Phylogenomic insights into species boundaries and population structure in South American silversides (Odontesthes, Atherinopsidae)

Abstract

Understanding the evolutionary relationships and population structure of South American silversides or pejerreyes (Odontesthes spp.) is essential to elucidate patterns of speciation, hybridization, and biogeography. Habitat transitions, salinity, and connectivity strongly influence gene flow and lineage formation. We analyzed 364 Odontesthes individuals using ddRADseq to investigate phylogenetic relationships, population structure, and species boundaries across Atlantic and Pacific basins. Phylogenetic reconstructions revealed two major clades corresponding to basin distributions. Several species (O. ledae, O. mirinensis, O. mauleanum, O. brevianalis, O. regia, O. gracilis) were non-monophyletic, suggesting historical admixture, while O. nigricans was included for the first time in a genomic-scale phylogeny. STRUCTURE, DAPC, and PCA analyses identified clear differentiation for O. smitti, coastal O. argentinensis, and O. perugiae, whereas southern Brazilian species and O. regia/O. gracilis formed intermixed clusters, reflecting ongoing gene flow. Mantel tests detected isolation-by-distance in O. bonariensis and the southern Brazilian species group, but not in O. argentinensis or the O. smitti/O. regia/O. gracilis complex. These results demonstrate that geographic isolation, habitat connectivity, and hybridization jointly shape population structure and evolutionary history in Odontesthes. This study provides the first genomic-scale perspective for several lesser-known species and highlights admixture as a key factor influencing genetic diversity and lineage boundaries in South American pejerreyes.