title: Dynamically heterogenous partitions and phylogenetic inference: an evaluation of analytical strategies with cytochrome b and ND6 gene sequences in cranes.
abstract: ki ctes 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.
authors.affiliation: Center for Systematic Biology, Southern Illinois University, Carbondale, Illinois 62901-6501, USA. careyk@sui.edu
authors.forename: C
authors.initials: C
authors.lastname: Krajewski
authors.forename: M G
authors.initials: MG
authors.lastname: Fain
authors.forename: L
authors.initials: L
authors.lastname: Buckley
authors.forename: D G
authors.initials: DG
authors.lastname: King
mesh_terms: D000465:Algorithms; D000818:Animals; D001717:Birds / Q000145:classification / Q000235:genetics*; D003573:Cytochrome b Group / Q000235:genetics*; D019143:Evolution, Molecular; D018740:Genetic Heterogeneity; D016013:Likelihood Functions; D016014:Linear Models; D008969:Molecular Sequence Data; D009245:NADH Dehydrogenase / Q000235:genetics*; D010802:Phylogeny
chemical_list: D003573:Cytochrome b Group; D009245:NADH Dehydrogenase