Integrating phylogenomics, natural history collection holdings, innovative morphology and paleontological data - The phylogeny and evolution of adephagan beetles as a case study

在过去的几十年里，分子系统学取得了巨大的进步。对六足类进化的研究在最近发表的一项研究中达到了高潮，该研究基于100多个末端分类群(1KITE)的1478个同源基因。同样，形态技术也得到了极大的改进，导致了对结构特征和一门被称为“进化形态学”的学科的探索的复兴。这些进展与对非常丰富的化石收藏的深入调查相结合，特别是在中国和俄罗斯的机构，为重建巨型六足动物的进化开辟了新的视角。这里我们使用的是Adephaga亚目的甲虫(45,000种。)作为一个典型案例。它们进化的一个耐人寻味的方面是，它们出现在非常不同的栖息地：陆生、湿润和水生。导致显著的生态多样性的进化模式仍然不够清楚。陆栖步甲科(Adephaga)最大的科(约38,000种)。然而，十个科中有八个是水生或半水栖(湿润生境)，它们在形态和生活方式上有令人印象深刻的多样性，包括显著不同的幼虫习性(例如，摄食和呼吸)和游泳适应(从完全缺乏到非常有效)。关于不同亚群的形态和分类的大量研究以及基于形态的系统发育学都是可用的。然而，基于分子数据的系统发育研究仍然不令人满意，结果相互矛盾(基于形态的树也是如此)，并且没有令人信服的系统发育覆盖所有主要的谱系，具有足够的分类样本。基因组分析缺失，基于可靠的系统发育假说和对彻底调查的化石进行校准的对进化史的正式评估仍然不足。该项目提出，她的目标是采用综合办法解决该群体的进化问题(主要侧重于水生科)，包括对基因组数据进行分类全面采样，利用创新技术(例如X射线显微断层照相术)提供广泛的形态证据，以及对丰富的化石记录进行新的评价。我们将为Adephaga开发一个目标DNA浓缩工作流程，这将在经济上补充转录组数据，并帮助将现有的收集与系统基因组管道连接起来。因此，项目目标是：使用Adephaga强大的、时间校准的系统发育推断来测试其形态和生态转变的假说；为常规将现有组织纳入系统发育分析提供工具，从而提出一种整合分子系统学、创新形态和广泛的古生物学数据的方法。

Molecular systematics has made a tremendous progress in the last decades. The investigation of the evolution of Hexapoda culminated with a recently published study based on 1,478 orthologous genes of more than 100 terminal taxa (1KITE). Similarly, morphological techniques have been greatly improved leading to a renaissance of the exploration of structural features and a discipline referred to as "Evolutionary Morphology". These advances combined with an intensified investigation of very rich fossil collections, especially in Chinese and Russian institutions, open new perspectives to reconstruct the evolution of megadiverse Hexapoda. Here we use beetles of the suborder Adephaga (45,000 spp.) as a model case. One of the intriguing aspects of their evolution is that they occur in very diverse habitats: terrestrial, hygropetric, and aquatic. The evolutionary pattern leading to the remarkable ecological versatility is still insufficiently understood. The terrestrial Carabidae are the largest family of Adephaga (ca. 38,000 spp.). However, eight of the ten families are aquatic or semiaquatic (hygropetric habitats), with an impressive diversity in their morphology and life styles, including remarkably different larval habits (e.g., feeding and breathing) and swimming adaptations (from lacking completely to extremely efficient). A large number of studies dealing with the morphology and taxonomy of different subgroups are available as well as morphology-based phylogenies. However, phylogenetic investigations based on molecular data are still unsatisfying, with conflicting results (also with morphology-based trees) and no convincing phylogeny covering all major lineages with a sufficient taxonomic sampling. Genomic analyses are missing and a formal evaluation of the evolutionary history based on a robust phylogenetic hypothesis and calibration with thoroughly investigated fossils is still wanting. The project proposed her aims to address the evolution of the group (with a main focus on the aquatic families) using an integrative approach, including taxonomically comprehensive sampling of genomic data, extensive morphological evidence using innovative techniques (e.g., x-ray microtomography), and a new evaluation of the rich fossil record. We will develop a target DNA enrichment workflow for Adephaga, which will economically complement transcriptome data, and help to link existing collections to the phylogenomic pipeline.The project goals are therefore: Use a robust, time calibrated phylogenetic inference for Adephaga to test hypotheses of their morphological and ecological transitions; provide the tools for routine incorporation of existing tissues in phylogenomic analyses and thus present an approach integrating molecular systematics, innovative morphology and extensive paleontological data.