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Phylogenetic Relationships of the Commercial Marine Shrimp Family Penaeidae from Persian Gulf

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Phylogenetic Relationships of the Commercial Marine Shrimp Family Penaeidae from Persian Gulf Iranian Journal Fisheries Sciences 15(1) 333-346 2016 Phylogenetic relationships of the commercial marine shrimp family Penaeidae from Persian Gulf Samadi S.1; Ghavam Mostafavi P.1; Rezvani Gilkolaii S.2*; Fatemi M.1; Fazli H.3 Received: July 2014 Accepted: December 2015 Abstract Phylogenetic relationships among all described species (total of 5 taxa) of the shrimp genus Penaeus, were examined with nucleotide sequence data from portions of mitochondrial gene and cytochrome oxidase subunit I (COI). There are twelve commercial shrimp in the Iranian coastal waters. The reconstruction of the evolution phylogeny of these species is crucial in revealing stock identity that can be used for the management of fish industries in Iran. Mitochondrial DNA sequences were used to reconstruct the phylogeny of the Penaeus species of marine shrimp. For this purpose, DNA was extracted using phenol- chloroform well as CTAB method. The evolutionary relationships among 5 species of the shrimp genus Penaeus were examined using 610 bp of mitochondrial (mt) DNA from the cytochrome oxidase subunit I gene. Finally the cladograms were compared and the resulting phylogenetic trees confirmed that the Iranian species originated from the Indo-west pacific species. The Iranian species, which were not grouped with the other Penaeid taxa, seem to always form a sister- clade to the Indo-west pacific species with strong bootstrap support of 100%. Although the Iranian species + Western Hemisphere clade is paraphyletic in our gene tree, the bootstrap support is high. However, we still lack any comprehensive and clear understanding of phylogenetic relationships in this group. Keywords: Mitochondrial DNA, Penaeidae, Persian Gulf, Phylogeny 1-Department of Marine Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran 2-Iranian Fisheries Science Research Institute, Agricultural Research, Education and Extension Organization, Tehran, Iran. 3- Caspian Sea Ecology Research Center, Iranian Fisheries Science Research Institute, Agricultural Research, Education and Extension *Corresponding author's email: [email protected] 334 Samadi et al., Phylogenetic relationships of the commercial marine shrimp family… Introduction has been reported (Chong and The Penaeid shrimp form a diverse Sasekumar, 1982). group of marine decapods with over As is known, mtDNA is a useful 400 species globally distributed and maternal marker because of its inhabiting both shallow waters and matrilineal mode of inheritance. In abyssal zones below 5000 m (Pérez animals, mtDNA genes such as COI are Farfante and Kensley, 1997). The particularly suitable for the Penaeid industry has grown rapidly determination of intraspecific genetic through the last 30 years and the diversity owing to a high evolutionary dominant species are Penaeus monodon rate found in this maternally transmitted (Fabricius 1798), P. vannamei (Boone genome (Avise et al., 1987). Therefore 1931), P. chinensis (Osbeck 1765) P. it has been widely used as a genetic stylirostris (Stimpson 1874), P. marker to assess the phylogeography japonicus (Bate 1888), P. merguiensis and phylogeny within numerous species (De Man 1888) and P. indicus (H. and genera (Baldwin et al., 1998; Milne Edwards 1837). O’Grady et al., 1998; Funk, 1999; Reed Shrimp of the genus Penaeus and Sperling, 1999; Masta, 2000; (Crustacea: Decapoda) are the most Walton et al., 2000). Baldwin et al. abundant group of marine groups in (1998) examined 13 different species of tropical and subtropical waters around Penaeus using 558 bp of mitochondrial the world. Due to the lack of research in DNA from COI and was able to Iran, to resolve phylogeny relationships successfully divide the genus into two within this group is the main reason to groups (Burkenroad, 1934). perform this study. It is important to Mitochondrial DNA (mtDNA) manage wild stocks differently than it sequences have proved extremely was done for P. monodon. P. useful in elucidating phylogenetic merguiensis. For example, P. indicus, relationships among many crustacean P. japonicus, and P. vannamei together groups (Cunningham et al., 1992). can be easily be matured in captivity Mitochondrial large subunit ribosomal without eyestalk ablation (Bailey-Brock RNA (16S rRNA) and cytochrome c and Moss, 1992). Unfortunately, oxidase subunit I (COI) genes have Chaitiamvong and Supongpan (1992) been particularly helpful in analyzing tolled the existence of over 50 Penaeid crustacean phylogeny at the species species in Thai waters, four of them (P. level (Chu et al., 2003). Baldwin et al. merguiensis, P. indicus, P. silasi, and P. (1998) examined the phylogenetic penicillatus) are considered relationships of 13 Penaeus s.l. species morphologically similar species. based on COI sequences. The Taxonomic difficulties about the evolutionary partitions resolved do not external morphology of P. merguiensis support the subgenus division but are concordant with biogeographic Iranian Journal of Fisheries Sciences 15(1) 2016 335 groupings within the genus. In the true relationships among all particular, their data show that Penaeus species, and we still lack any Litopenaeus and Farfantepenaeus are comprehensive and clear understanding not valid phylogenetic groupings, but of phylogenetic relationships in this are paraphyletic (Baldwin et al., 1998). group. To date, 28 species are recognized in The aim of this study was the Penaeus (Dall et al., 1990). There have molecular identification of 5 been two studies so far based on 16S commercial shrimp species of the rRNA or combined 16S and COI Persian Gulf and Oman Sea, using a sequences of the superfamily DNA sequencing analysis of Penaeoidea in which 16 species cytochrome oxidase subunit I (COI). In (Vázquez-Bader et al., 2004) and 11 the present study, the mitochondrial species (Quan et al., 2004) of the cytochrome oxidase subunit I gene was Penaeidae were included. Results from chosen for analysis as it has proven the studies, however, question the useful in studying phylogenetic monophyletic status of the family relationships at the species level in Penaeidae. Voloch et al. (2005) many arthropods (Howland and Hewitt, examining the phylogenetic 1995).This study provides new COI relationships of the Penaeidae by sequences from 5 species, allowing COI analyzing 16S and COI sequences of 39 phylogenetic analysis of almost the species of the Penaeidae based on entire group. The Indian-Pacific has the existing data (Tong et al., 2000; most diverse species, with about five Maggioni et al., 2001; Lavery et al., times of that found in the Atlantic, 2004; Quan et al., 2004). Since showing the region of the origin for this Penaeus s.l. shrimp are remarkably widespread genus (Dall et al., 1990). well-known and are of great economic The second goal of this study was to importance separating them into six determine whether the Indo-West genera can produce significant impact Pacific is the origin of the genus. on both scientific and commercial Finally, the material presented here practices. provides a phylogenetic framework for In recent years there have been a management of these important natural variety of phylogenetic researches on resources. Bernatchez (1995), reported Penaeus species using genetic markers wildlife management programs that to solve questions regarding their depend on an understanding of the taxonomy and evolution. Unfortunately, phylogenic relation. Marine shrimp of all previous analyses have been the superfamily Penaeoidea represent severely constrained by data limitations approximately a third of the world’s in the number of species and the commercially important shrimp species number of genetic characters. Overall and account for over 80% of the wild there is still considerable doubt about catch. In addition, members of the 336 Samadi et al., Phylogenetic relationships of the commercial marine shrimp family… genus Penaeus represent over 90% of The sampling sites and the number of the cultured species worldwide. specimens examined are listed in Table 1. Materials and methods The Chinese mud shrimp, Solenocera Collection of materials koelbeli De Man, 1911, of the family Five species of commercial shrimp Solenoceridae (Decapoda, belonging to the family Peneaidae, were Dendrobranchiata, Penaeoidea), was collected by fishing trawler vessel involved in the study that was chosen as Ferdows II from northern parts of the an outgroup (Table 1). Five individuals Persian Gulf and preserved in 95% of each species were used for molecular ethanol. The sampled species are the sequence analysis and the species were following: Parapenaeopsis stylifera identified using several shrimp species (H. Milne Edwards, 1837 [in H. Milne keys (Dall et al., 1990) and they were Edwards, 1834-1840]), Metapenaeus also identified by the researcher stebbingi Nobili, 1904, M. stridulans (Mohsen Safaiee), who is an (Alcock, 1905). P. semisulcatus, P. experienced shrimp taxonomist. (Fenneropenaeus) merguiensis. Table 1: Details of specimens and sequences used in this study. Species N Location GenBank Accession Nos.a P. (Farfantepenaeus) aztecus 1 Gulf of Mexico, USA AF279834 P. (Farfantepenaeus) brasiliensis 1 AF0293931 P. (Farfantepenaeus) californiensis 1 NC 012738 P. (Farfantepenaeus) duorarum 1 Gulf of Mexico, USA AF279835 P. (Farfantepenaeus) notialis 1 X84350 P. (Farfantepenaeus) paulensis 1 AF0293921 P. (Farfantepenaeus) subtilis 1 AF2485594 P. (Fenneropenaeus) chinensis 1 Zhujiang estuary, China AF279836 P. (Fenneropenaeus) indicus 1 Bonaparte Gulf, W. Australia AF279837 P.
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