Trypanosoma (Herpetosoma) diversity in rodents and lagomorphs of New Mexico with a focus on epizootological aspects of infection in Southern Plains woodrats (Neotoma micropus)

Protozoan parasites of the genus Trypanosoma infect a broad diversity of vertebrates and several species cause significant illness in humans. However, understanding of the phylogenetic diversity, host associations, and infection dynamics of Trypanosoma species in naturally infected animals is incomplete. This study investigated the presence of Trypanosoma spp. in wild rodents and lagomorphs in northern New Mexico, United States, as well as phylogenetic relationships among these parasites. A total of 458 samples from 13 rodent and one lagomorph species collected between November 2002 and July 2004 were tested by nested PCR targeting the 18S ribosomal RNA gene (18S rRNA). Trypanosoma DNA was detected in 25.1% of all samples, with the highest rates of 50% in Sylvilagus audubonii, 33.1% in Neotoma micropus, and 32% in Peromyscus leucopus. Phylogenetic analysis of Trypanosoma sequences revealed five haplotypes within the subgenus Herpetosoma (T. lewisi clade). Focused analysis on the large number of samples from N. micropus showed that Trypanosoma infection varied by age class and that the same Trypanosoma haplotype could be detected in recaptured individuals over multiple months. This is the first report of Trypanosoma infections in Dipodomys ordii and Otospermophilus variegatus, and the first detection of a haplotype phylogenetically related to T. nabiasi in North America in S. audubonii. This study lends important new insight into the diversity of Trypanosoma species, their geographic ranges and host associations, and the dynamics of infection in natural populations.

Ultraviolet vision in Ord’s kangaroo rat (Dipodomys ordii)

Knowledge of a species’ visual system has far reaching implications that affect our understanding of a species’ ecology and evolutionary history. As a model taxon, the heteromyid rodent genus Dipodomys has been valuable in elucidating patterns and mechanisms in biomechanics, ecology, adaptive physiology, biogeography, and more. Although studied extensively, the visual system of Dipodomys has not been described beyond anecdotal mention of their large eyes. Here, the transmittance parameters of the cornea and lens of Ord’s kangaroo rat (Dipodomys ordii) were analyzed and photoreceptor proteins (opsins) expressed in the retina were identified with immunohistochemical (IHC) labeling. Retina maps were constructed to illustrate the relative densities of photoreceptor cells expressing short wavelength (SWS1) opsins, middle/long wavelength (MW/LW) opsins, and rhodopsin (RH1). The retina of D. ordii has variable densities of SWS1 opsin with the highest density being ventral to the optic nerve, high density of MW/LW opsin, and uniform distribution and high density of RH1 across the retina. Our results suggest that D. ordii has a UV-sensitive visual system. Composition and densities of MW/LW- and SWS1-expressing cells resemble that of a crepuscular/diurnal species thereby supporting previous authors who have reported such activity patterns. Uniform retinal distribution of RH1 indicates visual acuity at night, also confirming the paradigm of D. ordii as primarily a nocturnal species and suggesting visual acuity at all times of the day in the species. These results demonstrate not only that the species is capable of UV vision and has a retina characteristic of a diurnal mammal, but that many previously unknown photic niche selective advantages likely have shaped the evolution and ecology of this model taxon.

V genes in rodents from whole genome sequencing data

We studied the V exons of 14 rodent species obtained from whole genome sequencing (WGS) datasets. Compared to other mammals, we found an increase in the number of immunoglobulin (IG) V genes in the heavy (IGH) and kappa chain (IGK) loci. We provide evidence for a reduction genes in lambda chain (IGL) locus, disappearing entirely in one of the species (Dipodomys ordii). We show relationships amongst the V genes of the T-cell receptors (TR) found in primates, possessing ortholog sequences between them. As compared with other mammals, there is an increase in the number of TRAV genes within rodents. Such an increase within this locus is caused by duplication events involving a few putative V genes. This duplication phenomenon does not occur in the TRBV locus. In those species that underwent an expansion of TRAV genes, we found that they also have a correspondingly larger number of MHC Class I genes. The results suggest that selective pressures have conditioned the expansion of V genomic repertoire the TRA, IGK and IGH loci during the diversification process of rodents.