Harnessing the power of whole genome sequencing for the conservation and management of marine organisms

Abstract

Whole genome sequencing (WGS) has become increasingly affordable, and it is particularly useful for characterizing the distribution of neutral and adaptive genetic variation across space and time in marine systems. In this dissertation, I provide practical resources for a cost-effective WGS strategy and use real and simulated data to demonstrate the utilities of WGS in the population genetics and conservation of marine organisms. Low-coverage WGS (lcWGS) has emerged as a powerful WGS approach. However, it requires specialized analytical tools. It is also unclear what the best practices are when designing a lcWGS experiment. In the first chapter, I provide an overview of software packages for low-coverage data. I assess the accuracy of different population genetic inferences under different sequencing designs. I show that spreading a given amount of sequencing effort across more samples is generally preferable, with a few exceptions. A key strength of lcWGS is that pre-existing datasets can be combined and reused. However, a common concern is that non-biological differences between datasets may confound real biological patterns, a problem known as batch effects. In the second chapter, I combine two lcWGS datasets and show that batch effects are rampant. I demonstrate that they result from multiple technical artifacts, and that they can be detected and mitigated with simple bioinformatic strategies. When combined with an artificial selection experiment, WGS becomes a powerful tool to detect the quantitative trait loci (QTLs) of complex traits. In the third chapter, I use forward genetic simulation to build a more realistic model of an artificial selection experiment. I study the power of QTL detection and show that this power is influenced by different aspects of trait architecture. These findings have important implications in the study of fisheries-induced evolution. The genomic processes accompanying a population collapse are a central topic in conservation genomics. In the fourth chapter, I use time-series WGS data to track an Atlantic cod population before and after its collapse. I find that overexploitation has eroded its genetic diversity. There is a lack of strong genetic signatures of fisheries-induced evolution, suggesting that it is potentially reversible on the genetic level.