Longevity evolution is accompanied by genome-wide strengthening of purifying selection with a lineage-specific chromosome maintenance overlay

## Summary This study demonstrates that genome-wide strengthening of purifying selection is a convergent response to increased somatic mutation risk in both multicellular transitions (volvocine green algae) and mammalian longevity evolution (62 species). By comparing normalized and unnormalized evolutionary rates, a "dual structure" is revealed: genome-wide constraint overlaid by additional strengthening of chromosome maintenance pathways. Stochastic character mapping estimates approximately 36 independent origins of exceptional longevity across 973 mammals. Convergent evolution analysis shows that independent long-lived lineages (Chiroptera and Primates) achieve longevity through different gene-specific constraint patterns. ### Contents - **data/** — Analysis result CSV files (PAML, RERconverge, stochastic character mapping, GO enrichment) - **scripts/** — R and Python scripts to reproduce all analyses (01–10, numbered in execution order) - **supplementary/** — Supplementary Tables S1–S7 - **SOURCES.md** — External data sources with accession numbers - **environment.yml** — Software dependencies - **R_sessionInfo.txt** — R package versions ### Reproducibility Scripts 03–09 can be run directly using the provided data files. Scripts 01–02 and 10 require raw genome data from NCBI (accession numbers listed in SOURCES.md).## 摘要 本研究表明，全基因组纯化选择的强化是多细胞演化过渡（如团藻目绿藻）与哺乳动物长寿演化（涵盖62个物种）中，应对体细胞突变风险升高的趋同响应。通过对比标准化与非标准化的演化速率，研究揭示了一种“双重结构”：全基因组约束之上，还叠加了染色体维持通路的额外强化作用。随机性状映射估算显示，在973个哺乳动物物种中，极长寿性状的独立起源约有36次。趋同演化分析表明，独立演化出长寿的支系（翼手目（Chiroptera）与灵长目（Primates））通过不同的基因特异性约束模式实现了长寿表型。 ### 数据集内容 - **data/** — 分析结果CSV文件（涵盖PAML、RERconverge、随机性状映射、基因本体（Gene Ontology, GO）富集分析结果） - **scripts/** — 可复现全部分析流程的R与Python脚本（编号01至10，按执行顺序排列） - **supplementary/** — 补充表S1至S7 - **SOURCES.md** — 带有登录号的外部数据源说明文档 - **environment.yml** — 软件依赖配置文件 - **R_sessionInfo.txt** — R包版本信息 ### 可复现性 脚本03至09可直接使用提供的数据集文件运行。脚本01、02及10则需要美国国家生物技术信息中心（National Center for Biotechnology Information, NCBI）的原始基因组数据，其登录号详见SOURCES.md文件。