Phylogenetic relationships among the phrynosomatid sand lizards inferred from mitochondrial DNA sequences generated by heterogeneous evolutionary processes.
Phylogenetic relationships among the phrynosomatid sand lizards inferred from mitochondrial DNA sequences generated by heterogeneous evolutionary processes.
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根据异质进化过程产生的线粒体 DNA 序列推断出蜥蜴之间的系统发育关系。
DOI：
10.1080/10635159950127411
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发表时间：
2000
影响因子：
6.5
通讯作者：
Kevin de Queiroz
中科院分区：
文献类型：
--
作者：
James C. Wilgenbusch;Kevin de Queiroz
线粒体蛋白编码细胞色素B（cyt B; 650 bp）和小亚基12 S核糖体RNA（约350 bp）基因的核苷酸序列被用于分析现存的沙蜥的系统发育关系，包括检查关于“无穗”进化的竞争假说。“序列是从所有目前公认的沙蜥蜴物种以及第一和第二外群的代表中获得的，并使用简约法和似然法进行分析。cyt B数据提供了强有力的支持，对应于相对较新的分歧和中度至低的支持关系，反映更古老的分歧内的分支。这些数据支持单系的“无耳”类群，放置乌玛作为姐妹类群的其他沙蜥蜴，和单系的所有四个类群传统上列为属。所有支持的关系在12 S染色体组中是完全一致的支持的关系在细胞色素B染色体组中，然而，12 S数据单独提供很少的支持更深层次的分歧。物种内的系统发育关系与地理一致，并建议模式的地理分化，包括结论，至少有一个目前公认的物种（Holbrookia maculata）实际上包括一个以上的物种。通过独立地优化各种数据子集的似然模型参数，我们发现核苷酸取代过程在基因之间以及在每个基因内的结构和功能区域或位点类别之间变化很大。因此，我们比较了竞争的系统发育假说，使用特定于这些子集的参数估计，分别分析子集和各种组合。在对整个数据集（包括最能解释数据的分区集）进行的5次比较中，除一次外，所有其他比较中cyt B数据支持的假设均优于竞争性假设，尽管我们无法自信地拒绝（P < 0.05）备择假设。我们的研究结果突出了优化模型和参数估计的重要性，为不同的基因或其部分-一种策略，利用合并和分区数据的优势。
Nucleotide sequences of the mitochondrial protein coding cytochrome b (cyt b; 650 bp) and small-subunit 12S ribosomal RNA (approximately 350 bp) genes were used in analyses of phylogenetic relationships among extant phrynosomatid sand lizards, including an examination of competing hypotheses regarding the evolution of "earlessness." Sequences were obtained from all currently recognized species of sand lizards as well as representatives of the first and second outgroups and analyzed using both parsimony and likelihood methods. The cyt b data offer strong support for relationships that correspond with relatively recent divergences and moderate to low support for relationships reflecting more ancient divergences within the clade. These data support monophyly of the "earless" taxa, the placement of Uma as the sister taxon to the other sand lizards, and monophyly of all four taxa traditionally ranked as genera. All well-supported relationships in the 12S phylogeny are completely congruent with well-supported relationships in the cyt b phylogeny; however, the 12S data alone provide very little support for deeper divergences. Phylogenetic relationships within species are concordant with geography and suggest patterns of phylogeographic differentiation, including the conclusion that at least one currently recognized species (Holbrookia maculata) actually consists of more than one species. By independently optimizing likelihood model parameters for various subsets of the data, we found that nucleotide substitution processes vary widely between genes and among the structural and functional regions or classes of sites within each gene. Therefore, we compared competing phylogenetic hypotheses, using parameter estimates specific to those subsets, analyzing the subsets separately and in various combinations. The hypothesis supported by the cyt b data was favored over rival hypotheses in all but one of the five comparisons made with the entire data set, including the set of partitions that best explained the data, although we were unable to confidently reject (P < 0.05) alternative hypotheses. Our results highlight the importance of optimizing models and parameter estimates for different genes or parts thereof--a strategy that takes advantages of the strengths of both combining and partitioning data.
线粒体 DNA 中取代率的逐位估计和速率相关性。
影响因子：
6.5
作者：
Nielsen,R
通讯作者：
Nielsen,R