What if conservation’s favorite marker (the microsatellite) could be sequenced and genotyped from next-generation data? This paper (sub) is the latest showing that possibility and specifically introduces a genotyping and phasing tool: HipSTR. Microsatellites have propelled much of conservation genetics and users are familiar with data analysis and interpretation of results. As next-generation sequencing has begun replacing microsatellites as the marker of choice in evolutionary analyses there has been increasing pressure for conservation to switch markers too. However, genomic sequencing and allele calling of microsatellites may bring the marker back. Although library cost and terminal-based (vs GUI-based) data processing remain barriers to genomic microsatellite analyses for many conservationists, it is exciting to see what was old become new again.
Where’s the Inbreeding?
This paper (sub) evaluated genetic diversity in the Montseny brook newt (Calotriton arnoldi) which is listed as critically endangered by IUCN. The paper highlights a conservation conundrum: isolated populations that show no signs of inbreeding. When genetic diversity is considered in conservation management of a population or species, maintaining high diversity as a way to prevent inbreeding is frequently a focus. The idea being that this will first, allow sufficient genetic diversity for adaptation into the future and second, prevent mating between kin which may increase deleterious alleles thus reducing fitness. Yet this system and others observe small populations with neither genetic nor phenotypic signatures of inbreeding. So, how are populations doing this? Is it a function of their biology or something wrong with our estimates of inbreeding? The authors of this paper suggest that Montseny brook newts avoid mating with relatives; but how are they doing this in an isolated population with a limited number of individuals? This issue of very low population size with lack of inbreeding is of great conservation interest and we have much to learn about the mechanisms, taxonomic variability, and potential for application in on-the-ground conservation efforts.
Side photo of the Montseny brook newt by Jan Van Der Voort via ARKive.