Unexpected but unsurprising lineage diversity within the most widespread Neotropical crocodilian genus <i>Caiman</i> (Crocodylia, Alligatoridae)

Species discovery methods utilizing coalescent-based approaches are powerful tools for detecting cryptic lineages within morphological conservative groups, thus being an important methodology of integrative taxonomic research. Crocodilians are a classic example of morphologically conserved group where coalescence-based species delimitation analyses resulted in the discovery of cryptic lineages and potentially new species. In this study, we used several single locus species discovery methods to analyze the phylogenetic diversity of the most widespread alligatorid genus of the Neotropics, the genus <i>Caiman.</i> We analyzed 479 specimens representing all named taxa, with the exception of <i>Caiman crocodilus apaporiensis</i>, and known geographic distribution of these taxa. We observed high lineage diversity within the <i>Caiman crocodilus</i>/<i>yacare</i> complex, ranging from 7 to 10 lineages, and three lineages within <i>Caiman latirostris</i>. We also provide a new dated phylogeny for all the delimited lineages. Oligocene and Miocene events triggered the diversification of the major lineages, with latter Pleistocene events influencing the final diversification of the genus. We demonstrate that the discovered lineages within the <i>Caiman</i> complex are compatible with being species and as such are candidates for an integrated taxonomic analysis. However, it is important to highlight that independent of the future recognition of these lineages as species, it is extremely important to protect these cryptic lineages as unique evolutionary entities, many of which are highly threatened by habitat loss from dam construction projects, tailing dam collapses, mining, agriculture and agricultural run-off across all of South America.

基于溯祖理论（coalescent theory）的物种发现方法，是在形态保守类群中检测隐秘支系（cryptic lineage）的有力工具，亦是整合分类学（integrative taxonomy）研究的重要方法论手段。鳄形目（Crocodilians）是形态保守类群的经典范例，基于溯祖理论的物种界定分析曾在此类群中发现隐秘支系及潜在新物种。本研究采用多种单基因座物种发现方法，对新热带界分布最广的短吻鳄科（Alligatoridae）属类群——凯门鳄属（*Caiman*）的系统发育多样性展开分析。本次分析涵盖了除*Caiman crocodilus apaporiensis*之外的所有已命名分类单元，共计479号标本，并整合了各分类单元的已知地理分布数据。研究团队在眼镜凯门鳄/巴拉圭凯门鳄复合体（*Caiman crocodilus*/*yacare* complex）中检测到极高的支系多样性，支系数量介于7至10个之间；而在宽吻凯门鳄（*Caiman latirostris*）类群中则存在3个支系。本研究同时为所有界定出的支系构建了全新的时间校准系统发育树。渐新世（Oligocene）与中新世（Miocene）的地质事件推动了该属主要支系的分化，而更新世（Pleistocene）后期的事件则对该属支系的最终分化产生了重要影响。本研究证实，凯门鳄属复合体中发现的支系符合物种界定标准，因此可作为整合分类学分析的候选研究对象。但需着重强调的是，无论未来是否将这些支系正式认定为物种，将这些隐秘支系作为独特的进化实体加以保护都极为重要——在整个南美洲范围内，诸多此类支系正面临着来自大坝建设、尾矿坝溃坝、采矿、农业活动及农业径流所导致的栖息地丧失的严重威胁。

搜集汇总

背景与挑战

背景概述

该数据集基于对凯门鳄属的系统发育研究，通过分析479个标本，发现Caiman crocodilus/yacare复合体存在7-10个隐性谱系，Caiman latirostris存在3个谱系，并提供了新的时间校准系统发育树。研究强调这些谱系可能是新物种，并呼吁保护这些受栖息地丧失威胁的独特进化实体。数据集包含三个Excel文件，涵盖遗传和进化数据，适用于物种发现和保育研究。