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 trait of fish that defines their roles in food webs and in regulating the functions of aquatic ecosystems. The role of evolutionary history, including conservatism and divergence, in diet shaping is poorly understood, especially for fish living in marine ecosystems such as seagrass beds. Using a series of phylogenetic comparative analyses, we investigate conservatism and divergence in the diet of fishes associated with seagrass beds globally over deep evolutionary time. We find that the trophic levels of seagrass bed fishes exhibit a strong phylogenetic pattern, with closely related fishes being more trophically similar. This phylogenetic pattern is also supported by macroevolutionary model inferences, with major diet divergences occurring deep in history. Consistently, phylogenetic relationships explain ~ 60% of the variation in the diet composition of seagrass bed fishes, whereas contemporary morphological, ecological, and geographical factors explain ~ 5% in total. These results reveal that the diet of seagrass bed fishes has been shaped by general conservatism, with rare divergences leading to abrupt diet shifts. Our study fills a key gap in understanding the shaping of fish diet in seagrass beds and suggests that diet specialists represent products of long-term evolution and have irreplaceable functions, warranting priority conservation. #####Files order by names###### # ALL (folder): the dataset and code used to perform the main analysis. ## ALL.R: the R code to conduct the analysis in our research except for data collection. ## all_covariates.xlsx: this file contains the data used for CPO and VPA in our analysis, including the variables representing ecological, geographical, and morphological factors. ## diets.xlsx: this file contains the diet compositions of the fishes extracted from Fishbase. ## ref.tre: the time-calibrated phylogeny used in our analysis (extracted from Rabosky et al. 2018). ## tree_mr.xlsx: this file contains the matrix representing the phylogenetic relationship produced by compute.mr() in phytools. ## trophic_level.xlsx: the trophic level of species estimated by dietr, using the data of diet composition. #Family10 (folder): the dataset and code used to perform the sub-analysis, which contains the data of all the fishes from families where the proportion of seagrass bed fishes exceeds 10%. ## diets.xlsx: this file contains the diet compositions of the fishes extracted from Fishbase. ## Family10.R: the R code to conduct the sub-analysis except for data collection. ## ref.tre: the time-calibrated phylogeny used in the sub-analysis (extracted from Rabosky et al. 2018). ## tree_mr.xlsx: this file contains the matrix representing the phylogenetic relationship produced by compute.mr() in phytools. ## trophic_level.xlsx: the trophic level of species estimated by dietr, using the data of diet composition. #JUV (folder): the dataset and code used to perform the sub-analysis, which contains the data of juveniles and recruits for the fishes included in our main analysis. ## diets.xlsx: this file contains the diet compositions of the fishes, extracted from Fishbase. ## JUV.R: the R code to conduct the sub-analysis except for data collection. ## ref.tre: the time-calibrated phylogeny used in the sub-analysis (extracted from Rabosky et al. 2018). ## tree_mr.xlsx: this file contains the matrix representing the phylogenetic relationship produced by compute.mr() in phytools. ## trophic_level.xlsx: the trophic level of species estimated by dietr, using the data of diet composition. #OSGB (folder): the dataset and code used to perform the sub-analysis, which contains data of adult fishes that were identified by the IUCN, for which seagrass beds serve as habitats of major importance. ## diets.xlsx: this file contains the diet compositions of the fishes extracted from Fishbase. ## OSGB.R: the R code to conduct the sub-analysis except for data collection. ## ref.tre: the time-calibrated phylogeny used in the sub-analysis (extracted from Rabosky et al. 2018). ## tree_mr.xlsx: this file contains the matrix representing the phylogenetic relationship produced by compute.mr() in phytools. ## trophic_level.xlsx: the trophic level of species estimated by dietr, using the data of diet composition. #species_list_of_each_dataset.xlsx: this file contains the species lists for the main analysis and each sub-analysis. 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根源》的研究相关数据集与R代码。 研究摘要：食性是鱼类的核心性状之一，决定了其在食物网中的生态位角色以及水生生态系统功能的调控路径。学界对演化历史（包括演化保守性与趋异）在塑造鱼类食性中的作用尚缺乏深入认知，尤其是对于海草床等海洋生态系统中的鱼类类群。本研究借助一系列系统发育比较分析（phylogenetic comparative analyses）方法，探究全球范围内海草床关联鱼类的食性在漫长演化时间尺度下的保守性与趋异现象。研究发现，海草床鱼类的营养层级呈现显著的系统发育模式：亲缘关系越近的鱼类，其营养生态位的相似性越高。该系统发育模式亦得到宏观演化模型推断的支持，主要的食性趋异事件多发生于演化早期。一致性的结果表明，系统发育关系可解释约60%的海草床鱼类食性组成变异，而当代形态学、生态学与地理学因素的总解释度仅约5%。上述结果揭示，海草床鱼类的食性主要受演化保守性塑造，仅少数趋异事件引发了食性的快速转变。本研究填补了海草床鱼类食性塑造机制研究的关键空白，同时表明食性特化类群是长期演化的产物，具备不可替代的生态功能，因此亟需优先开展保护工作。 #####按名称排序的文件###### # ALL（文件夹）：用于执行主分析的数据集与代码。 ## ALL.R：本研究主分析（数据收集除外）所用的R代码。 ## all_covariates.xlsx：本研究分析中用于CPO与VPA的数据集，包含代表生态学、地理学与形态学因素的变量。 ## diets.xlsx：包含从Fishbase数据库提取的鱼类食性组成数据。 ## ref.tre：本研究分析所用的时间校准系统发育树（提取自Rabosky等人2018年的研究）。 ## tree_mr.xlsx：包含由phytools包中compute.mr()函数生成的系统发育关系矩阵。 ## trophic_level.xlsx：通过dietr工具基于食性组成数据估算得到的物种营养层级数据。 # Family10（文件夹）：用于执行亚组分析的数据集与代码，该亚组分析涵盖了海草床鱼类占比超过10%的所有鱼类科的数据。 ## diets.xlsx：包含从Fishbase数据库提取的鱼类食性组成数据。 ## Family10.R：该亚组分析（数据收集除外）所用的R代码。 ## ref.tre：该亚组分析所用的时间校准系统发育树（提取自Rabosky等人2018年的研究）。 ## tree_mr.xlsx：包含由phytools包中compute.mr()函数生成的系统发育关系矩阵。 ## trophic_level.xlsx：通过dietr工具基于食性组成数据估算得到的物种营养层级数据。 # JUV（文件夹）：用于执行亚组分析的数据集与代码，该亚组分析包含主分析中涉及鱼类的幼体与补充群体数据。 ## diets.xlsx：包含从Fishbase数据库提取的鱼类食性组成数据。 ## JUV.R：该亚组分析（数据收集除外）所用的R代码。 ## ref.tre：该亚组分析所用的时间校准系统发育树（提取自Rabosky等人2018年的研究）。 ## tree_mr.xlsx：包含由phytools包中compute.mr()函数生成的系统发育关系矩阵。 ## trophic_level.xlsx：通过dietr工具基于食性组成数据估算得到的物种营养层级数据。 # OSGB（文件夹）：用于执行亚组分析的数据集与代码，该亚组分析涵盖了经国际自然保护联盟（IUCN）认定、以海草床为主要栖息地的成体鱼类数据。 ## diets.xlsx：包含从Fishbase数据库提取的鱼类食性组成数据。 ## OSGB.R：该亚组分析（数据收集除外）所用的R代码。 ## ref.tre：该亚组分析所用的时间校准系统发育树（提取自Rabosky等人2018年的研究）。 ## tree_mr.xlsx：包含由phytools包中compute.mr()函数生成的系统发育关系矩阵。 ## trophic_level.xlsx：通过dietr工具基于食性组成数据估算得到的物种营养层级数据。 # species_list_of_each_dataset.xlsx：包含主分析与各亚组分析所用的物种列表。 Excel文件中数据的元数据详见Metadata工作表。