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Recent habitat modification of a tropical dry forest hotspot drives population genetic divergence in the Mexican leaf frog: a landscape genetics approach

Heredity volume 134, pages 306–320 (2025)Cite this article

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Abstract

Tropical dry forests (TDF) are among the ecosystems with the highest deforestation and transformation rates. Because of habitat loss and fragmentation, modified landscapes can impose resistance to the movement of individuals, with important genetic consequences. One of the most affected taxa due to habitat alteration are amphibians, which currently face extreme population declines globally. Here, we used single nucleotide polymorphisms (SNPs) to evaluate genetic diversity, genetic structure, and the effect of landscape elements on genetic connectivity of the Mexican tree frog (Agalychnis dacnicolor) in a TDF biodiversity hotspot in Mexico. We collected samples of 96 individuals from 16 sites located within fragmented areas of TDF and within continuous forest in the Chamela-Cuixmala region. Sampling sites from the fragmented forest showed slightly lower genetic diversity and effective population size compared to those in the continuous forest. We detected three admixed genetic groups, in which most of the sites within the fragmented forest were differentiated from the sites within continuous forest. Although these analyses suggest historical gene flow, we did not detect significant recent migration among the three genetic groups. While original vegetation (TDF + tropical evergreen forest), and in some areas, agriculture facilitated genetic connectivity, open-areas (grasslands + human settlements + exposed soil), and agriculture in other areas limited genetic connectivity in A. dacnicolor. This study helps to understand the factors shaping contemporary population divergence in highly modified complex landscapes, and highlights the importance to maintain connectivity in a rapidly changing ecosystem.

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Fig. 1: Map of the study landscape indicating the 16 sampling sites where we collected 96 individuals of A. dacnicolor within continuous (green dots) and fragmented forest (yellow dots) in the Chamela–Cuixmala region.
Fig. 2: Assignment probabilities of Agalychnis dacnicolor individuals to genetic groups (K) performed in ADMIXTURE.
Fig. 3: Assignment probabilities of Agalychnis dacnicolor individuals to genetic groups (K) performed in Admixture.
Fig. 4: Discriminant analysis of principal components (DAPC).
Fig. 5: Current flow density maps from the combined optimized surface models that best explained genetic distance (original vegetation, open areas, and agriculture), showing a gradient of genetic connectivity of Agalychnis dacnicolor across the studied landscape.

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Data availability

Raw sequence reads and metadata are deposited to Sequence Read Archive (SRA) in NCBI, under BioProject PRJNA1233838 (accession nos. SAMN47280615 – SAMN47280700). SNPs dataset from the de novo alignment is accessible at OSF open platform (https://osf.io/ph623).

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Acknowledgements

We thank Pedro Castillo, Alberto Sánchez, Yessenia Fraga, Jorge Marroquin, and Ariana González for field assistance, as well as Katherine Renton and the staff of the Estación de Biología Chamela (UNAM) for their logistic support. We also thank N. Bayona from the BadDNA@UGA facility for library preparation and sequencing; Eva María Piedra and Violeta Patiño for advise in molecular work; Jessica Pérez, Victor Piñeros, Andreia Malpica and Christian Morán, María Camila Latorre, and Ingrid Lara for assistance with genomic analyses; Rafael Hernández-Guzmán and Xochiquetzal Cortés for their support in landscape analyses; Emmanuel Villafán for his help in using the computer cluster Huitzilin of the Instituto de Ecología, A. C.; Frank Hailer and three anonymous reviewers who provided useful comments on a previous version of the manuscript. This research was funded by the Consejo Nacional de Humanidades Ciencias y Tecnologías (CONAHCYT) through a project grant (PDCPN 2015-1250) to Clementina González. This study constitutes partial fulfilment of Sara Covarrubias’ doctoral degree (Programa Institucional de Doctorado en Ciencias Biológicas at the Universidad Michoacana de San Nicolás de Hidalgo).

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Author notes

  1. Sara Covarrubias

    Present address: Laboratorio de Investigación Interdisciplinaria, Escuela Nacional de Estudios Superiores Unidad León, Universidad Nacional Autónoma de México, León, Guanajuato, México

Authors and Affiliations

  1. Instituto de Investigaciones sobre los Recursos Naturales, Universidad Michoacana de San Nicolás de Hidalgo, San Juanito Itzicuaro s/n Col. Nva. Esperanza, 58337, Morelia, Michoacán, México

    Sara Covarrubias & Clementina González

  2. Red de Biología Evolutiva, Instituto de Ecología A.C. Carretera Antigua a Coatepec 351, El Haya, 91070, Xalapa, Veracruz, México

    Carla Gutiérrez-Rodríguez

Authors
  1. Sara Covarrubias
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  2. Carla Gutiérrez-Rodríguez
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  3. Clementina González
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Contributions

CG conceived the study. SC, CG-R and CG developed the ideas and designed data collection and analyses. SC collected and analyzed the data with input of CG and CG-R. SC, CG-R and CG participated in manuscript conceptualization and writing.

Corresponding authors

Correspondence to Carla Gutiérrez-Rodríguez or Clementina González.

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Competing interests

The authors declare no competing interests.

Ethical approval

All sampling procedures were conducted with the permissions of Mexico’s Secretaría de Medio Ambiente y Recursos Naturales, Subsecretaría de Gestión para la Protección Ambiental, Dirección General de Vida Silvestre (permit numbers: SGPA/DGVS/10390/17 and SGPA/DGVS/05374/19).

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Associate editor: Frank Hailer.

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Covarrubias, S., Gutiérrez-Rodríguez, C. & González, C. Recent habitat modification of a tropical dry forest hotspot drives population genetic divergence in the Mexican leaf frog: a landscape genetics approach. Heredity 134, 306–320 (2025). https://doi.org/10.1038/s41437-025-00761-1

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