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 Caiman. We analyzed 479 specimens representing all named taxa, with the exception of Caiman crocodilus apaporiensis, and known geographic distribution of these taxa. We observed high lineage diversity within the Caiman crocodilus/yacare complex, ranging from 7 to 10 lineages, and three lineages within Caiman latirostris. 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 Caiman 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.

中文翻译：

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在最广泛的新热带鳄鱼属凯门鳄（鳄鱼，鳄鱼科）中出乎意料但并不令人惊讶的谱系多样性

利用基于聚结的方法的物种发现方法是检测形态保守群体内神秘谱系的有力工具，因此是综合分类学研究的重要方法。鳄鱼是形态学上保守的群体的典型例子，其中基于聚结的物种定界分析导致发现了神秘的谱系和潜在的新物种。在这项研究中，我们使用了几种单基因座物种发现方法来分析新热带地区最广泛的鳄鱼属凯门鳄属的系统发育多样性。我们分析了代表所有命名分类群的 479 个标本，除了凯门鳄 apaporiensis，以及这些分类群的已知地理分布。我们观察到凯门鳄 / yacare 复合体内的高谱系多样性，范围从 7 到 10 个谱系，以及凯门鳄 latirostris 中的三个谱系。我们还为所有划定的谱系提供了新的过时系统发育。渐新世和中新世事件引发了主要谱系的多样化，更新世后期的事件影响了该属的最终多样化。我们证明在凯门鳄复合物中发现的谱系与物种兼容，因此是综合分类学分析的候选者。然而，重要的是要强调，独立于未来将这些谱系识别为物种，保护这些神秘谱系作为独特的进化实体极为重要，其中许多受到大坝建设项目栖息地丧失、尾矿坝倒塌的高度威胁, 采矿,