Integrating fossils with genomic data to clarify the evolution of the herring-like fishes (Clupeiformes: Clupeoidei)

硬骨鱼亚目（如鲱鱼、沙丁鱼、凤尾鱼）是硬骨鱼的一个大亚目，包括约400种现存的小到中等大小（<50厘米）的远洋鱼类。clupeids的种类具有重要的生态和经济作用，但它们的进化史仍然不清楚，尽管有一个良好的化石记录，包括大约160种基于关节骨骼的物种。这主要是由于对大部分化石物种缺乏详细的分类和系统发育研究。拟议项目的总体目标是将化石和活的棍棒类动物纳入一个统一的、时间校准的系统发育，并推断它们多样化的历史。该项目由两个连续的工作包（WP）组成，其中WP1持续三年，WP2持续两年。当WP1几乎完成时，WP2将开始进行。WP1的具体目标是：(1)基于已选择的化石和现存物种的骨骼特征分析，构建一个新的、全面的数据矩阵；(2)从新的矩阵构建系统发育树；(3)批判性地评估自渐新世和中新世以来化石记录中可观察到的化石物种数量的增加。WP2的具体目标是(i)将现有的分子数据与形态特征矩阵结合起来，（ii）从不同的数据集组合中构建系统发生树，（iii）使用最先进的方法从这些树中推断谱系分化时间，以及（iv）使用新的时间校准系统发生作为多样化模式分析的基础。新的数据将为clupeidei的进化史提供全新的见解，也将为化石记录中没有代表的现存物种的进化提供线索。棍棒类动物的进化目前是鱼类学研究的热门话题，有几个研究小组利用不同的数据来源（DNA、现存物种的形态和古生物学）进行研究。然而，目前还缺乏一种将化石和基因组数据结合起来的综合方法。这个项目旨在填补这一空白，因此预计将得到相当大的注意。

Clupeoidei (e.g. herrings, sardines, anchovies) constitutes a large suborder of teleost fishes, which encompasses some 400 extant, small to moderate-sized (<50 cm) pelagic species. Species of clupeoids play significant ecological and economic roles, but their evolutionary history remains obscure, despite the availability of a good fossil record comprising about 160 species based on articulated skeletons. This is mainly the result of the lack of detailed taxonomic and phylogenetic studies of a large part of the fossil species available. The overall aim of the proposed project is to incorporate fossil and living clupeoids into a unified, time-calibrated phylogeny and infer the history of their diversification. The project is made up of two successive work packages (WP), with WP1 lasting for three years and WP2 for two years. WP2 will get underway when WP1 is virtually complete. The specific objectives of WP1 are (i) to assemble a new, comprehensive data matrix based on analyses of skeletal characters for already selected fossil and extant species, (ii) to construct phylogenetic trees from the new matrix, and (iii) to critically evaluate the increase in numbers of fossil species that is observable in the fossil record since the Oligocene and Miocene. The specific aims of WP2 are (i) to combine available molecular data with the morphological character matrix, (ii) to construct phylogenetic trees from different combinations of datasets, (iii) to infer lineage divergence times from these trees using state-of-the art methods, and (iv) to use the new time-calibrated phylogenies as the basis for the analysis of diversification patterns. The new data will provide completely new insights into the evolutionary history of the Clupeoidei and also shed light on the evolution of extant species that are not represented in the fossil record. Clupeoid evolution is currently a hot topic in ichthyological research, with several groups working with different sources of data (DNA, morphology of extant species, and paleontology). However, an integrative approach, which brings together fossils and genomic data, is currently lacking. This project aims to fill that gap and is therefore expected to receive considerable attention.