Reconstructing historical baselines for the Persian/Arabian Gulf Dugong,Dugong dugon (Mammalia: Sirena)

Retrospective estimates of historic abundances and distributions of marine organisms are crucial to understanding the anthropogenic impacts on the structure and species of coastal ecosystems, especially in the case of vulnerable species such as the Dugong (Dugong dugon). The Persian/Arabian Gulf is home to the second largest Dugong population in the world, yet little is known about their current or past abundance, distribution, and ecological role. Here, we examine historical changes in dugong distribution and estimate perceived changes in their abundance. We create a ‘dugong discovery curve’ and compile global density estimates as proxies for the overall health of the population in the Gulf. We find that since 1950 dugong range may have contracted by one quarter, and despite their large population, their overall densities in the Gulf are far lower than in other areas within their range. Basic understanding of historical trajectories for Dugongs is needed in order to develop appropriate management plans and conservation targets, particularly in light of large and wide-spread coastal development projects in the region.     

Molecular identification and phylogenetic relationships of Coleoidea (Mollusca: Cephalopoda) from the Persian Gulf and Oman Sea reveals a case of cryptic diversity

The Persian Gulf and Oman Sea constitute one of the most important marine ecosystems and have many economically important aquatic species, including several coleoid cephalopods. Some coleoids are difficult to identify using traditional morphological characteristics. In this study, two mitochondrial fragments, cytochrome oxidase I (COI) and the large ribosomal subunit (16S rRNA), were used for identification of coleoid species in four regions in the northern Persian Gulf and Oman Sea. The study led to the identification of potential cryptic species of Sepia, Amphioctopus and Uroteuthis. Furthermore, Euprymna hyllebergi was reported for the first time from the Persian Gulf. A high diversity of Coeloidea was found in the study area. Mean intraspecific and interspecific nucleotide distances for COI were 0%–2% and 2%–7%, respectively, while these values for 16S rRNA sequences were 0%–1% and 1%–4%. Given the uncertainty about species identity and the high levels of intraspecific genetic diversity reported for some species in GenBank, a comprehensive global study will be needed to resolve the taxonomic status of several coleoid species.     

Evaluation of copper and vanadium concentration in the soft tissue of Tylosurus crocodilus in Bahregan region,Persian Gulf

Abstract

The present study has been carried out to evaluate the concentration of copper (Cu) and vanadium (V) elements in the muscle, skin, and gill tissues of Tylosurus crocodilus (Belonidae), an edible fish, in the Bahregan region which is located in the northern part of the Persian Gulf. For this purpose, 18 fish samples in three different length groups (small, medium, and large) were randomly collected in Bahregan region. Tissues were separated and concentration of the heavy metals was determined by atomic absorption. The results showed that mean concentration of Cu and V were 0.2851 ± 0.10036 and 1.1368 ± 0.12405, 0.1117 ± 0.02322 and 2.5091 ± 1.14201 and 0.1803 ± 0.03204 and 3.3133 ± 1.05995 μg g^-1 dry weight, in skin, muscle and gill tissues, respectively. Also, the results revealed a significant positive correlation between the standard length and Cu concentration in the muscle and gill tissues (P ≤ 0.05), as well as between the standard length and V concentration in all the tissues (P ≤0.05). The results indicated that the concentration of V was higher than the World Health Organization (WHO) standard but the concentration of Cu was lower. It is therefore highly recommended that usage of this carnivore species in the studied area is limited because of the high accumulation of V in its muscle tissue.     

Identification of the highest potential human health and environmental hazard in contaminated sediment near the point sources in the northwest Persian Gulf

Abstract

The overall goal of this work was to determine the concentration levels and the potential ecological risks of 30 polycyclic aromatic hydrocarbons in the Persian Gulf sediments, Iran. The study also predicted the bioaccumulation of PAHs using the Monte Carlo simulation. For these goals, 68 surface sediment samples were collected from the Persian Gulf in January 2017. Then, the experiments were performed with Soxhlet system, chromatographic column and GC-MS instrument. According to the Canadian Sediment Quality Guidelines, 35.29% of sampling sites exhibited high potential adverse biological effects and 79.41% of samples have a low probability of toxicity. The mean bioaccumulated concentrations of carcinogenic PAHs in the Persian Gulf were predicted as 207.78?±?262.23, 116.06?±?146.47 and 69.26?±?87.41?ng g^–1 for mollusks, shrimps and crabs, respectively. The mean Toxic Equivalency and Mutagenic Equivalent Quotient for sediments was 702.06?±?1012.37 and 500.37?±?665.71?ng g^?1, respectively. The 95th percentile carcinogenic and non-carcinogenic risks calculated for children and adults were lower than the threshold values of 10^?6 and 1.0, respectively, revealing no potential health risk. The highest potential risks for toxicity were observed at sampling sites close to the Nowruz oil field and Mahshahr petrochemical economic zone based on the highest TEQcarc and MEQcarc values in this area.     

Shell selection behaviour and spatial distribution of three species of intertidal hermit crabs from Hormuz Island,Persian Gulf (Crustacea: Paguroidea)

Shell selection behaviour and spatial distribution of three hermit crab species, Diogenes avarus, D. karwarensis, and Areopaguristes perspicax, were studied at six sites along the intertidal zones of Hormuz Island in the Persian Gulf. 1025 specimens were collected occupying altogether 31 shell species (D. avarus 28 species, A. perspicax 22 species, and D. karwarensis 8 species). Diogenes avarus was found to be by far the most abundant of these three crab species, and Cerithidea cingulata the dominant shell occupied by these hermit crabs. The distribution of the hermit crabs significantly varied (p<0.05) among the sites. The number and the wide diversity of shells occupied in different sites show that the main factor in shell selection for these hermit crabs is the abundance and distribution of shell species in the field.     

The metabolism of photosynthetically fixed carbon by isolated chloroplasts from Codium fragile (Chlorophyta: Siphonales) and by Elysia viridis (Mollusca: Sacoglossa)

The metabolism of photosynthetically fixed ¹⁴C by isolated chloroplasts from Codium fragile is compared with that by Elysia viridis (which contains C. fragile chloroplasts). There are marked differences between the two in the formation and subsequent metabolism of both soluble and insoluble products. Less than 6% of the carbon fixed by the isolated chloroplasts during a 15 min pulse of ¹⁴C-bicarbonate in the light is released into the medium over the succeeding 24 h. During photosynthesis glycollate and glucose monophosphate are the only labelled compounds released; after the pulse very little glycollate is released and over 24 h only glucose monophosphate and an unidentified compound are found in the medium. In E. viridis photosynthetically fixed carbon can be recovered from compounds of all major classes found in animals. Soon after the pulse, hexoses are the most heavily labelled compounds, but two hours later amino acids are more heavily labelled than hexoses. The unidentified compound is not found in the animals. E. viridis can absorb and metabolize exogenous glycollate and glucose. Earlier authors' suggestions that glucose is the compound which moves from the chloroplast to the animal cell are discussed, and it is proposed that both glucose monophosphate and glucose are formed outside the chloroplast from triose phosphate exported from it.     

Cytochrome c oxidase subunit 1 barcode data of fish of the Nayband National Park in the Persian Gulf and analysis using meta-data flag several cryptic species

We provide cytochrome c oxidase subunit 1 (COI) barcode sequences of fishes of the Nayband National Park, Persian Gulf, Iran. Industrial activities, ecological considerations and goals of The Fish Barcode of Life campaign make it crucial that fish species residing in the park be identified. To the best of our knowledge, this is the first report of barcoding data on fishes of the Persian Gulf. We examined 187 individuals representing 76 species, 56 genera and 32 families. The data flagged potentially cryptic species of Gerres filamentosus and Plectorhinchus schotaf. 16S rDNA data on these species are provided. Exclusion of these two potential cryptic species resulted in a mean COI intraspecific distance of 0.18%, and a mean inter- to intraspecific divergence ratio of 66.7. There was no overlap between maximum Kimura 2-parameter distances among conspecifics (1.66%) and minimum distance among congeneric species (6.19%). Barcodes shared among species were not observed. Neighbour-joining analysis showed that most species formed cohesive sequence units with little variation. Finally, the comparison of 16 selected species from this study with meta-data of conspecifics from Australia, India, China and South Africa revealed high interregion divergences and potential existence of six cryptic species. Pairwise interregional comparisons were more informative than global divergence assessments with regard to detection of cryptic variation. Our analysis exemplifies optimal use of the expanding barcode data now becoming available.     

COI-based DNA barcoding of Arcoida species (Bivalvia: Pteriomorphia) along the coast of China

DNA barcoding is a promising tool for the rapid and unambiguous identification of species. Some arcoid species are particularly difficult to distinguish with traditional morphological identification owing to phenotypic variation and the existence of closely related taxa. Here, we apply DNA barcoding based on mitochondrial cytochrome c oxidase I gene (COI) to arcoid species collected from the coast along China. Combining morphology with molecular data indicates the 133 specimens of Arcoida could be assigned to 24 species. Because of the deep genetic divergence within Tegillarca granosa, there was an overlap between genetic variation within species and variation between species. Nevertheless, NJ and Bayesian trees showed that all species fell into reciprocally monophyletic clades with high bootstrap values. Our results evidence that the COI marker can efficiently identify species, correct mistakes caused by morphological identification and reveal genetic differentiation among populations within species. This study provides a clear example of the usefulness of barcoding for arcoid identification. Furthermore, it also lays a foundation for other biological and ecological studies of Arcoida.     

Genetic diversity and population structure of Sepiella japonica (Mollusca: Cephalopoda: Decapoda) inferred by mitochondrial DNA (COI) variations

In order to describe the genetic diversity of five geographical populations of cuttlefish (Sepiella japonica) along with Chinese coast and determined their phylogenetic relationship, partial mitochondrial COI gene (681bp in length) was amplified from 96 individuals collected from these populations and sequenced. The 5 populations of cuttlefish inhabit Yellow Sea, East China Sea and South China Sea. Out of 22 polymorphic nucleotides identified, 8 were represented by a single sequence, 12 were parsimony informative, which defined 22 haplotypes. Haplotype and nucleotide diversity were low among populations. Of 22 haplotypes, 15 appeared only in a single population, 6 appeared in 2 or 3 populations and 1 was shared by all populations. The COI gene was monomorphic in Qingdao population. The haplotypes identified clustered into 2 clades, each covered individuals from 5 populations each. Pairwise F_ST were not proportional to the geographical distances. Among the 5 populations, relatively high level of genetic diversity was found in Ningde population which was recommended to be the best choice of germplasm resources for artificial releasing project.     

Significant correlation of Cd,Cu, Pb and Zn in sediments and oysters (Saccostrea cucullata) collected from Qeshm Island,Persian Gulf,Iran

Abstract

The relationships are evaluated between the heavy metal species in sediments and the accumulation by the soft tissues of Saccostrea cucullata collected from the northern and southern coasts of Qeshm Island, Persian Gulf. The sequential extraction technique was employed to fractionate the sediment into non resistant and resistant fractions. Data from sequential extractions indicated that the metals were mainly associated with the residual fraction at the north coast and with non residual fractions at the south coast. The results showed that the best correlations were observed between heavy metals concentrations in soft tissues and the fractions in the southern sediment. Note that the bioavailability of trace metals is influenced by the chemical characteristics and properties of the sediment. Therefore, the present results generally supported the use of soft tissues of S. cucullata as a more accurate biomonitoring organism for Cu, Pb and Cd in sediments from the southern coast of Qeshm Island, Persian Gulf.     

Description of a new species of Parasesarma (Crustacea; Decapoda; Brachyura; Sesarmidae) from the Persian Gulf, based on morphological and genetic characteristics

The genera Parasesarma and Perisesarma are common inhabitants of mangroves and estuaries of the Indo-West Pacific. These, overall similar, genera of sesarmid crabs can be told apart by the presence or absence of an anterolateral tooth, but recent and ongoing studies show that they are not reciprocally monophyletic. In recent years, detailed morphological studies have revealed a surprising number of undescribed new species within these genera. In the present paper, we describe a new species of the genus Parasesarma from the relatively poorly studied Persian Gulf. So far, these specimens had been referred to as Parasesarma plicatum (Latreille, 1803), but morphological and genetic characteristics clearly allow separation of the two species. Consequently, the species from the Persian Gulf is here described as new and morphological and mitochondrial genetic characters are provided that allow recognition of the species.     

The occurrence of two xanthochromic fish,Epiniphelus marginatus (Serranidae) and Diplodus vulgaris (Sparidae) (Osteichthyes) in the eastern Mediterranean

Xanthism in fishes has a genetic basis that causes abnormal skin colouration of yellow to orange-gold. Xanthochromic specimens are rare in nature. We report two cases of adult xanthochromic specimens from the Mediterranean Sea: Epinephelus marginatus from Israel and Diplodus vulgaris from Greece and discuss the reason for the paucity of reports of xanthochromic fish from the Mediterranean.     

Molecular identification of mosquitoes (Diptera: Culicidae) in southeastern Australia

DNA barcoding is a modern species identification technique that can be used to distinguish morphologically similar species, and is particularly useful when using small amounts of starting material from partial specimens or from immature stages. In order to use DNA barcoding in a surveillance program, a database containing mosquito barcode sequences is required. This study obtained Cytochrome Oxidase I (COI) sequences for 113 morphologically identified specimens, representing 29 species, six tribes and 12 genera; 17 of these species have not been previously barcoded. Three of the 29 species ─ Culex palpalis, Macleaya macmillani, and an unknown species originally identified as Tripteroides atripes ─ were initially misidentified as they are difficult to separate morphologically, highlighting the utility of DNA barcoding. While most species grouped separately (reciprocally monophyletic), the Cx. pipiens subgroup could not be genetically separated using COI. The average conspecific and congeneric p‐distance was 0.8% and 7.6%, respectively. In our study, we also demonstrate the utility of DNA barcoding in distinguishing exotics from endemic mosquitoes by identifying a single intercepted Stegomyia aegypti egg at an international airport. The use of DNA barcoding dramatically reduced the identification time required compared with rearing specimens through to adults, thereby demonstrating the value of this technique in biosecurity surveillance. The DNA barcodes produced by this study have been uploaded to the ‘Mosquitoes of Australia–Victoria’ project on the Barcode of Life Database (BOLD), which will serve as a resource for the Victorian Arbovirus Disease Control Program and other national and international mosquito surveillance programs.     

The role of kleptoplasts in the survival rates of Elysia timida (Risso, 1818): (Sacoglossa: Opisthobranchia) during periods of food shortage

The importance of photosynthetic products derived from kleptoplasts in several sacoglossan species is being investigated in different fields, such as chemistry, biomolecular genetics and ecology. This study analyzes the effect of kleptoplasts on the survival rates of Elysia timida by evaluating the development of chlorophyll concentration, total length and survival rates of starved E. timida specimens kept in the light and in the dark. Although chlorophyll concentration values were similar in both cases, after 28 days specimens kept in the dark showed a greater size decrease and a lower survival rate (up to 30% lower) than those kept in the light. It is evident that kleptoplasts provide the mollusc with extra energy at the primary metabolism level to compensate for a shortage in food.     

基于COI基因5′端与3′端序列田间常见粉虱的分子鉴定

【目的】粉虱种类繁多,个体微小,其种类识别与鉴定常需借助分子生物学技术。本研究旨在明确线粒体COI基因(mitochondrial cytochrome c oxidase subunit I gene) 5′端和3′端序列对常见种类粉虱识别鉴定的可行性。【方法】以我国田间常见的16种粉虱为对象,以COI基因5′端(641 bp)和3′端(738 bp)序列为靶标进行比对分析,以MEGA 5.10软件的K2-P模型计算种内与种间遗传距离,以邻接法(NJ法)构建进化树并进行系统发育分析。【结果】当以5′端为靶标时,16种粉虱的种内平均遗传距离为0.0015,种间平均遗传距离为0.2897,种间遗传距离为种内遗传距离的193.1倍;而且种内、种间遗传距离没有重叠区域。当以3′端为靶标时种内平均遗传距离为0.0007,种间平均遗传距离为0.2817,种间遗传距离为种内遗传距离的402.4倍;但桑粉虱Pealius mori与烟粉虱Bemisia tabaci Asia II 1的种内和种间遗传距离重叠。系统发育分析结果显示,以5′端为靶标时,16种粉虱可以形成独立的进化分支;以3′端为靶标时,除桑粉虱与传统分类学不一致外,其余种类均可形成独立的分支。【结论】结果表明,5′端序列更适用于基于DNA条形码技术的物种识别鉴定研究。     

DNA barcoding of stoneflies (Plecoptera) in a general genetics course

DNA Barcoding is a powerful molecular biology tool for the identification of species, analysis of gene flow from within and between populations and evaluating species concepts. The process can be incorporated into a college genetics or bioinformatics core curriculum. Here we demonstrate how, by simply using Plecoptera, we actively engaged students in DNA extraction, amplification and DNA Barcoding. As a result, 38 new DNA sequences were accepted by an international DNA database, with potentially three of them being new species to the database. More importantly, through multiple assessment measurements, students showed a high degree of learning took place and that all student learning objectives were met.     

基于线粒体COI基因序列的文蛤属（软体动物门：帘蛤科）系统发育关系

测定了4种文蛤属贝类的15个个体的COI基因序列,并从GenBank下载了短文蛤(M petechialis)的相应序列.比对后的序列长度为574bp,包括93个简约信息位点,A、T、C和G的平均含量分别为21.15%、44.71%、14.05%和20.09%.通过对序列的分析,共定义了12个单倍型:文蛤(M.meretrix)4个,斧文蛤(M.lamarckii)2个,丽文蛤(M.lusoria)3个,琴文蛤(M.lyrata)1个,短文蛤2个.以青蛤(cylina sinensis)为外群,用MP法和贝叶斯法构建系统树.结果显示,短文蛤、丽文蛤和文蛤为亲缘关系较近的物种,支持短文蛤和丽文蛤为文蛤的同物异名的观点.     

Slugs' last meals: molecular identification of sequestered chloroplasts from different algal origins in Sacoglossa (Opisthobranchia, Gastropoda)

Some sacoglossan sea slugs have become famous for their unique capability to extract and incorporate functional chloroplasts from algal food organisms (mainly Ulvophyceae) into their gut cells. The functional incorporation of the so-called kleptoplasts allows the slugs to rely on photosynthetic products for weeks to months, enabling them to survive long periods of food shortage over most of their life-span. The algal food spectrum providing kleptoplasts as temporary, non-inherited endosymbionts appears to vary among sacoglossan slugs, but detailed knowledge is sketchy or unavailable. Accurate identification of algal donor species, which provide the chloroplasts for long-term retention is of primary importance to elucidate the biochemical mechanisms allowing long-term functionality of the captured chloroplast in the foreign animal cell environment. Whereas some sacoglossans forage on a variety of algal species, (e.g. Elysia crispata and E. viridis) others are more selective. Hence, characterizing the range of functional sacoglossan-chloroplast associations in nature is a prerequisite to understand the basis of this enigmatic endosymbiosis. Here, we present a suitable chloroplast gene (tufA) as a marker, which allows identification of the respective algal kleptoplast donor taxa by analysing DNA from whole animals. This novel approach allows identification of donor algae on genus or even species level, thus providing evidence for the taxonomic range of food organisms. We report molecular evidence that chloroplasts from different algal sources are simultaneously incorporated in some species of Elysia. NeigborNet analyses for species assignments are preferred over tree reconstruction methods because the former allow more reliable statements on species identification via barcoding, or rather visualize alternative allocations not to be seen in the latter.     

Molecular identification and distribution of leatherjackets (Diptera: Tipulidae) in U.K. agricultural grassland

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Aggregata polibraxiona n. sp. (Apicomplexa: Aggregatidae) from Octopus bimaculatus Verrill, 1883 (Mollusca: Cephalopoda) from the Gulf of California,Mexico

The Apicomplexa Aggregata spp. are intracellular parasites of cephalopods that infect the intestinal tract of commercially important species such as Octopus bimaculatus, which sustains the octopus fishery in Baja California (B.C.), Mexico. In this study, Aggregata polibraxiona n. sp. was described from the cecum of O. bimaculatus collected from Bahia de Los Angeles, B. C. Light and electron microscopy revealed that oocysts and sporocysts were spherical to ovoid in shape. Sporulated oocysts (293–835 × 177–688 μm) contained 135–674 sporocysts (12–24 × 11–22 μm). The sporocyst wall was covered by tubular projections (0.55–2.19 μm in length) bifurcated in the top, unevenly distributed, covered by a thin membrane. Each sporocyst contains 11–13 sporozoites (16–26 × 1.20–3 μm). Three partial sequences of the 18S rDNA gene were obtained, and two phylogenetic approaches were performed according to Bayesian inference and Maximum Likelihood. In both phylogenetic reconstructions, the sequences of A. polibraxiona n. sp. were recovered as a monophyletic group within the genus Aggregata and placed as a sister group to Aggregata octopiana Lineage II. Aggregata polibraxiona n. sp. is the first Apicomplexa described from a cephalopod host from Mexico and extends the geographical range of Apicomplexa infecting cephalopods.