Weevil phylogenomics using hybrid enrichment
Massively parallel sequencing (aka next generation sequence [NGS]) enables rapid access to genomic-scale DNA data at a relatively low cost. Phylogenomics is a flourishing field that capitalizes on the power of NGS and uses hundreds or even thousands of loci, often amounting to millions of base pairs (bp), to reconstruct phylogenies. Methods for obtaining loci are many, varying in mainly marker design and library preparation.
I am taking a target enrichment approach to capture and sequence >500 loci or >1000,000 bp to reconstruct a phylogeny of weevils at the family or subfamily level. These loci are derived from seven previously published weevil transcriptomes. The program SISRS is used to determine homologous loci across these transcriptomes. The sequence data are provided to a company called MYcroarray, which designs and produces biotinylated RNA baits (MYbaits), used for hybridizing to and capturing target loci.
I have obtained a MYbaits kit for capturing 500 loci. At the initial stage I will work on 24 weevil samples. I am collaborating with Dr. Rachel Schwartz (author of 'SISRS') on this project. Dr. Schwartz has done the heavy lifting of selecting markers using SISRS. I will be performing library preparation (using MYbaits) and the subsequent analyses after sequencing. Sequencing will be done on a Illumina Miseq. Sequence reads will be assembled and homologous loci determined with SISRS.
I will be using the resulting phylogeny to test familial and to some extent subfamilial relationships within weevils. Some contested or unresolved systematics problems include, but are not limited to, the monophyly of Anthribidae, if Nemonychidae together with Anthribidae or the latter (or part of it) alone is the sister to the remainders of Curculionoidea, and the phylogenetic relationships within some families (e.g., Attelabidae).
To learn more about this project, you can read the powerpoint slides (above) I have prepared based on locus selection results.