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

线粒体基因组学：大规模系统发育分析中的鱼类遗传学调查和核苷酸特征取样分子系统学利用DNA的变异来重建生物体之间的历史关系，并调查导致地球生物多样性的进化过程。 随着DNA序列数据量的不断增加以及可用于进化研究的特征和/或物种数量的不断增加，系统发育分析和实验设计方法变得越来越重要。 直觉告诉我们，越多的数据可以应用到一个遗传学问题上，就越有可能得到一个准确的遗传学估计。 尽管系统发育的准确性可能与从一个特定群体中取样的物种数量呈正相关，但分子系统学中的一个基本问题仍然存在：需要多少核苷酸特征来解析给定数量物种的系统发育，特别是当一个群体的所有（或大多数）现存成员都被取样时？ 本项目将采用一个大型的、强大的系统发育分析来研究系统发育分析对核苷酸特征取样的敏感性。辐鳍鱼（Actinopterii纲）表现出极端的多样性，其现存的描述物种比所有其他脊椎动物类群的总和还要多，具有重要的生态和经济意义。 尽管有大量的形态学研究，但许多放线翼龙谱系之间的系统发育关系仍不清楚。 该项目将汇编一个完整的线粒体基因组数据集，来自73种鳍鱼，包括32个（42个）目的代表和广泛的采样，从两个最大的目，鲤形目和鲈形目。 线粒体基因组是一种小的染色体，其遗传独立于细胞核中的大部分DNA。 线粒体DNA的克隆、母系遗传特性使其在系统发育研究中特别有用。 线粒体基因组序列，沿着核基因序列，将被用来产生一个强有力的假设的系统发育关系的最重要的谱系鳍鱼。 这组数据将揭示鱼类多样性的模式，并为早期脊椎动物的进化提供重要的见解。 线粒体数据，结合最佳系统发育假设，将被用来研究核苷酸采样特性在系统发育分析中的作用。 对于每个子样品，将确定恢复正确的同源性所需的核苷酸数量，以及不同水平的支持。 几个重要的进化参数对系统发育准确性的影响将被调查。 这些参数包括a）样品中可变核苷酸位点的频率; B）分类群间进化差异的数量; c）所包含谱系间进化速率变异的数量;以及d）取样分类群间核苷酸组成偏差的程度和分布。 这些结果将提供一个更深入的了解的行为的核苷酸数据的遗传学分析，并应确定一个范围内的核苷酸样本大小所需的准确估计作为一个功能的类群调查和相关的进化条件。 这些客观的实验设计准则将对分子系统学领域的研究具有实际意义，可为资源的预算和分配提供指导，并可提高分子系统学研究的效率和准确性。

Mitochondrial phylogenomics: Investigation of fish phylogeny and nucleotide character sampling in large-scale phylogenetic analysis Molecular systematics employs variation in DNA to reconstruct historicalrelationships among organisms and investigate evolutionary processes thathave given rise to the earth's biodiversity. The growing volume of DNAsequence data and the increasing number of characters and/or species thatmay be included in evolutionary investigations have placed greaterimportance on methods of phylogenetic analysis and experimental design. Itis intuitive that the more data that can be applied to a phylogeneticquestion, the greater the probability of recovering an accurate estimate ofthe phylogeny. Although phylogenetic accuracy may be positively correlatedwith the number of species sampled from a particular group, a fundamentalquestion in molecular systematics remains: How many nucleotide charactersare required to resolve the phylogeny of a given number of species,particularly when all (or most) of the extant members of a group have beensampled? This project will employ a large, robust phylogeny to investigatethe sensitivity of phylogenetic analysis to nucleotide character sampling.The ray-finned fishes (class Actinopterygii) exhibit extreme diversitywith more extant described species than all other vertebrate groupscombined and are of major ecological and economic importance. Despiteextensive morphological study, phylogenetic relationships among manyactinopterygian lineages remain unclear. This project will compile a dataset of complete mitochondrial genomes from 73 species of ray-finned fishes,including representatives of 32 (out of 42) orders and extensive samplingfrom the two largest orders, Cypriniformes and Perciformes. Mitochondrialgenomes are small chromosomes that are inherited independently of themajority of DNA found in the nucleus. The clonal, maternal inheritance ofmitochondrial DNA makes it particularly useful in phylogenetic studies. Mitochondrial genome sequences, along with nuclear gene sequences, will beused to generate a robust hypothesis of phylogenetic relationships amongthe most important lineages of ray-finned fishes. This data set willreveal patterns of diversification among fishes and provide importantinsights on the evolution of early vertebrates. The mitochondrial data, inconjunction with the best phylogenetic hypothesis, will then be used toinvestigate nucleotide sampling properties in phylogenetic analysis.Sub-samples of different numbers of species will be drawn from the group of73 species. For each sub-sample, the number of nucleotides required torecover the correct phylogeny, with various levels of support, will bedetermined. The influence of several important evolutionary parameters onphylogenetic accuracy will be investigated. These parameters include a)the frequency of variable nucleotide sites in the sample; b) the amount ofevolutionary divergence among taxa; c) the amount of evolutionary ratevariation among included lineages; and d) the extent and distribution ofnucleotide compositional bias among sampled taxa. The results will providea deeper understanding of the behavior of nucleotide data in phylogeneticanalysis and should identify a range of nucleotide sample sizes requiredfor accurate estimation of phylogeny as a function of the number of taxaunder investigation and relevant evolutionary conditions. Such objectivecriteria for experimental design will be of practical benefit to the fieldof molecular systematics by providing guidance in budgeting and allocationof resources and by improving the efficiency and accuracy of molecularphylogenetic studies.