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Genetic diversity within a population of the southern plains woodrat was examined using DNA sequences (967 base pairs [bp]) obtained from the control or d-loop region of the mitochondrial genome. One hundred fourteen individuals from 10 collection sites were assigned to 42 haplotypes. Haplotype diversity values were moderate to high (0.974 overall and ranged from 0.524 to 0.964 across collecting sites), whereas nucleotide diversity values were low (0.008 overall and ranged from 0.001 to 0.010 across sites), indicating that this population possesses a high number of closely related haplotypes. Seventy-nine percent of the genetic variability was partitioned within groups that corresponded to the collecting sites. In addition, 13 samples from Texas, New Mexico, and Mexico were included as references for evaluating the evolutionary history of haplotypes. Nested clade analysis revealed that restricted gene flow with isolation by distance in conjunction with contiguous range expansion was responsible for the observed pattern of genetic diversity. A test of neutrality supported the diagnosis of restricted gene flow, but failed to support contiguous range expansion due solely to population growth. Examination of the spatial distribution of the haplotypes indicated that most haplotypes were restricted to a single collecting site; however, a small number of haplotypes were found at 2 or more sites. A phylogenetic analysis indicated that some haplotypes (28.6%) were restricted to the study area whereas the remaining haplotypes occupied a broader geographic region.

Nucleotide sequences from the mitochondrial control region and genotypes from 5 nuclear microsatellite loci were used to examine genetic structure and infer recent (within approximately the last 3,000 years) evolutionary history of a population (549 individuals) of the southern plains woodrat (Neotoma micropus). Observed heterozygosity values ranged from 0.61 to 0.89 across microsatellite loci and systematically were lower than expected heterozygosity values (0.66-0.95). Probability of unique identity using microsatellite data was high (1 individual in 66,005,424). Fifty-three mitochondrial haplotypes were obtained from 150 individuals. F(ST) values estimated from sequence and microsatellite data were 0.061 and 0.011, respectively, and the R(ST) for microsatellite data was 0.007. Within-group genetic variation ranged from 93.90% to 99.99% depending on whether sequence or microsatellite data were examined. Analyses of microsatellite data suggested that all sampled individuals belonged to a single population, albeit genetically diverse. However, combined data analyses suggested the presence of low levels of substructure attributable to maternal lineages within the population. Low nucleotide-diversity values (0.007-0.010) in addition to high haplotype-diversity values (0.915-0.933) indicate a high number of closely related haplotypes, and suggest that this population may have undergone a recent expansion. However, Fu's F(S) statistic did not fully support this finding, because it did not reveal a significant excess of recent mutations. A phylogenetic approach using the haplotype sequence data and a combined set including both haplotype and genotype data was used to test for evolutionary patterns and history.

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A total of 3941 rodents were captured during a 46-month prospective (mark-recapture) study on the ecology of Catarina virus in southern Texas. Antibody reactive against Catarina virus was found in 73 (11.9%) of 611 southern plains woodrats (Neotoma micropus) and none of 3330 other rodents; strains of Catarina virus were isolated from 6 antibody-negative and 9 antibody-positive southern plains woodrats; and the infections in at least 3 southern plains woodrats were chronic. These results affirm the notion that the southern plains woodrat is the principal host of Catarina virus and suggest that Catarina virus infection is highly specific to N. micropus.