Sampling Across 20 Years (1996–2017) Reveals Loss of Diversity and Genetic Connectivity in the Coachella Valley Fringe-Toed Lizard (Uma inornata)

Open-File Report 2019-1105
By: , and 



The Coachella Valley fringe-toed lizard (Uma inornata) is a federally threatened, aeolian sand dune obligate, endemic to the Coachella Valley, California. Historically, U. inornata is thought to have formed a large interconnected metapopulation across the valley, with local dune habitat and population size fluctuations linked to stochastic droughts and flooding. Since the 1950s, aeolian habitat in Coachella Valley has declined by 91–95 percent. What remains is highly fragmented by highways and development in the urban communities of the Coachella Valley, raising concerns that fringe-toed lizard movement and gene flow among remaining habitat fragments is limited or nonexistent. We examined population genetic structure across three sample periods (1996, 2008, and 2017). Over that time, this species has shifted from a panmictic condition (1996) with little or no genetic structure between sites to the current (2017) condition where there are now genetically distinct populations. Two severe droughts (2000–04 and 2012–16) may have accelerated this shift through drought-related population declines and subsequent genetic bottlenecks. Using a combination of microsatellite loci and single nucleotide polymorphisms, we found patterns of decreasing genetic connectivity and diversity over time. These patterns are consistent with reduced fringe-toed lizard movement and gene flow among isolated sand dune systems. Low effective population sizes were recovered in some sites, suggesting genetic drift in smaller and fluctuating populations is likely responsible for loss of genetic diversity. A U.S. Fish and Wildlife Service recovery objective for this species is to maintain genetic diversity; however, evidence of fragmentation suggests that genetic cohesiveness has been altered and that the diversity maintained in individual fragments is lower than in the total metapopulation. Management actions that increase genetic diversity could be implemented, including translocation. We modeled increasing gene flow between 1–10 percent, which showed that allelic richness could increase rapidly if translocated individuals can survive and reproduce. Establishing translocation protocols could help to avoid the high mortality that has occurred with other reptile translocations. Successful translocations could be a useful strategy to replenish lost genetic diversity after bottlenecks and could mitigate the loss of natural gene flow among populations.

Suggested Citation

Vandergast, A.G., Wood, D.A., Fisher, M., Barrows, C., Mitelberg, A., and Smith, J.G., 2019, Sampling across 20 years (1996–2017) reveals loss of diversity and genetic connectivity in the Coachella Valley fringe-toed lizard (Uma inornata): U.S. Geological Survey Open-File Report 2019–1105, 20 p.,

ISSN: 2331-1258 (online)

Study Area

Table of Contents

  • Abstract
  • Introduction
  • Methods
  • Results
  • Discussion
  • References Cited
  • Appendix 1. Microsatellite Allelic Richness
Publication type Report
Publication Subtype USGS Numbered Series
Title Sampling across 20 years (1996–2017) reveals loss of diversity and genetic connectivity in the Coachella Valley fringe-toed lizard (Uma inornata)
Series title Open-File Report
Series number 2019-1105
DOI 10.3133/ofr20191105
Year Published 2019
Language English
Publisher U.S. Geological Survey
Publisher location Reston, VA
Contributing office(s) Western Ecological Research Center
Description vi, 20 p.
Country United States
State California
Other Geospatial Coachella Valley
Online Only (Y/N) Y
Google Analytic Metrics Metrics page
Additional publication details