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Landscape anthropization explains the genetic structure of an endemic Mexican bird (Thryophilus sinaloa: Troglodytidae) across the tropical dry forest biodiversity hotspot

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Abstract

Context

Tropical dry forests (TDFs) are one of the richest and also one of the most threatened ecosystems in the world due to anthropization. In Mexico, only a minimal proportion of TDF is conserved in protected areas, typically surrounded by human-modified landscapes. Habitat modification can impact gene flow, affecting the populations’ genetic structure, and ultimately, the long-term persistence of natural populations.

Objectives

We examined the influence of landscape features on the genetic connectivity of Thryophilus sinaloa, a common and highly territorial TDF-associated bird species. We conducted our study in a Mexican landscape along the Pacific coast characterized by a protected area surrounded by a heterogenous human-modified landscape.

Methods

We genotyped 90 individuals from 20 localities at 24,549 SNPs derived from 3RADseq and de novo assembling techniques to examine the relationship between population genetic patterns and landscape features using a resistance surface optimization framework.

Results

Populations were genetically structured in two groups across the landscape. An open-areas resistance surface, along with geographic distance, reduced genetic connectivity. This finding suggests that protected areas are partially isolated from TDF fragments and other non-protected areas.

Conclusions

Our research highlights the impact of TDF landscape modification by human-induced activities on the genetic connectivity of a common bird. Our study reveals that the only TDF reserve in the region is mostly disconnected from other remnants of non-protected areas of continuous TDF. The increasing deterioration of the habitat could eventually cause a decrease in genetic diversity and effective population size. Moreover, genetic differentiation could be enhanced as habitat patches are more isolated, increasing the likelihood of local extinctions.

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Data availability

Neutral SNPs dataset from the de novo alignment is accessible at OSF open platform (https://osf.io/3unxt/). Scripts of the analyzes performed in R packages can be found in the supplementary information.

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Acknowledgements

We thank A. González-Rodríguez, Y. Rico, R. Hernández-Guzmán, R. Pérez-Rodríguez for providing useful comments on previous versions of the manuscript; L. Zamudio-Beltrán, V. González, M. Mejía, S. Covarrubias, U. Alejandre, A. Sánchez and A. Ceja for field assistance as well as Katherine Renton and the staff of the “Estación de Biología Chamela” (UNAM) for their logistic support; A. K. Howard from the BadDNA@UGA facility for processing and sequencing DNA samples; S. Covarrubias, V. Piñeros, L. Zamudio-Beltrán, J. Pérez-Alquicira, for assistance with genomic analyses; A. Flores-Manzanero for ResistanceGA support; C. Gutiérrez-Rodríguez and E. Villafán for their help using the Huitzilin cluster at INECOL; and M. Mejía for Fig. 1 elaboration. This study constitutes partial fulfillment of Andreia Malpica’ doctoral degree (Programa Institucional de Doctorado en Ciencias Biológicas) at the UMSNH.

Funding

Our research was funded by the Consejo Nacional de Humanidades Ciencias y Tecnologías (CONAHCYT, https://conacyt.mx) through project grant PDCPN 2015-1250 to CG and by a doctoral scholarship (371634) to AM; and by the American Ornithological Society (Alexander Wetmore Memorial Research Award) to AM.

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  1. Instituto de Investigaciones sobre los Recursos Naturales, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán, México

    Andreia Malpica & Clementina González

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  1. Andreia Malpica
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AM and CG conceived the ideas, designed the methodology and collected the data. AM and CG led the manuscript conceptualization and data analysis. AM wrote the original draft. Both authors reviewed, edited and gave final approval for publication.

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Correspondence to Clementina González.

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All sampling activities were adhered to the guidelines on the use of wild birds in research formulated by the Ornithological Council, and with the permission 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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Malpica, A., González, C. Landscape anthropization explains the genetic structure of an endemic Mexican bird (Thryophilus sinaloa: Troglodytidae) across the tropical dry forest biodiversity hotspot. Landsc Ecol 38, 3249–3268 (2023). https://doi.org/10.1007/s10980-023-01777-w

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