BACKGROUND Understanding the origins of genome content has long been a goal of molecular evolution and comparative genomics. By examining genome evolution through the guise of lineage-specific evolution, it is possible to make inferences about the evolutionary events that have given rise to species-specific diversification. Here we characterize the evolutionary trends found in chordate species using The Adaptive Evolution Database (TAED). TAED is a database of phylogenetically indexed gene families designed to detect episodes of directional or diversifying selection across chordates. Gene families within the database have been assessed for lineage-specific estimates of dN/dS and have been reconciled to the chordate species to identify retained duplicates. Gene families have also been mapped to the functional pathways and amino acid changes which occurred on high dN/dS lineages have been mapped to protein structures. RESULTS An analysis of this exhaustive database has enabled a characterization of the processes of lineage-specific diversification in chordates. A pathway level enrichment analysis of TAED determined that pathways most commonly found to have elevated rates of evolution included those involved in metabolism, immunity, and cell signaling. An analysis of protein fold presence on proteins, after normalizing for frequency in the database, found common folds such as Rossmann folds, Jelly Roll folds, and TIM barrels were overrepresented on proteins most likely to undergo directional selection. A set of gene families which experience increased numbers of duplications within short evolutionary times are associated with pathways involved in metabolism, olfactory reception, and signaling. An analysis of protein secondary structure indicated more relaxed constraint in β-sheets and stronger constraint on alpha Helices, amidst a general preference for substitutions at exposed sites. Lastly a detailed analysis of the ornithine decarboxylase gene family, a key enzyme in the pathway for polyamine synthesis, revealed lineage-specific evolution along the lineage leading to Cetacea through rapid sequence evolution in a duplicate gene with amino acid substitutions causing active site rearrangement. CONCLUSION Episodes of lineage-specific evolution are frequent throughout chordate species. Both duplication and directional selection have played large roles in the evolution of the phylum. TAED is a powerful tool for facilitating this understanding of lineage-specific evolution.

中文翻译：

---

表征谱系特定的进化和推动脊索动物基因组多样化的过程。

背景技术了解基因组内容的起源长期以来一直是分子进化和比较基因组学的目标。通过以谱系特定进化的幌子来检查基因组进化，可以推断出引起物种特定多样化的进化事件。在这里，我们使用自适应进化数据库（TAED）描述了在碳酸盐物种中发现的进化趋势。TAED是系统发育索引基因家族的数据库，旨在检测跨脊索的方向性或多样化选择。数据库中的基因家族已针对dN / dS的谱系特异性评估进行了评估，并已与碳酸盐物种核对，以鉴定保留的重复序列。基因家族也已被定位到功能途径，高dN / dS谱系中发生的氨基酸变化已被定位到蛋白质结构。结果对该详尽的数据库进行的分析使人们能够表征和弦中特定于谱系的多样化过程。TAED的途径水平富集分析确定，最常发现进化速率升高的途径包括那些参与代谢，免疫和细胞信号转导的途径。在对数据库中的频率进行归一化后，对蛋白质上蛋白质折叠的存在进行了分析，发现常见的折叠（例如Rossmann折叠，果冻卷折叠和TIM桶）在最有可能进行方向选择的蛋白质上过多代表。一组在短进化时间内经历重复次数增加的基因家族与参与代谢，嗅觉接收和信号传导的途径有关。对蛋白质二级结构的分析表明，在β-折叠中更宽松的约束和对α螺旋的更强约束，在暴露位点普遍倾向于取代。最后，对鸟氨酸脱羧酶基因家族（一种多胺合成途径中的关键酶）的详细分析显示，沿谱系的特定进化是通过重复基因的快速序列进化而导致的鲸类的进化，该重复基因被氨基酸取代导致活性位点重排。结论整个有脉动物物种中，谱系特异性进化的情节很常见。复制和方向选择在门的进化中都发挥了重要作用。TAED是一种强大的工具，可促进对特定谱系进化的这种理解。