 754-755.
-
(2001)
Bioinformatics
, vol.17
, pp. 754-755
-
-
Huelsenbeck, J.P.1
Ronquist, F.2
-
38
-
-
0004248459
-
PAUP*: Phylogenetic analysis using parsimony (and other methods)
-
Sinauer Associates, Underland, Massachusetts, Version 4.0
-
Swofford DL, (1996) PAUP*: Phylogenetic analysis using parsimony (and other methods). Sinauer Associates, Underland, Massachusetts, Version 4.0.
-
(1996)
-
-
Swofford, D.L.1
-
40
-
-
72049128651
-
Unifying vertical and nonvertical evolution: A stochastic ARG-based framework
-
Bloomquist EW, Suchard MA, (2010) Unifying vertical and nonvertical evolution: A stochastic ARG-based framework. Syst Biol 59: 27-41.
-
(2010)
Syst Biol
, vol.59
, pp. 27-41
-
-
Bloomquist, E.W.1
Suchard, M.A.2
-
41
-
-
33750437728
-
Widespread discordance of gene trees with species tree in Drosophila: evidence for incomplete lineage sorting
-
doi:10.1371/journal.pgen.0020173
-
Pollard DA, Iyer VN, Moses AM, Eisen MB, (2006) Widespread discordance of gene trees with species tree in Drosophila: evidence for incomplete lineage sorting. PLoS Genet 2: e173 doi:10.1371/journal.pgen.0020173.
-
(2006)
PLoS Genet
, vol.2
-
-
Pollard, D.A.1
Iyer, V.N.2
Moses, A.M.3
Eisen, M.B.4
-
43
-
-
43749105558
-
Linkage disequilibrium - understanding the evolutionary past and mapping the medical future
-
Slatkin M, (2008) Linkage disequilibrium - understanding the evolutionary past and mapping the medical future. Nature Rev Genet 9: 477-485.
-
(2008)
Nature Rev Genet
, vol.9
, pp. 477-485
-
-
Slatkin, M.1
-
44
-
-
0041817551
-
Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci
-
Rannala B, Yang Z, (2003) Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci. Genetics 164: 1645-1656.
-
(2003)
Genetics
, vol.164
, pp. 1645-1656
-
-
Rannala, B.1
Yang, Z.2
-
45
-
-
34548575126
-
Species trees from gene trees: Reconstructing Bayesian posterior distributions of a species phylogeny using estimated gene tree distributions
-
Liu L, Pearl DK, (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
-
46
-
-
77249086587
-
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
-
47
-
-
79951561454
-
The accuracy of species tree estimation under simulation: A com- parison of methods
-
Leaché AD, Rannala B, (2011) The accuracy of species tree estimation under simulation: A com- parison of methods. Syst Biol 60: 126-137.
-
(2011)
Syst Biol
, vol.60
, pp. 126-137
-
-
Leaché, A.D.1
Rannala, B.2
-
48
-
-
63549118031
-
STEM: species tree estimation using maximum likelihood for gene trees under coalescence
-
Kubatko LS, Carstens BC, Knowles LL, (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
-
49
-
-
77958059433
-
Sources of error inherent in species-tree estimation: Impact of mutational and coalescent effects on accuracy and implications for choosing among different methods
-
Huang H, He Q, Kubatko LS, Knowles LL, (2010) Sources of error inherent in species-tree estimation: Impact of mutational and coalescent effects on accuracy and implications for choosing among different methods. Syst Biol 59: 573-583.
-
(2010)
Syst Biol
, vol.59
, pp. 573-583
-
-
Huang, H.1
He, Q.2
Kubatko, L.S.3
Knowles, L.L.4
-
50
-
-
0035923699
-
Evaluation of methods for detecting recombination from dna sequences: Computer simulations
-
Posada D, Crandall KA, (2001) Evaluation of methods for detecting recombination from dna sequences: Computer simulations. P Natl Acad Sci USA 98: 13757-13762.
-
(2001)
P Natl Acad Sci USA
, vol.98
, pp. 13757-13762
-
-
Posada, D.1
Crandall, K.A.2
-
51
-
-
33646167864
-
A simple and robust statistical test for detecting the presence of recombination
-
Bruen TC, Philippe H, Bryant D, (2002) A simple and robust statistical test for detecting the presence of recombination. Genetics 172: 2665-2681.
-
(2002)
Genetics
, vol.172
, pp. 2665-2681
-
-
Bruen, T.C.1
Philippe, H.2
Bryant, D.3
-
52
-
-
84857002599
-
RECOMP: A parsimony-based method for detecting recombination
-
In: Proceedings of the 4th Asia Pacific Bioinformatics Conference
-
Ruths D, Nakhleh L, (2006) RECOMP: A parsimony-based method for detecting recombination. pp. 59-68 In: Proceedings of the 4th Asia Pacific Bioinformatics Conference.
-
(2006)
, pp. 59-68
-
-
Ruths, D.1
Nakhleh, L.2
-
53
-
-
79960041437
-
Detecting phylogenetic breakpoints and discordance from genome-wide alignments for species tree reconstruction
-
Ané C, (2011) Detecting phylogenetic breakpoints and discordance from genome-wide alignments for species tree reconstruction. Genome Biol Evol 3: 246-258.
-
(2011)
Genome Biol Evol
, vol.3
, pp. 246-258
-
-
Ané, C.1
-
54
-
-
84860552871
-
Is recombination a problem for species-tree analyses?
-
In press: DOI:10.1093/sysbio/syr128
-
Lanier H, Knowles L, (2012) Is recombination a problem for species-tree analyses? Syst Biol In press: DOI:10.1093/sysbio/syr128.
-
(2012)
Syst Biol
-
-
Lanier, H.1
Knowles, L.2
-
55
-
-
65649112683
-
-
Greenwood Village, CO, Roberts & Company
-
Wakeley J, (2008) Coalescent Theory Greenwood Village, CO Roberts & Company.
-
(2008)
Coalescent Theory
-
-
Wakeley, J.1
-
57
-
-
49249091441
-
Using supernetworks to distinguish hybridization from lineage-sorting
-
Holland B, Benthin S, Lockhart P, Moulton V, Huber K, (2008) Using supernetworks to distinguish hybridization from lineage-sorting. BMC Evol Biol 8: 202.
-
(2008)
BMC Evol Biol
, vol.8
, pp. 202
-
-
Holland, B.1
Benthin, S.2
Lockhart, P.3
Moulton, V.4
Huber, K.5
|