Mitochondrial Phylogenomics: Investigation of Fish Phylogeny and Nucleotide Character Sampling in Large-scale Phylogenetic analysis

University Of Oklahoma Norman Campus, Norman OK

Investigators

Abstract

Mitochondrial phylogenomics: Investigation of fish phylogeny and nucleotide character sampling in large-scale phylogenetic analysis Molecular systematics employs variation in DNA to reconstruct historical relationships among organisms and investigate evolutionary processes that have given rise to the earth's biodiversity. The growing volume of DNA sequence data and the increasing number of characters and/or species that may be included in evolutionary investigations have placed greater importance on methods of phylogenetic analysis and experimental design. It is intuitive that the more data that can be applied to a phylogenetic question, the greater the probability of recovering an accurate estimate of the phylogeny. Although phylogenetic accuracy may be positively correlated with the number of species sampled from a particular group, a fundamental question in molecular systematics remains: How many nucleotide characters are required to resolve the phylogeny of a given number of species, particularly when all (or most) of the extant members of a group have been sampled? This project will employ a large, robust phylogeny to investigate the sensitivity of phylogenetic analysis to nucleotide character sampling. The ray-finned fishes (class Actinopterygii) exhibit extreme diversity with more extant described species than all other vertebrate groups combined and are of major ecological and economic importance. Despite extensive morphological study, phylogenetic relationships among many actinopterygian lineages remain unclear. This project will compile a data set of complete mitochondrial genomes from 73 species of ray-finned fishes, including representatives of 32 (out of 42) orders and extensive sampling from the two largest orders, Cypriniformes and Perciformes. Mitochondrial genomes are small chromosomes that are inherited independently of the majority of DNA found in the nucleus. The clonal, maternal inheritance of mitochondrial DNA makes it particularly useful in phylogenetic studies. Mitochondrial genome sequences, along with nuclear gene sequences, will be used to generate a robust hypothesis of phylogenetic relationships among the most important lineages of ray-finned fishes. This data set will reveal patterns of diversification among fishes and provide important insights on the evolution of early vertebrates. The mitochondrial data, in conjunction with the best phylogenetic hypothesis, will then be used to investigate nucleotide sampling properties in phylogenetic analysis. Sub-samples of different numbers of species will be drawn from the group of 73 species. For each sub-sample, the number of nucleotides required to recover the correct phylogeny, with various levels of support, will be determined. The influence of several important evolutionary parameters on phylogenetic accuracy will be investigated. These parameters include a) the frequency of variable nucleotide sites in the sample; b) the amount of evolutionary divergence among taxa; c) the amount of evolutionary rate variation among included lineages; and d) the extent and distribution of nucleotide compositional bias among sampled taxa. The results will provide a deeper understanding of the behavior of nucleotide data in phylogenetic analysis and should identify a range of nucleotide sample sizes required for accurate estimation of phylogeny as a function of the number of taxa under investigation and relevant evolutionary conditions. Such objective criteria for experimental design will be of practical benefit to the field of molecular systematics by providing guidance in budgeting and allocation of resources and by improving the efficiency and accuracy of molecular phylogenetic studies.