The evolution and phenotypic convergence in Malagasy tenrecs (Afrosoricida, Tenrecidae): a combined molecular and morphological perspective

马达加斯加以其本土哺乳动物的高度地域性而闻名于世。其中，马达加斯加石龙科(Tenresidae)因其辐射到类地鼠、类鼹鼠、类刺猬和半水生态而出类拔萃。然而，我们对马达加斯加殖民后它们的演变和多样化的了解仍然有限。Tenrecs长期以来一直与其他小型、以昆虫为食的、在许多方面具有多形性的哺乳动物，如地鼠、鼹鼠和刺猬结合在一起，归入食虫纲。然而，随着系统基因组数据的出现，可能表明食虫目包含两个甚至不是密切相关的胎盘哺乳动物谱系：起源于北部大陆(劳亚大陆)的Eulipotyphla(地鼠、鼹鼠、刺猬)和具有非洲-马达加斯加分布的AFrosoricida(田鼠、金鼹鼠、水獭)。这进一步表明，马达加斯加的Tenrec生态形体代表了北方大陆的地鼠、鼹鼠和刺猬的汇聚进化的一个明显例子。由于系统发育问题和缺乏分子资源，这种表型趋同背后的基因组基础和形态进化速度如何受到殖民后辐射的影响尚不清楚。因此，该项目与实地生物学家和生物信息学家合作，旨在重新组装涵盖所有系统发育和生态谱系的七个Tenrec物种的基因组。此外，我们的目标是组装一种水獭的基因组，作为与Tenrecs最接近的一种，以及一种半水生的Eulipotyphlan地鼠的基因组，以补充我们广泛的比较基因组样本。通过结合最先进的PacBio Hifi长阅读测序技术和最近开发的电子配对方法，我们提出了一种全面但具有成本效益的方法，该方法将使我们能够(I)重建马达加斯加藤类的系统发育历史；(Ii)比较藤类系统树上的形态进化速度；以及(Iii)鉴定马达加斯加藤类和劳拉西亚食虫动物(地鼠、鼹鼠、刺猬)之间的全基因组分子趋同/并行性。为了克服以前基于候选的收敛分析的缺陷，我们将实施一种全基因组、功能不可知的方法，该方法将考虑背景收敛，并寻求对组织和器官的收敛效应，而不是对单个基因的收敛效应。总而言之，这些结果有望为形成多样性的进化过程提供新的见解。他们将进一步帮助阐明表型趋同是如何与哺乳动物之间的分子趋同和形态比率的变化平行的。

Madagascar is renowned for the strikingly high endemicity of its native mammalian fauna. Among this, Malagasy tenrecs (Tenrecidae) are outstanding for their radiation into shrew-like, mole-like, hedgehog-like and semiaquatic ecomorphs. Yet, our understanding of their evolution and diversification after the colonization of Madagascar is still limited. Tenrecs have long been united with other small-sized, insect-feeding and in many aspects plesiomorphic mammals, such as shrews, moles and hedgehogs, into the taxon Insectivora. With the emergence of phylogenomic data, however, it could be shown that Insectivora contains two, not even closely related lineages of placental mammals: the Eulipotyphla (shrews, moles, hedgehogs) that originated on northern continents (Laurasia), and the Afrosoricida (tenrecs, golden moles, otter shrews) with Afro-Malagasy distribution. This further implies that Malagasy tenrec ecomorphs represent a conspicuous case of convergent evolution with regards to shrews, moles and hedgehogs of northern continents. Due to phylogenetic issues and the lack of molecular resources, the genomic basis behind this phenotypic convergence and how rates of morphological evolution were affected by post-colonization radiation is poorly understood. In collaboration with field biologists and bioinformaticians, this project therefore aims to de-novo assemble the genomes of seven tenrec species covering all phylogenetic and ecomorphological lineages. In addition, we aim to assemble the genomes of an otter shrew as closest relative to tenrecs and a semi-aquatic eulipotyphlan shrew to complement our extensive comparative genomic sample. By combining state-of-the-art PacBio Hifi long-read sequencing technologies and recently developed in-silico mate-pair approaches, we propose a comprehensive yet cost-effective approach that will enable us (I) to reconstruct the phylogenomic history of Malagasy tenrecs; (II) to compare the rates of morphological evolution along the phylogenomic tree of tenrecs; and (III) to identify genome-wide molecular convergence/parallelism among Malagasy tenrecs and Laurasian insectivorans (shrews, moles, hedgehogs). To overcome the pitfalls of previous candidate-based convergence analyses, we will implement a genome-wide, functionally agnostic approach that will take background convergence into account and that seeks for convergent effects on tissues and organs rather than on individual genes. Altogether, the results are expected to provide novel insights into the evolutionary processes that shaped the diversity. They will further help to elucidate how phenotypic convergence is paralleled by molecular convergence and shifts in morphological rates among mammals.