Mitochondrial DNA sequences and multiple data sets: a phylogenetic study of phytophagous beetles (Chrysomelidae: Ophraella).
Mitochondrial DNA sequences and multiple data sets: a phylogenetic study of phytophagous beetles (Chrysomelidae: Ophraella).
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线粒体 DNA 序列和多个数据集：植食性甲虫（叶甲科：Ophraella）的系统发育研究。
DOI：
10.1093/oxfordjournals.molbev.a040242
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发表时间：
1995
影响因子：
10.7
通讯作者：
A. Meyer
中科院分区：
文献类型：
--
作者：
D. J. Funk;D. Futuyma;G. Ortí;A. Meyer
本文介绍了系统发育的基础设施，为综合历史和实验研究的主机使用进化的chrysomelid叶甲属Ophraella。我们报告的16S核糖体RNA（446 bp）和细胞色素氧化酶亚基I（420 bp）的线粒体基因的序列数据收集的12种Ophraella和两个外类群。序列分析表明，一个强大的A + T核苷酸的偏见，高种间COI序列的分歧（高达21.4%），大大超过了16 S（高达5.9%），高种内COI分歧（高达3.8%），缺乏氨基酸取代COI，和不同的取代模式，在核糖体茎和环。COI单倍型的种内变异普遍支持Ophraella谱系的系谱一致性，同时表明两种并系种的情况。16S和COI数据集的单独系统发育分析产生了很大程度上一致的树。一个组合的16S + COI分析产生了一个最短的树下的最大简约，是相同的树提供的逐次逼近，相邻连接，和最大似然方法。这种拓扑结构被证明对各种形式的加权是鲁棒的，并且大多数节点都得到了高度支持（通过自助分析）。线粒体DNA和以前收集的形态学和电形态学数据集的单独简约分析显示，除了一个分支内的所有分支关系一致的估计。合并的数据集的分析，另外提供了支持的基础放置两个物种从这个分支，虽然其余物种的拓扑结构弱支持和不一致的线粒体DNA树。每个数据集包含显着结构化的系统发育信号相对于这个分支，和数据集表现出有限的冲突（字符不一致）彼此。然而，合并后的数据集被发现缺乏系统发育信号。这些观察结果可能意味着汇集异质进化的数据类掩盖了每个系统发育信号，这是组合方法的潜在限制。
This paper presents the phylogenetic infrastructure for an integrated historical and experimental study of host use evolution in the chrysomelid leaf beetle genus Ophraella. We report the collection of sequence data from the 16S ribosomal RNA (446 bp) and the cytochrome oxidase subunit I (420 bp) mitochondrial genes from 12 species of Ophraella and two outgroups. Sequence analysis revealed a strong A + T nucleotide bias, high interspecific COI sequence divergences (up to 21.4%) that greatly exceeded those for 16S (up to 5.9%), high intraspecific COI divergences (up to 3.8%), a dearth of amino acid substitutions in COI, and differing substitution patterns in ribosomal stems and loops. Intraspecific variation in COI haplotypes generally supported the genealogical coherence of Ophraella lineages, while suggesting two cases of paraphyletic species. Separate phylogenetic analyses of 16S and COI data sets yielded largely congruent trees. A combined 16S + COI analysis yielded a single shortest tree under maximum parsimony that was identical to trees provided by successive approximations, neighbor-joining, and maximum-likelihood methods. This topology proved robust to various forms of weighting and most nodes were highly supported (by bootstrap analysis). Separate parsimony analyses of mtDNA and previously collected morphological and electromorphic data sets revealed congruent estimates of all cladistic relationships except those within one clade. Analysis of the pooled data sets in a combined approach additionally provided support for the basal placement of two species from this clade, although the topology for the remaining species was weakly supported and incongruent with the mtDNA tree. Each data set contained significantly structured phylogenetic signal with respect to this clade, and data sets exhibited limited conflict (character incongruence) with each other. The combined data set, however, was found to lack phylogenetic signal. These observations may imply that pooling heterogeneously evolving classes of data obscured the phylogenetic signal in each, a potential limitation of the combined approach.