Genomic Diversity and Introgression in O. sativa Reveal the Impact of Domestication and Breeding on the Rice Genome

The domestication of Asian rice (Oryza sativa) was a complex process punctuated by episodes of introgressive hybridization among and between subpopulations. Deep genetic divergence between the two main varietal groups (Indica and Japonica) suggests domestication from at least two distinct wild populations. However, genetic uniformity surrounding key domestication genes across divergent subpopulations suggests cultural exchange of genetic material among ancient farmers.In this study, we utilize a novel 1,536 SNP panel genotyped across 395 diverse accessions of O. sativa to study genome-wide patterns of polymorphism, to characterize population structure, and to infer the introgression history of domesticated Asian rice. Our population structure analyses support the existence of five major subpopulations (indica, aus, tropical japonica, temperate japonica and GroupV) consistent with previous analyses. Our introgression analysis shows that most accessions exhibit some degree of admixture, with many individuals within a population sharing the same introgressed segment due to artificial selection. Admixture mapping and association analysis of amylose content and grain length illustrate the potential for dissecting the genetic basis of complex traits in domesticated plant populations.Genes in these regions control a myriad of traits including plant stature, blast resistance, and amylose content. These analyses highlight the power of population genomics in agricultural systems to identify functionally important regions of the genome and to decipher the role of human-directed breeding in refashioning the genomes of a domesticated species

Best Management Practices for Trapping Furbearers in the United States

Humans have used wild furbearers for various purposes for thousands of years. Today, furbearers are sustainably used by the public for their pelts, leather, bones, glands, meat, or other purposes. In North America, contemporary harvest of furbearers has evolved along with trap technologies and societal concerns, and is now highly regulated and more closely coupled with harvest analysis and population monitoring. Traps and regulated trapping programs provide personal or cultural rewards that can also support conservation, and can assist with advancing ecological knowledge through research, protecting endangered species, restoring populations or habitats, protecting personal property, and enhancing public health and safety. However, animal welfare and trap selectivity remain important topics for furbearer management in North America, as they have for more than a century. A related international challenge to modern furbearer management came with the Wild Fur Regulation by the European Union, which passed in 1991. This regulation prohibited use of foothold traps in many European countries and the importation of furs and manufactured fur products to Europe from countries that allowed use of foothold traps or trapping methods that did not meet internationally agreed‐upon humane trapping standards. To address existing national concerns and requirements of the Wild Fur Regulation, the United States and European Union signed a non‐binding bilateral understanding that included a commitment by the United States to evaluate trap performance and advance the use of improved traps through development of best management practices (BMPs) for trapping. Our testing followed internationally accepted restraining‐trap standards for quantifying injuries and capture efficiency, and we established BMP pass‐fail thresholds for these metrics. We also quantified furbearer selectivity, and qualitatively assessed practicality and user safety for each trap, yielding overall species‐specific performance profiles for individual trap models. We present performance data for 84 models of restraining traps (6 cage traps, 68 foothold traps, 9 foot‐encapsulating traps, and 1 power‐activated footsnare) on 19 furbearing species, or 231 trap‐species combinations. We conducted post‐mortem examinations on 8,566 furbearers captured by trappers. Of the 231 trap model‐species combinations tested, we had sufficient data to evaluate 173 combinations, of which about 59% met all BMP criteria. Pooling species, cage traps produced the lowest average injury score (common injuries included tooth breakage), with minimal differences across other trap types; species‐specific patterns were generally similar, with the exception of raccoons (Procyon lotor) for which foot‐encapsulating traps performed better than other foot‐restraining trap types. Padded‐jaw foothold traps performed better than standard‐jaw models for many species, though often similar to and occasionally worse than offset‐ or laminatedjaw models.Most traps we tested had high capture efficiency; only 5 (3%) failed BMP standards strictly because of poor efficiency. Average furbearer selectivity was high across all trap types we evaluated and was lowest for footsnares (88%) and highest for foot‐encapsulating traps (99%). Mortality from trap‐related injury in restraining traps we tested was very rare for furbearers (0.5% of animals). In over 230,000 trap‐nights across a 21‐year period, no individuals of a threatened or endangered species were captured. Of 9,589 total captures, 11% were non‐furbearers, of which 83% were alive upon trap inspection; nearly all non‐furbearer mortalities were birds, rabbits, or squirrels. Approximately 2% of total captures were feral or free‐ranging dogs (Canis familiaris), of which none died or were deemed in need of veterinary care by either our technicians or the owners (if located). Similarly, 3% of total captures were feral or free‐ranging cats (Felis catus); 2 were dead, and although locating potential owners was often impossible, none of the remaining cats were deemed in need of veterinary care by technicians or owners. Our results show that furbearer selectivity was high for all trap types evaluated, mortality or significant injury was very rare for domestic (or feral) animals, and the most potential for mortality or injury of non‐furbearers was with smaller animals, a majority of which were squirrels and rabbits. Our results suggest that injury scores for a given trap‐species combination are unlikely to vary significantly across states or regions of the United States, provided similar methods are employed. Our data also suggest that taxonomic affiliation and body‐size groupings are correlated with injury scores, presumably through morphological, physiological, or behavioral adaptations or responses that influence injury potential during restraint; higher injury scores in foot‐restraining trap types were more likely in smaller or more dexterous species, whereas injury scores were typically lowest for the felids we evaluated. For some species (e.g., American badger [Taxidea taxus], bobcat [Lynx rufus]), most restraining traps we tested met BMP standards, whereas few restraining traps we tested met standards for other species (e.g., muskrat [Ondatra zibethicus], striped skunk [Mephitis mephitis]). Comparison of our results with survey information collected during 2015 on trap use in the United States indicates that approximately 75% of all target furbearers harvested were taken in BMP‐compliant traps, with another 10% taken in traps yet to be tested on that species. Future trap testing and development should focus on commonly used traps not yet tested on a species, species for which few passing traps currently pass BMP criteria, and trap models and modifications most likely to minimize trap injuries given a species morphology, physiology, and behavior. Outreach efforts should focus on general BMP awareness, discouraging use of traps that fail BMP standards for a given species, and public outreach on trapping. Restraining (and other) traps have evolved substantially in recent decades and offer numerous benefits to individuals, conservation, and society. However, continuing to address societal concerns remains a critical component of modern regulated trapping and furbearer management. Published trapping BMPs are regularly updated online and may include additional approved restraining and killing traps that were evaluated as part of testing by Canada. We will periodically update the trap performance tables and figures we presented and make them available online at the Association of Fish and Wildlife Agencies website