Population Genomics and Land-Use Change Analysis for Quercus mulleri, a Oaxacan Endemic

Tania Martínez León, Cecilia Liana Alfonso Corrado, Ricardo Clark Tapia, Jorge E. Campos, Nelly Jazmín Pacheco Cruz, and Juan J. Von Thaden Ugalde

Published May 2026 in International Oaks No. 37: 41–48

Abstract

Quercus mulleri is an endemic species of the Sierra Sur of Oaxaca, classified as Critically Endangered by the IUCN due to its small population size and restricted distribution area. However, it is not currently categorized as at risk in Mexico according to NOM-059. Population genomics studies and land-use change analyses are important for the conservation of threatened and endemic species because they allow us to describe patterns of genetic diversity and structure, as well as population size. Additionally, analyses of changes in vegetation cover complement genetic analyses and allow us to infer how these changes have affected genetic diversity and structure. The main objective of this study was to assess genomic and population structural variation, along with conducting an analysis of land-use change between 1979 and 2022 in the locality of San Pedro Sosoltepec in the Sierra Sur of Oaxaca. For genomic variation and population structure, single nucleotide polymorphisms (SNPs) were obtained as molecular markers for the species using a “pools” sequencing approach. A total of 5,541 and 3,726 SNPs were identified for the 11 and 10 analyzed pools, respectively. Intermediate to low levels of genetic diversity were found (He ~ 0.2) with low structuring (FST= 0.021). Overall, the species behaves as a single population, except for pool 2, which showed greater genetic differentiation. The study area experienced a 6.87% loss of forest cover during the evaluated period. Based on these findings, it is suggested to prioritize the conservation and monitoring of the species throughout its distribution area.

Keywords

conservation genomics, single nucleotide polymorphisms, pool sequencing, threatened oak species, habitat fragmentation

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