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Population genomics applications for conservation: the case of the tropical dry forest dweller Peromyscus melanophrys

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Abstract

Recent advances in genomic sequencing have opened new horizons in the study of population genetics and evolution in non-model organisms. However, very few population genomic studies have been performed on wild mammals to understand how the landscape affects the genetic structure of populations, useful information for the conservation of biodiversity. Here, we applied a genomic approach to evaluate the relationship between habitat features and genetic patterns at spatial and temporal scales in an endangered ecosystem, the Tropical Dry Forest (TDF). We studied populations of the Plateau deer mouse Peromyscus melanophrys to analyse its genomic diversity and structure in a TDF protected area in the Huautla Mountain Range (HMR), Mexico based on 8209 SNPs obtained through Genotyping-by-Sequencing. At a spatial scale, we found a significant signature of isolation-by-distance, few significant differences in genetic diversity indices among study sites, and no significant differences between habitats with different levels of human perturbation. At a temporal scale, while genetic diversity levels fluctuated significantly over time, neither seasonality nor disturbance levels had a significant effect. Also, outlier analysis revealed loci potentially under selection. Our results suggest that the population genetics of P. melanophrys may be little impacted by anthropogenic disturbances, or by natural spatial and temporal habitat heterogeneity in our study area. The genome-wide approach adopted here provides data of value for conservation planning, and a baseline to be used as a reference for future studies on the effects of habitat fragmentation and seasonality in the HMR and in TDF.

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Acknowledgements

Computations were performed using the Cornell University Biotechnology Resource Center (BRC) and Bioportal (University of Oslo). Trapping was done under permit FAUT-0251 extended to DVG. Valentino Sorani provided data for analysis of satellite images. The Centro de Investigación en Biodiversidad y Conservación, Universidad Autónoma del Estado de Morelos (CIByC-UAEM) provided logistical facilities. DVG thanks field assistance of Martín Cadena, Edgard Mason, Evodio Rendón and Amantina Lavalle (CIByC-UAEM). We acknowledge Robert Elshire, Sharon E. Mitchell and Charlotte Acharya (Institute for Genomic Diversity, Cornell University) for their help on Genotyping-by-Sequencing.

Funding

This project was partly funded by the Cornell Center for Comparative and Population Genomics (3CPG), Consejo Nacional de Ciencia y Tecnología (CONACyT; J3490-V), Secretaría de Medio Ambiente-CONACyT (C01-0794) and Programa Volkswagen “Por Amor al Planeta”. RV was funded by the Programa de Becas Postdoctorales, Universidad Nacional Autónoma de México (UNAM). EVD acknowledges financial support from the Instituto de Ecología, UNAM.

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    1. Ecology Research Group, Section of Life Sciences, School of Human and Life Sciences, Canterbury Christ Church University, North Holmes Road, Canterbury, Kent, CT1 1QU, UK

      Rodrigo Vega & Thomas A. White

    2. Department of Ecology and Evolutionary Biology, Cornell University, Corson Hall, Ithaca, NY, 14853-2701, USA

      Rodrigo Vega, Thomas A. White & Jeremy B. Searle

    3. Departamento de Ecología de la Biodiversidad, Instituto de Ecología, Universidad Nacional Autónoma de México (UNAM), Ciudad Universitaria, 04510, México, DF, México

      Rodrigo Vega & Ella Vázquez-Domínguez

    4. Centro de Investigación en Biodiversidad y Conservación (CIByC), Universidad Autónoma del Estado de Morelos (UAEM), Cuernavaca, Morelos, México

      David Valenzuela-Galván

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    Rodrigo Vega and Ella Vázquez-Domínguez have contributed equally to this work.

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    Vega, R., Vázquez-Domínguez, E., White, T.A. et al. Population genomics applications for conservation: the case of the tropical dry forest dweller Peromyscus melanophrys . Conserv Genet 18, 313–326 (2017). https://doi.org/10.1007/s10592-016-0907-5

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