@ARTICLE{TreeBASE2Ref14702,
author = {Natalia M. Belfiore and Leo X. Liu and Craig Moritz},
title = {Multilocus Phylogenetics of a Rapid Radiation in the Genus Thomomys (Rodentia: Geomyidae)},
year = {2008},
keywords = {},
doi = {10.1080/10635150802044011},
url = {},
pmid = {},
journal = {Systematic Biology},
volume = {57},
number = {2},
pages = {294--310},
abstract = {Species complexes undergoing rapid radiation present a challenge in molecular systematics because of the possibility that ancestral polymorphism is retained in component gene trees. Coalescent theory has demonstrated that gene trees often fail to match lineage trees when taxon divergence times are less than the ancestral effective population sizes. Suggestions to increase the number of loci and the number of individuals per taxon have been proposed; however, phylogenetic methods to adequately analyze these data in a coalescent framework are scarce. We compare two approaches to estimating lineage (species) trees using multiple individuals and multiple loci: the commonly used partitioned Bayesian analysis of concatenated sequences, and a modification of a newly developed hierarchical Bayesian method (BEST) that simultaneously estimates gene trees and species trees from multilocus data. We test these approaches on a phylogeny of rapidly radiating species wherein divergence times are likely to be smaller than effective population sizes, and incomplete lineage sorting is known, in the rodent genus, Thomomys. We use seven independent non-coding nuclear sequence loci (total ~ 4300 bp), and between one and 12 individuals per taxon to construct a phylogenetic hypothesis for eight Thomomys species. The majority-rule consensus tree from the partitioned concatenated analysis included 14 strongly supported bipartitions, corroborating monophyletic species status of five of the eight named species. The BEST tree strongly supported only the split between the two subgenera, and showed very low support for any other clade. Comparison of both lineage trees to individual gene trees revealed that the concatenation method appears to ignore conflicting signals among gene trees, whereas the BEST tree considers conflicting signals and downweights support for those nodes. Bayes factor analysis of posterior tree distributions from both analyses strongly favor the model underlying the BEST analysis. This comparison underscores the risks of over-reliance on results from concatenation, and ignoring the properties of coalescence, especially in cases of recent, rapid radiations.}
}
Matrix 3079 of Study 2005
Citation title:
"Multilocus Phylogenetics of a Rapid Radiation in the Genus Thomomys (Rodentia: Geomyidae)".
This study was previously identified under the legacy study ID S1997
(Status: Published).
Matrices
Title: TBO72
Description: Legacy TreeBASE Matrix ID = M3718
Rows
Taxon Label |
Row Segments |
Characters 1?–30 |
Thomomys townsendii relictus |
(none)
|
GCAACCTTCTCCTTTCATTGCTCCCCCCCC |
Thomomys umbrinus chihuahuae |
(none)
|
GCAACCTTCTCCTTCCATTGCTCCCCCCCC |
Thomomys umbrinus atroavarius |
(none)
|
GCCACCTTCTCCTTCCATTGCTCCCCCCCC |
Geomys breviceps |
(none)
|
?????????????????????????????? |
Orthogeomys heterodus |
(none)
|
?????????????????????????????? |
Thomomys bottae awahnee a |
(none)
|
??????????????????????CCCCCCCC |
Thomomys bottae awahnee b |
(none)
|
???????????????????????CCCCCCC |
Thomomys bottae xerophilus |
(none)
|
??????????????????????CCCCCCCC |
Thomomys bottae cactophilus |
(none)
|
??????????????????????CCCCCCCC |
Thomomys bottae albatus |
(none)
|
???????????????????????CCCCCCC |
Thomomys bottae ruidosae |
(none)
|
??????????????????????CCCCCCCC |
Thomomys bottae bottae |
(none)
|
??????????????????????CCCCCCCC |
Thomomys bottae alpinus |
(none)
|
??????????????????????CCCCCCCC |
Thomomys bottae riparius |
(none)
|
???????????????????????CCCCCCC |
Thomomys bottae mewa |
(none)
|
??????????????????????CCCCCCCC |
Thomomys bottae saxatilis |
(none)
|
???????????????????????CCCCCCC |
Thomomys bottae laticeps |
(none)
|
??????????????????????CCCCCCCC |
Thomomys bulbivorus |
(none)
|
GCAACCTTCTCCTTCCATTGCTCCCCCTCC |
Thomomys talpoides ocius |
(none)
|
?????CTTCTCCTTCCATTGCTCCCCCTCC |
Thomomys idahoensis pygmaeus a |
(none)
|
GCAACCTTCTCCTTCCATTGCTCCCCCTCC |
Thomomys idahoensis pygmaeus b |
(none)
|
?CAACCTTCTCCTTCCATTGCTCCCCCTCC |
Thomomys mazama mazama |
(none)
|
??CACCTTCTCCTTCCATTGCTCCCCCTCC |
Thomomys mazama nasicus |
(none)
|
GCAACCTTCTCCTTCCATTGCTCCCCCTCC |
Thomomys monticola a |
(none)
|
?????????????TTCATTGCTCCCCCTCC |
Thomomys monticola b |
(none)
|
GCAACCTTCTCCTTCCATTGCTCCCCCTCC |
Thomomys talpoides yakimensis |
(none)
|
?????????????????????????????? |
Thomomys talpoides bridgeri |
(none)
|
GCAACCTTCTCCTTTCATTGCTCCCCCTCC |
Thomomys townsendii townsendii |
(none)
|
GCAACCTTCTCCTTCCATTGCTCCCCCCCC |
Columns
None of the columns has a description.