Population genomics of the arboreal alligator lizard, Abronia campbelli

Authors

Natalie Winters, Rebecca Meyer, Morgan Muell, and Jamie Oaks

Introduction

Abronia alligator lizards are arboreal reptiles spanning southern Mexico and Central America. Some Abronia species endemic to eastern Guatemala, such as Abronia campbelli and Abronia frosti, are classified as critically endangered (Ariano-Sánchez & Melendez, 2009); the expansion of farmland in this area has left many populations of A. campbelli isolated to single trees. Understanding how the isolation and fragmentation of populations can affect genetic diversity and structure of a species is critical for informing conservation and management efforts. The goal of this project was to investigate whether recent extreme isolation of the agricultural populations has left a signature in the lizard’s genomes.

Methods

Collection, Genomic Library Prep and Sequencing

Blood samples from 45 Abronia lizards located in various populations in Eastern Guatemala were preserved on FTA cards.

Assembly of Genomic Loci

After extracting DNA from the blood samples, we sequenced tens of thousands of regions of the lizards’ genomes associated with the restriction sites (Bayona-Vásquez et al.). To assemble and align the sequence data across the lizard samples, we used ipyrad (Eaton & Overcast, 2020).

Principal Component Analysis (PCA)

To visualize the genetic variation among the Abronia alligator lizards, we used a principal component analysis.

IQ-TREE

To estimate the phylogenetic relationships among the sampled Abronia lizards, we used a maximum-likelihood search in IQ-TREE (Wong et al., 2025).

Results

From the estimated phylogenetic tree (Figure 1), we can observe a monophyletic group of 20 individuals from five separate populations of various levels of isolation. The members of this clade group together along the first principal component in our PCA analysis (Figure 2).

This clade and group in the PCA does not correspond with any of the isolated agricultural locations from which the lizards were sampled. We do not see obvious signatures in the genomic diversity of the lizards left by recent extreme isolation

Conclusions

Within populations of Abronia campbelli in Eastern Guatemala, our principal component analysis, phylogenetic tree, and satellite data do not indicate a correspondence between extreme isolation imposed by agriculture and genomic divergence.

A better understanding of genetic variation among these isolated populations of Abronia in eastern Guatemala can be used to inform further conservation efforts and strategies.

References

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2. Eaton DAR, Overcast I. 2020. ipyrad: Interactive assembly and analysis of RADseq datasets. Bioinformatics 36:2592–2594. DOI: 10.1093/bioinformatics/btz966. Link.
3. Ariano-Sánchez D, Melendez L. 2009. Arboreal Alligator Lizards in the Genus \textitAbronia: Emeralds from the Cloud Forests of Guatemala. Reptiles & Amphibians 16. DOI: 10.17161/randa.v16i1.15938. Link.
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