Putting fish fossils in trees: using advanced phylogenetic methods to co-estimate the phylogeny and temporal diversification patterns of living and fossil Gobioidei

虾虎鱼是小型底栖鱼类，是硬骨鱼类中最大的亚目之一，现存约2200种。它们是浅海、河口和淡水生态系统的重要组成部分，对研究进化过程特别有吸引力，因为它们显示出许多适应性。然而，很少有人知道他们的进化历史，尽管有一个很好的化石记录，包括约25种基于骨骼和约60种基于孤立的耳石（耳石）。该项目的目的是利用虎鱼的形态特征，将化石和活的类群联系在一个统一的、有时间尺度的进化史中，并推断它们的多样化历史。将根据所有已知化石分类群和所有现存科和谱系的代表的骨架、鳞片和耳石特征编制一个矩阵，并将apogonids和kurtids作为外群;将为现存物种添加可用的分子数据。特别注意将给予系统发育信息的耳石字符的识别，因为耳石以前从未被用于系统发育分析。将（i）对形态学数据，（ii）对形态学数据与DNA序列数据的组合，以及（iii）通过添加形态学数据集中未显示的分类群的可用DNA序列数据，进行简约性、最大似然和贝叶斯分析。结果将使用化石限制的“尖端测年”进行分析，这是一种评估系统发育节点年龄的新方法。传统的系统发育年代测定方法仅使用化石作为日期校准;化石不直接包括在定年的系统发育中。在尖端年代测定中，带有编码形态学数据的化石标本作为尖端被包括在树中，沿着来自活物种标本的DNA和形态学。化石和现存物种的系统发育关系，然后估计同时在树中的物种形成事件的日期。尖定年的虎鱼树将建立一个新的时间框架虎鱼的进化。目前有几个研究小组正在研究虾虎鱼的分子遗传和进化，我们的化石和分子数据的结合将是一个令人兴奋的方法，以显着推进这一科学领域。此外，这个项目将是第一个主要的小费约会研究之一，并会得到很多关注的结果。

Gobioids are small benthic fishes that constitute one of the largest suborders of teleost fishes, with about 2200 extant species. They form a significant component of shallow marine, estuarine and freshwater ecosystems and are particularly attractive for studying evolutionary processes because they display numerous adaptations. However, little is known about their evolutionary history despite the availability of a good fossil record comprising about 25 species based on skeletons and about 60 species based on isolated otoliths (ear stones). The objective of the proposed project is to use morphological characters of gobioids to link fossil and living taxa in a unified, time-scaled phylogeny and infer their history of diversification. A matrix will be prepared based on skeleton, scale and otolith characters for all known fossil taxa and for representatives from all living families and lineages, with apogonids and kurtids as outgroups; available molecular data will be added for the extant species. Special attention will be given to the identification of phylogenetic informative otolith characters because otoliths have never before been used in phylogenetic analyses. Parsimony, maximum-likelihood and Bayesian analyses will be performed (i) for the morphological data, (ii) for the morphological data in combination with the DNA sequence data, and (iii) by adding available DNA sequence data from taxa not represented in the morphological dataset. The outcome will be analysed using fossil constrained "tip-dating", which is a novel method for assessing phylogenetic node ages. Traditional phylogenetic dating methods use fossils only as date calibrations; the fossils are not included directly in the dated phylogeny. In tip-dating, fossil specimens with coded morphological data are included as tips in the tree, along with DNA and morphology from specimens of living species. The phylogenetic relationships of the fossils and living species are then estimated simultaneously with the dates of speciation events in the tree. Tip-dating the gobioid tree will establish a new temporal framework for gobioid evolution. Several groups are currently studying the molecular phylogeny and evolution of gobioids, and our combination of fossil and molecular data will be an exciting approach to significantly advance this field of science. Moreover, this project will be one of the first major tip-dating studies, and will get a lot of attention as a result.