Landscape limits gene flow and drives population structure in Agassiz’s desert tortoise (Gopherus agassizii)

Abstract

Distance, environmental heterogeneity and local adaptation can strongly influence population structure and connectivity. Understanding how these factors shape the genomic landscape of threatened species is a major goal in conservation genomics and wildlife management. Herein, we use thousands (6,859) of single nucleotide polymorphism markers and spatial data from hundreds of individuals (n = 646) to re-evaluate the population structure of Agassiz’s desert tortoise (Gopherus agassizii). Analyses resolve from 4 to 8 spatially well-defined clusters across the range. Western, central, and southern populations within the Western Mojave recovery unit are consistent throughout, while analyses sometimes merge other recovery units depending on the level of clustering. Causal modeling consistently associates genetic connectivity with least-cost distance, based on multiple landscape features associated with tortoise habitat, better than geographic distance. Some features include elevation, soil depth, rock volume, precipitation, and vegetation coverage, suggesting that physical, climatic, and biotic landscape features have played a strong evolutionary role restricting gene flow between populations. Further, 12 highly differentiated outlier loci have associated functions that may be involved with neurogenesis, wound healing, lipid metabolism, and possibly vitellogenesis. Together, these findings have important implications for recovery programs, such as translocations, population augmentation, reproduction in captivity and the identification of ecologically important genes, opening new venues for conservation genomics in desert tortoises.

Using movement to inform conservation corridor design for Mojave desert tortoise

“…Dispersal is still poorly understood within the Gopherus genus, and we did not have any tortoises with GPS loggers make large dispersal movements during the study period. While populations of the Mojave desert tortoise were historically continuously distributed across suitable habitat in the Mojave and Colorado deserts [31,32], populations of the closely related Sonoran desert tortoise, Gopherus morafkai, are mostly confined to discrete foothill habitats [96,112,113]. Genetic analysis has shown that these patchy populations were historically connected by individuals dispersing through relatively unsuitable resident habitat in valleys; this behavior of dispersing through unsuitable resident habitat is not known in Mojave desert tortoise but could occur and play a role in maintaining genetic connectivity [108].…”

A range‐wide model of contemporary, omnidirectional connectivity for the threatened Mojave desert tortoise

“…Fish and Wildlife Service 2011). A number of genetic connectivity studies have shed light on restricted gene flow due to the long-term limiting factors on dispersal (i.e., over multiple generations; Hagerty et al 2011, S anchez-Ram ırez et al 2018). Although the model we present here represents a first approximation of potential habitat connectivity for the Mojave desert tortoise, it does account for many of the underlying, contemporary drivers of movement and dispersal that are not reflected in existing models or maps.…”

“…, Sánchez‐Ramírez et al. ). However, genetic studies might not detect the effects of landscape fragmentation for many generations, which can amount to over a century for this long‐lived species (U.S.…”

Refining genetic boundaries for Agassiz’s desert tortoise (Gopherus agassizii) in the western Sonoran Desert: the influence of the Coachella Valley on gene flow among populations in southern California

“…Although GUs have been defined for G. agassizii (Murphy et al 2007, Sánchez-Ramírez et al 2018, these studies did not include sampling from near the southwestern limits of the species range (e.g., populations surrounding the Coachella Valley; Berry and Murphy 2019). The low density or absence of tortoises in much of the area surrounding the Coachella Valley is due to the lack of suitable habitat in such low elevation areas (much of which is below sea level) and environmental conditions that are physiologically challenging for sustaining G. agassizii populations (reviewed by Ernst andLovich 2009, Berry andMurphy 2019).…”