Genetic consequences of postglacial range expansion in two codistributed rodents (genus Dipodomys) depend on ecology and genetic locus.

How does range expansion affect genetic diversity in species with different ecologies, and do different types of genetic markers lead to different conclusions? We addressed these questions by assessing the genetic consequences of postglacial range expansion using mitochondrial DNA (mtDNA) and nuclear restriction site-associated DNA (RAD) sequencing in two congeneric and codistributed rodents with different ecological characteristics: the desert kangaroo rat (Dipodomys deserti), a sand specialist, and the Merriam's kangaroo rat (Dipodomys merriami), a substrate generalist. For each species, we compared genetic variation between populations that retained stable distributions throughout glacial periods and those inferred to have expanded since the last glacial maximum. Our results suggest that expanded populations of both species experienced a loss of private mtDNA haplotypes and differentiation among populations, as well as a loss of nuclear single-nucleotide polymorphism (SNP) private alleles and polymorphic loci. However, only D. deserti experienced a loss of nucleotide diversity (both mtDNA and nuclear) and nuclear heterozygosity. For all indices of diversity and differentiation that showed reduced values in the expanded areas, D. deserti populations experienced a greater degree of loss than did D. merriami populations. Additionally, patterns of loss in genetic diversity in expanded populations were substantially less extreme (by two orders of magnitude in some cases) for nuclear SNPs in both species compared to that observed for mitochondrial data. Our results demonstrate that ecological characteristics may play a role in determining genetic variation associated with range expansions, yet mtDNA diversity loss is not necessarily accompanied by a matched magnitude of loss in nuclear diversity.

Chihuahuan Desert kangaroo rats: nonlinear effects of population dynamics, competition, and rainfall.

Using long-term data on two kangaroo rats in the Chihuahuan Desert of North America, we fitted logistic models including the exogenous effects of seasonal rainfall patterns. Our aim was to test the effects of intraspecific interactions and seasonal rainfall in explaining and predicting the numerical fluctuations of these two kangaroo rats. We found that logistic models fit both data sets quite well; Dipodomys merriami showed lower maximum per capita growth rates than Dipodomys ordii, and in both cases logistic models were nonlinear. Summer rainfall appears to be the most important exogenous effect for both rodent populations; models including this variable were able to predict independent data better than models including winter rainfall. D. merriami was also negatively affected by another kangaroo rat (Dipodomys spectabilis), consistent with previous experimental evidence. We hypothesized that summer rainfall influences the carrying capacity of the environment by affecting seed availability and the intensity of intraspecific competition.

Geographic patterns of genetic differentiation within the restricted range of the endangered Stephens' kangaroo rat Dipodomys stephensi.

Using mtDNA variation in the kangaroo rat Dipodomys stephensi, we found no support for the hypothesis that a species with an historically restricted range will exhibit low levels of genetic polymorphism and little genetic structure. Dipodomys stephensi has long been restricted to a few interior coastal valleys in southern California encompassing an area of approximately 70 x 40 km; however, we found high levels of genetic variation over much of its range and significant genetic structure both within and between regions. We also found evidence for a recent range expansion. Dipodomys stephensi is a federally endangered species that is separated from D. panamintinus, its presumed sister taxon, by a mountain range to the north. We assessed genetic variation by sequencing 645 bases of the mitochondrial d-loop from 61 individuals sampled from 16 locations across the species range and rooted their relationship using two D. panamintinus individuals. Despite its limited geographic range, the level of mtDNA variation in D. stephensi is comparable to that of other rodents, including that of the more widely distributed D. panamintinus. This variation revealed significant regional differentiation. The northern, central, and southern regions of the range differ in both the level and the distribution of genetic variation. Phylogenetic analysis revealed that the center of the range contains the most diversity of lineages, including the most basal. In this region and in the north, most haplotypes were found at only a single location (25/29), or at a pair of nearby locations (3/29). In addition, related haplotypes clustered geographically. These results are consistent with long-term demographic stability characterized by limited dispersal and high local effective population size. Further support for this conclusion is the finding of unique diversity in two northern peripheral populations, Norco and Potrero Creek (PC). However, in sharp contrast, one haplotype (CC) was found at five of 11 central and northern locations and comprised 18% of individuals sampled. The atypical distribution of the CC haplotype reflected a pattern seen more strongly in the southern region. Here the CC haplotype comprised 69% of the sample and was found at all five sampling locations. Consequently, the southern region had very low genetic variability. We propose that this dominance of CC was probably due to a local population bottleneck that occurred during a recent range expansion into the southern region.