Genomes of three Sympatric Species of an Adaptive Radiation: Cyprinodon variegatus, C. desquamator, and C. brontotheroides

Speciation is a central process in evolutionary biology that involves the formation of reproductive barriers between diverging populations. This process can occur through multiple ecological, behavioral, and genetic mechanisms that ultimately lead to changes within a population leading to the formation of distinct species. The relatively young adaptive radiation of Cyprinodon pupfishes in the lakes of San Salvador Island provides a powerful system to study the drivers of speciation in species that exist both sympatrically and allopatrically. The three species; C. variegatus, C. desquamator, and C. brontotheroides, can be found in many lakes on the island, exhibit distinct morphological adaptations relating to feeding, and, when in sympatry, the three species have overlapping habitats and breeding grounds. Species boundaries are maintained by asymmetric mate choice by both males and females, which reinforce extreme fitness costs of hybridization. Here we present high-quality annotated reference genomes for these three species generated using PacBio hifi sequencing. The assemblies resulted in a genome size of approximately 1.2 Gb for each species with most sequences scaffolding into 24 chromosomes with BUSCO analysis indicating a >99% level of completion. The annotation of these three genomes generated over 21,500 protein coding genes with BUSCO analysis indicating a >86 completion. These genomes provide a key resource for studying the genomic architecture of ecological specialization, reproductive isolation in sympatry, and rapid speciation and will facilitate future comparative and population genomic studies on adaptive radiations.