Gordon Luikart | Search bioRxiv

bioRxiv2016

Genomic data reveal similar genetic differentiation between invertebrates living under and on a riverine floodplain

Little is known about the life histories, population connectivity, or dispersal mechanisms of shallow groundwater organisms. Here we used RAD-seq to analyze population structure in two aquifer species: Paraperla frontalis, a stonefly with groundwater larvae and aerial adults, and Stygobromus sp., a groundwater-obligate amphipod. We found similar levels of connectivity in each species between floodplains separated by ~70 river km in the Flathead River basin of NW Montana, USA. Given that Stygobromous lacks the aboveground life stage of P. frontalis, our findings suggest that aquifer-obligate species might have previously unrecognized dispersal capacity.

Genomics↗

bioRxiv2015

RAD Capture (Rapture): Flexible and efficient sequence-based genotyping.

Massively parallel sequencing has revolutionized many areas of biology but sequencing large amounts of DNA in many individuals is cost-prohibitive and unnecessary for many studies. Genomic complexity reduction techniques such as sequence capture and restriction enzyme-based methods enable the analysis of many more individuals per unit cost. Despite their utility, current complexity reduction methods have limitations, especially when large numbers of individuals are analyzed. Here we develop a much improved restriction site associated DNA (RAD) sequencing protocol and a new combinatorial method called Rapture (RAD capture). The new RAD protocol improves versatility by separating RAD tag isolation and sequencing library preparation into two distinct steps. This protocol also recovers more unique (non-clonal) RAD fragments and produces better data for both standard RAD and Rapture analysis. Rapture then uses an in-solution capture of chosen RAD tags to target sequencing reads to desired loci. Rapture combines the benefits of both RAD and sequence capture, i.e. very inexpensive and rapid library preparation for many individuals as well as high specificity in the number and location of genomic loci analyzed. Our results demonstrate that Rapture is a rapid and flexible technology capable of analyzing a very large number of individuals with minimal sequencing and library preparation cost. The methods presented here should improve the efficiency of genetic analysis for many aspects of agricultural, environmental, and biomedical science.

Genetics↗