DNA barcoding of penaeidae (Decapoda; crustacea): Non-distance-based species delimitation of the most economically important shrimp family

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

Research output: Contribution to journalArticlepeer-review

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.

Original languageEnglish
Article number460
JournalDiversity
Volume13
Issue number10
DOIs
StatePublished - Oct 2021

Bibliographical note

Funding Information:
This study was funded by Concytec/Fondecyt (C?rculos de Investigaci?n 023-2016) and DNA Barcoding Brazilian Network. Marine Organisms-Molecular Identification of Biodiversity (MCT/CNPq/FNDCT-50/2010). P.M.G.J. and P.D.F. thank Conselho Nacional de Desenvolvimento Cient?fico e Tecnol?gico (CNPq, 303524/2019-7and 304477/2018-4, respectively) and Centro de Oceanografia Integrada INCT Mar COI (MCT/CNPq/FNDCT/FAP-71/2010, Institutos Nacionais de Ci?ncia e Tecnologia). P.D.F. thank S?o Paulo State Research Support Foundation (Fapesp 2011/21384-6; 2012/17322-8). C.G.M. and L.S. received grants from Conselho Nacional de Desenvolvimento Cient?fico e Tecnol?gico (CNPq), Brazil.

Publisher Copyright:
© 2021 by the authors. Licensee MDPI, Basel, Switzerland.

Keywords

  • COI
  • GMYC
  • Hidden diversity
  • PTP
  • Penaeids

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