Peru is one of the world’s leading fishing nations and its seafood industry relies on the trade of a vast variety of aquatic resources, playing a key role in the country’s socio-economic development. DNA barcoding has become of paramount importance for systematics, conservation, and seafood traceability, complementing or even surpassing conventional identification methods when target organisms show similar morphology during the early life stages, have recently diverged, or have undergone processing. Aiming to increase our knowledge of the species diversity available across the Peruvian supply chain (from fish landing sites to markets and restaurants), we applied full and mini-barcoding approaches targeting three mitochondrial genes (COI, 16S, and 12S) and the control region to identify samples purchased at retailers from six departments along the north-central Peruvian coast. DNA barcodes from 131 samples were assigned to 55 species (plus five genus-level taxa) comprising 47 families, 24 orders, and six classes including Actinopterygii (45.03%), Chondrichthyes (36.64%), Bivalvia (6.87%), Cephalopoda (6.11%), Malacostraca (3.82%), and Gastropoda (1.53%). The identified samples included commercially important pelagic (anchovy, bonito, dolphinfish) and demersal (hake, smooth-hound, Peruvian rock seabass, croaker) fish species. Our results unveiled the marketing of protected and threatened species such as whale shark, Atlantic white marlin, smooth hammerhead (some specimens collected during closed season), shortfin mako, and pelagic thresher sharks. A total of 35 samples (26.72%) were mislabeled, including tilapia labeled as wild marine fish, dolphinfish and hake labeled as grouper, and different shark species sold as “smooth-hounds”. The present study highlights the necessity of implementing traceability and monitoring programs along the entire seafood supply chain using molecular tools to enhance sustainability efforts and ensure consumer choice.

Early detection of non-indigenous species is crucial to reduce, mitigate, and manage their impacts on the ecosystems into which they were introduced. However, assessment frameworks for identifying introduced species on the Pacific Coast of South America are scarce and even non-existent for certain countries. In order to identify species’ boundaries and to determine the presence of non-native species, through morphological examinations and the analysis of the plastid ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit (rbcL-5P) gene, we investigated the phylogenetic relationships among species of the class Florideophyceae from the coast of Ancash, Peru. The rbcL-5P dataset revealed 10 Florideophyceae species distributed in the following four orders: Gigartinales, Ceramiales, Halymeniales, and Corallinales, among which the Asian species, Melanothamnus japonicus (Harvey) Díaz-Tapia & Maggs was identified. M. japonicus showed a pairwise divergence of 0% with sequences of M. japonicus from South Korea, the USA, and Italy, the latter two being countries where M. japonicus has been reported as introduced species. Our data indicate a recent introduction event of M. japonicus in Peru, and consequently, the extension of its distribution into South America. These findings could help to adopt management strategies for reducing the spread and impact of M. japonicus on the Pacific Coast of South America.

The Penaeidae family includes some of the most economic and ecological important marine shrimp, comprising hundreds of species. Despite this importance and diversity, the taxonomic classification for penaeid shrimp has constantly been revised, and issues related to the species identification are common. In this study, we implemented DNA barcoding analyses in addition to single-gene species delimitation analyses in order to identify molecular operational taxonomy units (MOTUs) and to generate robust molecular information for penaeid shrimp based on the cytochrome oxidase subunit I (COI) mitochondrial gene. Our final data set includes COI sequences from 112 taxa distributed in 23 genera of penaeids. We employed the general mixed Yule coalescent (GMYC) model, the Poisson tree processes (PTP), and the Bayesian PTP model (bPTP) for MOTUs delimitation. Intraspecific and interspecific genetic distances were also calculated. Our findings evidenced a high level of hidden diversity, showing 143 MOTUs, with 27 nominal species not agreeing with the genetic delimitation obtained here. These data represent potential new species or highly structured populations, showing the importance of including a non-distance-based species delimitation approach in biodiversity studies. The results raised by this study shed light on the Penaeidae biodiversity, addressing important issues about taxonomy and mislabeling in databases and contributing to a better comprehension of the group, which can certainly help management policies for shrimp fishery activity in addition to conservation programs.

No abstract

No abstract

Objective The advancement of molecular techniques in an era in which high-throughput sequencing has revolutionized biology renders old-fashioned alternatives to high-throughput methods obsolete. Such advanced molecular techniques, however, are not yet accessible to economically disadvantaged region-based laboratories that still obtain DNA profiles using gel-based techniques. To explore whether cost-efficient techniques can produce results that are as robust as those obtained using high-throughput methods, we compared the performance of polyacrylamide gel electrophoresis (PAGE)- and capillary electrophoresis (CE)-derived genomic data in estimating genetic diversity and inferring relatedness using 70 individuals of fine flounder (Paralichthys adspersus) selected from a hatchery population and genotyped for five microsatellite loci. Results Here, we show that PAGE- and CE-derived genomic datasets yield comparable genetic diversity levels regarding allelic diversity measures and heterozygosity. However, relatedness inferred from each dataset showed that the categorization of dyads in the different relationship categories strongly differed. This suggests that while scientists can reliably use PAGE-derived genomic data to estimate genetic diversity, they cannot use the same for parentage testing. The findings could help laboratories committed to population research not be discouraged from using the PAGE system if high-throughput technologies are unavailable and the method is adequate to address the biological question.

No abstract

The present‐day population structure of a species reflects the combination of oceanographic currents, life‐history traits, and historical events. However, little is known about the mechanisms that have shaped the gene lineage distribution of marine species inhabiting the Southeast Pacific. Here, we provide a comprehensive phylogeographical study of a species distributed along the Southeast Pacific coastal region by analyzing the endemic gastropod Thaisella chocolata (Duclos, 1832). Sequencing of mitochondrial cytochrome c oxidase subunit 1 (CO1) and 16S rRNA revealed strikingly high haplotypic nucleotide and genetic diversity but a lack of significant population differentiation within the survey area. In addition, a star‐shaped phylogeny and significantly negative Tajima's D and Fu's Fs tests of neutrality suggested historical occurrence of rapid demographic expansion. Mismatch distributions and Bayesian inference analyses also confirmed T. chocolata to have undergone two ancestral demographic expansions. Calculations suggested that these expansions began in the lower and middle Pleistocene epoch, likely due to continental shelf development and climatic conditions. These findings could help establish a genetic baseline for T. chocolata as the first step toward sustainable spatial management of this species, as well as understand this species’ response to future climate change.