<b>Supplemental Data &amp; Code:</b>Convergent relaxation of molecular constraint in mammalian herbivores highlights the roles of liver and kidney functions in carnivory

Mammalia comprises a great diversity of diet types and associated adaptations. An understanding of the genomic mechanisms underlying these adaptations may offer insights for improving human health. Comparative genomic studies of diet that employ taxonomically restricted analyses or simplified diet classifications may suffer reduced power to detect molecular convergence associated with diet evolution. Here, we used a quantitative carnivory score—indicative of the amount of animal protein in the diet—for 80 mammalian species to detect significant correlations between the relative evolutionary rates of genes and changes in diet. We identified six genes—<i>ACADSB</i>, <i>CLDN16</i>, <i>CPB1</i>, <i>PNLIP</i>, <i>SLC13A2</i>, and <i>SLC14A2</i>—that experienced significant changes in evolutionary constraint alongside changes in carnivory score, becoming less constrained in lineages evolving more herbivorous diets. We further considered the biological functions associated with diet evolution and observed that pathways related to amino acid and lipid metabolism, biological oxidation, and small molecule transport experienced reduced purifying selection as lineages became more herbivorous. Liver and kidney functions showed similar patterns of constraint with dietary change. Our results indicate that, in highly carnivorous lineages, selection acts on the liver and kidneys to maintain sufficient metabolism and excretion of substances found in excess in carnivorous diets. These biological functions become less important with the evolution of increasing herbivory, so experience a relaxation of constraint in more herbivorous lineages.哺乳纲（Mammalia）拥有极为多样的饮食类型及其相关适应性演化特征。解析这些适应性背后的基因组机制，可为改善人类健康提供重要研究视角。过往针对饮食的比较基因组研究，若采用分类学受限的分析策略或简化的饮食分类体系，可能会降低检测与饮食演化相关的分子趋同（molecular convergence）现象的效力。本研究针对80个哺乳类物种，采用可反映饮食中动物蛋白占比的量化肉食性得分（quantitative carnivory score），以检测基因相对演化速率与饮食变化之间的显著关联。本研究鉴定出6个基因：ACADSB、CLDN16、CPB1、PNLIP、SLC13A2及SLC14A2，它们的演化约束（evolutionary constraint）程度随肉食性得分的变化发生了显著改变——在向更植食性饮食演化的支系中，这些基因的演化约束被显著放松。本研究进一步分析了与饮食演化相关的生物学功能，发现随着支系向更植食性方向演化，氨基酸与脂质代谢、生物氧化以及小分子转运相关的通路所受的纯化选择（purifying selection）压力显著减弱。肝脏与肾脏的功能也呈现出随饮食变化而改变的约束模式。研究结果表明，在高度肉食性的支系中，自然选择作用于肝脏与肾脏，以维持对肉食性饮食中过量摄入物质的正常代谢与排泄功能。随着植食性程度不断升高的演化过程，这些生物学功能的重要性逐渐降低，因此在更偏向植食性的支系中，相关基因的演化约束得以放松。