Swine global genomic resources: insights into wild and domesticated populations.

Suids, both domesticated and wild, are found on all continents except for Antarctica and provide valuable food resources for humans in addition to serving as important models for biomedical research. Continuing advances in genome sequencing have allowed researchers to compare the genomes from diverse populations of suids helping to clarify their evolution and dispersal. Further analysis of these samples may provide clues to improve disease resistance/resilience and productivity in domestic suids as well as better ways of classifying and conserving genetic diversity within wild and captive suids. Collecting samples from diverse populations of suids is resource intensive and may negatively impact endangered populations. Here we catalog extensive tissue and DNA samples from suids in collections in both Europe and North America. We include samples that have previously been used for whole genome sequencing, targeted DNA sequencing, RNA sequencing, and reduced representation bisulfite sequencing (RRBS). This work provides an important centralized resource for researchers who wish to access published databases.

First assessment of weeks-to-negative processing fluids in breeding herds after a Senecavirus A outbreak.

Senecavirus A (SVA) causes vesicular disease in swine and has been responsible for a rampant increase in the yearly number of foreign animal disease investigations conducted in the United States. Diagnostic investigations for SVA are typically performed by sampling animals individually, which is labor-intensive and stressful. Developing an alternative aggregate sampling method would facilitate the detection of this virus at the population level. In a preliminary study, SVA was detected in processing fluids (PF) collected in a breeding herd before and after outbreak detection. The objective of this study was to estimate the average number of weeks PF remain SVA-positive after an SVA outbreak. Ten farrow-to-wean breeding herds volunteered to participate in this studyby longitudinally collecting PF samples after an SVA outbreak was detected and submitting samples for RT-rtPCR testing. The PF samples from the 10 farms were SVA-positive for an average of 11.8 weeks after the outbreak. Here, we show that testing of PF may be a cost-effective method to detect SVA and help halt its spread in SVA-endemic regions.

Elephant natural history: a genomic perspective.

We review DNA-based studies of elephants and recently extinct proboscideans. The evidence indicates that little or no nuclear gene flow occurs between African savanna elephants (Loxodonta africana) and African forest elephants (Loxodonta cyclotis), establishing that they comprise separate species. In all elephant species, males disperse, whereas females remain with their natal social group, leading to discordance in the phylogeography of nuclear and mitochondrial DNA patterns. Improvements in ancient DNA methods have permitted sequences to be generated from an increasing number of proboscidean fossils and have definitively established that the Asian elephant (Elephas maximus) is the closest living relative of the extinct woolly mammoth (Mammuthus primigenius). DNA-based methods have been developed to determine the geographic provenance of confiscated ivory in an effort to aid the conservation of elephants.