Rob Roy Ramey

Evolution of mammals and their gut microbes

Mammals are metagenomic in that they are composed of not only their own gene complements but also those of all of their associated microbes. To understand the coevolution of the mammals and their indigenous microbial communities, we conducted a network-based analysis of bacterial 16S ribosomal RNA gene sequences from the fecal microbiota of humans and 59 other mammalian species living in two zoos and in the wild. The results indicate that host diet and phylogeny both influence bacterial diversity, which increases from carnivory to omnivory to herbivory; that bacterial communities codiversified with their hosts; and that the gut microbiota of humans living a modern life-style is typical of omnivorous primates.

Genetic relatedness of the Preble's meadow jumping mouse (Zapus hudsonius preblei) to nearby subspecies of Z. hudsonius as inferred from variation in cranial morphology, mitochondrial DNA and microsatellite DNA: implications for taxonomy and conservation

The Preble’s meadow jumping mouse (Zapus hudsonius preblei) is listed as a threatened subspecies under the United States Endangered Species Act (US-ESA). The quantitative description of this subspecies was based on cranial measurements of only three adult specimens. It is one of twelve subspecies of Z. hudsonius and is a peripheral population at the western edge of its range. We tested the uniqueness of Z. h. preblei relative to other nearby subspecies of Z. hudsonius using a hypothesis testing approach and analyses of cranial morphometric, mtDNA sequence and nuclear microsatellite data obtained from museum specimens and archived tissues. Morphometric analysis of variance did not support the original description of Z. h. preblei as a subspecies. Principal component analysis of these data showed Z. h. preblei within the range of variation found in Z. h. campestris and Z. h. intermedius. Discriminant analysis correctly classified only 42% of Z. h. preblei skulls at jackknifed posterior probabilities >0.95 relative to Z. h. campestris. All mtDNA haplotypes found in Z. h. preblei were also found in Z. h. campestris. Simulation based estimates of current and historical gene flow (MDIV) revealed low, but non-zero, mtDNA gene flow among Z. h. preblei and several nearby subspecies. Analyses of five nuclear microsatellite loci using population pairwise FST, BAPS and STRUCTURE were consistent with morphometric and mtDNA results. These revealed low levels of genetic structure and evidence of recent gene flow and bottlenecks inZ.h.preblei. Due to a lack of clearly recognisable genetic, morphological, or adaptive differences, we synonymise Z. h. preblei and Z. h. intermedius with Z. h. campestris. We suggest that candidates for listing under the US-ESA, or similar biodiversity laws, be evaluated for genetic and/or morphological uniqueness to prevent the misallocation of resources to non-distinct taxa like Z. h. preblei.

Spatial relationships and matrilineal kinship in African savanna elephant (Loxodonta africana) clans

African savanna elephants, Loxodonta africana, live in stable family groups consisting of adult females and their dependent offspring. During the dry season, “clans” consisting of several family groups typically share a common home range. We compared spatial relationships and mitochondrial DNA (mtDNA) haplotypes among 14 adult female elephants within 3 clans during the dry season in northern Zimbabwe. Spatial relationships were studied by radio-tracking. Home-range similarity was quantified by correlating the estimated utilization distributions of all pairs of elephants. Clans were identified by cluster analysis of the home-range similarity values. All three clans contained at least two of the five mtDNA haplotypes that were found, indicating that clan members are not necessarily matrilineally related. Within clans, home ranges of elephants with the same haplotype were not significantly more similar to each other than those of elephants with different haplotypes. Most elephants within each clan used their shared home ranges independently of each other: the distribution of distances between their positions at any given time did not differ from the distribution expected by chance. However, 8 out of the 26 within-clan pairs exhibited long-term coordination of space use by remaining within known hearing distance of each other’s low-frequency calls significantly more often than expected by chance. At least four of these coordinated pairs consisted of animals in different family groups. Elephants in three of the four different-family pairs whose movements were coordinated had different haplotypes. Further research is needed to determine the relationship between these coordinated movements and conventionally defined bond-group behavior.