Orthology inference in nonmodel organisms using transcriptomes and low-coverage genomes: improving accuracy and matrix occupancy for phylogenomics.
Bottom Line: The procedure significantly increased the completeness and accuracy of the inferred homologs and orthologs.We also found that data sets that are more recently diverged and/or include more high-coverage genomes had more complete sets of orthologs.They have been implemented in python with independent scripts for each step, making it easy to modify or incorporate them into existing pipelines.
Affiliation: Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor firstname.lastname@example.org email@example.com.Show MeSH
Mentions: Species trees reconstructed from the HYM data set were overall highly consistent among all four orthology inference methods in topology, branch lengths, and support values (fig. 3). They had identical topologies to those in the analysis by Johnson et al. (2013). All branches received a support value of 100% from both the bootstrap and 30% jackknife analyses. Branches received less-than-perfect support values using STAR or PhyloNet in Johnson et al. (2013) similarly received less-than-perfect jackknife support values in our 10% and/or 20 gene jackknife analyses. The node uniting Formicidae and Apoidea (marked with an arrow in fig. 3) received 81–97% jackknife support with around 100 loci and around 60% with 20 loci. Given that five of the nine taxa in this clade were from annotated genomes and the entire tree was otherwise well supported, this Formicidae + Apoidea node warrants further investigation of the source of the conflict.Fig. 3.
Affiliation: Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor firstname.lastname@example.org email@example.com.