Clocklike genes in Komodo dragon dataset

Individual gene trees for 1,394 single copy orthologs across 15 reptile species, three birds, and four mammals were used to estimate a species phylogeny. The 15 reptile species used were Varanus komodoensis, Shinisaurus crocodilurus, Ophisaurus gracilis, Anolis carolinensis, Pogona vitticeps, Python molurus bivittatus, Eublepharis macularius, Gekko japonicus, Pelodiscus sinensis, Chelonia mydas, Chrysemys picta bellii, Alligator sinensis, Alligator mississippiensis, Gavialis gangeticus, and Crocodylus porosus. The three birds used were Gallus gallus, Meleagris gallopavo, and Taeniopygia guttata, and the four mammals were Ornithorhynchus anatinus, Mus musculus, Canis familiaris, and Homo sapiens. Each set of orthologous proteins were aligned using PRANK v.170427. Gene trees were constructed using IQ-TREE and rooted on mammals as an outgroup.<br>Informative metrics for finding clock-like genes was performed with SortaDate (https://github.com/FePhyFoFum/SortaDate). These metrics are root-to-tip variance, tree length, and bipartition support compared to the reference concatenation phylogeny. This can be used to identify genes evolving in a clock-like manner for phylogenetic analyses.针对15种爬行类、3种鸟类以及4种哺乳类共1394个单拷贝直系同源基因（single copy orthologs），我们构建了各自的基因树，并以此估算物种系统发育树。本次使用的15种爬行类分别为科莫多巨蜥（Varanus komodoensis）、鳄蜥（Shinisaurus crocodilurus）、细脆蛇蜥（Ophisaurus gracilis）、安乐蜥（Anolis carolinensis）、鬃狮蜥（Pogona vitticeps）、缅甸蟒（Python molurus bivittatus）、豹纹守宫（Eublepharis macularius）、无蹼壁虎（Gekko japonicus）、中华鳖（Pelodiscus sinensis）、绿海龟（Chelonia mydas）、西部锦龟（Chrysemys picta bellii）、扬子鳄（Alligator sinensis）、密西西比短吻鳄（Alligator mississippiensis）、恒河鳄（Gavialis gangeticus）以及湾鳄（Crocodylus porosus）；3种鸟类分别为红原鸡（Gallus gallus）、火鸡（Meleagris gallopavo）、斑胸草雀（Taeniopygia guttata）；4种哺乳类分别为鸭嘴兽（Ornithorhynchus anatinus）、小家鼠（Mus musculus）、家犬（Canis familiaris）以及智人（Homo sapiens）。 所有直系同源蛋白集均使用PRANK v.170427进行多序列比对。随后利用IQ-TREE构建基因树，并以哺乳类作为外类群对基因树进行定根。 我们使用SortaDate（https://github.com/FePhyFoFum/SortaDate）计算了用于筛选类钟基因的信息度量指标，这些指标包括根到端方差、树长，以及与参考串联系统发育树的二分支持度。该方法可用于识别在系统发育分析中以类钟方式演化的基因。