Dynamically Heterogenous Partitions and Phylogenetic Inference: An Evaluation of Analytical Strategies with Cytochrome b and ND6 Gene Sequences in Cranes

Dynamically Heterogenous Partitions and Phylogenetic Inference: An Evaluation of Analytical... Debates over whether molecular sequence data should be partitioned for phylogenetic analysis often confound two types of heterogeneity among partitions. We distinguish historical heterogeneity (i.e., different partitions have different evolutionary relationships) from dynamic heterogeneity (i.e., different partitions show different patterns of sequence evolution) and explore the impact of the latter on phylogenetic accuracy and precision with a two-gene, mitochondrial data set for cranes. The well-established phylogeny of cranes allows us to contrast tree-based estimates of relevant parameter values with estimates based on pairwise comparisons and to ascertain the effects of incorporating different amounts of process information into phylogenetic estimates. We show that codon positions in the cytochrome b and NADH dehydrogenase subunit 6 genes are dynamically heterogenous under both Poisson and invariable-sites + gamma-rates versions of the F84 model and that heterogeneity includes variation in base composition and transition bias as well as substitution rate. Estimates of transition-bias and relative-rate parameters from pairwise sequence comparisons were comparable to those obtained as tree-based maximum likelihood estimates. Neither rate-category nor mixed-model partitioning strategies resulted in a loss of phylogenetic precision relative to unpartitioned analyses. We suggest that weighted-average distances provide a computationally feasible alternative to direct maximum likelihood estimates of phylogeny for mixed-model analyses of large, dynamically heterogenous data sets. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Molecular Phylogenetics and Evolution Elsevier

Dynamically Heterogenous Partitions and Phylogenetic Inference: An Evaluation of Analytical Strategies with Cytochrome b and ND6 Gene Sequences in Cranes

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Publisher
Elsevier
Copyright
Copyright © 1999 Academic Press
ISSN
1055-7903
eISSN
1095-9513
DOI
10.1006/mpev.1999.0646
pmid
10603258
Publisher site
See Article on Publisher Site

Abstract

Debates over whether molecular sequence data should be partitioned for phylogenetic analysis often confound two types of heterogeneity among partitions. We distinguish historical heterogeneity (i.e., different partitions have different evolutionary relationships) from dynamic heterogeneity (i.e., different partitions show different patterns of sequence evolution) and explore the impact of the latter on phylogenetic accuracy and precision with a two-gene, mitochondrial data set for cranes. The well-established phylogeny of cranes allows us to contrast tree-based estimates of relevant parameter values with estimates based on pairwise comparisons and to ascertain the effects of incorporating different amounts of process information into phylogenetic estimates. We show that codon positions in the cytochrome b and NADH dehydrogenase subunit 6 genes are dynamically heterogenous under both Poisson and invariable-sites + gamma-rates versions of the F84 model and that heterogeneity includes variation in base composition and transition bias as well as substitution rate. Estimates of transition-bias and relative-rate parameters from pairwise sequence comparisons were comparable to those obtained as tree-based maximum likelihood estimates. Neither rate-category nor mixed-model partitioning strategies resulted in a loss of phylogenetic precision relative to unpartitioned analyses. We suggest that weighted-average distances provide a computationally feasible alternative to direct maximum likelihood estimates of phylogeny for mixed-model analyses of large, dynamically heterogenous data sets.

Journal

Molecular Phylogenetics and EvolutionElsevier

Published: Nov 1, 1999

References

  • Separate versus combined analysis of phylogenetic evidence
    de Queiroz, A.; Donoghue, M.J.; Kim, J.
  • Phylogenies from molecular sequences: Inference and reliability
    Felsenstein, J.
  • Phylogeny estimation and hypothesis testing using maximum likelihood
    Huelsenbeck, J.P.; Crandall, K.A.
  • A multigene assessment of phylogenetic relationships in the dasyurid marsupial subfamily Sminthopsinae
    Krajewski, C.; Blacket, M.; Buckley, L.; Westerman, M.
  • Phylogenetic frameworks: Towards a firmer foundation for the comparative approach
    Lanyon, S.
  • Phylogenetic inference
    Swofford, D.L.; Olsen, G.J.; Waddell, P.J.; Hillis, D.M.

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