Data from: Evolution of the snake body form reveals homoplasy in amniote Hox gene function

Hox genes regulate regionalization of the axial skeleton in vertebrates, and changes in their expression have been proposed to be a fundamental mechanism driving the evolution of new body forms. The origin of the snake-like body form, with its deregionalized pre-cloacal axial skeleton, has been explained as either homogenization of Hox gene expression domains9, or retention of standard vertebrate Hox domains with alteration of downstream expression that suppresses development of distinct regions. Both models assume a highly regionalized ancestor, but the extent of deregionalization of the primaxial domain (vertebrae, dorsal ribs) of the skeleton in snake-like body forms has never been analysed. Here we combine geometric morphometrics and maximum-likelihood analysis to show that the pre-cloacal primaxial domain of elongate, limb-reduced lizards and snakes is not deregionalized compared with limbed taxa, and that the phylogenetic structure of primaxial morphology in reptiles does not support a loss of regionalization in the evolution of snakes. We demonstrate that morphometric regional boundaries correspond to mapped gene expression domains in snakes, suggesting that their primaxial domain is patterned by a normally functional Hox code. Comparison of primaxial osteology in fossil and modern amniotes with Hox gene distributions within Amniota indicates that a functional, sequentially expressed Hox code patterned a subtle morphological gradient along the anterior–posterior axis in stem members of amniote clades and extant lizards, including snakes. The highly regionalized skeletons of extant archosaurs and mammals result from independent evolution in the Hox code and do not represent ancestral conditions for clades with snake-like body forms. The developmental origin of snakes is best explained by decoupling of the primaxial and abaxial domains and by increases in somite number, not by changes in the function of primaxial Hox genes.Hox基因（Hox gene）可调控脊椎动物轴骨的区域特化，其表达模式的改变被认为是驱动新型躯体形态演化的核心机制。针对伴随泄殖腔前轴骨区域化缺失的蛇形躯体起源，既往研究提出两种解释：一是Hox基因表达域的同质化⁹，二是保留脊椎动物标准Hox表达域，但通过改变下游表达以抑制特定区域的发育。两类模型均假设祖先类群的轴骨具有高度区域化特征，但蛇形躯体类群中骨骼原轴域（primaxial domain，即椎骨与背肋）的区域化缺失程度，此前从未被系统分析过。 本研究结合几何形态测量学（geometric morphometrics）与最大似然分析（maximum-likelihood analysis），结果显示：与具附肢的类群相比，长身、附肢退化的蜥蜴与蛇类的泄殖腔前原轴域并未出现区域化缺失；爬行类原轴形态的系统发育结构，也不支持蛇类演化过程中存在区域化程度降低的现象。本研究证实，形态学的区域边界与蛇类中已定位的基因表达域相匹配，这表明其原轴域由正常发挥功能的Hox密码（Hox code）所调控。 通过对比化石与现生羊膜动物（amniote）的原轴骨学特征，结合羊膜动物类群内的Hox基因分布数据，本研究表明：具备序列表达功能的Hox密码，在羊膜类支系的基干类群与现生蜥蜴（包括蛇类）中，沿前后体轴构建了细微的形态梯度。现生主龙类（archosaurs）与哺乳类的高度区域化骨骼，是Hox密码独立演化的结果，并不代表蛇形躯体类群的祖先状态。蛇类的发育起源，最佳解释应为原轴域与轴旁域（abaxial domain）的解耦以及体节（somite）数量的增加，而非原轴Hox基因功能的改变。