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Citation for 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).

Citation

Struck T., Nesnidal M., Purschke G., & Halanych K. 2008. Detecting Possibly Saturated Positions in 18S and 28S Sequences and their Influence on Phylogenetic Reconstruction of Annelida (Lophotrochozoa). Molecular Phylogenetics and Evolution, 48(2): 628-645.

Authors

Struck T.
Nesnidal M.
Purschke G.
Halanych K.

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.

Keywords

C factor, O/E ratio, Annelida, Saturation, rRNA, Phylogeny, Iss

External links

DOI: 10.1016/j.ympev.2008.05.015

About this resource

Canonical resource URI: http://purl.org/phylo/treebase/phylows/study/TB2:S2046
Other versions: Nexus NeXML

Show BibTeX reference

		@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.}
}

Show RIS reference

TY - JOUR
ID - 9908
AU - Struck,Torsten H.
AU - Nesnidal,Maximilian P.
AU - Purschke,Guenter
AU - Halanych,Kenneth M.
T1 - Detecting Possibly Saturated Positions in 18S and 28S Sequences and their Influence on Phylogenetic Reconstruction of Annelida (Lophotrochozoa).
PY - 2008
KW - C factor
KW - O/E ratio
KW - Annelida
KW - Saturation
KW - rRNA
KW - Phylogeny
KW - Iss
UR - http://dx.doi.org/10.1016/j.ympev.2008.05.015
N2 - 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.
L3 - 10.1016/j.ympev.2008.05.015
JF - Molecular Phylogenetics and Evolution
VL - 48
IS - 2
SP - 628
EP - 645
ER -