Conservation Genetics

, Volume 16, Issue 5, pp 1025–1039 | Cite as

Defining population structure and genetic signatures of decline in the giant gartersnake (Thamnophis gigas): implications for conserving threatened species within highly altered landscapes

  • Dustin A. WoodEmail author
  • Brian J. Halstead
  • Michael L. Casazza
  • Eric C. Hansen
  • Glenn D. Wylie
  • Amy G. Vandergast
Research Article


Anthropogenic habitat fragmentation can disrupt the ability of species to disperse across landscapes, which can alter the levels and distribution of genetic diversity within populations and negatively impact long-term viability. The giant gartersnake (Thamnophis gigas) is a state and federally threatened species that historically occurred in the wetland habitats of California’s Great Central Valley. Despite the loss of 93 % of historic wetlands throughout the Central Valley, giant gartersnakes continue to persist in relatively small, isolated patches of highly modified agricultural wetlands. Gathering information regarding genetic diversity and effective population size represents an essential component for conservation management programs aimed at this species. Previous mitochondrial sequence studies have revealed historical patterns of differentiation, yet little is known about contemporary population structure and diversity. On the basis of 15 microsatellite loci, we estimate population structure and compare indices of genetic diversity among populations spanning seven drainage basins within the Central Valley. We sought to understand how habitat loss may have affected genetic differentiation, genetic diversity and effective population size, and what these patterns suggest in terms of management and restoration actions. We recovered five genetic clusters that were consistent with regional drainage basins, although three northern basins within the Sacramento Valley formed a single genetic cluster. Our results show that northern drainage basin populations have higher connectivity than among central and southern basins populations, and that greater differentiation exists among the more geographically isolated populations in the central and southern portion of the species’ range. Genetic diversity measures among basins were significantly different, and were generally lower in southern basin populations. Levels of inbreeding and evidence of population bottlenecks were detected in about half the populations we sampled, and effective population size estimates were well below recommended minimum thresholds to avoid inbreeding. Efforts focused on maintaining and enhancing existing wetlands to facilitate dispersal between basins and increase local effective population sizes may be critical for these otherwise isolated populations.


Population structure Genetic diversity Thamnophis gigas Microsatellite Bottleneck Effective population size Fragmentation 



We wish to thank Tag N. Engstrom for contributing tissues and DNAs from previous studies. We also wish to thank Jimmy Jo Rabbers for his assistance with the copious number of DNA extractions. Finally, we thank Erica Fleishman, Jonathan Richmond, and anonymous reviewers for their comments that greatly improved this manuscript. Support for this project was provided by the Brookfield Natomas LLC and the Western Ecological Research Center. Samples for this project were collected under U.S. Fish and Wildlife Service recovery permit TE-157216-2 and California Scientific Collecting Permit 003004 and accompanying Memorandum of Understanding. Support for tissues collected by the California Department of Fish and Wildlife at Gray Lodge Wildlife Area was provided through an Endangered Species Act Section 6 grant administered by the U.S. Fish and Wildlife Service. This study was approved by the Western Ecological Research Center Animal Care and Use Committee in association with the University of California, Davis. Any use of trade, product, or firm names is for descriptive purposes only and does not imply endorsement by the U.S. Government.

Supplementary material

10592_2015_720_MOESM1_ESM.docx (1.4 mb)
Supplementary material 1 (DOCX 1457 kb)


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Copyright information

© Springer Science+Business Media Dordrecht (outside the USA) 2015

Authors and Affiliations

  • Dustin A. Wood
    • 1
    Email author
  • Brian J. Halstead
    • 2
  • Michael L. Casazza
    • 2
  • Eric C. Hansen
    • 3
  • Glenn D. Wylie
    • 2
  • Amy G. Vandergast
    • 1
  1. 1.U.S. Geological SurveyWestern Ecological Research CenterSan DiegoUSA
  2. 2.U.S. Geological SurveyWestern Ecological Research CenterDixonUSA
  3. 3.Consulting Environmental BiologistSacramentoUSA

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