@ARTICLE{TreeBASE2Ref2124,
author = {Jeffrey L. Boore and Stuart J. Longhorn and Susan E. Masta},
title = {Arachnid relationships based on mitochondrial genomes: asymmetric nucleotide and amino acid bias affects phylogenetic analyses.},
year = {2008},
keywords = {},
doi = {},
url = {},
pmid = {},
journal = {Molecular Phylogenetics and Evolution},
volume = {},
number = {},
pages = {},
abstract = {Phylogenetic analyses based on mitochondrial DNA have yielded widely differing relationships among members of the arthropod lineage Arachnida, depending on the nucleotide coding schemes and models of evolution used. We enhanced taxonomic coverage within the Arachnida greatly by sequencing seven new arachnid mitochondrial genomes from five orders. We then used all 13 mitochondrial protein-coding genes from these genomes to evaluate patterns of nucleotide and amino acid biases. Our data show that two of the six orders of arachnids (spiders and scorpions) have experienced shifts in both nucleotide and amino acid usage in all their protein-coding genes, and that these biases mislead phylogeny reconstruction. These biases are most striking for the hydrophobic amino acids isoleucine and valine, which appear to have evolved asymmetrical exchanges in response to shifts in nucleotide composition. To improve phylogenetic accuracy based on amino acid differences, we tested two recoding methods: (1) removing all isoleucine and valine sites and (2) recoding amino acids based on their physiochemical properties. We find that these methods yield phylogenetic trees that are consistent in their support of ancient intraordinal divergences within the major arachnid lineages. Further refinement of amino acid recoding methods may help us better delineate interordinal relationships among these diverse organisms.}
}
Matrix 3595 of Study 2187

Citation title:
"Arachnid relationships based on mitochondrial genomes: asymmetric nucleotide and amino acid bias affects phylogenetic analyses.".

This study was previously identified under the legacy study ID S2195
(Status: Published).
Matrices
Title: Arachnids
Description: Legacy TreeBASE Matrix ID = M4162
Rows
Taxon Label |
Row Segments |
Characters 1?–30 |
Limulus polyphemus |
(none)
|
RWLYSTNHKDIGTMYLIFGIWAAMVGTALS |
Ornithodoros moubata |
(none)
|
RWFYSTNHKDIGTMYLLLGSWSMMIGMSLS |
Haemaphysalis flava |
(none)
|
RWMFSTNHKDIGTMYLIFGTWAGMLGLSMS |
Ixodes hexagonus |
(none)
|
RWLFSTNHKDIGTMYLIFGSWSTMVGMSMS |
Rhipicephalus sanguineus |
(none)
|
RWMYSTNHKDIGTMYLIFGAWSGMLGLSMS |
Varroa destructor |
(none)
|
RWLFSCNHKDIGTIYFIFSLWSGVLGMMLS |
Heptathela hangzhouensis |
(none)
|
RWLFSTNHKDIGTMYLILGVWSSMMGTALS |
Ornithoctonus huwena |
(none)
|
RWLFSTNHSDIGTLYLLFGVWSAMVGTAMS |
Aphonopelma sp |
(none)
|
RWFYSTNHSDIGSLYFFFGVWSAMVGTAMS |
Hypochilus thorelli |
(none)
|
RWIYSTNHKDIGTLYLIFGLWASVLGTAMS |
Habronattus oregonensis |
(none)
|
RWLYSTNHKDIGTLYLIFGAWAAMVGTAMS |
Eremobates |
(none)
|
RWLYSTNHKDIGTLYLIFGAWSAMFGTALS |
Buthus occitanus |
(none)
|
RWLYSTNHKDIGTMYLVLGIWASMVGTALS |
Centruroides limpidus |
(none)
|
RWLYSTNHKDIGTMYLVLGIWASMVGTALS |
Uroctonus mordax |
(none)
|
RWLFSTNHKDIGTMYLILGGWASMVGTALS |
Phrynus sp |
(none)
|
RWFYSTNHKDIGTMYLLLGVWAAMIGTSLS |
Mastigoproctus giganteus |
(none)
|
RWLFSTNHKDIGTLYLILGLWAALSGSALS |
Lithobius forficatus |
(none)
|
RWMFSTNHKDIGTMYFVLGIWSAMIGTGLS |
Scutigera coleoptrata |
(none)
|
RWFFSTNHKDIGTMYLIFGAWAAMVGTALS |
Narceus annularus |
(none)
|
RWLFSTNHKDIGTMYLIFGAWAAMVGTALS |
Thyropygus sp |
(none)
|
RWLFSTNHKDIGTMYLIFGAWAAMIGTSLS |
Columns
None of the columns has a description.