Shaping species with ephemeral boundaries: the distribution and genetic structure of desert tortoise


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Journal of Biogeography, Article first published online: November 10, 2015

Taylor Edwards1,2,*,
Mercy Vaughn3,
Philip C. Rosen1,
Cristina Meléndez Torres4,
Alice E. Karl5,
Melanie Culver1,6 and
Robert W. Murphy7

Author Information
1School of Natural Resources and the Environment, The University of Arizona, Tucson, AZ, USA
2University of Arizona Genetics Core, University of Arizona, Tucson, AZ, USA
3Sundance Biology, Inc., Paso Robles, CA, USA
4Comisión de Ecología y Desarrollo Sustentable del Estado de Sonora, Sonora, Mexico
5Davis, CA, USA
6U.S. Geological Survey, Arizona Cooperative Fish and Wildlife Research Unit, University of Arizona, Tucson, AZ, USA
7Royal Ontario Museum, Toronto, ON, Canada
* Correspondence: Taylor Edwards, University of Arizona Genetics Core, 1657 E. Helen Street, room 111, Tucson, AZ 85721, USA.
E-mail: [email protected]

Editor: Brett Riddle
This is an open access article under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non-commercial and no modifications or adaptations are made.



We examine the role biogeographical features played in the evolution of Morafka's desert tortoise (Gopherus morafkai) and test the hypothesis that G. morafkai maintains genetically distinct lineages associated with different Sonoran Desert biomes. Increased knowledge of the past and present distribution of the Sonoran Desert region's biota provides insight into the forces that drive and maintain its biodiversity.


Sonoran Desert biogeographical region; Sonora and Sinaloa, Mexico and Arizona, USA.


We examined wild tortoises from Mexico (n = 155) and Arizona (n = 78), spanning their known distribution. We used mtDNA sequences to reconstruct matrilineal relationships and 25 microsatellite (STR) loci for Bayesian analyses of gene flow. We performed clinal analyses on both mtDNA and STR loci to determine the position and amount of introgression where lineages co-occur. We used GIS to assess the association of genetic structuring with ecological features. We used these data in a hypothesis-driven approach to assess different models of how genetic diversity is maintained and distributed in G. morafkai.


Gopherus morafkai was found to comprise genetically and geographically distinct ‘Sonoran’ and ‘Sinaloan’ lineages. Both lineages occurred in a relatively narrow zone of overlap in Sinaloan thornscrub, where it transitions into Sonoran desertscrub. Limited introgression occurred at the contact zone. The best-fit model suggests that these lineages diverged in parapatry where the distribution of genotypes is environment-dependent and introgression is inhibited by exogenous selection.

Main conclusions

The historically shifting ecotone between tropical deciduous forest and Sonoran desertscrub appears to be a boundary that fostered divergence between parapatric lineages of tortoises. The sharp genetic cline between the two lineages suggests that periods of isolation in temporary refugia due to Pleistocene climatic cycling influenced divergence. Despite incomplete reproductive isolation, the Sonoran and Sinaloan lineages of G. morafkai are on separate evolutionary trajectories.

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