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Desert landscape features influencing the microgeographic genetic structure of Nelson’s pocket mouse Chaetodipus nelsoni

Heredity volume 134, pages 21–32 (2025)Cite this article

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Abstract

Elucidating the factors that drive the genetic patterns of natural populations is key in evolutionary biology, ecology and conservation. Hence, it is crucial to understand the role that environmental features play in species genetic diversity and structure. Landscape genetics measures functional connectivity and evaluates the effects of landscape composition, configuration, and heterogeneity on microevolutionary processes. Deserts constitute one of the world’s most widespread biomes and exhibit a striking heterogeneity of microhabitats, yet few landscape genetics studies have been performed with rodents in deserts. We evaluated the relationship between landscape and functional connectivity, at a microgeographic scale, of the Nelson’s pocket mouse Chaetodipus nelsoni in the Mapimí Biosphere Reserve (Chihuahuan desert). We used single-nucleotide polymorphisms and characterized the landscape based on on-site environmental data and from Landsat satellite images. We identified two distinct genetic clusters shaped by elevation, vegetation and soil. High elevation group showed higher connectivity in the elevated zones (1250–1350 m), with scarce vegetation and predominantly rocky soils; whereas that of Low elevation group was at <1200 m, with denser vegetation and sandy soils. These genetic patterns are likely associated with the species’ locomotion type, feeding strategy and building of burrows. Interestingly, we also identified morphological differences, where hind foot size was significantly smaller in individuals from High elevation compared to Low elevation, suggesting the possibility of ecomorphs associated with habitat differences and potential local adaptation processes, which should be explored further. These findings improve our understanding of the genetics and ecology of C. nelsoni and other desert rodents.

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Fig. 1: Map of the study site at the Mapimí Biosphere Reserve (MBR), Mexico for the Nelson’s pocket mouse.
Fig. 2: Raster layers of the four landscape variables at the study site and sampling localities of Chaetodipus nelsoni.
Fig. 3: Morphological metrics of Chaetodipus nelsoni at the study site in the Mapimí Biosphere Reserve, Mexico.
Fig. 4: Genetic structure of Chaetodipus nelsoni at the study site in the Mapimí Biosphere Reserve, Mexico.
Fig. 5: Surface optimization and response curves for Chaetodipus nelsoni at the study site in the Mapimí Biosphere Reserve, Mexico.
Fig. 6: Landscape genetics patterns for Chaetodipus nelsoni.

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Data availability

Input files for population genetic analyses (raw and filtered genomic data files) have been made available on Dryad (https://doi.org/10.5061/dryad.qbzkh18sz).

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Acknowledgements

We are grateful with L. Eguiarte-Fruns and R. López Wilchis for discussions throughout the entire project, with R. Medina and Ó. Romero-Báez for assistance with genomic analyses, and with J. Searle and the people from his laboratory for their help and friendship during GP-S scientific visit. We deeply thank the Instituto de Ecología A.C. and Mr. Francisco Herrera and Mrs. Ernestina Rojas for their devoted support at the Mapimí Field Station. Our gratitude with A. Flores-Manzanero, T. Garrido-Garduño, M. Suárez-Atilano and M. Luna-Bárcenas for their enthusiastic help during fieldwork, S. Castañeda‐Rico and T. Garrido‐Garduño for molecular advice, and A. González and M. Baltazar for computational support. We truly thank the anonymous reviewers which helped us improve the manuscript. GP-S had a scholarship provided by CONACyT (becario 661803) for her Master’s in the Programa de Maestría en Ciencias Biológicas de la Universidad Nacional Autónoma de México (UNAM) and financial support from Programa de Estudios de Posgrado (PAEP 2017 and 2018). The project had financial support from Programa de Apoyo a Proyectos de Investigación e Innovación Tenconlógica granted to EV-D (research grant Papiit IN201716). EV-D received financial support for a sabbatical at the Estación Biológica de Doñana-CSIC from Dirección General de Asuntos del Personal Académico (DGAPA, UNAM; PASPA No. 067/2023) and Consejo Nacional de Humanidades, Ciencias y Tecnologias (CONAHCyT).

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  1. Departamento de Ecología de la Biodiversidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Coyoacán, 04510, Ciudad de México, México

    Gissella Pineda-Sánchez & Ella Vázquez-Domínguez

  2. Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Edificio D, 1er Piso, Unidad de Posgrado, 04510, Ciudad de México, México

    Gissella Pineda-Sánchez

  3. Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana (EBD-CSIC), 41092, Sevilla, España

    Ella Vázquez-Domínguez

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  1. Gissella Pineda-Sánchez
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EV-D conceived the original idea, designed the research and obtained the financial support. EV-D and GP-S conducted the fieldwork. GP-S performed the laboratory work. EV-D and GP-S performed the analyses. EV-D wrote the manuscript and GP-S agreed on the final version and submission of the manuscript.

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Correspondence to Ella Vázquez-Domínguez.

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Procedures were conducted in strict accordance with the guidelines of the American Society of Mammalogists for use of wild mammal species (Sikes 2016) and with the corresponding collecting permits (FAUT 0168). No institutional ethical approval was required given no experimental procedures or killing of individuals were performed.

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Pineda-Sánchez, G., Vázquez-Domínguez, E. Desert landscape features influencing the microgeographic genetic structure of Nelson’s pocket mouse Chaetodipus nelsoni. Heredity 134, 21–32 (2025). https://doi.org/10.1038/s41437-024-00732-y

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