Population structure and gene flow in a heavily disturbed habitat: implications for the management of the imperilled Red Hills salamander (Phaeognathus hubrichti)

Abstract

Estimating levels of gene flow and assessing levels of population connectivity are of critical importance to the field of conservation genetics, especially for imperiled species. Many factors can influence dispersal and therefore gene-flow patterns across a natural landscape. These patterns can be substantially altered by the impacts of habitat modification by humans or natural phenomena. Landscape-genetic studies that address both historical and contemporary influences on gene flow can be critical to demonstrating whether isolated populations with low levels of genetic variation are typical of the species or a result of strong negative effects of such modification. We used 10 microsatellite markers to investigate the spatial genetic patterns of the Red Hills salamander (Phaeognathus hubrichti), a federally listed species. Bayesian clustering revealed five well-supported demes within the range of P. hubrichti. Gene-flow analysis suggested that overall migration levels for P. hubrichti are low, but coalescent methods indicate that migration levels were significantly higher before habitat modification by humans. By accounting for history and species characteristics, our results suggest that loss and fragmentation of habitat have strongly negatively affected P. hubrichti by reducing migration, increasing bottlenecks, and promoting high levels of inbreeding.

Parnassius apollo nevadensis: identification of recent population structure and source–sink dynamics

“…It has been demonstrated by theoretical models and field studies that the maintenance of genetic diversity and population viability is critically dependent on gene flow among local populations (Swindell and Bouzat 2005;Apodaca et al 2012). When habitat fragmentation compromises gene flow, the viability of the population and individual fitness will be theoretically affected as inbreeding accumulates deleterious mutations (Lynch et al 1995;Saccheri et al 1998).…”

The problem of estimating recent genetic connectivity in a changing world

“…To investigate the effects of human‐induced landscape change (e.g., habitat fragmentation) on genetic connectivity, some have compared these 2 estimates of connectivity to make inferences (e.g., Apodaca et al. ; Sharma et al. ; Blakney et al.…”

Informing management of endemic habitat specialists: Multiscale habitat selection by the Red Hills salamander

“…However, we do not suggest that land managers should focus on individual sites to the exclusion of the landscape. Long‐term conservation plans for P. hubrichti must consider the ability for populations to recover following disturbance (Lindenmayer et al ); an intact landscape is likely important to maintain P. hubrichti dispersal and genetic connectivity (Apodaca et al ) and the ability for the species to (re)colonize sites. In addition, an intact landscape likely facilitates the presence of high‐quality habitat within occupied ravines (J. Godwin, Auburn University, unpublished data).…”

“…In addition, the species has relatively low reproductive rates, as compared to other salamanders (Salthe ), and this is likely to increase the risk of extinction. Certain logging practices are detrimental to P. hubrichti populations (Dodd ) and may have affected migration rates and resulting genetic diversity (Apodaca et al ), perhaps because of disturbance of overlying mesic‐hardwood canopy cover (Jordan and Mount , Dodd ). Thus, P. hubrichti may accurately be considered at high risk of extinction because of a combination of its natural history and anthropogenic modification of the landscape (Purvis et al ).…”