Pedigree-based assessment of recent population connectivity in a threatened rattlesnake

Managing endangered species in fragmented landscapes requires estimating
dispersal rates between populations over contemporary timescales. Here we
develop a new method for quantifying recent dispersal using genetic
pedigree data for close and distant kin. Specifically, we describe an
approach that infers missing shared ancestors between pairs of kin in
habitat patches across a fragmented landscape. We then apply a
stepping-stone model to assign unsampled individuals in the pedigree to
probable locations based on minimizing the number of movements required to
produce the observed locations in sampled kin pairs. Finally, we use all
pairs of reconstructed parent-offspring sets to estimate dispersal rates
between habitat patches under a Bayesian model. Our approach measures
connectivity over the timescale represented by the small number of
generations contained within the pedigree and so is appropriate for
estimating the impacts of recent habitat changes due to human activity. We
used our method to estimate recent movement between newly discovered
populations of threatened Eastern Massasauga Rattlesnakes (Sistrurus
catenatus) using data from 2996 RAD-based genetic loci. Our pedigree
analyses found no evidence for contemporary connectivity between five
genetic groups, but, as validation of our approach, showed high dispersal
rates between sample sites within a single genetic cluster. We conclude
that these five genetic clusters of Eastern Massasauga Rattlesnakes have
small numbers of resident snakes and are demographically isolated
conservation units. More broadly, our methodology can be widely applied to
determine contemporary connectivity rates, independent of bias from shared
genetic similarity due to ancestry that impacts other approaches.