Molecular Systematics of the Eastern Fence Lizard (Sceloporus undulatus): A Comparison of Parsimony, Likelihood, and Bayesian Approaches

Abstract

Phylogenetic analysis of large datasets using complex nucleotide substitution models under a maximum likelihood framework can be computationally infeasible, especially when attempting to infer confidence values by way of nonparametric bootstrapping. Recent developments in phylogenetics suggest the computational burden can be reduced by using Bayesian methods of phylogenetic inference. However, few empirical phylogenetic studies exist that explore the efficiency of Bayesian analysis of large datasets. To this end, we conducted an extensive phylogenetic analysis of the wide-ranging and geographically variable Eastern Fence Lizard (Sceloporus undulatus). Maximum parsimony, maximum likelihood, and Bayesian phylogenetic analyses were performed on a combined mitochondrial DNA dataset (12S and 16S rRNA, ND1 protein-coding gene, and associated tRNA; 3,688 bp total) for 56 populations of S. undulatus (78 total terminals including other S. undulatus group species and outgroups). Maximum parsimony analysis resulted in numerous equally parsimonious trees (82,646 from equally weighted parsimony and 335 from weighted parsimony). The majority rule consensus tree derived from the Bayesian analysis was topologically identical to the single best phylogeny inferred from the maximum likelihood analysis, but required approximately 80% less computational time. The mtDNA data provide strong support for the monophyly of the S. undulatus group and the paraphyly of "S. undulatus" with respect to S. belli, S. cautus, and S. woodi. Parallel evolution of ecomorphs within "S. undulatus" has masked the actual number of species within this group. This evidence, along with convincing patterns of phylogeographic differentiation suggests "S. undulatus" represents at least four lineages that should be recognized as evolutionary species.

Molecular phylogeny of the brachyuran crab superfamily Majoidea indicates close congruence with trees based on larval morphology

“…Mitochondrial (16S and COI) single-locus trees supported a clade of eastern Pacific epialtid species (Pugettia producta, P. richii, P. dalli, P. gracilis, and Mimulus foliatus; bootstrap and bpp support = 69-100). For single-locus trees, Bayesian support values were generally higher than ML bootstrap support, as has been noted in other studies (Erixon et al, 2003;Huelsenbeck et al, 2002;Leache and Reeder, 2002).…”

“…In this study, we focus on model-based approaches to phylogenetic inference, specifically Bayesian and maximum likelihood methods, because their ability to incorporate information about the model of evolution for a particular locus decreases statistical inconsistency (e.g., by correcting for multiple substitutions) (Bergsten, 2005;Huelsenbeck et al, 2002Huelsenbeck et al, , 2001Leache and Reeder, 2002). We used the program MrBayes v3.1.2 (Hulsenbeck and Ronquist, 2001;Ronquist and Hulsenbeck, 2003) to construct trees using single-locus and combined datasets, as MrBayes allows different partitions (i.e., loci) to evolve under different models of evolution.…”

“…We used the program MrBayes v3.1.2 (Hulsenbeck and Ronquist, 2001;Ronquist and Hulsenbeck, 2003) to construct trees using single-locus and combined datasets, as MrBayes allows different partitions (i.e., loci) to evolve under different models of evolution. However, since Bayesian posterior probability support values (bpp) can often be inflated for certain clades relative to bootstrap values from maximum-likelihood (ML) and maximum parsimony methods (Erixon et al, 2003;Huelsenbeck et al, 2002;Leache and Reeder, 2002), we also constructed trees using each single-locus dataset using ML. For ML searches, we used the program PhyML (Guindon and Gascuel, 2003;Guindon et al, 2005) to construct 100 ML bootstrap replicates using the full complement of species sequenced for each individual locus.…”

Systematic relationships of Oriental tiny frogs of the family Microhylidae (Amphibia, Anura) as revealed by mtDNA genealogy

“…We a priori regarded tree nodes with bootstrap value 70% or greater as sufficiently resolved (Huelsenbeck and Hillis, 1993), and those between 50% and 70% as tendencies. In the BI analysis, we considered nodes with a BPP of 95% or greater significant (Leaché and Reeder, 2002).…”

Molecular systematics of the damselfishes (Teleostei: Pomacentridae): Bayesian phylogenetic analyses of mitochondrial and nuclear DNA sequences

“…ML results are thus more difficult to interpret in comparison to the straightforward assessment of Bayesian support for a phylogenetic hypothesis. The relative novelty of the Bayesian approach has limited its inspection in comparison to alternative phylogenetic methods, but such scrutiny is rapidly expanding (e.g., Buckley et al, 2002;Huelsenbeck et al, 2002;Leache and Reeder, 2002).…”