Effects of Character Weighting and Species Sampling on Phylogeny Reconstruction: A Case Study Based on DNA Sequence Data in Cetaceans
Different phylogenetic analyses of the same genetic data set can yield conflicting results, depending on the choic of parameter settings and included taxa. This is particularly true in studies involving data sets where levels of homoplasy are high and likely to obscure the phylogenetic signal. Filte...
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ftpubmed:oai:pubmedcentral.nih.gov:1207731 2023-05-15T15:37:10+02:00 Effects of Character Weighting and Species Sampling on Phylogeny Reconstruction: A Case Study Based on DNA Sequence Data in Cetaceans Milinkovitch, M. C. LeDuc, R. G. Adachi, J. Farnir, F. Georges, M. Hasegawa, M. 1996-12 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1207731 http://www.ncbi.nlm.nih.gov/pubmed/8978067 en eng http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1207731 http://www.ncbi.nlm.nih.gov/pubmed/8978067 Investigations Text 1996 ftpubmed 2013-08-30T13:27:09Z Different phylogenetic analyses of the same genetic data set can yield conflicting results, depending on the choic of parameter settings and included taxa. This is particularly true in studies involving data sets where levels of homoplasy are high and likely to obscure the phylogenetic signal. Filtering of this phylogenetic noise can be attempted, with varying degrees of success, by using different weighting schemes and ingroup/outgroup choices, but it can be difficult to decide objectively which approach is best. Using a cytochrome b data set from cetaceans and artiodactyls, we examined the effects of a suite of parameter settings on the outcome of phylogenetic analyses. We tested 2968 combinations among the seven parameters that most often vary among phylogenetic studies. It is our contention that this sensitivity analysis identifies portions of the multidimensional parameter space where phylogenetic signal is most reliably recovered, and simple rules are given to guide the choice of settings. Portions of this data set have been used in previous studies with conflicting results, namely the monophyly vs. paraphyly of one of the two major recognized cetacean suborders, the toothed whales. This analysis strongly supports the sister relationship between sperm whales and baleen whales. Text baleen whales toothed whales PubMed Central (PMC) |
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Investigations Milinkovitch, M. C. LeDuc, R. G. Adachi, J. Farnir, F. Georges, M. Hasegawa, M. Effects of Character Weighting and Species Sampling on Phylogeny Reconstruction: A Case Study Based on DNA Sequence Data in Cetaceans |
topic_facet |
Investigations |
description |
Different phylogenetic analyses of the same genetic data set can yield conflicting results, depending on the choic of parameter settings and included taxa. This is particularly true in studies involving data sets where levels of homoplasy are high and likely to obscure the phylogenetic signal. Filtering of this phylogenetic noise can be attempted, with varying degrees of success, by using different weighting schemes and ingroup/outgroup choices, but it can be difficult to decide objectively which approach is best. Using a cytochrome b data set from cetaceans and artiodactyls, we examined the effects of a suite of parameter settings on the outcome of phylogenetic analyses. We tested 2968 combinations among the seven parameters that most often vary among phylogenetic studies. It is our contention that this sensitivity analysis identifies portions of the multidimensional parameter space where phylogenetic signal is most reliably recovered, and simple rules are given to guide the choice of settings. Portions of this data set have been used in previous studies with conflicting results, namely the monophyly vs. paraphyly of one of the two major recognized cetacean suborders, the toothed whales. This analysis strongly supports the sister relationship between sperm whales and baleen whales. |
format |
Text |
author |
Milinkovitch, M. C. LeDuc, R. G. Adachi, J. Farnir, F. Georges, M. Hasegawa, M. |
author_facet |
Milinkovitch, M. C. LeDuc, R. G. Adachi, J. Farnir, F. Georges, M. Hasegawa, M. |
author_sort |
Milinkovitch, M. C. |
title |
Effects of Character Weighting and Species Sampling on Phylogeny Reconstruction: A Case Study Based on DNA Sequence Data in Cetaceans |
title_short |
Effects of Character Weighting and Species Sampling on Phylogeny Reconstruction: A Case Study Based on DNA Sequence Data in Cetaceans |
title_full |
Effects of Character Weighting and Species Sampling on Phylogeny Reconstruction: A Case Study Based on DNA Sequence Data in Cetaceans |
title_fullStr |
Effects of Character Weighting and Species Sampling on Phylogeny Reconstruction: A Case Study Based on DNA Sequence Data in Cetaceans |
title_full_unstemmed |
Effects of Character Weighting and Species Sampling on Phylogeny Reconstruction: A Case Study Based on DNA Sequence Data in Cetaceans |
title_sort |
effects of character weighting and species sampling on phylogeny reconstruction: a case study based on dna sequence data in cetaceans |
publishDate |
1996 |
url |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1207731 http://www.ncbi.nlm.nih.gov/pubmed/8978067 |
genre |
baleen whales toothed whales |
genre_facet |
baleen whales toothed whales |
op_relation |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1207731 http://www.ncbi.nlm.nih.gov/pubmed/8978067 |
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1766367630329905152 |