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Examining the utility of categorical models and alleviating artifacts in phylogenetic reconstruction of the Squamata (Reptilia).

Douglas, Desiree LU and Arnason, Ulfur LU (2009) In Molecular Phylogenetics and Evolution 52. p.784-796
Abstract
Reconstruction artifacts are a serious hindrance to the elucidation of phylogenetic relationships and a number of methods have been devised to alleviate them. Previous studies have demonstrated a striking disparity in the evolutionary rates of the mitochondrial (mt) genomes of squamate reptiles (lizards, worm lizards and snakes) and the reconstruction artifacts that may arise from this. Here, to examine basal squamate relationships, we have added the mt genome of the blind skink Dibamus novaeguineae to the mitogenomic dataset and applied different models for resolving the squamate tree. Categorical models were found to be less susceptible to artifacts than were the commonly used noncategorical phylogenetic models GTR and mtREV. The... (More)
Reconstruction artifacts are a serious hindrance to the elucidation of phylogenetic relationships and a number of methods have been devised to alleviate them. Previous studies have demonstrated a striking disparity in the evolutionary rates of the mitochondrial (mt) genomes of squamate reptiles (lizards, worm lizards and snakes) and the reconstruction artifacts that may arise from this. Here, to examine basal squamate relationships, we have added the mt genome of the blind skink Dibamus novaeguineae to the mitogenomic dataset and applied different models for resolving the squamate tree. Categorical models were found to be less susceptible to artifacts than were the commonly used noncategorical phylogenetic models GTR and mtREV. The application of different treatments to the data showed that the removal of the fastest evolving sites in snakes improved phylogenetic signal in the dataset. Basal divergences remained, nevertheless, poorly resolved. The proportion of both fast-evolving and conserved sites in the squamate mt genomes relative to sites with intermediate rates of evolution suggests rapid early divergences among squamate taxa and at least partly explains the short internal relative to external branches in the squamate tree. Thus, mt and nuclear trees may never reach full agreement because of the short branches characterizing these divergences. (Less)
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author
organization
publishing date
type
Contribution to journal
publication status
published
subject
in
Molecular Phylogenetics and Evolution
volume
52
pages
784 - 796
publisher
Elsevier
external identifiers
  • wos:000268265800020
  • pmid:19481165
  • scopus:67649662203
ISSN
1095-9513
DOI
10.1016/j.ympev.2009.05.020
language
English
LU publication?
yes
id
f9a6ca98-3154-4995-9d5a-794b04d9caea (old id 1434723)
date added to LUP
2009-07-01 15:28:57
date last changed
2017-01-01 05:05:22
@article{f9a6ca98-3154-4995-9d5a-794b04d9caea,
  abstract     = {Reconstruction artifacts are a serious hindrance to the elucidation of phylogenetic relationships and a number of methods have been devised to alleviate them. Previous studies have demonstrated a striking disparity in the evolutionary rates of the mitochondrial (mt) genomes of squamate reptiles (lizards, worm lizards and snakes) and the reconstruction artifacts that may arise from this. Here, to examine basal squamate relationships, we have added the mt genome of the blind skink Dibamus novaeguineae to the mitogenomic dataset and applied different models for resolving the squamate tree. Categorical models were found to be less susceptible to artifacts than were the commonly used noncategorical phylogenetic models GTR and mtREV. The application of different treatments to the data showed that the removal of the fastest evolving sites in snakes improved phylogenetic signal in the dataset. Basal divergences remained, nevertheless, poorly resolved. The proportion of both fast-evolving and conserved sites in the squamate mt genomes relative to sites with intermediate rates of evolution suggests rapid early divergences among squamate taxa and at least partly explains the short internal relative to external branches in the squamate tree. Thus, mt and nuclear trees may never reach full agreement because of the short branches characterizing these divergences.},
  author       = {Douglas, Desiree and Arnason, Ulfur},
  issn         = {1095-9513},
  language     = {eng},
  pages        = {784--796},
  publisher    = {Elsevier},
  series       = {Molecular Phylogenetics and Evolution},
  title        = {Examining the utility of categorical models and alleviating artifacts in phylogenetic reconstruction of the Squamata (Reptilia).},
  url          = {http://dx.doi.org/10.1016/j.ympev.2009.05.020},
  volume       = {52},
  year         = {2009},
}