@ARTICLE{TreeBASE2Ref18607,
author = {A. D. Leach?},
title = {Species Tree Discordance Traces to Phylogeographic Clade Boundaries in North American Fence Lizards (Sceloporus)},
year = {2009},
keywords = {},
doi = {10.1093/sysbio/syp057},
url = {},
pmid = {},
journal = {Systematic Biology},
volume = {58},
number = {6},
pages = {547?559},
abstract = {I investigated the impacts of phylogeographic sampling decisions on species tree estimation in the Sceloporus undulatus species group, a recent radiation of small, insectivorous lizards connected by para- and peripatric distribution across North America, using a variety of species tree inference methods (BEST, BUCKy and minimize deep coalescences). Phylogenetic analyses of 16 specimens representing four putative species within S. undulatus using complete (8 loci, > 5.5kb) and incomplete (29 loci; > 23.6 kb) nuclear datasets result in species trees that share features with the mitochondrial DNA (mtDNA) genealogy at the phylogeographic level, but provide new insights into the evolutionary history of the species group. The concatenated nuclear data and mtDNA data both recover four major clades connecting populations across North America; however, instances of discordance are localized at the contact zones between adjacent phylogeographic groups. A random sub-sampling experiment designed to vary the phylogeographic samples included across hundreds of replicate species tree inferences suggests that inaccurate species assignments can result in inferred phylogenetic relationships that are dependent upon which particular populations are used as exemplars to represent species and can lead to increased estimates of effective population size (Θ). For the phylogeographic data presented here, reassigning specimens with introgressed mtDNA genomes to their prospective species, or excluding them from the analysis altogether, produce species tree topologies that are distinctly different from analyses that utilize mtDNA-based species assignments. Evolutionary biologists working at the interface of phylogeography and phylogenetics are likely to encounter multiple processes influencing gene trees congruence, which increases the relevance of estimating species trees with multilocus nuclear data and models that accommodate incomplete deep coalescence.}
}
Matrix 4610 of Study 10116
Citation title:
"Species Tree Discordance Traces to Phylogeographic Clade Boundaries in North American Fence Lizards (Sceloporus)".
This study was previously identified under the legacy study ID S2457
(Status: Published).
Matrices
Title: combined nuclear data A
Description: Legacy TreeBASE Matrix ID = M4675
Rows
Taxon Label |
Row Segments |
Characters 1?–30 |
Sceloporus tristichus AZa |
(none)
|
GTTTGCAAGAATATCATGGAAGACCTTCTC |
Sceloporus tristichus AZ |
(none)
|
GTTTGCAAGAATATCATGGAAGACCTTCTC |
Sceloporus tristichus WY |
(none)
|
GTTTGCAAGAATATCATGGAAGACCTTCTC |
Sceloporus tristichus CO |
(none)
|
GTTTGCAAGAATATCATGGAAGACCTTCTC |
Sceloporus cowlesi TX |
(none)
|
????????????????????????CTTCTC |
Sceloporus cowlesi NMa |
(none)
|
GTTTGCAAGAATATCATGGAAGACCTTCTC |
Sceloporus cowlesi NM |
(none)
|
GTTTGCAAGAATATCATGGAAGACCTTCTC |
Sceloporus cowlesi AZ |
(none)
|
GTTTGCAAGAATATCATGGAAGACCTTCTC |
Sceloporus consobrinus KS |
(none)
|
GTTTGCAAGAATATCATGGAAGATCTTCTC |
Sceloporus consobrinus MS |
(none)
|
GTTTGCAAGAATATCATGGAAGACCTTCTC |
Sceloporus consobrinus TX |
(none)
|
????????????????????????CTTCTC |
Sceloporus consobrinus CO |
(none)
|
GTTTGCAAGAATATCATGGAAGATCTTCTC |
Sceloporus undulatus AL |
(none)
|
GTTTGCAAGAATATCATGGAAGACCTTCTC |
Sceloporus undulatus FL |
(none)
|
GTTTGCAAGAATATCATGGAAGACCTTCTC |
Sceloporus undulatus NC |
(none)
|
GTTTGCAAGAATATCATGGAAGACCTTCTC |
Sceloporus undulatus NJ |
(none)
|
GTTTGCAAGAATATCATGGAAGACCTTCTC |
Sceloporus cautus |
(none)
|
GTTTGCAAGAATATCATGAAAGACCTTCTC |
Sceloporus virgatus |
(none)
|
GTTTGCAAGAATATCATGAAAGACCTTCTC |
Sceloporus occidentalis |
(none)
|
?????????????????????????????? |
Sceloporus woodi |
(none)
|
GTTTGCAAGAATATCATGGAAGACCTTCTC |
Sceloporus olivaceus |
(none)
|
GTTTGCAAAAATATCATGAAAGACCTTCTC |
Columns
None of the columns has a description.