Spatial patterns of immunogenetic and neutral variation underscore the conservation value of small, isolated American badger populations

Abstract

Small and isolated populations often exhibit low genetic diversity due to drift and inbreeding, but may simultaneously harbour adaptive variation. We investigate spatial distributions of immunogenetic variation in American badger subspecies (Taxidea taxus), as a proxy for evaluating their evolutionary potential across the northern extent of the species’ range. We compared genetic structure of 20 microsatellites and the major histocompatibility complex (MHC DRB exon 2) to evaluate whether small, isolated populations show low adaptive polymorphism relative to large and well‐connected populations. Our results suggest that gene flow plays a prominent role in shaping MHC polymorphism across large spatial scales, while the interplay between gene flow and selection was stronger towards the northern peripheries. The similarity of MHC alleles within subspecies relative to their neutral genetic differentiation suggests that adaptive divergence among subspecies can be maintained despite ongoing gene flow along subspecies boundaries. Neutral genetic diversity was low in small relative to large populations, but MHC diversity within individuals was high in small populations. Despite reduced neutral genetic variation, small and isolated populations harbour functional variation that likely contribute to the species evolutionary potential at the northern range. Our findings suggest that conservation approaches should focus on managing adaptive variation across the species range rather than protecting subspecies per se.

Development of a genotype‐by‐sequencing immunogenetic assay as exemplified by screening for variation in red fox with and without endemic rabies exposure

“…(). Our observed heterozygosity is also high compared to reported estimates of expected heterozygosity in Polish red fox (72%, Mullins et al., ) and that of other carnivores, including the American badger (81%; Rico et al., ) and Canadian black bear (55%–81%; Pelletier et al., ). Possible causes of the conflicting results include amplification bias and allelic dropout in their dataset that is suggested by the large difference in observed homozygotes (1.6% vs. 28.1%) or challenges in our dataset in aligning sequences to generate accurate genotypes and hence the larger number of heterozygotes.…”

The evolution of the major histocompatibility complex in upstream versus downstream river populations of the longnose dace

“…Of our 26 samples that were amplified and sequenced twice, only one (from Edworthy Park, BOW1) was assigned a different genotype in each of two replicates; thus, our estimated repeatability rate was 96.2% across the library preparation, sequencing, and bioinformatic procedure. This rate is higher than that from other studies that used a similar approach to estimate repeatability (e.g., 87.1% in Herdegen, Babik, & Radwan, ; 81.5% in Rico et al., ). We excluded that one sample from subsequent analyses.…”

Prelude to a panzootic: Gene flow and immunogenetic variation in northern little brown myotis vulnerable to bat white-nose syndrome

“…This requires a backdrop of robust data on neutral genetic diversity against which immunogenetic diversity can be contrasted (Ekblom et al 2007;Rico et al 2016). However, studies of immune response to infectious diseases rarely consider more than one pathogen at a time and often focus on particular immune genes (as we have done here).…”

“…Genetic structure can sometimes predict the spread of host-dispersed pathogens by estimating the magnitude and direction of dispersal among populations, or identifying barriers to dispersal that could limit pathogen spread (Blanchong et al 2008;Biek and Real 2010;Wilder et al 2015). Delimiting neutral population structure is also a prerequisite for assessing local adaptation because it allows the effects of genetic drift and selection to be separated (Ekblom et al 2007;Spurgin and Richardson 2010;Rico et al 2016). …”