Phylogenomic insights into the evolutionary history of the Amazonian Creole pig using nuclear genome data and maximum-likelihood analyses

Abstract

The Peruvian Creole pig represents an underexplored zoogenetic resource whose evolutionary history remains poorly resolved due to the limited availability of high-resolution genomic studies. Here, we present the first nuclear phylogenomic analysis of the Amazonian Creole pig based on whole-genome sequencing data, integrating four local individuals with 45 reference genomes representing domestic, wild, and outgroup lineages of Sus scrofa. A high-confidence dataset comprising over 38 million SNPs was generated and used to infer phylogenetic relationships under a maximum likelihood framework. The four Creole individuals formed a strongly supported monophyletic clade, clearly differentiated from European and Asian commercial breeds. This lineage was recovered as a sister group to traditional European breeds, supporting a historical origin linked to colonial introductions followed by local divergence. In addition, evidence of internal substructure within the Creole group suggests potential geographic differentiation and may be associated with local adaptation processes, although further analyses are required to test these hypotheses explicitly. The overall consistency of the dataset supports the robustness of the inferred relationships. Overall, our results indicate that the Amazonian Creole pig represents a distinct nuclear lineage within S. scrofa, with important evolutionary and conservation implications. This study provides a valuable genomic resource for future research on genetic diversity, population structure, and adaptation in Latin American pig populations. Supplementary Information The online version contains supplementary material available at 10.1038/s41598-026-48764-0. Keywords: Genetic diversity, Population structure, Local adaptation, Conservation genomics, Whole-genome sequencing Subject terms: Evolution, Genetics