Engstrom Tag N, Shaffer H Bradley, McCord William P
Center for Population Biology and Section of Evolution and Ecology, University of California, Davis, CA 95616, USA.
Syst Biol. 2004 Oct;53(5):693-710. doi: 10.1080/10635150490503053.
We present a phylogenetic hypothesis and novel, rank-free classification for all extant species of softshell turtles (Testudines:Trionychidae). Our data set included DNA sequence data from two mitochondrial protein-coding genes and a approximately 1-kb nuclear intron for 23 of 26 recognized species, and 59 previously published morphological characters for a complimentary set of 24 species. The combined data set provided complete taxonomic coverage for this globally distributed clade of turtles, with incomplete data for a few taxa. Although our taxonomic sampling is complete, most of the modern taxa are representatives of old and very divergent lineages. Thus, due to biological realities, our sampling consists of one or a few representatives of several ancient lineages across a relatively deep phylogenetic tree. Our analyses of the combined data set converge on a set of well-supported relationships, which is in accord with many aspects of traditional softshell systematics including the monophyly of the Cyclanorbinae and Trionychinae. However, our results conflict with other aspects of current taxonomy and indicate that most of the currently recognized tribes are not monophyletic. We use this strong estimate of the phylogeny of softshell turtles for two purposes: (1) as the basis for a novel rank-free classification, and (2) to retrospectively examine strategies for analyzing highly homoplasious mtDNA data in deep phylogenetic problems where increased taxon sampling is not an option. Weeded and weighted parsimony, and model-based techniques, generally improved the phylogenetic performance of highly homoplasious mtDNA sequences, but no single strategy completely mitigated the problems of associated with these highly homoplasious data. Many deep nodes in the softshell turtle phylogeny were confidently recovered only after the addition of largely nonhomoplasious data from the nuclear intron.
我们提出了一个系统发育假说以及针对所有现存鳖科物种（龟鳖目：鳖科）的全新、无等级分类。我们的数据集包括来自26个已确认物种中23个物种的两个线粒体蛋白质编码基因的DNA序列数据以及一个约1千碱基的核内含子，还有另外24个物种补充数据集的59个先前发表的形态学特征。该组合数据集为这个全球分布的龟类分支提供了完整的分类学覆盖，不过有少数分类单元的数据不完整。尽管我们的分类抽样是完整的，但大多数现代分类单元是古老且分歧很大的谱系的代表。因此，由于生物学现实，我们的抽样在一个相对较深的系统发育树中包含了几个古老谱系的一个或几个代表。我们对组合数据集的分析得出了一组得到充分支持的关系，这与传统鳖类系统学的许多方面一致，包括圆鳖亚科和鳖亚科的单系性。然而，我们的结果与当前分类学的其他方面存在冲突，表明目前大多数公认的族并非单系的。我们将这种对鳖科系统发育的有力估计用于两个目的：（1）作为全新无等级分类的基础，（2）回顾性地研究在增加分类单元抽样不可行的深度系统发育问题中分析高度同塑的线粒体DNA数据的策略。去除冗余和加权简约法以及基于模型的技术，总体上提高了高度同塑的线粒体DNA序列的系统发育性能，但没有单一策略能完全缓解与这些高度同塑数据相关的问题。只有在加入来自核内含子的基本非同塑数据后，鳖科系统发育中的许多深层节点才得到可靠恢复。
