Kohlsdorf Tiana, Cummings Michael P, Lynch Vincent J, Stopper Geffrey F, Takahashi Kazuhiko, Wagner Günter P
Department of Ecology and Evolutionary Biology, Yale University, 165 Prospect Street, New Haven, CT 06520, USA.
J Mol Evol. 2008 Dec;67(6):581-93. doi: 10.1007/s00239-008-9156-7.
The homeobox gene Hoxa-13 codes for a transcription factor involved in multiple functions, including body axis and hand/foot development in tetrapods. In this study we investigate whether the loss of one function (e.g., limb loss in snakes) left a molecular footprint in exon 1 of Hoxa-13 that could be associated with the release of functional constraints caused by limb loss. Fragments of the Hoxa-13 exon 1 were sequenced from 13 species and analyzed, with additional published sequences of the same region, using relative rates and likelihood-ratio tests. Five amino acid sites in exon 1 of Hoxa-13 were detected as evolving under positive selection in the stem lineage of snakes. To further investigate whether there is an association between limb loss and sequence variation in Hoxa-13, we used the random forest method on an alignment that included shark, basal fish lineages, and "eu-tetrapods" such as mammals, turtle, alligator, and birds. The random forest method approaches the problem as one of classification, where we seek to predict the presence or absence of autopodium based on amino acid variation in Hoxa-13 sequences. Different alignments tested were associated with similar error rates (18.42%). The random forest method suggested that phenotypic states (autopodium present and absent) can often be correctly predicted based on Hoxa-13 sequences. Basal, nontetrapod gnat-hostomes that never had an autopodium were consistently classified as limbless together with the snakes, while eu-tetrapods without any history of limb loss in their phylogeny were also consistently classified as having a limb. Misclassifications affected mostly lizards, which, as a group, have a history of limb loss and limb re-evolution, and the urodele and caecilian in our sample. We conclude that a molecular footprint can be detected in Hoxa-13 that is associated with the lack of an autopodium; groups with classification ambiguity (lizards) are characterized by a history of repeated limb loss and possible limb re-evolution.
同源框基因Hoxa - 13编码一种参与多种功能的转录因子，包括四足动物的体轴和手足发育。在本研究中，我们调查了一种功能的丧失（例如蛇类肢体的丧失）是否在Hoxa - 13的外显子1中留下了分子印记，这可能与肢体丧失导致的功能限制的解除有关。从13个物种中对Hoxa - 13外显子1的片段进行测序并分析，结合该区域已发表的其他序列，使用相对速率和似然比检验。在蛇类的主干谱系中，检测到Hoxa - 13外显子1中的五个氨基酸位点在正选择下进化。为了进一步研究肢体丧失与Hoxa - 13序列变异之间是否存在关联，我们在一个包含鲨鱼、基底鱼类谱系以及哺乳动物、龟、短吻鳄和鸟类等“真四足动物”的比对中使用了随机森林方法。随机森林方法将该问题视为一个分类问题，即我们试图根据Hoxa - 13序列中的氨基酸变异来预测是否存在 autopodium。测试的不同比对具有相似的错误率（18.42%）。随机森林方法表明，基于Hoxa - 13序列通常可以正确预测表型状态（存在autopodium和不存在autopodium）。从未有过autopodium的基底非四足有颚脊椎动物与蛇类一起始终被归类为无肢，而在其系统发育中没有任何肢体丧失历史的真四足动物也始终被归类为有肢体。错误分类主要影响蜥蜴，作为一个群体，蜥蜴有肢体丧失和肢体重新进化的历史，以及我们样本中的有尾目动物和蚓螈。我们得出结论，在Hoxa - 13中可以检测到与缺乏autopodium相关的分子印记；具有分类歧义的群体（蜥蜴）的特征是有反复肢体丧失和可能的肢体重新进化的历史。
