Capturing nuclear exons for phylogenetic reconstructions targeting basal Clupeocephalans.

Today, next generation sequencing offers the possibility to sequence hundreds or thousands of genes for phylogenetic reconstructions in a single run. Targeted gene capturing using RNA bait libraries enables to obtain suitable loci prior to sequencing in DNA libraries.

Here, we report on a methodology for capturing nuclear exons of diverse and distantly related fish taxa to attain datasets with strong phylogenetic signal. These datasets could provide sound resolution on both, shallow and deeper nodes within phylogenetic relations which have been much debated in multiple studies - often delivering controversial results.

We are aiming to sequence up to 14,000 loci from a set of Clupeocephalan fishes for reviewing current phylogenies. Sequence information of putative ortholog exons was attained from the publicly available genome of the zebrafish, Danio rerio, serving as a matrix for RNA bait design. First results on the usage of this method for phylogenetic reconstruction are promising.