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

Combining morphology and molecular data to improve <i>Drosophila paulistorum</i> (Diptera, Drosophilidae) taxonomic status

<p>The <i>willistoni</i> species subgroup has been the subject of several studies since the latter half of the past century and is considered a Neotropical model for evolutionary studies, given the many levels of reproductive isolation and different evolutionary stages occurring within them. Here we present for the first time a phylogenetic reconstruction combining morphological characters and molecular data obtained from 8 gene fragments (C<i>OI, COII, Cytb, Adh, Ddc, Hb, kl-3</i> and <i>per</i>). Some relationships were incongruent when comparing morphological and molecular data. Also, morphological data presented some unresolved polytomies, which could reflect the very recent divergence of the subgroup. The total evidence phylogenetic reconstruction presented well-supported relationships and summarized the results of all analyses. The diversification of the <i>willistoni</i> subgroup began about 7.3 Ma with the split of <i>D. insularis</i> while <i>D.paulistorum</i> complex has a much more recent diversification history, which began about 2.1 Ma and apparently has not completed the speciation process, since the average time to sister species separation is one million years, and some entities of the <i>D. paulistorum</i> complex diverge between 0.3 and 1 Ma. Based on the obtained data, we propose the categorization of the former “semispecies” of <i>D. paulistorum</i> as a subspecies and describe the subspecies <i>D. paulistorum amazonian, D. paulistorum andeanbrazilian, D. paulistorum centroamerican, D. paulistorum interior, D. paulistorum orinocan</i> and <i>D. paulistorum transitional.</i></p

Extended Bayesian skyline plot showing the effective population size fluctuation of three South American sea lions populations throughout time based on the mtDNA control region.

<p>Internal thick lines are median estimates and thin lines and coloured areas are the 95% Central Posterior Density (CPD) intervals. Nef, effective female population size (log scale), ka, thousands of years ago. Time was truncated at 50 ka.</p

Migration rates (%, standard error in parenthesis) between the six sampling areas along the South America based on microsatellite data.

<p>The migration rate is the proportion of individuals in a population that immigrated from a source population per generation. Values in bold are inter-oceanic comparisons.</p

Bayesian phylogenetic tree of South American sea lion and related species <i>cyt b</i> sequences (381 bp).

<p>The two <i>Otaria flavescens</i> clades have a posterior probability of 1 and their median divergence time (in Mya) is indicated, with 95% credibility interval within parentheses.</p

Mitochondrial genetic and microsatellites diversities in each locality: N number of individuals analyzed (averaged over loci for microsatellites); Hd, haplotype diversity; π, nucleotide diversity; H, number of haplotypes; K, average number of alleles; Ho, observed heterozygosity; He, expected heterozygosity.

<p>Mitochondrial genetic and microsatellites diversities in each locality: N number of individuals analyzed (averaged over loci for microsatellites); Hd, haplotype diversity; π, nucleotide diversity; H, number of haplotypes; K, average number of alleles; Ho, observed heterozygosity; He, expected heterozygosity.</p

Pairwise microsatellite R_ST (above diagonal) and mtDNA control region Φ_ST distance values (below diagonal) between the six sampling areas. Negative values were adjusted to zero.

<p>Pairwise microsatellite R_ST (above diagonal) and mtDNA control region Φ_ST distance values (below diagonal) between the six sampling areas. Negative values were adjusted to zero.</p

Unrooted neighbour-joining tree for South American sea lion populations using D_SW genetic distance on microsatellite data.

<p>Numbers are bootstrap values (%).</p