Collaborative Research: Inferring admixture history in non-model organisms using local ancestry detection

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What happens when geological, climatic, or other events cause recently diverged species to be reintroduced to one another? If their evolved genetic differences are not great, the two species may mate and produce hybrid offspring. Between-species crossbreeding, once considered a rare and mostly inconsequential phenomenon, has now been documented in a wide variety of species pairs including brown/polar bears, dog/wolf, cow/bison, and even human/Neanderthal. Importantly, in each of these cases, at least some of the hybrid offspring were viable and fertile as evidenced by tracking genetic exchanges between these species pairs. Each of these past crossbreeding events can be considered a natural experiment across what were thought to be species barriers. This project will develop tools for detecting and analyzing genes that have moved across species. Application of the tool will focus on two species pairs for which past hybridization has been particularly important. Cows and bison were intentionally crossbred by ranchers in the early 1900s, such that most bison carry cow genes. Brown bears and polar bears had several episodes of past crossbreeding,and this continues to occur. Analysis of these species pairs will reveal which genes are refractory to movement across species and which are not. This information will be key to understanding the extent and consequences of future hybridization of any species pair of interest. Outreach to the public, students, and pre-service teachers will occur through a focus on the California Golden Bear and associated educational programs at the California Academy of Sciences. The new flexible ancestry inference tool will be capable of localizing introgressed genomic regions even when only low-coverage DNA sequence data are available. The tool will incorporate complex demographic scenarios, such as multiple pulses of admixture, and will pinpoint regions of the genome that are of potential evolutionary significance by virtue of being high frequency or devoid of admixed ancestry. The application of this tool to two species pairs with known admixture histories will provide new insights into the processes of speciation and local adaptation, with the potential to inform management practices that seek to limit admixed ancestry in populations that are targeted for conservation. In addition, the tool will satisfy the growing need for improved methods of signal detection to infer evolutionary processes, providing the research community with a valuable tool for transforming genomic data into scientific inference.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.