@ARTICLE{TreeBASE2Ref21966,
author = {Carl J. Rothfels and Eric Schuettpelz},
title = {Accelerated Rate of Molecular Evolution for Vittarioid Ferns is Strong and Not Due to Selection},
year = {2013},
keywords = {Adiantum, Calciphilopteris, codon models, divergence time dating, local clocks, model selection, molecular clock, mutation rate, nucleotide substitution rate, Pteridaceae, rate heterogeneity, relaxed clocks, trigenomic analyses},
doi = {},
url = {http://},
pmid = {},
journal = {Systematic Biology},
volume = {},
number = {},
pages = {},
abstract = {Molecular evolutionary rate heterogeneity?the violation of a molecular clock?is a prominent feature of many phylogenetic datasets. It has particular importance to systematists not only because of its biological implications, but also for its practical effects on our ability to infer and date evolutionary events. Here we show, using both maximum likelihood and Bayesian approaches, that a remarkably strong increase in substitution rate in the vittarioid ferns is consistent across the nuclear and plastid genomes. Contrary to some expectations, this rate increase is not due to selective forces acting at the protein level in our focal loci; the vittarioids bear no signature of the change in the relative strengths of selection and drift that one would expect if the rate increase was caused by altered post-mutation fixation rates. Instead, the substitution rate increase appears to stem from an elevated supply of mutations, perhaps limited to the vittarioid ancestral branch. This generalized rate increase is accompanied by extensive fine-scale heterogeneity in rates across loci, genomes, and taxa. Our analyses demonstrate the effectiveness and flexibility of trait-free investigations of rate heterogeneity within a model selection framework, emphasize the importance of explicit tests for signatures of selection prior to invoking selection-related or demography-based explanations for patterns of rate variation, and illustrate some unexpected nuances in the behavior of relaxed clock methods for modeling rate heterogeneity, with implications for our ability to confidently date divergence events. In addition, our data provide strong support for the monophyly of Adiantum, and for the position of Calciphilopteris in the cheilanthoid ferns, two relationships for which convincing support was previously lacking. }
}
Citation for Study 14194
Citation title:
"Accelerated Rate of Molecular Evolution for Vittarioid Ferns is Strong and Not Due to Selection".
Study name:
"Accelerated Rate of Molecular Evolution for Vittarioid Ferns is Strong and Not Due to Selection".
This study is part of submission 14194
(Status: Published).
Citation
Rothfels C., & Schuettpelz E. 2013. Accelerated Rate of Molecular Evolution for Vittarioid Ferns is Strong and Not Due to Selection. Systematic Biology, .
Authors
-
Rothfels C.
-
Schuettpelz E.
Abstract
Molecular evolutionary rate heterogeneity?the violation of a molecular clock?is a prominent feature of many phylogenetic datasets. It has particular importance to systematists not only because of its biological implications, but also for its practical effects on our ability to infer and date evolutionary events. Here we show, using both maximum likelihood and Bayesian approaches, that a remarkably strong increase in substitution rate in the vittarioid ferns is consistent across the nuclear and plastid genomes. Contrary to some expectations, this rate increase is not due to selective forces acting at the protein level in our focal loci; the vittarioids bear no signature of the change in the relative strengths of selection and drift that one would expect if the rate increase was caused by altered post-mutation fixation rates. Instead, the substitution rate increase appears to stem from an elevated supply of mutations, perhaps limited to the vittarioid ancestral branch. This generalized rate increase is accompanied by extensive fine-scale heterogeneity in rates across loci, genomes, and taxa. Our analyses demonstrate the effectiveness and flexibility of trait-free investigations of rate heterogeneity within a model selection framework, emphasize the importance of explicit tests for signatures of selection prior to invoking selection-related or demography-based explanations for patterns of rate variation, and illustrate some unexpected nuances in the behavior of relaxed clock methods for modeling rate heterogeneity, with implications for our ability to confidently date divergence events. In addition, our data provide strong support for the monophyly of Adiantum, and for the position of Calciphilopteris in the cheilanthoid ferns, two relationships for which convincing support was previously lacking.
Keywords
Adiantum, Calciphilopteris, codon models, divergence time dating, local clocks, model selection, molecular clock, mutation rate, nucleotide substitution rate, Pteridaceae, rate heterogeneity, relaxed clocks, trigenomic analyses
External links
About this resource
- Canonical resource URI:
http://purl.org/phylo/treebase/phylows/study/TB2:S14194
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- Show BibTeX reference
@ARTICLE{TreeBASE2Ref21966,
author = {Carl J. Rothfels and Eric Schuettpelz},
title = {Accelerated Rate of Molecular Evolution for Vittarioid Ferns is Strong and Not Due to Selection},
year = {2013},
keywords = {Adiantum, Calciphilopteris, codon models, divergence time dating, local clocks, model selection, molecular clock, mutation rate, nucleotide substitution rate, Pteridaceae, rate heterogeneity, relaxed clocks, trigenomic analyses},
doi = {},
url = {http://},
pmid = {},
journal = {Systematic Biology},
volume = {},
number = {},
pages = {},
abstract = {Molecular evolutionary rate heterogeneity?the violation of a molecular clock?is a prominent feature of many phylogenetic datasets. It has particular importance to systematists not only because of its biological implications, but also for its practical effects on our ability to infer and date evolutionary events. Here we show, using both maximum likelihood and Bayesian approaches, that a remarkably strong increase in substitution rate in the vittarioid ferns is consistent across the nuclear and plastid genomes. Contrary to some expectations, this rate increase is not due to selective forces acting at the protein level in our focal loci; the vittarioids bear no signature of the change in the relative strengths of selection and drift that one would expect if the rate increase was caused by altered post-mutation fixation rates. Instead, the substitution rate increase appears to stem from an elevated supply of mutations, perhaps limited to the vittarioid ancestral branch. This generalized rate increase is accompanied by extensive fine-scale heterogeneity in rates across loci, genomes, and taxa. Our analyses demonstrate the effectiveness and flexibility of trait-free investigations of rate heterogeneity within a model selection framework, emphasize the importance of explicit tests for signatures of selection prior to invoking selection-related or demography-based explanations for patterns of rate variation, and illustrate some unexpected nuances in the behavior of relaxed clock methods for modeling rate heterogeneity, with implications for our ability to confidently date divergence events. In addition, our data provide strong support for the monophyly of Adiantum, and for the position of Calciphilopteris in the cheilanthoid ferns, two relationships for which convincing support was previously lacking. }
}
- Show RIS reference
TY - JOUR
ID - 21966
AU - Rothfels,Carl J.
AU - Schuettpelz,Eric
T1 - Accelerated Rate of Molecular Evolution for Vittarioid Ferns is Strong and Not Due to Selection
PY - 2013
KW - Adiantum
KW - Calciphilopteris
KW - codon models
KW - divergence time dating
KW - local clocks
KW - model selection
KW - molecular clock
KW - mutation rate
KW - nucleotide substitution rate
KW - Pteridaceae
KW - rate heterogeneity
KW - relaxed clocks
KW - trigenomic analyses
UR - http://dx.doi.org/
N2 - Molecular evolutionary rate heterogeneity?the violation of a molecular clock?is a prominent feature of many phylogenetic datasets. It has particular importance to systematists not only because of its biological implications, but also for its practical effects on our ability to infer and date evolutionary events. Here we show, using both maximum likelihood and Bayesian approaches, that a remarkably strong increase in substitution rate in the vittarioid ferns is consistent across the nuclear and plastid genomes. Contrary to some expectations, this rate increase is not due to selective forces acting at the protein level in our focal loci; the vittarioids bear no signature of the change in the relative strengths of selection and drift that one would expect if the rate increase was caused by altered post-mutation fixation rates. Instead, the substitution rate increase appears to stem from an elevated supply of mutations, perhaps limited to the vittarioid ancestral branch. This generalized rate increase is accompanied by extensive fine-scale heterogeneity in rates across loci, genomes, and taxa. Our analyses demonstrate the effectiveness and flexibility of trait-free investigations of rate heterogeneity within a model selection framework, emphasize the importance of explicit tests for signatures of selection prior to invoking selection-related or demography-based explanations for patterns of rate variation, and illustrate some unexpected nuances in the behavior of relaxed clock methods for modeling rate heterogeneity, with implications for our ability to confidently date divergence events. In addition, our data provide strong support for the monophyly of Adiantum, and for the position of Calciphilopteris in the cheilanthoid ferns, two relationships for which convincing support was previously lacking.
L3 -
JF - Systematic Biology
VL -
IS -
ER -