DNA Barcoding of Penaeidae (Decapoda; Crustacea): Non-Distance-Based Species Delimitation of the Most Economically Important Shrimp Family

Jorge L Ramirez,Patricia D Freitas,Lorenzo E Reyes-Flores,Jaqueline Gusmão,Carolina Tavares,Luisa Simbine,Adolfo S López,Eliana Zelada-Mázmela,Carla G Marques,Pedro M Galetti

doi:10.3390/d13100460

Abstract

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.

Highlights

The mean intra-group distances, the maximum intra-group distance, the nearest neighbor (NN), and the NN’s minimum distance for both consensus MOTUS and nominal species are shown in Supplementary Material (Table S2)
Our integrated approach, combining DNA barcoding with non-distance-based singlegene species delimitation methods, was efficient in raising some issues and pointing inconsistences out for the penaeids analyzed
It is known that such strategy can constitute a powerful tool for molecular operational taxonomy units (MOTUs) delimitation, aiding the knowledge about species diversity in different taxa [1,28,50,51,52]

Summary

Introduction

Especially in tropical and subtropical regions, the Penaeidae family includes some of the most important marine shrimp, comprising, up until 2020, 32 genera with 224 species [1], some of which are considered the crustaceans of most major economic importance in the world [2,3,4]. The world production of shrimp, adding catches and shrimp farming, represents the most important fish product traded internationally in terms of value. While catches of shrimp reached new records in recent years, the world aquaculture production of crustaceans in 2018, for instance, consisted of 9.4 million tons, representing 11.4% of the world total aquaculture production of aquatic animals [3]. In several tropical developing countries, shrimp fishing represents the most valuable export product and an important employment-generating activity [5]

Methods

Results

Conclusion