Confirming the phylogeny of mammals by use of large comparative sequence data sets - PubMed (original) (raw)

Comparative Study

. 2008 Sep;25(9):1795-808.

doi: 10.1093/molbev/msn104. Epub 2008 May 2.

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Comparative Study

Confirming the phylogeny of mammals by use of large comparative sequence data sets

Arjun B Prasad et al. Mol Biol Evol. 2008 Sep.

Abstract

The ongoing generation of prodigious amounts of genomic sequence data from myriad vertebrates is providing unparalleled opportunities for establishing definitive phylogenetic relationships among species. The size and complexities of such comparative sequence data sets not only allow smaller and more difficult branches to be resolved but also present unique challenges, including large computational requirements and the negative consequences of systematic biases. To explore these issues and to clarify the phylogenetic relationships among mammals, we have analyzed a large data set of over 60 megabase pairs (Mb) of high-quality genomic sequence, which we generated from 41 mammals and 3 other vertebrates. All sequences are orthologous to a 1.9-Mb region of the human genome that encompasses the cystic fibrosis transmembrane conductance regulator gene (CFTR). To understand the characteristics and challenges associated with phylogenetic analyses of such a large data set, we partitioned the sequence data in several ways and utilized maximum likelihood, maximum parsimony, and Neighbor-Joining algorithms, implemented in parallel on Linux clusters. These studies yielded well-supported phylogenetic trees, largely confirming other recent molecular phylogenetic analyses. Our results provide support for rooting the placental mammal tree between Atlantogenata (Xenarthra and Afrotheria) and Boreoeutheria (Euarchontoglires and Laurasiatheria), illustrate the difficulty in resolving some branches even with large amounts of data (e.g., in the case of Laurasiatheria), and demonstrate the valuable role that very large comparative sequence data sets can play in refining our understanding of the evolutionary relationships of vertebrates.

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Figures

F<sc>IG</sc>. 1.—

FIG. 1.—

ML tree derived from the analysis of the coding sequence partition using RY-coded bases and a codon position partitioned CF + Γ model. Branch lengths indicate likelihood-inferred substitutions per site with a GTR + Γ model. ML bootstrap proportions are listed above Bayesian posterior probabilities for all branches at less than 100% bootstrap proportion and 1.0 Bayesian posterior probability support. Platypus was constrained to the mammals (its branch is marked with an asterisk to reflect this). The fishes (Tetraodon and Fugu) were used to root, but their branches are not shown. Branch lengths were optimized using ML from nucleotide-coded data with a GTR + Γ model.

F<sc>IG</sc>. 2.—

FIG. 2.—

ML tree derived from the analysis of coding plus conserved noncoding sequence matrix using RY-coded bases. A CF + Γ model was used, with 4 partitions: 3 for codon positions and 1 for conserved noncoding sequence. Long branches leading to platypus and chicken were abbreviated for clarity. Other features are the same as indicated in figure 1.

F<sc>IG</sc>. 3.—

FIG. 3.—

ML trees for each of 10 sequential, equal-sized partitions from the coding plus conserved noncoding sequence matrix. Numbers (1–10) reflect the specific partition used. The arrangement of taxa and branches indicated in colors other than black vary among partitions. Nodes annotated with hollow circles have less than 50% bootstrap proportions, those with shaded circles have 50% to 75% bootstrap proportions, and those with solid circles have 75% bootstrap proportions or greater. Branches that are the same in all trees are indicated in black, with some collapsed to higher level taxa for simplicity.

F<sc>IG</sc>. 4.—

FIG. 4.—

Three possible roots for Placentalia. SH test results from the coding plus conserved noncoding sequence matrix for both nucleotide- and RY-coded matrices. (A) Hypothesis rooting Placentalia between Xenarthra and Epitheria (Boreoeutheria + Afrotheria). (B) Hypothesis rooting Placentalia between Afrotheria and Exafroplacentalia (Boreoeutheria + Afrotheria). (C) Hypothesis rooting Placentalia between Boreoeutheria and Atlantogenata (Afrotheria + Xenarthra).

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