Population structure and genetic variation in the endangered Giant Kangaroo Rat (Dipodomys ingens)

Abstract

Populations of the endangered giant kangaroo rat, Dipodomys ingens (Heteromyidae), have suffered increasing fragmentation and isolation over the recent past, and the distribution of this unique rodent has become restricted to 3% of its historical range. Such changes in population structure can significantly affect effective population size and dispersal, and ultimately increase the risk of extinction for endangered species.To assess the fine-scale population structure, gene flow, and genetic diversity of remnant populations of Dipodomys ingens, we examined variation at six microsatellite DNA loci in 95 animals from six populations. Genetic subdivision was significant for both the northern and southern part of the kangaroo rat's range although there was considerable gene flow among southern populations. While regional gene diversity was relatively high for this endangered species, hierarchical F-statistics of northern populations in Fresno and San Benito counties suggested non-random mating and genetic drift within subpopulations. We conclude that effective dispersal, and therefore genetic distances between populations, is better predicted by ecological conditions and topography of the environment than linear geographic distance between populations. Our results are consistent with and complimentary to previous findings based on mtDNA variation of giant kangaroo rats. We suggest that management plans for this endangered rodent focus on protection of suitable habitat, maintenance of connectivity, and enhancement of effective dispersal between populations either through suitable dispersal corridors or translocations.

Reconstructing the evolutionary history of an endangered subspecies across the changing landscape of the Great Central Valley of California

“…Reconstructing the evolutionary history of populations or species that occupy highly altered landscapes such as the San Joaquin Valley is challenging because, in many cases, much of the history may have been erased through population extinction. Even in remnant populations, dramatic demographic fluctuations associated with habitat fragmentation and degradation may have substantially altered historic patterns of genetic variation through drift or inbreeding (Loew et al 2005;Keyghobadi 2007). Developing a view of history on such landscapes requires an integrative approach that includes data from parts of the genome that capture different aspects of population history (nuclear and mitochondrial genomes) and provide insight into different depths of evolutionary history (slowly and rapidly evolving loci).…”

Evaluating current and future range limits of an endangered, keystone rodent (Dipodomys ingens)

“…These differences in climatic factors could alter their response to environmental change and disparate reactions to species interactions. Although previous work (Good, Williams, Ralls, & Fleischer, ; Loew, Williams, Ralls, Pilgrim, & Fleischer, ) found relatively low genetic differentiation in neutral microsatellites between the Panoche and Carrizo, indicating recent or no divergence, more recent work relying on unique haplotypes in cytochrome b suggested a much earlier (~6,800 years) splitting time (Statham et al, ). In two divergent populations with large effective population size, selection for specific climatic regimes may occur relatively rapidly (Hoffman & Sgrò, ).…”

“…However, the historical model, which modelled the species' historical environmental niche, predicted even less range contraction than the local models. This could be because it (Good, Williams, Ralls, & Fleischer, 1997;Loew, Williams, Ralls, Pilgrim, & Fleischer, 2005) found relatively low genetic differentiation in neutral microsatellites between the Panoche and Carrizo, splitting time (Statham et al, 2019). In two divergent populations with large effective population size, selection for specific climatic regimes may occur relatively rapidly (Hoffman & Sgrò, 2011).…”

Conserving the endangered Mexican fishing bat (Myotis vivesi): genetic variation indicates extensive gene flow among islands in the Gulf of California

“…Most of the historically recorded extinctions have occurred on islands (Ricketts et al 2005), and many of the presently threatened species persist only in insular habitat fragments (e.g., Garner et al 2005;Loewl et al 2005). When insular populations go extinct, efforts often are made to restore habitat at those sites in the hope that dispersers from extant populations will recolonize empty patches (Scott et al 2001).…”