SG: Selection in Bottlenecked Populations

University Of California-Los Angeles, Los Angeles CA

Investigators

Abstract

This study will examine genetic changes in sea otter populations using samples from Pre-Columbian to Modern times. Many rare or endangered species have experienced sharp population declines known as population "bottlenecks". These bottlenecks can have deleterious genetic impacts similar to inbreeding and affect the probability of species recovery. Understanding and quantifying these effects in populations allows for more effective management and better prediction of survival outcomes. A model example of a species that has experienced population bottlenecks is the sea otter. It was hunted almost to extinction, with numerical declines of >99% during the course of the 18th -19th century fur trade. The small number of surviving otters increased over the 20th century under careful monitoring and enhanced protection. In this project, the researchers will endeavor to determine whether the fur trade decline had lasting impacts on the sea otter genome that can be observed in extant populations. The researchers will compare genomes of sea otters that lived before the fur trade to those living today across the entire geographic range. Native American rubbish deposits, known as middens, dating back to Pre-Columbian times will supply the prehistoric and historical samples. The researchers will use cutting-edge gene sequencing technology to identify deleterious genes and predict their effect on individuals and populations. The results will inform future management plans for these populations and provide a new precedent for research on rare and endangered species. Researchers also will work with the Monterey Bay Aquarium and Smithsonian Conservation Biology Institute to create exhibits demonstrating how genome sequencing can aid conservation efforts and provide new genomic insights into a charismatic species that has an essential role in maintaining coastal kelp forest ecosystems. This project will utilize low and high coverage genome sequencing of individuals from six modern and three ancient pre-bottlenecked sea otter populations to reconstruct demographic history and quantify patterns of deleterious variation as a proxy for genetic load. A novel analytical framework will be developed using genetic variation data across multiple time points to study the relationship between small population size and patterns of deleterious mutations. Using forward-in-time simulations, null expectations of how genetic drift should act on different genomic elements will be developed for comparison to the empirical genomic dataset, and the importance of natural selection in preserving and purging deleterious variation will be quantified. The roles of purifying, relaxed and balancing selection will be examined by testing for enrichment of deleterious variation across genic regions. This research will provide a framework for distinguishing between moderately and strongly deleterious mutations and for evaluating the effects of bottlenecks on natural selection at the molecular level that can be applicable to other systems. As a result of this research, a variety of recent demographic events in a species with a complex demographic history will be detected and quantified, patterns of deleterious mutations across multiple time points will be compared, and patterns of genetic load will be predicted. Finally, the ways in which purifying and balancing selection are affected by small population sizes will be evaluated. The replication of recent extreme demographic events across sea otter populations and the abundance of pre-fur trade otter samples in Pre-Columbian middens provide unprecedented opportunities to isolate the effects of a bottleneck on deleterious variation and genetic load. The results and methods developed in this study will be broadly applicable to understanding the biology of small populations, especially those that are endangered.