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TEST FOR SIMULTANEOUS DIVERGENCE USING APPROXIMATE BAYESIAN COMPUTATION

Comparative phylogeographic studies often reveal disparate levels of sequence divergence between lineages spanning a common geographic barrier, leading to the conclusion that isolation was nonsynchronous. However, only rarely do researchers account for the expected variance associated with ancestral... Full description

Journal Title: Evolution 2006, Vol.60 (12), p.2435-2453
Main Author: Hickerson, Michael J.
Other Authors: Stahl, Eli A. , Lessios, H. A.
Format: Electronic Article Electronic Article
Language: English
Subjects:
Publisher: Oxford, UK: Blackwell Publishing Ltd
ID: ISSN: 0014-3820
Link: https://www.ncbi.nlm.nih.gov/pubmed/17263107
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title: TEST FOR SIMULTANEOUS DIVERGENCE USING APPROXIMATE BAYESIAN COMPUTATION
format: Article
creator:
  • Hickerson, Michael J.
  • Stahl, Eli A.
  • Lessios, H. A.
subjects:
  • Animals
  • Approximate Bayesian computation
  • Bayes Theorem
  • Bayesian analysis
  • Bayesian statistical decision theory
  • Biological Evolution
  • Biology
  • coalescent
  • comparative phylogeography
  • Datasets
  • Descriptive statistics
  • Divergent evolution
  • echinoid
  • Estimated taxes
  • Estimation methods
  • Estimators
  • Evolutionary genetics
  • Genetic mutation
  • Genetic research
  • Genetics
  • hierarchical model
  • Identification and classification
  • Meta-analysis
  • Mitochondrial DNA
  • Modeling
  • Models, Biological
  • Panama
  • Phenetics
  • Sea Urchins
  • Statistical variance
  • Taxa
  • Time Factors
  • vicariance
ispartof: Evolution, 2006, Vol.60 (12), p.2435-2453
description: Comparative phylogeographic studies often reveal disparate levels of sequence divergence between lineages spanning a common geographic barrier, leading to the conclusion that isolation was nonsynchronous. However, only rarely do researchers account for the expected variance associated with ancestral coalescence and among-taxon variation in demographic history. We introduce a flexible approximate Bayesian computational (ABC) framework that can test for simultaneous divergence (TSD) using a hierarchical model that incorporates idiosyncratic differences in demographic history across taxon pairs. The method is tested across a range of conditions and is shown to be accurate even with single-locus mitochondrial DNA (mtDNA) data. We apply this method to a landmark dataset of putative simultaneous vicariance, eight geminate echinoid taxon pairs thought to have been split by the Isthmus of Panama 3.1 million years ago. The ABC posterior estimates are not consistent with a history of simultaneous vicariance given these data. Subsequent ABC estimates under a constrained model that assumes two divergence times across the eight taxon pairs suggests simultaneous divergence 3.1 million years ago in seven of the taxon pairs and a more recent divergence in the remaining taxon pair. These ABC estimates on the simultaneous divergence of the seven taxon pairs correspond to a DNA substitution rate of approximately 1.59% per lineage per million years at the mtDNA cytochrome oxidase I gene. This ABC framework can easily be modified to analyze single taxon-pair datasets and/or be expanded to include multiple loci, migration, recombination, and other idiosyncratic demographic histories. The flexible aspect of ABC and its built-in evaluation of estimator bias and statistical power has the potential to greatly enhance statistical rigor in phylogeographic studies.
language: eng
source:
identifier: ISSN: 0014-3820
fulltext: no_fulltext
issn:
  • 0014-3820
  • 1558-5646
url: Link


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titleTEST FOR SIMULTANEOUS DIVERGENCE USING APPROXIMATE BAYESIAN COMPUTATION
creatorHickerson, Michael J. ; Stahl, Eli A. ; Lessios, H. A.
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descriptionComparative phylogeographic studies often reveal disparate levels of sequence divergence between lineages spanning a common geographic barrier, leading to the conclusion that isolation was nonsynchronous. However, only rarely do researchers account for the expected variance associated with ancestral coalescence and among-taxon variation in demographic history. We introduce a flexible approximate Bayesian computational (ABC) framework that can test for simultaneous divergence (TSD) using a hierarchical model that incorporates idiosyncratic differences in demographic history across taxon pairs. The method is tested across a range of conditions and is shown to be accurate even with single-locus mitochondrial DNA (mtDNA) data. We apply this method to a landmark dataset of putative simultaneous vicariance, eight geminate echinoid taxon pairs thought to have been split by the Isthmus of Panama 3.1 million years ago. The ABC posterior estimates are not consistent with a history of simultaneous vicariance given these data. Subsequent ABC estimates under a constrained model that assumes two divergence times across the eight taxon pairs suggests simultaneous divergence 3.1 million years ago in seven of the taxon pairs and a more recent divergence in the remaining taxon pair. These ABC estimates on the simultaneous divergence of the seven taxon pairs correspond to a DNA substitution rate of approximately 1.59% per lineage per million years at the mtDNA cytochrome oxidase I gene. This ABC framework can easily be modified to analyze single taxon-pair datasets and/or be expanded to include multiple loci, migration, recombination, and other idiosyncratic demographic histories. The flexible aspect of ABC and its built-in evaluation of estimator bias and statistical power has the potential to greatly enhance statistical rigor in phylogeographic studies.
editionReceived October 13, 2005. Accepted September 12, 2006.
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subjectAnimals ; Approximate Bayesian computation ; Bayes Theorem ; Bayesian analysis ; Bayesian statistical decision theory ; Biological Evolution ; Biology ; coalescent ; comparative phylogeography ; Datasets ; Descriptive statistics ; Divergent evolution ; echinoid ; Estimated taxes ; Estimation methods ; Estimators ; Evolutionary genetics ; Genetic mutation ; Genetic research ; Genetics ; hierarchical model ; Identification and classification ; Meta-analysis ; Mitochondrial DNA ; Modeling ; Models, Biological ; Panama ; Phenetics ; Sea Urchins ; Statistical variance ; Taxa ; Time Factors ; vicariance
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titleTEST FOR SIMULTANEOUS DIVERGENCE USING APPROXIMATE BAYESIAN COMPUTATION
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abstractComparative phylogeographic studies often reveal disparate levels of sequence divergence between lineages spanning a common geographic barrier, leading to the conclusion that isolation was nonsynchronous. However, only rarely do researchers account for the expected variance associated with ancestral coalescence and among-taxon variation in demographic history. We introduce a flexible approximate Bayesian computational (ABC) framework that can test for simultaneous divergence (TSD) using a hierarchical model that incorporates idiosyncratic differences in demographic history across taxon pairs. The method is tested across a range of conditions and is shown to be accurate even with single-locus mitochondrial DNA (mtDNA) data. We apply this method to a landmark dataset of putative simultaneous vicariance, eight geminate echinoid taxon pairs thought to have been split by the Isthmus of Panama 3.1 million years ago. The ABC posterior estimates are not consistent with a history of simultaneous vicariance given these data. Subsequent ABC estimates under a constrained model that assumes two divergence times across the eight taxon pairs suggests simultaneous divergence 3.1 million years ago in seven of the taxon pairs and a more recent divergence in the remaining taxon pair. These ABC estimates on the simultaneous divergence of the seven taxon pairs correspond to a DNA substitution rate of approximately 1.59% per lineage per million years at the mtDNA cytochrome oxidase I gene. This ABC framework can easily be modified to analyze single taxon-pair datasets and/or be expanded to include multiple loci, migration, recombination, and other idiosyncratic demographic histories. The flexible aspect of ABC and its built-in evaluation of estimator bias and statistical power has the potential to greatly enhance statistical rigor in phylogeographic studies.
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doi10.1111/j.0014-3820.2006.tb01880.x
tpages19
editionReceived October 13, 2005. Accepted September 12, 2006.
oafree_for_read