@ARTICLE{TreeBASE2Ref9908,
author = {Torsten H. Struck and Maximilian P. Nesnidal and Guenter Purschke and Kenneth M. Halanych},
title = {Detecting Possibly Saturated Positions in 18S and 28S Sequences and their Influence on Phylogenetic Reconstruction of Annelida (Lophotrochozoa).},
year = {2008},
keywords = {C factor, O/E ratio, Annelida, Saturation, rRNA, Phylogeny, Iss},
doi = {10.1016/j.ympev.2008.05.015},
url = {http://},
pmid = {},
journal = {Molecular Phylogenetics and Evolution},
volume = {48},
number = {2},
pages = {628--645},
abstract = {Phylogenetic reconstructions may be hampered by multiple substitutions in nucleotide positions obliterating signal, a phenomenon called saturation. Traditionally, plotting ti/tv ratios against genetic distances has been used to reveal saturation by assessing when ti/tv stabilizes at 1. However, interpretation of results and assessment of comparability between different data sets or partitions are rather subjective. Herein, we present the new C factor, which quantifies convergence of ti/tv ratios, thus allowing comparability. Furthermore, we introduce a comparative value for homoplasy, the O/E ratio, based on alterations of tree length. Simulation studies and an empirical example, based on annelid rRNA-gene sequences, show that the C factor correlates with noise, tree length and genetic distance and therefore is a proxy for saturation. The O/E ratio correlates with the C factor, which does not provide an intrinsic threshold of exclusion, and thus both together can objectively guide decisions to exclude saturated nucleotide positions. However, analyses also showed that, for reconstructing annelid phylogeny using Maximum Likelihood, an increase in numbers of positions improves tree reconstruction more than does the exclusion of saturated positions.}
}
Matrix 602 of Study 2046
Citation title:
"Detecting Possibly Saturated Positions in 18S and 28S Sequences and their Influence on Phylogenetic Reconstruction of Annelida (Lophotrochozoa).".
This study was previously identified under the legacy study ID S2045
(Status: Published).
Matrices
Title: Eukaryotic HMG-CoA
Description: Legacy TreeBASE Matrix ID = M1501
Rows
|
Taxon Label |
Row Segments |
Characters 1?–30 |
| Phycomyces blakesleeanus |
(none)
|
ENVIGYMPIPVGVAGPMNIDGDLIHIPMAT |
| Aspergillus terreus 1 |
(none)
|
ENVVGYLPLPLGVAGPMVIDGQALFIPMAT |
| Candida utilis |
(none)
|
ENVIGYMPLPVGVAGPLIIDGKPYHIPMAT |
| Saccharomyces cerervisiae 1 |
(none)
|
ENVIGYMPIPVGVIGPLIIDGTSYHIPMAT |
| Schizosaccharomyces pombe 1 |
(none)
|
ENVIGYMPLPLGVAGPLIIDGKPFYIPMAT |
| Gibberella fujikuroi |
(none)
|
ENVIGYMPLPVGVAGPLVIDGQSYFIPMAT |
| Strongylocentrotus purpuratus |
(none)
|
ENVIGYMPVPVGVAGPLLLDGQEFQVPMAT |
| Blattella germanica |
(none)
|
ENVIGYMPVPVGVAGPLNLDGRLVHVPLAT |
| Dendroctonus jeffreyi |
(none)
|
ENVIGYMPIPVGYAGPLLLDGRELYIPMAT |
| Ips paraconfusus |
(none)
|
ENVIGYMPIPVGYAGPLVLDGKEIYVPMAT |
| Xenopus laevis |
(none)
|
ENVIGYMPIPVGVAGPLLLNNKEYQVPMAT |
| Oryctolagus cuniculus |
(none)
|
ENVIGYMPIPVGVVGPLCLDGKEFQVPMAT |
| Rattus norvegicus |
(none)
|
ENVIGYMPIPVGVAGPLCLDGKEYQVPMAT |
| Cricetulus griseus |
(none)
|
ENVIGYMPIPVGVAGPLCLDGKEYQVPMAT |
| Agrotis ipsilon |
(none)
|
ENVIGYVGVPVGYAGPLVVDGKPYMIPMAT |
| Drosophila melanogaster |
(none)
|
ENVLGYVPIPVGYAGPLLLDGETYYVPMAT |
| Homo sapiens |
(none)
|
ENVIGYMPIPVGVAGPLCLDEKEFQVPMAT |
Columns
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Citation
Taxa
Matrices
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Analyses
