Computational protocol: Evolution of gremlin 2 in cetartiodactyl mammals: gene loss coincides with lack of upper jaw incisors in ruminants

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Protocol publication

[…] We annotated gremlin 2 genes in representative species of laurasiatherian mammmals. Our study included representative species from the orders Carnivora: cat (Felis catus), Siberian tiger (Panthera tigris), dog (Canis familiaris), ferret (Mustela putorius), Weddell seal (Leptonychotes weddellii), Pacific walrus (Odobenus rosmarus), panda (Ailuropoda melanoleuca); Perissodactyla: Przewalsk’s horse (Equus ferus), horse (Equus caballus), donkey (Equus asinus), Eulipotyphla: European hedgehog (Erinaceus europaeus); Chiroptera: Black flying fox (Pteropus alecto), Large flying fox (Pteropus vampyrus), Egyptian fruit bat (Rousettus aegyptiacus); Cetartiodactyla: pig (Sus Scrofa), alpaca (Vicugna pacos), dromedary (Camelus dromedarius) and Bactrian camel (Camelus bactrianus); and Pholidota (Manis javanica) (). Mouse and kangaroo rat sequences were used as outgroups. Amino acid sequences were aligned using the L-INS-i strategy from MAFFT v.6 (). Nucleotide alignment was generated using the amino acid alignment as a template using the software PAL2NAL (). Phylogenetic relationships were estimated using maximum likelihood and Bayesian approaches. We used the propose model tool of IQ-Tree () to select the best-fitting models for each codon position (TVMe+I, K2P+G4 and HKY+G4, for first, second and third codon positions, respectively). We performed a maximumlikelihood analysis to obtain the best tree using the program IQ-Tree (); and nodes support was assessed with 1,000 bootstrap pseudoreplicates using the ultrafast routine. Bayesian searches were conducted in MrBayes v.3.1.2 (); two independent runs of six simultaneous chains for 20 × 106 generations were set, and every 2,500 generations were sampled using default priors. The run was considered to have reached convergence once the likelihood scores reached an asymptote and the average standard deviation of the split frequencies remained <0.01. We discarded all trees that were sampled before convergence, and we evaluated support for the nodes and parameter estimates from a majority rule consensus of the last 4,000 trees. […]

Pipeline specifications

Software tools MAFFT, PAL2NAL, IQ-TREE, MrBayes
Applications Phylogenetics, Nucleotide sequence alignment
Organisms Sus scrofa, Camelus dromedarius