DNA barcoding of marine fishes from Saudi Arabian waters of the Gulf.

We used the cytochrome oxidase subunit I (coI) gene DNA to barcode 117 endemic Gulf and cosmopolitan Indo-West Pacific fish species belonging to 54 families and 13 orders. Novel DNA barcodes were provided for 18 fish species (Trachinocephalus sp., Nematalosa sp., Herklotsichthys lossei, Upeneus doriae, Trachurus indicus, Apogonichthyoides taeniatus, Verulux cypselurus, Favonigobius sp., Suezichthus gracilis, Sillago sp., Brachirus orientalis, Pegusa sp., Lepidotrigla bispinosa, Lepidotrigla sp., Grammoplites suppositus, Hippichthys sp., Paramonacanthus sp. and Triacanthus sp.). The species delimitation analysis, conducted with Poisson tree processes- Bayesian PTP (PTP-bPTP) and nucleotide-divergence-threshold (NDT) models), found 137 and 119 entities respectively. Overall, NDT method, neighbour-joining species tree and the prior taxonomic assessment provided similar results. Among the 54 families considered, only 10 (Ariommatidae, Ephippidae, Leiognathidae, Nemipteridae, Plotosidae, Pomacanthidae, Pomacentridae, Priacanthidae and Rachycentridae) showed the occurrence of molecular diagnostic pure characters. The DNA barcoding database developed during this study will help ichthyologists to identify and resolve the taxonomic ambiguities they may encounter with the fishes occurring in The Gulf and throughout the region.

Mitochondrial haplotypes indicate parapatric-like phylogeographic structure in blue-spotted maskray (Neotrygon kuhlii) from the Coral Triangle region.

Phylogeographic structure was investigated in the blue-spotted maskray, Neotrygon kuhlii, focusing on the Coral Triangle region. We used as genetic marker a 519-bp fragment of the cytochrome c-oxidase subunit I (COI) gene, sequenced in a total of 147 individuals from 26 sampling locations. The parsimony network of COI haplotypes was split into seven distinct clades within the Coral Triangle region. Different clades had exclusive but contiguous geographic distributions, indicating parapatric-like phylogeographic structure. Strong genetic differences were also inferred between local populations within a clade, where reciprocal monophyly between geographically adjacent samples was observed on several instances. Nearly 25% of the total molecular variance could be ascribed to differences between geographic samples within a clade, whereas interclade variation accounted for >65% of the total variance. The strong phylogeographic structure observed within a clade can be explained by either sedentarity or female philopatry. We interpret the parapatric distribution of clades as the joint result of 1) expansion from refuge populations at times of low sea level, and 2) possible enhanced competition between individuals from different clades, or assortative mating, or hybrid zones, along lines of secondary contact. The parapatric-like structure uncovered in the present study parallels regional differences at nuclear marker loci, thus pointing to incipient speciation within Coral Triangle N. kuhlii.

DNA barcoding of marine teleost fishes (Teleostei) in Cebu, the Philippines, a biodiversity hotspot of the coral triangle.

A morphology-based barcoding library of market teleost fishes (Teleostei) in Cebu is built based on cytochrome c oxidase subunit I (COI) sequences and voucher specimens which aimed to establish a reliable reference of frequently traded fishes in the province, a biodiversity hotspot at the center of the Philippine archipelago. A total of 1721 specimens were collected from 18 fish markets and landing sites around the province, in which 538 specimens were sequenced belonging to 393 species from 229 genera, 86 families, and 37 orders. Most speciose families are coral reef or reef-related shallow-water species. Twelve species from 11 families are newly recorded in the Philippine waters, among which 7 species are deep-sea inhabitants, while 3 species have expanded their distribution range. Only 20 taxa could not be identified to the species level due to the difficulty in morphological examinations, absence of matched reference sequences in online databases, and/or problematic species awaiting further studies. This first comprehensive DNA barcoding survey of Cebu fishes can facilitate further taxonomic research as well as the conservation and management of fisheries in the Philippines.

Characterization of mitochondrial genome of Indian Ocean blue-spotted maskray, Neotrygon indica and its phylogenetic relationship within Dasyatidae Family.

The present study characterized complete mitochondrial genome of Blue-spotted maskray, Neotrygon indica and studied the evolutionary relationship of the species within the Dasyatidae family. The total length of the mitogenome was 17,974 bp including 37 genes and a non-coding control region. The average frequency of nucleotides in protein-coding genes was A: 29.1 %, T: 30.2 %, G: 13.0 % and C: 27.7 % with AT content of 59.3 %. The values of AT and GC skewness were -0.018 and -0.338, respectively. Comparative analyses showed a large number of average synonymous substitutions per synonymous site (Ks) in gene NADH4 (5.07) followed by NADH5 (4.72). High values of average number of non-synonymous substitutions per non-synonymous site (Ka) were observed in genes ATPase8 (0.54) and NADH2 (0.44). Genes NADH4L and NADH2 showed high interspecific genetic distance values of 0.224 ± 0.001 and 0.213 ± 0.002, respectively. Heat map analysis showed variation in codon usage among different species of the Dasyatidae family. The phylogenetic tree showed a sister relationship between the Dasyatinae and the Neotrygoninae subfamilies. Neotrygon indica formed as a sister species to the clade consisting of N. varidens and N. orientalis. Based on the present results, Neotrygon indica could have diverged from the common ancestor of the two latter in the Plio-Pleistocene. The present study showed distinct characteristics of N. indica from its congeners through comparative mitogenomics.

Planiliza lauvergnii (Eydoux & Souleyet, 1850), a senior synonym of Planiliza affinis (Günther, 1861) with a re-evaluation of keeled back mullets (Mugiliformes: Mugilidae).

The taxonomic status of the keeled back mullets (Teleostei: Mugilidae) has been reinvestigated. Two nominal mugilid species having keeled backs from East Asia: Mugil lauvergnii Eydoux & Souleyet, 1850 and Mugil affinis Günther, 1861 have been re-evaluated through examination of the holotypes and fresh specimens. Comparison of morpho-meristic characters of the holotypes shows that both species are identical. Phylogenetic analysis based on mitochondrial cytochrome c oxidase 1 (CO1) confirmed morphological data by highlighting presence of a single clade from East Asia. Mugil lauvergnii (=Planiliza lauvergnii) is thus the sole keeled back mullet from East Asia and a senior synonym of Mugil affinis (=Planiliza affinis). The taxonomic status of two other keeled back mullets, Planiliza carinata and P. klunzingeri, is also contentious due to their similar morphology. Meristic and morphometric variation as well as sequence divergence between the two species are limited but phylogenetic analyses delineate well-supported clades consistent with biogeography and currently accepted taxonomy. Planiliza carinata and P. klunzingeri share a recent common ancestor in a Maximum Likelihood tree, with separate distribution ranges while P. lauvergnii formed a paraphyletic lineage. Based on present findings, we suggest maintenance of the taxonomic distinction of P. klunzingeri and P. carinata and discuss its evolutionary significance.

Plio-Pleistocene sea level and temperature fluctuations in the northwestern Pacific promoted speciation in the globally-distributed flathead mullet Mugil cephalus.

BACKGROUND: The study of speciation in the marine realm is challenging because of the apparent absence of physical barriers to dispersal, which are one of the main drivers of genetic diversity. Although phylogeographic studies using mitochondrial DNA (mtDNA) information often reveal significant genetic heterogeneity within marine species, the evolutionary significance of such diversity is difficult to interpret with these markers. In the northwestern (NW) Pacific, several studies have emphasised the potential importance of sea-level regression during the most recent glaciations as a driver of genetic diversity in marine species. These studies have failed, however, to determine whether the period of isolation was long enough for divergence to attain speciation. Among these marine species, the cosmopolitan estuarine-dependent fish Mugil cephalus represents an interesting case study. Several divergent allopatric mtDNA lineages have been described in this species worldwide, and three occur in sympatry in the NW Pacific. RESULTS: Ten nuclear microsatellites were surveyed to estimate the level of genetic isolation of these lineages and determine the role of sea-level fluctuation in the evolution of NW Pacific M. cephalus. Three cryptic species of M. cephalus were identified within this region (NWP1, 2 and 3) using an assignment test on the microsatellite data. Each species corresponds with one of the three mtDNA lineages in the COI phylogenetic tree. NWP3 is the most divergent species, with a distribution range that suggests tropical affinities, while NWP1, with a northward distribution from Taiwan to Russia, is a temperate species. NWP2 is distributed along the warm Kuroshio Current. The divergence of NWP1 from NWP2 dates back to the Pleistocene epoch and probably corresponds to the separation of the Japan and China Seas when sea levels dropped. Despite their subsequent range expansion since this period of glaciation, no gene flow was observed among these three lineages, indicating that speciation has been achieved. CONCLUSIONS: This study successfully identified three cryptic species in M. cephalus inhabiting the NW Pacific, using a combination of microsatellites and mitochondrial genetic markers. The current genetic architecture of the M. cephalus species complex in the NW Pacific is the result of a complex interaction of contemporary processes and historical events. Sea level and temperature fluctuations during Plio-Pleistocene epochs probably played a major role in creating the marine species diversity of the NW Pacific that is found today.

The complete mitogenome of the Greytail angelfish Chaetodontoplus poliourus and its phylogenetic relationships (Perciformes: Pomacanthidae).

The mitogenome of the Greytail angelfish Chaetodontoplus poliourus (Pomacanthidae) was decoded using next-generation sequencing techniques. The de novo assembled mitogenome consists of 16,961 bp, including 13 protein-coding genes, 2 ribosomal RNAs and 22 transfer RNA genes. The gene arrangement is identical to the other available Pomacanthidae mitogenomes submitted to NCBI. The overall base composition of the C. poliourus mitogenome was estimated to be 28.0% A, 30.9% C, 15.8% G and 25.3% T. The phylogenetic analysis of the C. poliourus mitogenome suggests a closer genetic relationship with Vermiculated angelfish Chaetodontoplus mesoleucus as expected from their similar color patterns. The overall pairwise identity except D-loop is 93.7% for these two sister species. The decoding of the C. poliourus mitogenome has enriched gene database for further evolutionary studies and conservation assessments of this uncommon and newly described marine angelfish.

Delimitation of Tigertooth Croaker Otolithes Species (Teleostei: Sciaenidae) from the Western Arabian Gulf Using an Integrative Approach, with a Description of Otolithes arabicus sp. nov.

Two species, Otolithes ruber and Otolithes cuvieri, are currently recognized in the sciaenid genus Otolithes. Recent findings suggest that Otolithes ruber likely has multiple genetically and morphologically distinct lineages and one of them, Otolithes sp. West Indian Ocean II group (WIO II group), has been previously identified in the Arabian Gulf. In this study, the specimens of Otolithes sp. collected from the western Arabian Gulf were examined using an integrative approach by combining mitochondrial cytochrome c oxidase 1 gene, morphological characteristics, and otolith-shape analyses. Three groups were found to have small within-group and large between-group genetic distance: the Otolithes sp. Western Arabian Gulf (WA) group, and the Otolithes sp. WIO II groups type A and type B. Accordingly, three primary species hypotheses were proposed. Evidence from conventional morphological comparisons, multivariate statistical analysis, geometric morphometric landmark analysis on morphological characteristics, and otolith shape analysis based on wavelet transformation all favor the hypothesis that the Otolithes sp. WA group is a distinct lineage. For this new species, the name Otolithes arabicus sp. nov. is proposed. A detailed description of Otolithes arabicus sp. nov. and a key to identifing species in the genus Otolithes are also provided. However, the primary species hypotheses for Otolithes sp. West Indian Ocean II group type A and type B cannot be fully supported because of partial congruence, which may result from recent divergence.

Johnius taiwanensis, a new species of Sciaenidae from the Taiwan Strait, with a key to Johnius species from Chinese waters.

A new sciaenid fish, Johnius taiwanensis, is described from the southeast coast of mainland China from Zhejiang to Guangdong, Hong Kong, and west coast of Taiwan. Johnius taiwanensis sp. nov. can be distinguished from other Johnius species by having a grayish dorsal half of body divided by a clear line from a whitish ventral half, and a black spot at the dorsal half of pectoral-fin axil, appearing as a distinct dot at the most dorsal point of the pectoral-fin base. First dorsal fin black tipped, other fins pale to dusky but never darkly pigmented. The species lacks distinctly enlarged teeth on upper and lower jaws. Body scales ctenoid, moderately large, with five or six rows between first dorsal-fin origin and lateral line. It is one of the most abundant sciaenids found in the shallow coastal waters (20 m) of southeast mainland China and the west coast of Taiwan. It has often been misidentified as J. macrorhynus in the region. Phylogenetic analysis from all 27 sciaenid species found in Chinese waters based on the complete COI and 16S rRNA gene sequences confirmed that the genus Johnius is monophyletic and J. taiwanensis is placed as a sister species of J. trewavasae. Acoustic analysis has shown that J. taiwanensis produces a unique sound among fishes in Taiwan coastal waters.

Neotrygon indica sp. nov., the Indian Ocean blue-spotted maskray (Myliobatoidei, Dasyatidae).

The blue-spotted maskray, previously N. kuhlii, consists of up to eleven lineages representing separate species. Nine of these species (N. australiae, N. bobwardi, N. caeruleopunctata, N. malaccensis, N. moluccensis, N. orientale, N. vali, N. varidens, N. westpapuensis) have already been formally described and two (Indian Ocean maskray and Ryukyu maskray) remain undescribed. Here, the Indian Ocean maskray is described as a new species, Neotrygon indica sp. nov. Specimens of the new species were generally characterized on their dorsal side by a moderately large number of small ocellated blue spots, a low number of medium-sized ocellated blue spots, the absence of large ocellated blue spots, a high number of dark speckles, a few dark spots, and a conspicuous occipital mark. The new species formed a distinct haplogroup in the tree built from concatenated nucleotide sequences at the CO1 and cytochrome b loci. A diagnosis based on colour patterns and nucleotide sequences at the CO1 and cytochrome b loci is proposed. The distribution of N. indica sp. nov. includes the Indian coast of the Bay of Bengal, the Indian coast of the Laccadives Sea, and Tanzania. Considerable sampling effort remains necessary for an in-depth investigation of the phylogeographic structure of the Indian Ocean maskray.

Complete mitochondrial genome and the phylogenetic position of the pelagic octopus Tremoctopus violaceus (Mollusca: Tremoctopodidae).

Tremoctopus violaceus is a small species of pelagic octopods which inhabit in subtropical and tropical open oceans. The mitogenome of T. violaceus is 16,015 base pairs (bp) in length and contained 13 protein-coding genes, two rRNA genes, and 22 tRNA genes. Sequence analysis showed that the overall base composition is 31.5% for A, 40.47% for T, 7.79% for C, and 20.24% for G. The newly characterized complete mitochondrial genome of T. violaceus will provide essential data for further studies of this endangered species.

The complete mitochondrial genome of the palette surgeonfish, Paracanthurus hepatus (Perciformes: Acanthuridae).

In this study, the complete mitogenome sequence of the palette surgeonfish, Paracanthurus hepatus (Perciformes: Acanthuridae), has been sequenced by next-generation sequencing method. The assembled mitogenome was 16 498 bp in length, consisted of 13 protein-coding genes, 22 transfer RNAs, 2 ribosomal RNAs genes. The overall base composition of palette surgeonfish was 28.6% for A, 28.6% for C, 16.3% for G, 26.4% for T and showed 87% identities to somber surgeonfish Zebrasoma flavescens. The complete mitogenome of the palette surgeonfish provides essential and important DNA molecular data for further phylogeography and evolutionary analysis for surgeonfish's phylogeny.

The complete mitochondrial genome of the Royal dottyback Pictichromis paccagnellae (Perciformes: Pseudochromidae).

In this study, the complete mitogenome sequence of the Royal dottyback, Pictichromis paccagnellae (Perciformes: Pseudochromidae), has been sequenced by the next-generation sequencing method. The assembled mitogenome was of 16 976 bp in length, consisting of 13 protein-coding genes, 22 transfer RNAs, and two ribosomal RNAs genes. The overall base composition was 27.4% for A, 28.1% for C, 17.3% for G, and 27.2% for T and showed 76% identities to Fire-tail devil Labracinus cyclophthalmus in the same family. The complete mitogenome of P. paccagnellae provides essential and important DNA molecular data for further phylogeography and evolutionary analysis for Pseudochromidae.

Next-generation sequencing yields the complete mitochondrial genome of the Redbelly yellowtail fusilier, Caesio cuning (Teleostei: Caesionidae).

In this study, the complete mitogenome sequence of Redbelly yellowtail fusileer, Caesio cuning (Teleostei: Caesionidae), has been sequenced by the next-generation sequencing method. The assembled mitogenome, consisting of 16 508 bp, had the typical vertebrate mitochondrial gene arrangement, including 13 protein-coding genes, 22 transfer RNAs, 2 ribosomal RNAs genes and a non-coding control region of D-loop. D-loop contains 826 bp length that is located between tRNA-Pro and tRNA-Phe. The overall base composition of C. cuning is 28.1% for A, 31.1% for C, 16.3% for G and 24.4% for T. The complete mitogenome may provide essential and important DNA molecular data for further phylogenetic and evolutionary analysis for Caesionidae.

The complete chloroplast genome of Tianshan Snow Lotus (Saussurea involucrata), a famous traditional Chinese medicinal plant of the family Asteraceae.

abtract We decoded the complete chloroplast DNA (cpDNA) sequence of the Tianshan Snow Lotus (Saussurea involucrata), a famous traditional Chinese medicinal plant of the family Asteraceae, by using next-generation sequencing technology. The genome consists of 152 490 bp containing a pair of inverted repeats (IRs) of 25 202 bp, which was separated by a large single-copy region and a small single-copy region of 83 446 bp and 18 639 bp, respectively. The genic regions account for 57.7% of whole cpDNA, and the GC content of the cpDNA was 37.7%. The S. involucrata cpDNA encodes 114 unigenes (82 protein-coding genes, 4 rRNA genes, and 28 tRNA genes). There are eight protein-coding genes (atpF, ndhA, ndhB, rpl2, rpoC1, rps16, clpP, and ycf3) and five tRNA genes (trnA-UGC, trnI-GAU, trnK-UUU, trnL-UAA, and trnV-UAC) containing introns. A phylogenetic analysis of the 11 complete cpDNA from Asteracease showed that S. involucrata is closely related to Centaurea diffusa (Diffuse Knapweed). The complete cpDNA of S. involucrata provides essential and important DNA molecular data for further phylogenetic and evolutionary analysis for Asteraceae.

Next generation sequencing yields the complete mitogenome of nereid worm, Namalycastis abiuma (Annelida: Nereididae).

In this study, the complete mitogenome sequence of nereid worm, Namalycastis abiuma (Annelida: Nereididae), has been decoded for the first time by low coverage genome sequencing method. The overall base composition of N. abiuma mitogenome is 30.8% for A, 24.6% for C, 14.0% for G and 30.6% for T, and has GC content of 38.6%. The assembled mitogenome, consisting of 15 265 bp, has unique 13 protein-coding genes (PCGs), 21 transfer RNAs and two ribosomal RNA genes. The complete mitogenome of N. abiuma shows 69% identities to Tylorrhynchus heterochaetus. All PCGs, tRNA and rRNA genes were encoded on H-strand. The potential D-loop is 827 bp in length and located between tRNA-Gly and tRNA-Trp. The complete mitogenome provides essential and important DNA molecular data for further phylogenetic and evolutionary analysis for Annelida.

Next generation sequencing yields the complete mitochondrial genome of the Hornlip mullet Plicomugil labiosus (Teleostei: Mugilidae).

In this study, the complete mitogenome sequence of hornlip mullet Plicomugil labiosus (Teleostei: Mugilidae) has been sequenced by next-generation sequencing method. The assembled mitogenome, consisting of 16,829 bp, had the typical vertebrate mitochondrial gene arrangement, including 13 protein coding genes, 22 transfer RNAs, 2 ribosomal RNAs genes and a non-coding control region of D-loop. D-loop contains 1057 bp length is located between tRNA-Pro and tRNA-Phe. The overall base composition of P. labiosus is 28.0% for A, 29.3% for C, 15.5% for G and 27.2% for T. The complete mitogenome may provide essential and important DNA molecular data for further population, phylogenetic and evolutionary analysis for Mugilidae.

Complete mitogenomes of Guinean angelfish (Holacanthus africanus) and Rock beauty (Holacanthus tricolor) (Teleostei: Pomacanthidae).

In this study, we used the next-generation sequencing method to deduce two complete mitogenomes of Guinean angelfish (Holacanthus africanus) and Rock beauty (Holacanthus tricolor) for the first time. The assembled mitogenome, consisting of 16,819 bp and 16,625 bp in length, shows 87% similarity with each other. Both mitogenomes follow the typical vertebrate arrangement, including 13 protein-coding genes, 22 transfer RNAs, 2 ribosomal RNAs genes, and a non-coding control region of D-loop. The D-loop contains 1107 bp in H. africanus and 905 bp in H. tricolor and is located between tRNA-Pro and tRNA-Phe. The overall GC content is 46.2% for H. africanus and 45.6% for H. tricolor. The complete mitogenome of Guinean angelfish and Rock beauty deduced in this study provides essential and important DNA molecular data for further phylogenetic and evolutionary analysis for marine angelfish.