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

线粒体系统学：大规模系统发育分析中鱼类系统发育和核苷酸特征采样的研究分子系统学利用DNA的变异来重建生物之间的历史关系，并研究导致地球生物多样性的进化过程。DNA序列数据的增长和进化研究中可能包含的特征和/或物种的数量的增加，使得系统发育分析和实验设计的方法变得更加重要。直观的是，可以应用于系统发育问题的数据越多，恢复对系统发育的准确估计的可能性就越大。尽管系统发育的准确性可能与从特定类群中采样的物种的数量呈正相关，但分子系统学中的一个基本问题仍然是：需要多少核苷酸特征才能解决给定数量的物种的系统发育问题，特别是当一个种群的所有(或大多数)现有成员都已被采样时？这个项目将使用一个大型的、强大的系统发育来研究系统发育分析对核苷酸特征采样的敏感性。放射鳍鱼类(放线鸟纲)表现出极大的多样性，所描述的物种比所有其他脊椎动物类别的总和还要多，具有重要的生态和经济意义。尽管进行了广泛的形态研究，但许多放线蕨类谱系之间的系统发育关系仍然不清楚。该项目将汇编73种鳍鱼的完整线粒体基因组数据集，其中包括42个目中的32个目的代表和来自两个最大的目--鲤形目和贻贝目的大量样本。线粒体基因组是独立于核中发现的大多数DNA而遗传的小染色体。线粒体DNA的克隆母系遗传使其在系统发育研究中特别有用。线粒体基因组序列和核基因序列将被用来产生一个强有力的假设，即最重要的鳍鱼谱系之间的系统发育关系。这个数据集将揭示鱼类之间的多样化模式，并为早期脊椎动物的进化提供重要的见解。线粒体数据，结合最好的系统发育假说，将被用于在系统发育分析中调查核苷酸采样特性。不同数量的物种的亚样本将从73个物种的组中提取。对于每个亚样本，将确定恢复正确的系统发育所需的核苷酸数量，并得到不同程度的支持。我们将研究几个重要的进化参数对系统发育准确性的影响。这些参数包括a)样本中可变核苷酸位置的频率；b)分类群之间的进化差异量；c)所包括的谱系之间的进化率变异量；以及d)抽样分类群之间核苷酸组成偏差的程度和分布。这些结果将有助于更深入地理解核苷酸数据在系统发育分析中的行为，并应确定准确估计系统发育所需的一系列核苷酸样本大小，作为正在调查的类群数量和相关进化条件的函数。这种客观的实验设计标准将为分子系统学领域提供资源预算和分配的指导，并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.