Modeling nucleotide evolution at the mesoscale: The phylogeny of the Neotropical pitvipers of the Porthidium group (Viperidae: Crotalinae)

• Published in: Molecular phylogenetics and evolution Vol. 37; no. 3; pp. 881 - 898
• Main Authors: Castoe, Todd A., Sasa, Mahmood M., Parkinson, Christopher L.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 01-12-2005
• Subjects: Akaike weights; Animals; Atropoides; Base Sequence; Bayes factors; Bayes Theorem; Central America; Cerrophidion; DNA, Mitochondrial - genetics; Evolution, Molecular; MCMC model testing; Mexico; Models, Genetic; Molecular Sequence Data; Phylogeny; Porthidium; Relative Bayes factors; Sequence Analysis, DNA; Viperidae - classification; Viperidae - genetics; Central America; Mexico; Relative Bayes factors; MCMC model testing; Bayes factors; Atropoides; Akaike weights; Porthidium; Cerrophidion
• ISSN: 1055-7903; 1095-9513
• DOI: 10.1016/j.ympev.2005.05.013

We analyzed the phylogeny of the Neotropical pitvipers within the
Porthidium group (including intra-specific through inter-generic relationships) using 1.4
kb of DNA sequences from two mitochondrial protein-coding genes (ND4 and cyt-
b). We investigated how Bayesian Markov chain Monte-Carlo (MCMC) phylogenetic hypotheses based on this ‘mesoscale’ dataset were affected by analysis under various complex models of nucleotide evolution that partition models across the dataset. We develop an approach, employing three statistics (Akaike weights, Bayes factors, and relative Bayes factors), for examining the performance of complex models in order to identify the best-fit model for data analysis. Our results suggest that: (1) model choice may have important practical effects on phylogenetic conclusions even for mesoscale datasets, (2) the use of a complex partitioned model did not produce widespread increases or decreases in nodal posterior probability support, and (3) most differences in resolution resulting from model choice were concentrated at deeper nodes. Our phylogenetic estimates of relationships among members of the
Porthidium group (genera:
Atropoides,
Cerrophidion, and
Porthidium) resolve the monophyly of the three genera. Bayesian MCMC results suggest that
Cerrophidion and
Porthidium form a clade that is the sister taxon to
Atropoides. In addition to resolving the intra-specific relationships among a majority of
Porthidium group taxa, our results highlight phylogeographic patterns across Middle and South America and suggest that each of the three genera may harbor undescribed species diversity.