Journal
MOLECULAR BIOLOGY AND EVOLUTION
Volume 33, Issue 8, Pages 2117-2134Publisher
OXFORD UNIV PRESS
DOI: 10.1093/molbev/msw069
Keywords
Markov cluster; protein homology; spiders; Araneae; transcriptomics; genomics
Funding
- National Science Foundation [DEB1144492, DEB114417, DEB1457300, DEB1457539]
- Gonzalo Giribet
- GWU Harlan Summer Fellowship
- GWU Weintraub Graduate Fellowship
- Direct For Biological Sciences
- Division Of Environmental Biology [1457300] Funding Source: National Science Foundation
- Division Of Environmental Biology
- Direct For Biological Sciences [1144492] Funding Source: National Science Foundation
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Current sequencing technologies are making available unprecedented amounts of genetic data for a large variety of species including nonmodel organisms. Although many phylogenomic surveys spend considerable time finding orthologs from the wealth of sequence data, these results do not transcend the original study and after being processed for specific phylogenetic purposes these orthologs do not become stable orthology hypotheses. We describe a procedure to detect and document the phylogenetic distribution of orthologs allowing researchers to use this information to guide selection of loci best suited to test specific evolutionary questions. At the core of this pipeline is a new phylogenetic orthology method that is neither affected by the position of the root nor requires explicit assignment of outgroups. We discuss the properties of this new orthology assessment method and exemplify its utility for phylogenomics using a small insects dataset. In addition, we exemplify the pipeline to identify and document stable orthologs for the group of orb-weaving spiders (Araneoidea) using RNAseq data. The scripts used in this study, along with sample files and additional documentation, are available at https://github.com/ballesterus/UPhO.
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