Genomic assessment reveals signal of adaptive selection in populations of the Spotted rose snapper Lutjanus guttatus from the Tropical Eastern Pacific.

Background: The lack of barriers in the marine environment has promoted the idea of panmixia in marine organisms. However, oceanographic conditions and habitat characteristics have recently been linked to genetic structure in marine species. The Tropical Eastern Pacific (TEP) is characterized by dynamic current systems and heterogeneous oceanographic conditions. The Gulf of Panama (part of the equatorial segment for the TEP) is influenced by a complex current system and heterogeneous environment, which has been shown to limit the gene flow for shoreline species. Next Generation Sequencing (NGS) has contributed to detect genetic differences in previously reported panmictic species by the assessment of loci associated with selection and to understand how selection acts affects marine populations. Lutjanus guttatus is a species distributed in the TEP for which previous studies using mitochondrial data recovered a panmictic pattern along its distributional range. In this study, we used SNP data of L. guttatus individuals sampled along its range to evaluate population genetic structure and investigate whether oceanographic factors influence the species' genetic architecture. Finally, we assessed the role of adaptive selection by evaluating the contribution of outlier and neutral loci to genetic divergence. Methods: The RADcap method was used to obtain 24 million paired reads for 123 individuals of L. guttatus covering nearly all its distributional area. Genetic variation was assessed using both spatial and non-spatial methods by comparing three different data sets: (i) a Combined Loci (CL dataset = 2003 SNPs); a search for putative loci under selection allowed the evaluation of (ii) Neutral Loci (NL dataset = 1858 SNPs) and (iii) Outlier Loci (OL dataset = 145 SNPs). We used the estimating effective migration surface (EEMS) approach to detect possible barriers to gene flow. Results: Genetic differences were found in the OL dataset, showing two clusters (Northern and Southern), whereas NL showed no differences. This result may be related to the Selection-Migration balance model. The limit between the Northern and Southern groups was in the Gulf of Panama, which has been previously identified as a barrier to gene flow for other species, mainly due to its heterogeneous oceanographic conditions. The results suggest that selection plays an important role in generating genetic differences in Lutjanus guttatus. A migration corridor was detected that coincides with the Costa Rica Coastal Current that flows from Central America to the Gulf of California, allowing the homogenization of the northern population. In the Southern cluster, a migration corridor was observed with the OL from Panama to Colombia, which could be associated with the currents found in the Gulf of Panama. Genetic variation found in the OL of Lutjanus guttatus highlights the usefulness of NGS data in evaluating the role of selection in population differentiation.

Genetic differentiation in the genus Characodon: implications for conservation and taxonomy.

The subfamily Goodeinae is a group of fishes endemic to the Mexican highlands. Most of the species are restricted to small and isolated streams or springs. Within this subfamily, the genus Characodon is the earliest diverging lineage of which three species have been described: C. lateralis, C. audax, and C. garmani, with the latter, considered extinct. Characodon lateralis and C. audax are classed as endangered, and have been the subject of taxonomic controversy since their description: previous studies have recognized a genetic differentiation in two groups separated by the El Salto waterfall, but morphological analyses contradict these genetic results. We perform a phylogeographic study using the mitochondrial cytb gene and d-loop region to elucidate the evolutionary history of C. lateralis and C. audax. The results with both markers show the presence of two highly differentiated haplogroups; one distributed north and the other distributed south of the waterfall, with genetic distances of 1.7 and 13.1% with cytb and d-loop respectively, and divergence calculated to have occurred 1.41 Mya. Significant genetic structure was found within each haplogroup and suggests the existence of at least four Evolutionary Significant Units (ESUs) within the examined populations. The possible processes identified as contributing to the formation of differentiated genetic groups are isolation, low population size, recurrent bottlenecks, and the strong sexual selection exhibited by the genus.