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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.
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.
