Data from: Deep evolutionary roots of diet in seagrass bed fishes

Provided here are the datasets and R code for the study entitled "Deep evolutionary roots of diet in seagrass bed fishes". Summary of the study: Diet is a fundamental ecological trait of species that defines their roles in food webs and in regulating the functions of natural ecosystems. How diet has been shaped over deep evolution remains poorly understood, especially for marine species. Using a series of phylogenetic comparative analyses, we investigated conservatism and divergences in the diet evolution of fishes associated with seagrass beds globally. We find strong conservatism in fish trophic level, with closely related fishes being more trophically similar. However, rare, but profound diet divergences took place following seagrass recolonization of the ocean and diverfication around 70-100 mya. Furthermore, phylogeny explains >60% of the variation in diet composition, even when morphological, ecological, and geographical covariates are accounted for. These results highlight the importance of evolutionary history in shaping diet and provide a conciliation for diet divergence versus conservatism from a group of globally distributed and ecologically and economically important species. #####Files ordered by file name###### # all_covariates.xlsx This file contains the data of ecological, geographical, and morphological covariates. # diet.xlsx This file contains the data of fish diet compositions extracted from FishBase. #final.R This file contains the R code (version 1) to conduct all the analyses in our study. #final_tree.nex This file contains the time-calibrated phylogeny we produced using BEAST. #o_finaltree.phy This file contains the reduced tree of the final_tree.nex for fish species that were reported in FishBase to be associated only with seagrass beds. #regimes.xlsx This file contains the assumed regimes to reconstruct a MOU model. #seq_id.xslx This file contains the sequence ID for the genetic sequences used to construct the phylogeny. #species_list.xlsx This file contains the scientific names and their taxonomy. #tree_mr.csv This file contains the matrix representing the phylogenetic relationship produced by compute.mr() in phytools. #trophic_level.xlsx This file contains the trophic level data of fish species estimated using dietr. The metadata for interpreting the data in the Excel files are included in the Metadata sheet.

本资源提供了题为《海草床鱼类食性的深层演化起源》的研究相关数据集与R代码。
研究概述：食性是物种的核心生态性状，决定了其在食物网中的生态位以及对自然生态系统功能的调控作用。目前学界对食性在深层演化历程中的塑造机制仍知之甚少，针对海洋物种的相关研究尤为匮乏。本研究通过一系列系统发育比较分析，对全球范围内与海草床相关的鱼类的食性演化保守性与分化模式展开探究。
研究结果显示，鱼类的营养级存在显著的演化保守性，亲缘关系越近的鱼类，其营养级相似性越高。然而，在约7000万至1亿年前海洋重新被海草床定植并发生辐射演化后，鱼类食性出现了罕见但影响深远的分化。此外，即便在控制形态、生态与地理协变量的情况下，系统发育仍可解释食性组成60%以上的变异。本研究结果凸显了演化历史在塑造物种食性中的重要性，并为全球分布广泛、兼具生态与经济价值的鱼类类群的食性分化与保守性之间的矛盾提供了调和方案。
#####按文件名排序的文件#####
# all_covariates.xlsx 该文件包含生态、地理与形态协变量数据。
# diet.xlsx 该文件包含从FishBase（全球鱼类数据库）中提取的鱼类食性组成数据。
# final.R 该文件包含用于复现本研究所有分析的R代码（版本1）。
# final_tree.nex 该文件包含我们使用BEAST构建的时间校准系统发育树。
# o_finaltree.phy 该文件包含final_tree.nex的精简版系统发育树，对应仅在FishBase中被记录为仅与海草床相关的鱼类物种。
# regimes.xlsx 该文件包含用于构建多变量奥尔特-乌伦贝克（MOU）模型的预设演化状态区域数据。
# seq_id.xslx 该文件包含用于构建系统发育树的遗传序列的序列ID。
# species_list.xlsx 该文件包含鱼类的学名及其分类学信息。
# tree_mr.csv 该文件包含由phytools包中compute.mr()函数生成的系统发育关系矩阵。
# trophic_level.xlsx 该文件包含使用dietr包估算的鱼类物种营养级数据。
所有Excel文件的元数据均包含在Metadata工作表中。