DNA barcoding reveals taxonomic uncertainty in <i>Salminus</i> (Characiformes)

<p><i>Salminus</i> is a genus composed of four species of migratory fishes and top predators. Although this group has great economic and ecological importance, the species level diversity of <i>Salminus</i> is not yet completely clarified. Our goal was to detect if this taxonomic problem is the consequence of lineage divergence within species, and, if so, whether these divergences are sufficient to flag potentially undescribed taxa. We employed the standard DNA barcoding analyses and a generalized mixed Yule-coalescent model (GMYC) using one mitochondrial (COI) marker and Bayesian Inference (BI) reconstruction for one nuclear (RAG2) marker for all currently recognized species of <i>Salminus</i>, sampled across different hydrographic basins. Eight MOTUs (Molecular Operational Taxonomic Units) were determined by distance and model-based analyses, and recovered with BI analyses for COI. Only <i>Salminus affinis</i> and <i>Salminus franciscanus</i> formed monophyletic haplogroups. <i>Salminus brasiliensis</i> and <i>Salminus hilarii</i> had two and four distinct mitochondrial lineages, respectively, and higher intraspecific K2P distances than the adopted optimum threshold. The RAG2 gene tree supported two lineages of <i>S. hilarii</i> (<i>S. hilarii</i> Amazon and <i>S</i>. <i>hilarii</i> Araguaia), while the other mitochondrial lineages of <i>S. hilarii</i> and <i>S. brasiliensis</i> were not supported. All lineages of both species, corresponded to morphological variation described in previous studies. We suggest, based on the DNA barcoding analysis, a new taxonomic scenario and conservation polices for <i>Salminus</i> in the Brazilian territory.</p

Gene Ontology (GO) biological process description for outlier loci under positive selection.

*associated with populations. **associated with host strains and populations. Loci with no mark are associated with host strains. (DOCX)</p

PCA analysis generated with (A) 2,853 neutral SNPs, (B) 456 outliers.

Dots represent different individuals of each location.</p

Outlier loci under positive selection with blast hits in NCBI with > 90% similarity.

*associated with populations. **associated with host strains and populations. Loci with no mark are associated with host strains. (DOCX)</p

Fall armyworm sampling locations in Brazil and Argentina according to ecoregions.

Shapefile of limits of countries in South America: IBGE-Mapas (IBGE—Brazilian Institute of Geography and Statistics; Available at: https://geoftp.ibge.gov.br/cartas_e_mapas/bases_cartograficas_continuas/bc250/versao2021/shapefile/bc250_shapefile_2021_11_18.zip>; Acessed on February 26, 2023) QGIS v3.28.3 (Available at: https://qgis.org/en/site/>; Acessed on: February 26, 2023). DATUM: SIRGAS 2000.</p

Admixture analysis of fall armyworm populations based on (A) 2,853 neutral SNP loci and (B) 456 outlier SNP loci.

Bar plot colors indicate estimated proportions of ancestry for each individual shown as a vertical line.</p

Discriminant Analysis of Principal Components (DAPC) scatterplot showing the first two linear discriminants.

Geographic locations are represented by different colors, and dots represent different individuals. The inset shows BIC values for different number of k clusters. Analysis performed with (A) All SNP loci, (B) 2,853 neutral SNPs, (C) 456 outliers. Plots generated using adegenet package for R software. Sampling locations were considered as priori groupings. (TIF)</p

Detection of outlier SNPs under positive selection using Pcadapt, FstHet, and FLK.

The Venn diagrams shows the number of outlier SNPs associated to (A) FAW host strains and (B) populations. (TIF)</p

Outlier SNPs under positive selection using Pcadapt, FstHet, and FLK.

(A) GO categories of putative loci under selection generated from WEGO. The results are presented in three main categories: biological process, cellular component, and molecular function. The left y-axis indicates the percentage of a specific category of genes in the main category. The right y-axis indicates the number of genes in each category. (B) Manhattan plot of FST analysis comparing C-strain and R-strain against the position of SNPs on each of the 31 chromosomes. Chromosome 1 corresponds to the sex chromosome Z. Each SNP is represented by a dot. Chromosomes are represented by blue (odd) and orange (even).</p

Cross-validation method implemented in ADMIXTURE v1.3.0 to estimate the number of ancestral populations (k) inferred from (A) neutral markers and (B) outlier markers.

Cross-validation method implemented in ADMIXTURE v1.3.0 to estimate the number of ancestral populations (k) inferred from (A) neutral markers and (B) outlier markers.</p