RAD-Sequencing reveals deep genetic divides between populations of vernal pool branchiopods in California

Shannon Rose Kieran and Joshua M. Hull, Department of Animal Science, University of California, Davis, CA, Andrea Schreier and Amanda J. Finger, University of California, Davis, Alisha Goodbla, Dept. of Animal Science, University of California-Davis, Davis, CA

Background/Question/Methods
California's vernal pools contain many endemic, passively-dispersed species which are threatened by the enormous loss and fragmentation of vernal pool habitat that California has experienced over the past three centuries. Despite limited dispersal ability, many of these species occur across the Central Valley in geographically disjunct vernal pool complexes. Whether these disjunct populations are genetically isolated, or whether avian, anthropic or other vectors create long-distance transport between populations, is an important question for conservationists and managers. For many of California's vernal pool branchiopods including fairy shrimp and tadpole shrimp, the extent of genetic differentiation between populations is currently unknown. This hinders recovery efforts which may include introductions and translocations that would greatly benefit from knowledge about inter-population relationships.

In order to better understand the genetic relationships between populations of Californian branchiopods, we collected specimens of Branchinecta lynchi (the Vernal Pool Fairy Shrimp), Linderiella occidentalis (The California Fairy Shrimp) and Lepidurus packardi (The Vernal Pool Tadpole Shrimp) from populations across their respective ranges in California and Southern Oregon. We performed Restriction-enzyme Associated Digest (RAD) Sequencing on 544 specimens within these three species. We assembled de novo RAD reference assemblies for each species and analyzed the populations at 6,488-12,701 RAD loci per species.

Results/Conclusions
We found overall high levels of genetic divergence between populations as measured by FST and Cavalli-Sforza and Edwards Chord Distance. We additionally found evidence of the widespread genetic isolation of populations in all three species. We found no evidence of recent migration between populations of Branchinecta lynchi at geographic scales >50 km, but we did find that some geographically disjunct populations were genetically similar, suggesting recent colonization or historical migration compared to other population pairs. We found significant geographic structuring in all three species as determined by a Mantel test. Neighbor-joining trees and phylogenetic analysis suggest a stepping-stone dispersal pattern rather than frequent long-distance colonization or migration events, although it does not rule out long-distance movement as an occasional process that affects the dispersal of these species. We conclude that genetic isolation and divergence of populations is likely to continue or increase as more habitat is lost, and that populations must be managed in tandem to maintain the genetic diversity of the species as a whole.