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

马达加斯加因其本土哺乳动物的高度地方性而闻名。其中，马达加斯加的藤蔓（藤蔓科）以其辐射成鼩鼱状、鼹鼠状、刺猬状和半水生的ecomorphs而闻名。然而，我们对它们在马达加斯加被殖民后的进化和多样化的理解仍然有限。长期以来，田鼠一直与其他小型的、以昆虫为食的哺乳动物，如鼩鼱、鼹鼠和刺猬等，在许多方面都属于半形哺乳动物，并被归入食虫纲。然而，随着系统基因组学数据的出现，我们可以证明，食虫科包含两个甚至不密切相关的胎盘哺乳动物谱系：起源于北部大陆（月牙）的Eulipotyphla（鼩鼱、鼹鼠、刺猬），以及分布在非洲马达加斯加的Afrosoricida （tenrecs、金鼹鼠、水獭鼩）。这进一步表明马达加斯加的节肢动物代表了与北方大陆的鼩鼱、鼹鼠和刺猬相关的趋同进化的一个显著案例。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以及形态进化的速度如何受到定殖后辐射的影响尚不清楚。因此，该项目与野外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形态学谱系的7种tentrec物种的基因组。此外，我们的目标是组装与tenrecs最接近的水獭鼩和半水生高脂鼩鼱的基因组，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长读测序技术和最近开发的计算机配对方法，我们提出了一种全面而具有成本效益的方法，使我们能够(1)重建马达加斯加线虫的系统基因组史；（II）比较藤本植物系统基因组树的形态进化速率；（III）鉴定马达加斯加藤蔓类和月牙虫类（鼩鼱、鼹鼠、刺猬）的全基因组分子趋同/平行性。为了克服先前基于候选基因的趋同分析的缺陷，我们将实施一种全基因组、功能不确定的方法，该方法将考虑背景趋同，并寻求对组织和器官的趋同效应，而不是对单个基因的趋同效应。总之，这些结果有望为形成多样性的进化过程提供新的见解。它们将进一步帮助阐明哺乳动物的分子趋同和形态速率的变化是如何与表型趋同并行的。

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.