Using genomics to quantify Desert tortoise habitat fragmentation

Focus Area

Wildlife & Ecosystems


Natural Resources






1-2 years

Research Idea Scope

Even in remote areas of California, roads are challenging for wildlife-they lead to car strikes, changes in microhabitat characteristics along road boundaries, and large-scale habitat fragmentation. We all suspect that fragmentation in particular is a major effect of roads, and that such fragmentation may have long-term effects on population viability and persistence. However, quantifying these effects is extremely challenging, given the recent construction of most roads. Particularly when using genetic tools to measure gene flow and fragmentation, it may take many generations to accumulate measureable effects of such fragmentation using traditional genetic tools and approaches. We have recently begun working with the California Department of Fish and Wildlife and the US Fish and Wildlife Service to develop and implement a genome-scale approach to studying habitat movements, appropriate habitat corridors, and population fragmentation for the federally endangered desert tortoise, Gopherus agassizii. Here, we propose to build on the data set we are already assembling to examine two critical aspects of the effects of roads on desert tortoise population connectivity. Our proposed project specifically focuses new sampling and analysis on tortoise samples that span a series of highways in the Mojave Desert to examine two specific aspects of highways on tortoise movement and population viability. First, we will increase our sampling of desert tortoises from roughly 250 to about 500 tortoises across the Mojave Desert (California and Nevada) to gain a detailed understanding of the impacts of 1) Interstate highways (I-10, I-15, I-40), US and California state highways (US 395, US 95, CA 247, CA 62, CA 58), and smaller roads (Camp Rock Road, Kelso-Cima Road are two examples) on desert tortoise population connectivity and movement patterns. Second, we will focus on one specific area along California State Highway 58 to evaluate the population genomic consequences of fencing the highway to reduce tortoise mortality (see “Effectiveness of Fences and Culverts for Protecting Desert Tortoises along California State Highway 58. Report to California Energy Commission. William I. Boarman, 1994.” for more details on this fenced roadway). Because we are generating full genome data (that is, sequencing the entire ~3 billion base pairs of the tortoise genome) for each individual tortoise, we have an unprecedented opportunity to quantify the effects of roads and fences on population connectivity in natural tortoise populations. In addition, our unique modeling approach, working with colleagues at USC and UC Davis, allows us to interpret our population genomics data in terms of population viability in the future. This unique approach will allow us to evaluate the effects of different road types, and of road fencing, on the future population viability of tortoises compared to situations with no road or fence, or where structures are in place to reduce the impacts of highways on population fragmentation.

Urgency and Payoff

The desert tortoise is arguably the most important endangered vertebrate in the Mojave with respect to policy issues regarding the effects of roads on conservation and management. It is wide-ranging, slow-moving, iconic and federally listed, making it a key species in our goal of understanding and mitigating the effects of roads on long-term population persistence, and the effects of management tools like fencing on population stability. The species is also continuing to decline, even with the enormous efforts that have been focused on different aspects of its recovery. As alternative energy and tourism continue to grow in importance in the Mojave, roads will become increasingly scrutinized as a key element in tortoise declines. Our ability to quantify the effects of different classes of roads, with different traffic levels, including the efficacy of tortoise-proof fences as a management strategy, are absolutely critical at this point in the development of the desert. Our project will provide this information in a timely manner, and its urgency is at an all-time high. The anticipated benefits of this work are enormous. By quantifying the effects of different classes of highways, with different potential impacts on tortoise movement, we can determine the importance of highways for effective tortoise conservation, including real solutions to those problems. For example, tortoise-proof fences presumably reduce road mortalities but increase the isolating effects of the roads that they flank. Our work will quantify both of these costs and benefits, and work them into population viability models for tortoises in the Mojave, allowing us to make concrete recommendations on whether, and in what cases, fences are an appropriate management tool. Similarly, if our work determines that high-traffic roads form impenetrable barriers to tortoise movement, and if that fragmentation increases the probability that local populations will go extinct, then this creates a powerful incentive to create underpasses or overpasses that allow tortoises to move freely across highways. Such solutions are feasible, but quantifying their benefits has always been a challenge. Our work with tortoise genomics will provide the fine-scale data necessary to evaluate the effectiveness of such solutions across the desert, and whether they are cost-effective. Finally, our approach can be applied to any species with respect to roads, as long as tissue samples are obtainable. We therefore also view our work as a model for additional studies using genome-level data to study the impacts of highways on natural populations, and the solutions to those impacts.

Suggested By

H. Bradley Shaffer UCLA 530-902-3078

[email protected]