Genomic resources for the North American water vole (Microtus richardsoni) and the montane vole (Microtus montanus)

BackgroundVoles of the genus Microtus are important research organisms, yet genomic resources in the genus are lacking. Providing such resources would benefit future studies of immunology, phylogeography, cryptic diversity, and more.FindingsWe sequenced and assembled nuclear genomes from two subspecies of water vole (Microtus richardsoni) and from the montane vole (Microtus montanus). The water vole genomes were sequenced with Illumina and 10X Chromium plus Illumina sequencing, resulting in assemblies with ~1,600,000 and ~30,000 scaffolds respectively. The montane vole was assembled into ~13,000 scaffolds using Illumina sequencing also. In addition to the nuclear assemblies, mitochondrial genome assemblies were also performed for both species. We conducted a structural and functional annotation for the best water vole nuclear genome, which resulted in ~24,500 annotated genes, with 83% of these receiving functional annotations. Finally, we find that assembly quality statistics for our nuclear assemblies fall within the range of genomes previously published in the genus Microtus, making the water vole and montane vole genomes useful additions to currently available genomic resources.

Babesiosis Survey of Voles of Grand Teton National Park

First described in 1885 by Viktor Babes, babesiosis was the first known arthropod vector-borne disease and the general term for the malaria-like infection due to protozoan parasites of the family Babesiidae of which there are on the order of 100 known species of worldwide distribution (CDC, Hunfeld et al. 2008). The overarching objective of this study is to examine the phylogenetic relatedness of the endemic strain(s) of Babesia microti isolated from voles (Microtus montanus, M. pennsylvanicus) in the Grand Teton National Park to previously described babesia species/strains. In the United States the rodent parasite B. microti is the etiological agent of babesiosis in areas of endemicity with the primary reservoir often described as the white-footed mouse (Peromyscus leucopus) and borne by the arthropod vector the black-legged tick (Ixodes scapularis) (Persing et al. 1992, Mitchell et al. 1996) The primary reservoir within the Grand Teton National Park region has been shown to be the meadow vole (Microtus pennsylvanicus) and the montane vole (Microtus montanus) (Watkins et al. 1991, Peck 1998) It is these reservoir host animals which the present research proposes to investigate. To this end, the research aspects specific to our IACUC proposal are to obtain blood samples for subsequent genotyping of B. microti samples for comparison to those previously isolated from wild populations of voles from the Grand Teton National Park region (Peck 1998). This research generally involves comparing DNA sequences from isolates to those of previously described strains focusing on the B-tubulin genes. This was selected to give a more particular phylogeny than was possible by previously employed methods such as immunoassay, which lacks sensitivity and suffers cross-reactivity, and 16s-ribosomal DNA of the past decade, which lacks specificity relative to the less highly-conserved B-tubulin. These samples will be genotyped by sequencing and comparison against the relatively more recent Genbank B-tubulin sequence data submissions for B. microti variants.

Long-Term Response of Small Mammal Communities to the 1988 Huckleberry Mountain Fire

Biologists have long been interested in the response of small mammals and their habitat following natural disturbances. The Greater Yellowstone Area (GYA) fires of 1988 have provided opportunities to study short and long term responses. This study continues investigations conducted in the 1990’s following identical methodology at the same sites now 21 years post-fire. We live trapped 256 Clethrionomys gapperi (Red-backed Vole), 116 Peromyscus maniculatus (Deer Mouse), 44 Tamius minimus (Least Chipmunk), 28 Zapus princeps (Western Jumping Mouse), two Microtus montanus (Montane Vole), 1 Thomomys talpoides (Northern Pocket Gopher) and 37 shrews (Sorex ssp.). These results support findings from other investigations regarding the initial early dominance of P. maniculatus in burn areas and C. gapperi in control or non-burn areas, and as time has progressed since the burn, differences between burn and control sites (as measured by community diversity indices) has decreased. As expected calculated Shannon diversity indices (H’) in 2009 are higher for at least one of the burn sites than in previous years as the habitat recovers to pre-burn conditions.