Conservation genetics in the age of high-throughput sequencing: new tools for old dilemmas

A combination of complex geological and climatological history in California have created a biodiversity “hotspot” with numerous endemic species. Most of the wetlands in the region, such as rivers and coastal lagoons, were shaped by uplift, sea-level change and climatic fluctuations creating a physical template on which genetic diversification of the aquatic biota could unfold. Coastal lagoons, for example, provide important ecological services as well as habitat and nursery for endemic and endangered animals, such as the steelhead (Oncorhynchus mykiss), red-legged frog (Rana aurora draytonii), and the tidewater goby (Eucyclogobius newberryi). However, anthropogenic impacts on the landscape, such as urbanization and water management for human use and/or flood control, have had major impacts on the landscape threatening much of the fauna associated with these wetlands. Such is the case of the rare and endangered unarmored threespine stickleback, Gasterosteus aculeatus williamsoni, found in only a few drainages in southern California. Most of the populations are now extirpated and those that persist have suffered isolation and bottlenecks, as well as inadvertent mixture of distinct lineages and introduction of non-native predators. Many conservation and restoration efforts led by numerous governmental units and NGOs are underway in California. These require decisions informed by more comprehensive understanding of current and extirpated populations, as such information will lead to more successful and effective planning and management. Advancements in molecular techniques, particularly the development of high-throughput sequencing, has made it possible to not only deepen our knowledge on evolution but also to use it as a tool in conservation biology. This revolution allows us to unravel genomic signals of demography and selection, investigate historic data from museum material, and even look at environmental samples collected from soil and water. All the work presented here explores the use of high-throughput sequencing and bioinformatic tools to target relevant conservation issues related to endangered species and habitats in southern California. We expect that results will have an impact on conservation efforts, and techniques can be applied to other systems and fields of interest