Data from: The origin of snakes: revealing the ecology, behavior, and evolutionary history of early snakes using genomics, phenomics, and the fossil record

Background: The highly derived morphology and astounding diversity of snakes has long inspired debate regarding the ecological and evolutionary origin of both the snake total-group (Pan-Serpentes) and crown snakes (Serpentes). Although speculation abounds on the ecology, behavior, and provenance of the earliest snakes, a rigorous, clade-wide analysis of snake origins has yet to be attempted, in part due to a dearth of adequate paleontological data on early stem snakes. Here, we present the first comprehensive analytical reconstruction of the ancestor of crown snakes and the ancestor of the snake total-group, as inferred using multiple methods of ancestral state reconstruction. We use a combined-data approach that includes new information from the fossil record on extinct crown snakes, new data on the anatomy of the stem snakes Najash rionegrina, Dinilysia patagonica, and Coniophis precedens, and a deeper understanding of the distribution of phenotypic apomorphies among the major clades of fossil and Recent snakes. Additionally, we infer time-calibrated phylogenies using both new ‘tip-dating’ and traditional node-based approaches, providing new insights on temporal patterns in the early evolutionary history of snakes. Results: Comprehensive ancestral state reconstructions reveal that both the ancestor of crown snakes and the ancestor of total-group snakes were nocturnal, widely foraging, non-constricting stealth hunters. They likely consumed soft-bodied vertebrate and invertebrate prey that was subequal to head size, and occupied terrestrial settings in warm, well-watered, and well-vegetated environments. The snake total-group – approximated by the Coniophis node – is inferred to have originated on land during the middle Early Cretaceous (~128.5 Ma), with the crown-group following about 20 million years later, during the Albian stage. Our inferred divergence dates provide strong evidence for a major radiation of henophidian snake diversity in the wake of the Cretaceous-Paleogene (K-Pg) mass extinction, clarifying the pattern and timing of the extant snake radiation. Although the snake crown-group most likely arose on the supercontinent of Gondwana, our results suggest the possibility that the snake total-group originated on Laurasia. Conclusions: Our study provides new insights into when, where, and how snakes originated, and presents the most complete picture of the early evolution of snakes to date. More broadly, we demonstrate the striking influence of including fossils and phenotypic data in combined analyses aimed at both phylogenetic topology inference and ancestral state reconstruction.

研究背景：蛇类高度特化的形态特征与惊人的物种多样性，长期以来引发学界围绕蛇类总类群（Pan-Serpentes，泛蛇类）与冠群蛇类（Serpentes，真蛇类）的生态起源与演化起源的广泛争论。尽管学界针对最早期蛇类的生态习性、行为模式与起源地存在诸多推测，但迄今尚未开展过严格的、覆盖全支系的蛇类起源分析，其部分原因在于早期茎干蛇类缺乏足够的古生物学数据支撑。本文首次采用多种祖先状态重建（ancestral state reconstruction）方法，完成了冠群蛇类祖先与蛇类总类群祖先的综合解析重建。本研究采用整合数据策略，纳入了已灭绝冠群蛇类化石记录的新信息、茎干蛇类Najash rionegrina、Dinilysia patagonica与Coniophis precedens的解剖学新数据，以及对化石与现生蛇类主要支系中表型衍征（phenotypic apomorphies）分布的更深入认知。此外，本研究同时采用新型末端定年法（tip-dating）与传统节点定年法（node-based approaches）推断时间校准系统发育树（time-calibrated phylogenies），为蛇类早期演化历史的时间格局提供了新的认知视角。
研究结果：综合祖先状态重建结果显示，冠群蛇类祖先与蛇类总类群祖先均为夜行性、广泛觅食的非绞杀型伏击猎手。它们大概率以体型与头部尺寸相当的软体无脊椎动物与脊椎动物为食，栖息于温暖、湿润且植被繁茂的陆地生境中。以Coniophis分支为代表的蛇类总类群，被推断起源于早白垩世中期（约1.285亿年前）的陆地环境，冠群蛇类则在约2000万年后的阿尔必阶出现。我们推断的分化时间为白垩纪-古近纪（K-Pg）大灭绝后原蛇下目蛇类多样性的大规模辐射提供了有力证据，厘清了现生蛇类辐射演化的模式与时间节点。尽管冠群蛇类大概率起源于冈瓦纳超大陆，但本研究结果表明蛇类总类群可能起源于劳亚大陆。
研究结论：本研究为蛇类起源的时间、地点与方式提供了新的认知视角，并构建了迄今最为完整的蛇类早期演化图景。从更广泛的层面来看，本研究证实了在同时针对系统发育拓扑结构推断与祖先状态重建的整合分析中，纳入化石数据与表型数据所产生的显著影响。