New molecular phylogeny of the squids of the family Loliginidae with emphasis on the genus Doryteuthis Naef, 1912: Mitochondrial and nuclear sequences indicate the presence of cryptic species in the southern Atlantic Ocean João Bráullio de Luna Sales a,⇑ , Paul W. Shaw b , Manuel Haimovici c , Unai Markaida d , Divino B. Cunha a , Jonathan Ready a , Wilsea M.B. Figueiredo-Ready a , Horacio Schneider a , Iracilda Sampaio a a Universidade Federal do Pará, Campus Universitário de Bragança, Laboratório de Genética e Biologia Molecular, Bragança/PA CEP 68600-000, Brazil b Institute of Biological, Environmental and Rural Science (IBERS), Aberystwyth University, Penglais, Aberystwyth SY23 3DA, UK c Universidade Federal do Rio Grande (FURG), Laboratório de Recursos Demersais e Cefalópodes, Caixa Postal 474, Rio Grande/RS CEP 96201-900, Brazil d Laboratorio de Pesquerías Artesanales, El Colegio de La Fronteira Sur, Unidad Campeche, 24500 Campeche, Mexico article info Article history: Received 6 December 2012 Revised 23 March 2013 Accepted 25 March 2013 Available online 6 April 2013 Keywords: Cephalopoda Loliginidae Cryptic species Phylogeny South Atlantic Ocean Molecular systematics abstract The family Loliginidae Lesueur, 1821, is currently considered to include seven genera and approximately 50 species of neritic and coastal squids. These commercially important species occur in tropical and tem- perate coastal waters around the world. The taxonomy of the family has been revised a number of times in recent years, focusing in particular on genera such as Doryteuthis, Sepioteuthis, Alloteuthis, and Uroteu- this, which are represented by populations in the New World, Oceania, Europe/Africa, and Asia. However, no detailed phylogenetic analysis is available for the loliginids of the southern Atlantic, in particular the genus Doryteuthis. The present molecular study analyzed 81 loliginid taxa from around the world. The partial sequencing of the mitochondrial 16S and Cytochrome Oxidase I genes, and the nuclear rhodopsin gene revealed a number of important patterns, recovering the monophyletic status of the majority of the genera and revealing possible cryptic species in Doryteuthis plei D. pealei, Uroteuthis duvauceli and Sepio- teuthis lessoniana. Ó 2013 Elsevier Inc. All rights reserved. 1. Introduction The phylogenetic relationships and systematic arrangement of most groups of mollusks are unclear, and taxonomic inferences tend to be ambiguous or hampered by a variety of factors. One of these factors is the considerable variation in the phenotypic char- acters traditionally used for taxonomic analysis and the lack of reli- able morphological data for the definition of specific diagnostic traits. These factors are especially relevant in the case of the cephalopods. The family Loliginidae Lesueur, 1821, encompasses an ample group of commercially important species of neritic and coastal cephalopods. This family contains seven genera and approximately fifty species that occur in coastal oceanic waters of tropical and temperate regions worldwide (Anderson, 2000b). The taxonomy of the family has been the subject of a number of revisions in re- cent years. In 1988, the Cephalopod International Advisory Council (CIAC) organized a symposium dedicated to the Loliginidae, at which modifications to the traditional taxonomic scheme were proposed (Vecchione et al., 1998). The family was divided into five genera with four subgenera: Sepioteuthis Blainville, 1824; Lolligun- cula (Lolliguncula) Steenstrup, 1881; Lolliguncula (Loliolopsis) Steenstrup, 1881; Uroteuthis (Uroteuthis) Rehder, 1945; Uroteuthis (Photololigo) Rehder, 1945; Loliolus (Loliolus) Steenstrup, 1856; Lol- iolus (Nipponololigo) Steenstrup, 1856; Loligo (Loligo) Lamarck, 1798, and Loligo (Alloteuthis) Lamarck, 1798. However, during sub- sequent years, new cladistic analyses based on morphological (Alexeyev, 1989; Anderson, 1996, 2000a) and molecular tech- niques (Anderson, 2000a; Brierley et al., 1996) have introduced alternative insights into the taxonomic status of the family. In a more recent symposium on the systematics of the loliginids (CIAC, 2003), a new classification was proposed, which includes ten genera and nine valid subgenera (Vecchione et al., 2005). However, many species remain undetermined (Table 1). The phylogenetic status of a number of genera has been tested over the years. These genera include Doryteuthis, found in the Americas, Sepioteuthis (Caribbean and Oceania), Alloteuthis (Europe/Africa), and Uroteuthis (Asia). In a phylogeographic analy- sis of the North American populations of Doryteuthis (Loligo) plei and Doryteuthis (Loligo) pealei, Herke and Foltz (2002) distin- guished two populations representing each species within a vast 1055-7903/$ - see front matter Ó 2013 Elsevier Inc. All rights reserved. http://dx.doi.org/10.1016/j.ympev.2013.03.027 ⇑ Corresponding author. Address: Universidade Federal do Pará, IECOS, Laborató- rio de Genética e Biologia Molecular, Alameda Leandro Ribeiro s/n, Bairro Aldeia, Bragança/PA, CEP 68600-000, Brazil. E-mail address: braziliancephalopod@gmail.com (J.B.L Sales). Molecular Phylogenetics and Evolution 68 (2013) 293–299 Contents lists available at SciVerse ScienceDirect Molecular Phylogenetics and Evolution journal homepage: www.elsevier.com/locate/ympev