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

Journal article


Vega, R., Vázquez-Domínguez, E., White, T., Valenzuela-Galván, D. and Searle, J. 2016. Population genomics applications for conservation: the case of the tropical dry forest dweller Peromyscus melanophrys. Conservation Genetics. https://doi.org/10.1007/s10592-016-0907-5
AuthorsVega, R., Vázquez-Domínguez, E., White, T., Valenzuela-Galván, D. and Searle, J.
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 8,209 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.

KeywordsPeromyscus melanophrys; Population genomics; Population genetics
Year2016
JournalConservation Genetics
PublisherSpringer
ISSN1566-0621
Digital Object Identifier (DOI)https://doi.org/10.1007/s10592-016-0907-5
FunderCornell Center for Comparative and Population Genomics (3CPG)
Consejo Nacional de Ciencia y Tecnologia (CONACyT; J3490-V)
Secretaria de Medio Ambiente-CONACyT (C01-0794)
Programa Volkswagen Por Amor al Planeta
Programa de Becas Postdoctorales, Universidad Nacional Autonoma de Mexico (UNAM)
Instituto de Ecologia, UNAM.
Publication dates
Online04 Nov 2016
Publication process dates
Deposited09 Nov 2016
Accepted01 Nov 2016
Accepted author manuscript
Output statusPublished
Additional information

Electronic supplementary material The online version of this
article (doi:10.1007/s10592-016-0907-5) contains supplementary
material, which is available to authorized users.

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