Statistical analysis of CHD dS, dN, and dN/dS.

Classical cadherins (CDH) comprise a family of single-pass transmembrane glycoproteins that contribute to tissue morphogenesis by regulating cell-cell adhesion, cytoskeletal dynamics, and cell signaling. CDH are grouped into type I (CDH 1, 2, 3, 4 and 15) and type II (CDH 5, 6, 7, 8, 9, 10, 11, 12, 18, 20, 22 and 24), based on the folding of the cadherin binding domain involved in trans-dimer formation. CDH are exclusively found in metazoans, and the origin and expansion of the gene family coincide with the emergence of multicellularity and vertebrates respectively. This study examined the evolutionary changes of CDH orthologs in primates and the factors that influence selective pressure to investigate the varying constraints exerted among CDH. Pairwise comparisons of the number of amino acid substitutions and of the ratio of non-synonymous substitutions per non-synonymous sites (dN) over synonymous substitutions per synonymous sites (dS), show that CDH2, CDH4, and most type II CDH have been under significantly higher negative selective pressure as compared to CDH1, CDH3, CDH5 and CDH19. Evaluation of gene essentiality as determined by the effect of germline deletion on animal viability, morphogenic phenotype, and reproductive fitness, show no correlation with the with extent of negative selection observed on CDH. Spearman’s correlation analysis shows a positive correlation between CDH expression levels (E) in mouse and human tissues and their rate of evolution (R), as observed in most proteins expressed on the cell surface. However, CDH expression in the CNS show a significant E-R negative correlation, indicating that the strong negative selection exerted on CDH2, CDH4, and most type II CDH is associated with their expression in the CNS. CDH participate in a variety of cellular processes in the CNS including neuronal migration and functional assembly of neural circuits, which could profoundly influence animal fitness. Therefore, our findings suggest that the unusually high negative selective pressure exerted on CDH2, CDH4 and most type II CDH is due to their role in CNS formation and function and may have contributed to shape the evolution of the CNS in primates.经典钙粘蛋白（Classical cadherins, CDH）是一类单次跨膜糖蛋白家族，通过调控细胞间黏附、细胞骨架动力学与细胞信号转导参与组织形态发生过程。根据参与反式二聚体形成的钙粘蛋白结合域折叠方式，CDH可分为I型（CDH 1、2、3、4及15）与II型（CDH 5、6、7、8、9、10、11、12、18、20、22及24）两大类。CDH仅存在于后生动物（metazoans）中，该基因家族的起源与扩张分别对应多细胞性与脊椎动物的出现事件。本研究针对灵长类动物中CDH直系同源基因的演化变化，以及影响选择压力的因素展开分析，以探究不同CDH所受选择约束的差异。通过比对氨基酸替换数，以及非同义位点每非同义替换率（dN）与同义位点每同义替换率（dS）的比值（dN/dS），研究发现CDH2、CDH4与多数II型CDH所受的负选择压力显著高于CDH1、CDH3、CDH5及CDH19。通过生殖系敲除对动物生存能力、形态发生表型及生殖适合度的影响评估基因必需性的分析显示，其与CDH所受负选择程度无相关性。斯皮尔曼相关性分析（Spearman’s correlation analysis）结果表明，与多数细胞表面表达蛋白一致，小鼠与人类组织中CDH的表达水平（E）与其进化速率（R）呈正相关。但中枢神经系统（Central Nervous System, CNS）中的CDH表达则呈现显著的E-R负相关，提示CDH2、CDH4及多数II型CDH所受的强负选择与其在中枢神经系统中的表达密切相关。CDH参与中枢神经系统内多种细胞过程，包括神经元迁移与神经环路的功能性组装，这些过程可显著影响动物的适合度。因此，本研究结果表明，CDH2、CDH4及多数II型CDH所受异常强烈的负选择压力，源于其在中枢神经系统形成与功能发挥中的作用，且可能参与塑造了灵长类中枢神经系统的演化历程。