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Depauperate major histocompatibility complex variation in the endangered reticulated flatwoods salamander (Ambystoma bishopi)

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Abstract

Reticulated flatwoods salamander (Ambystoma bishopi) populations began decreasing dramatically in the 1900s. Contemporary populations are small, isolated, and may be susceptible to inbreeding and reduced adaptive potential because of low genetic variation. Genetic variation at immune genes is especially important as it influences disease susceptibility and adaptation to emerging infectious pathogens, a central conservation concern for declining amphibians. We collected samples from across the extant range of this salamander to examine genetic variation at major histocompatibility complex (MHC) class Iα and IIβ exons as well as the mitochondrial control region. We screened tail or toe tissue for ranavirus, a pathogen associated with amphibian declines worldwide. Overall, we found low MHC variation when compared to other amphibian species and did not detect ranavirus at any site. MHC class Iα sequencing revealed only three alleles with a nucleotide diversity of 0.001, while MHC class IIβ had five alleles with a with nucleotide diversity of 0.004. However, unique variation still exists across this species’ range with private alleles at three sites. Unlike MHC diversity, mitochondrial variation was comparable to levels estimated for other amphibians with nine haplotypes observed, including one haplotype shared across all sites. We hypothesize that a combination of a historic disease outbreak and a population bottleneck may have contributed to low MHC diversity while maintaining higher levels of mitochondrial DNA variation. Ultimately, MHC data indicated that the reticulated flatwoods salamander may be at an elevated risk from infectious diseases due to low levels of immunogenetic variation necessary to combat novel pathogens.

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Acknowledgments

We are thankful to A. Perez-Umphrey, C. Rutt, A. Snider, A. Settlecowski, A. Bresnan, and T. Turner for extensive edits to this manuscript as well as Dr. Kim Terrell and Dr. Chris Austin, for their support and helpful comments. Thank you to everyone who helped in sample acquisition: K. Jones, B. Rincon, V. Porter, C. Abeles, A. Farmer, P. Hill, L. Smith, R. Bilbow, J. de Silva, K. Erwin, B. Moore, J. Sandoval, and E. Browning. We are grateful to A. Wendt who extracted all of the samples collected on Eglin and to Dr. M. Allender for providing a linearized ranavirus plasmid. Portions of this research were conducted with high-performance computational resources provided by the Louisiana Optical Network Infrastructure (http://www.loni.org). This material is based upon work that is supported by the National Institute of Food and Agriculture, U.S. Department of Agriculture, McIntire Stennis program. Collection of tissue samples and extraction of DNA from salamanders on Eglin Air Force Base was supported by Eglin Air Force Base Jackson Guard, the US Air Force Civil Engineer Center, and the US Fish and Wildlife Service. Salamander samples from Eglin Air Force Base were collected under US Fish and Wildlife Service Threatened and Endangered Species Permit #TE049502 and Virginia Tech IACUC protocols #13-129 and #16-100. Samples from Mayhaw WMA were collected under Georgia Department of Natural Resources scientific collection permit #029, and samples at Garcon Point and Escribano Point were collected under the section 6 agreement between USFWS and Florida Fish and Wildlife Conservation Commission.

Funding

This work would not be possible without the funding provided by Audubon Center for Research of Endangered Species (ACRES) grant. This project/work used Genomics core facilities that are supported in part by COBRE (NIH8 1P30GM118430-02) and NORC (NIH 2P30DK072476) center grants from the National Institutes of Health.

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  1. School of Renewable Natural Resources, Louisiana State University AgCenter, Baton Rouge, LA, 70806, USA

    Steven Tyler Williams & Sabrina S. Taylor

  2. Department of Fish and Wildlife Conservation, Virginia Tech, Blacksburg, VA, 24061, USA

    Carola A. Haas

  3. Department of Biology, Georgia Southern University, Statesboro, GA, 30458, USA

    James H. Roberts

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  1. Steven Tyler Williams
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Williams, S.T., Haas, C.A., Roberts, J.H. et al. Depauperate major histocompatibility complex variation in the endangered reticulated flatwoods salamander (Ambystoma bishopi). Immunogenetics 72, 263–274 (2020). https://doi.org/10.1007/s00251-020-01160-y

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