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 choice 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. Filt...
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ftunivbruxelles:oai:dipot.ulb.ac.be:2013/164268 2023-05-15T15:37:11+02:00 Effects of character weighting and species sampling on phylogeny reconstruction: A case study based on DNA sequence data in cetaceans Milinkovitch, Michel Leduc, Richard R.G. Adachi, Jun Farnir, Frédéric Georges, Michel Hasegawa, Masami 1996-12 No full-text files http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/164268 en eng uri/info:pmid/8978067 uri/info:scp/0030469275 http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/164268 Genetics, 144 (4 Biologie info:eu-repo/semantics/article info:ulb-repo/semantics/articlePeerReview info:ulb-repo/semantics/openurl/article 1996 ftunivbruxelles 2022-06-12T21:25:39Z Different phylogenetic analyses of the same genetic data set can yield conflicting results, depending on the choice 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 weighing 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 cetacean suborders, the toothed whales. This analysis strongly supports the sister relationship between sperm whales and baleen whales. SCOPUS: ar.j info:eu-repo/semantics/published Article in Journal/Newspaper baleen whales toothed whales DI-fusion : dépôt institutionnel de l'Université libre de Bruxelles (ULB) |
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DI-fusion : dépôt institutionnel de l'Université libre de Bruxelles (ULB) |
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ftunivbruxelles |
language |
English |
topic |
Biologie |
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Biologie Milinkovitch, Michel Leduc, Richard R.G. Adachi, Jun Farnir, Frédéric Georges, Michel Hasegawa, Masami Effects of character weighting and species sampling on phylogeny reconstruction: A case study based on DNA sequence data in cetaceans |
topic_facet |
Biologie |
description |
Different phylogenetic analyses of the same genetic data set can yield conflicting results, depending on the choice 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 weighing 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 cetacean suborders, the toothed whales. This analysis strongly supports the sister relationship between sperm whales and baleen whales. SCOPUS: ar.j info:eu-repo/semantics/published |
format |
Article in Journal/Newspaper |
author |
Milinkovitch, Michel Leduc, Richard R.G. Adachi, Jun Farnir, Frédéric Georges, Michel Hasegawa, Masami |
author_facet |
Milinkovitch, Michel Leduc, Richard R.G. Adachi, Jun Farnir, Frédéric Georges, Michel Hasegawa, Masami |
author_sort |
Milinkovitch, Michel |
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://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/164268 |
genre |
baleen whales toothed whales |
genre_facet |
baleen whales toothed whales |
op_source |
Genetics, 144 (4 |
op_relation |
uri/info:pmid/8978067 uri/info:scp/0030469275 http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/164268 |
_version_ |
1766367635586416640 |