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Genes in space: what Mojave desert tortoise genetics can tell us about landscape connectivity

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Abstract

Habitat loss and fragmentation in the Mojave desert have been increasing, which can create barriers to movement and gene flow in populations of native species. Disturbance and degradation of Mojave desert tortoise habitat includes linear features (e.g. highways, railways, a network of dirt roads), urbanized areas, mining activities, and most recently, utility-scale solar facilities. To evaluate the spatial genetic structure of tortoises in an area experiencing rapid habitat loss, we genotyped 299 tortoises at 20 microsatellite loci from the Ivanpah valley region along the California/Nevada border. We used a Bayesian clustering analysis to quantify population genetic structure across valley and mountain pass habitats. A spatial principal components analysis was used to further investigate patterns with isolation-by-distance. To explicitly consider landscape features (e.g. habitat and anthropogenic linear barriers), we used maximum likelihood population effects analyses. We quantified recent gene flow through relatedness using a maximum likelihood pedigree approach. We detected three genetic clusters that generally corresponded to valleys separated by mountains, with one genetically distinguishable population in a mountain pass. Pedigree analyses showed second order relationships up to 60 km apart suggesting a greater range of interactions and inter-relatedness than previously suspected. Our results support historical gene flow with isolation-by-resistance and reveal reduced genetic connectivity across two parallel linear features bisecting our study area (a railway and a highway). Our work demonstrates the potential for tortoises to use a range of habitats, spanning valleys to mountain passes, but also indicates habitat fragmentation limits connectivity with relatively rapid genetic consequences.

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Acknowledgements

We thank the many individuals who have contributed to the acquisition of data including Kristina Drake, Felicia Chen, Ben Gottsacker, Amanda McDonald, Jordan Schwart, Sara Murray, Steve Hromada, Brett Dickson, and Ironwood Consulting. This work was supported by the U.S. Bureau of Land Management, the U.S. Fish and Wildlife Service, the National Fish and Wildlife Foundation, and the U.S. Geological Survey Ecosystems Mission Area Energy and Wildlife Program. We are particularly grateful to Amy Fesnock (BLM—California) and Mark Slaughter (BLM—Nevada) for their support of our desert tortoise research program. All tortoises were handled according with USFWS Permit (permit TE-030659-10), Nevada Department of Wildlife Scientific Collection Permit 317351, University of Nevada, Reno Animal Care and Use Committee protocol (IACUP 00671), and a Memorandum of Understanding with the California Department of Fish and Wildlife (all to T. Esque). Any use of trade, firm, or product names is for descriptive purposes only and does not imply endorsement by the U.S. Government.

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  1. Department of Geography, University of Nevada, Reno, 1664 N. Virginia St., Reno, NV, 89557, USA

    Kirsten E. Dutcher, Jill S. Heaton & Ken E. Nussear

  2. U.S. Geological Survey, Western Ecological Research Center - San Diego Field Station, 4165 Spruance Rd., Suite 200, San Diego, CA, 92101, USA

    Amy G. Vandergast & Anna Mitelberg

  3. U.S. Geological Survey, Western Ecological Research Center - Henderson Field Station, 160 N. Stephanie St., Henderson, NV, 89074, USA

    Todd C. Esque

  4. Department of Natural Resources and Environmental Science, Program in Ecology, Evolution, and Conservation Biology, University of Nevada, Reno, 1664 N. Virginia St., Reno, NV, 89557, USA

    Marjorie D. Matocq

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  1. Kirsten E. Dutcher
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Dutcher, K.E., Vandergast, A.G., Esque, T.C. et al. Genes in space: what Mojave desert tortoise genetics can tell us about landscape connectivity. Conserv Genet 21, 289–303 (2020). https://doi.org/10.1007/s10592-020-01251-z

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