Species-specific molecular signature of Commiphora species of Saudi Arabia inferred from internal transcribed spacer sequences of nuclear ribosomal DNA

The deciduous habit and tendency to produce flowers prior to developing leaves, and a predominantly dioecious system of breeding in the genus Commiphora leads to difficulties in its taxonomic identification at species level. The characteristics of easy amplification by universal primer, shorter length and higher discrimination power at the species level makes the internal transcribed spacer (ITS) sequence of nuclear ribosomal DNA (nrDNA) to a smart gene for generating species-specific phylogenetic inferences in most of the plants groups. The present study deals the ITS sequence of nrDNA based molecular genotyping of seven species of the genus Commiphora of Saudi Arabia. The molecular phylogenetic analysis of ITS sequences of nrDNA of Commiphora species distributed in Saudi Arabia reveals the the occurrence of C. madagascariens in Saudi Arabia.     

Molecular diagnosis of begomovirus associated with Chilli leaf curl disease in Jeddah,Saudi Arabia

Chilli (Capsicum annum L.) is well known as ‘wonder spice’. This is a very valuable cash crop grown as a vegetable globally. Chilli leaf curl disease is a major threat and global concern for the cultivation of Chilli by farmers and growers. In this work, the molecular diagnosis, genetic diversity, phylogenetic relationship, and begomovirus association with Chilli leaf curl disease have been discussed. The infected leaves were randomly harvested from the Chilli field, at Jeddah, Saudi Arabia. A group of begomovirus vector, whiteflies were also observed on the Chilli crop and infected weeds growing in the neighboring field. The begomovirus was confirmed by coat protein gene specific primer, dot blot hybridization, sequencing and sequence analysis. The full coat protein gene was found to have 774 nucleotides. The nucleotide sequences analysis shared the highest identity with Tomato yellow leaf curl virus reported earlier infecting tomato from Saudi Arabia, and the lowest identity was observed with Tomato yellow leaf curl virus Oman isolate. The overall sequence identity ranged from more than ninety percent among the analyzed sequences. The phylogenetic relationship analysis formed the major three clusters and showed the closed clustering with Tomato yellow leaf curl virus isolates. The natural spread of the Tomato yellow leaf curl virus on the Chilli crop from other crops poses an important and serious threat to Chili cultivation in the Kingdom of Saudi Arabia. Based on the literature review and current evidence, this is the first report of leaf curl disease of Chilli from Saudi Arabia.     

Two newly recognized species of Hemidactylus (Squamata,Gekkonidae) from the Arabian Peninsula?and Sinai,Egypt

A recent molecular phylogeny of the Arid clade of the genus Hemidactylus revealed that the recently described H. saba and two unnamed Hemidactylus species from Sinai, Saudi Arabia and Yemen form a well-supported monophyletic group within the Arabian radiation of the genus. The name ‘Hemidactylus saba species group’ is suggested for this clade. According to the results of morphological comparisons and the molecular analyses using two mitochondrial (12S and cytb) and four nuclear (cmos, mc1r, rag1, rag2) genes, the name Hemidactylus granosus Heyden, 1827 is resurrected from the synonymy of H. turcicus for the Sinai and Saudi Arabian species. The third species of this group from Yemen is described formally as a new species H. ulii sp. n. The phylogenetic relationships of the members of ‘Hemidactylus saba species group’ are evaluated and the distribution and ecology of individual species are discussed.     

Using multilocus approach to uncover cryptic diversity within Pseudotrapelus lizards from Saudi Arabia

The agamid Pseudotrapelus lizards inhabit the mountainous areas of the Arabian Peninsula and eastern North Africa. Currently six Pseudotrapelus species are recognised, though diagnostic morphological characters are still lacking, creating great difficulty in describing new species. Recently, two specimens of Pseudotrapelus were collected from the vicinity of Riyadh in central Saudi Arabia, an area that was not sampled in previous phylogenetic studies. In here we used both mitochondrial and nuclear data to investigate the phylogenetic position of the new samples, and assess their phylogenetic relationships with the other recognised species of Pseudotrapelus from across the distribution range of the genus. We used a multilocus approach of haplotype networks, concatenated datasets and species trees, performed mitochondrial and nuclear species delimitation analyses, and estimated divergence times. In general, our results support previous molecular studies and uncover the presence of cryptic diversity within Pseudotrapelus. The phylogenetic structure of the genus is of two major clades and within them seven distinct, delimited phylogenetic groups belonging to the six recognised species and the seventh to the individuals from Riyadh. The Riyadh specimens were distinct in all analyses performed. We suggest that the new specimens from the Riyadh area are a distinct lineage, forming a clade with their phylogenetic relatives, P. sinaitus and P. chlodnickii. The clade formed by these three species diverged during the Late Miocene around 6.4 Ma, with cladogenesis possibly facilitated by vicariance and isolation caused due to climatic fluctuations and the progression of sandy areas. Our results suggest further morphological research is necessary to revise the taxonomic status of this lineage and of the entire genus.     

Sea cucumbers of the Arabian Peninsula and Iran – A review of historical and current research trends

Sea cucumbers are benthic marine invertebrates with immense ecological and commercial value. Processed sea cucumbers known as “Beche-de-mer” are a delicacy in southeast Asian countries with an ever-increasing demand depleting wild stocks on a global scale. Aquaculture techniques are well developed for commercially important species (e.g. Holothuria scabra) to aid in conservation and trade. In the Arabian Peninsula and Iran, where the major land mass is surrounded by marginal seas (Arabian Gulf, Gulf of Oman, Arabian Sea, Gulf of Aden, and Red Sea), studies on sea cucumbers are rather limited and its economic value is underestimated. Historical and current research trends indicate impoverished diversity (82 species) due to environmental extremes. Artisanal fisheries exist for the sea cucumbers of Iran, Oman, and Saudi Arabia, with Yemen and United Arab Emirates (UAE) playing a key role in collection and export to Asian countries. Stock assessment and data on export indicates depletion of natural stocks in Saudi Arabia and Oman. Aquaculture trials of high value species (H. scabra) were successful in Saudi Arabia, Oman and Iran with prospects for further expansion. Research on ecotoxicological properties and bioactive substances conducted in Iran demonstrates an immense research potential. Molecular phylogeny, biology, use in bioremediation, and characterisation of bioactive compounds were identified as potential gaps in research. Expanding aquaculture operations could revive exports and recuperate damaged stocks through sea ranching. Furthermore, regional cooperation, networking, training, and capacity building could help fill the gaps in sea cucumber research, which will aid in its effective conservation and management.     

Sea cucumbers of the Arabian Peninsula and Iran – A review of historical and current research trends

Sea cucumbers are benthic marine invertebrates with immense ecological and commercial value. Processed sea cucumbers known as “Beche-de-mer” are a delicacy in southeast Asian countries with an ever-increasing demand depleting wild stocks on a global scale. Aquaculture techniques are well developed for commercially important species (e.g. Holothuria scabra) to aid in conservation and trade. In the Arabian Peninsula and Iran, where the major land mass is surrounded by marginal seas (Arabian Gulf, Gulf of Oman, Arabian Sea, Gulf of Aden, and Red Sea), studies on sea cucumbers are rather limited and its economic value is underestimated. Historical and current research trends indicate impoverished diversity (82 species) due to environmental extremes. Artisanal fisheries exist for the sea cucumbers of Iran, Oman, and Saudi Arabia, with Yemen and United Arab Emirates (UAE) playing a key role in collection and export to Asian countries. Stock assessment and data on export indicates depletion of natural stocks in Saudi Arabia and Oman. Aquaculture trials of high value species (H. scabra) were successful in Saudi Arabia, Oman and Iran with prospects for further expansion. Research on ecotoxicological properties and bioactive substances conducted in Iran demonstrates an immense research potential. Molecular phylogeny, biology, use in bioremediation, and characterisation of bioactive compounds were identified as potential gaps in research. Expanding aquaculture operations could revive exports and recuperate damaged stocks through sea ranching. Furthermore, regional cooperation, networking, training, and capacity building could help fill the gaps in sea cucumber research, which will aid in its effective conservation and management.     

Modelling potential habitat suitability for critically endangered Arabian leopards (Panthera pardus nimr) across their historical range in Saudi Arabia

Camera trapping can detect and monitor rare species in landscapes spanning thousands of square kilometres but placement of cameras in areas where the animals most likely occur will increase detection success. This vital information is lacking for the critically endangered Arabian leopard (Panthera pardus nimr) that has undergone a 90% decline across its range in Saudi Arabia. We aimed to identify suitable Arabian leopard habitat and potential population capacity in Saudi Arabia using data from leopards living in ecologically analogous habitat in South Africa and Oman. We developed a resource selection function (RSF) from 14 leopards’ GPS data in the Cederberg, South Africa, and validated the model using three leopards in the Little Karoo, and two Arabian leopards in Oman. We then projected the model to the historical range of Arabian leopards in Saudi Arabia to estimate likely leopard locations and potential population sizes based on home range metrics. The RSF successfully discriminated between used and available locations (specificity = 96.7%) and had high predictive ability (Rho > 0.9). Leopards selectively used areas away from human settlements and roads, with high enhanced vegetation index, and intermediate slopes and elevations. Saudi Arabia could theoretically host 4 distinct populations totalling 162–362 Arabian leopard females, depending on home range size. Camera traps deployed in the south-western mountains of Saudi Arabia may be most likely to detect remnant populations of Arabian leopards. Further research is needed into the local abundance of prey species and human activity to ensure the persistence of suitable leopard ranges and inform conservation actions.     

Geographical distribution and molecular detection of Nosema ceranae from indigenous honey bees of Saudi Arabia

The aim of the study was to detect the infection level of honey bees with Nosema apis and/or Nosema ceranae using microscopic and molecular analysis from indigenous honeybee race of eight Saudi Arabian geographical regions. A detailed survey was conducted and fifty apiaries were chosen at random from these locations. Infection level was determined both by microscope and Multiplex-PCR and data were analyzed using bioinformatics tools and phylogenetic analysis. Result showed that N. ceranae was the only species infecting indigenous honeybee colonies in Saudi Arabia. As determined by microscope, Nosema spores were found to be in 20.59% of total samples colonies, while 58% of the samples evaluated by PCR were found to be positive for N. ceranae, with the highest prevalence in Al-Bahah, a tropical wet and dry climatic region, whereas low prevalence was found in the regions with hot arid climate. Honeybees from all eight locations surveyed were positive for N. ceranae. This is the first report about the N. ceranae detection, contamination level and distribution pattern in Saudi Arabia.     

An ITS-based phylogenetic framework for the genus Vorticella: finding the molecular and morphological gaps in a taxonomically difficult group

Vorticella includes more than 100 currently recognized species and represents one of the most taxonomically challenging genera of ciliates. Molecular phylogenetic analysis of Vorticella has been performed so far with only sequences coding for small subunit ribosomal RNA (SSU rRNA); only a few of its species have been investigated using other genetic markers owing to a lack of similar sequences for comparison. Consequently, phylogenetic relationships within the genus remain unclear, and molecular discrimination between morphospecies is often difficult because most regions of the SSU rRNA gene are too highly conserved to be helpful. In this paper, we move molecular systematics for this group of ciliates to the infrageneric level by sequencing additional molecular markers—fast-evolving internal transcribed spacer (ITS) regions—in a broad sample of 66 individual samples of 28 morphospecies of Vorticella collected from Asia, North America and Europe. Our phylogenies all featured two strongly supported, highly divergent, paraphyletic clades (I, II) comprising the morphologically defined genus Vorticella. Three major lineages made up clade I, with a relatively well-resolved branching order in each one. The marked divergence of clade II from clade I confirms that the former should be recognized as a separate taxonomic unit as indicated by SSU rRNA phylogenies. We made the first attempt to elucidate relationships between species in clade II using both morphological and multi-gene approaches, and our data supported a close relationship between some morphospecies of Vorticella and Opisthonecta, indicating that relationships between species in the clade are far more complex than would be expected from their morphology. Different patterns of helix III of ITS2 secondary structure were clearly specific to clades and subclades of Vorticella and, therefore, may prove useful for resolving phylogenetic relationships in other groups of ciliates.     

Fatty acid production of thraustochytrids from Saudi Arabian mangroves

This is the first report of thraustochytrids from Saudi Arabia. A total of 108 isolates of thraustochytrid were cultured from Syhat mangroves, Arabian Gulf, Saudi Arabia. Isolated thraustochytrids belonged to five genera: Aplanochytrium, Aurantiochytrium, Schizochytrium, Thraustochytrium and Ulkenia. Cultured thraustochytrids isolated from decaying leaves of Avicennia marina (77 isolates), sediment (15), seawater (10) and decaying thalli of Sargassum (6). Of the 108 isolates, three strains (SY25, SY38 and SY52) were selected based on their high biomass productivity and high percentages of PUFAs. Phylogenetic analyses based on 18S rDNA placed the three strains within the Aurantiochytrium clade with high statistical support. Species of Aurantiochytrium formed six separate clades, the two strains (SY38 and SY52) formed a separate clade that is a sister clade to the one that contains the type species A. limacinum, while SY25 grouped with Aurantiochytrium sp. TA4, that is also isolated from mangroves in Iran, Arabian Gulf. The strains (SY38 and SY52) shared the phylogenetic placement, their morphology and fatty acid profile. The strain SY25 have different shape of sporangia that divide to give zoospores directly, sporogenous cells are surrounded by thick gelatinous sheath and produce high levels of Linoleic and Oleic essential unsaturated fatty acids. The three studied strain produced high levels of Palmitic acid (ranged between 31.1 and 65.3 % of total fatty acids) that can be further optimized for biofuel production.     

Small and overlooked: Phylogeny of the genus Trigonodactylus (Squamata: Gekkonidae), with the first record of Trigonodactylus arabicus from Jordan

Geckos of the genus Trigonodactylus are widely distributed in the sand deserts of the Arabian Peninsula. Three species of this genus are currently recognized, with a fourth one, Stenodactylus pulcher, which placement within Trigonodactylus has been tentatively suggested, but not yet confirmed. We present a phylogenetic analysis of the genus Trigonodactylus with new specimens collected in central Saudi Arabia and southern Jordan. New genetic data has been generated from three mitochondrial markers to investigate the phylogenetic relationships of all species of the genus and to assess the putative generic assignment of S. pulcher. Our results confirm that S. pulcher indeed belongs within Trigonodactylus, branching as a sister lineage to all other species of the genus. The new samples cluster within Trigonodactylus arabicus, thus confirming the genetic homogeneity of the species across its large and seemingly inhospitable range. The new specimen collected in southern Jordan represents the first record for the country and a considerable range extension to the northwest from all previously reported localities. Our findings and discovery of a new species for Jordan highlight the need of more field surveys to be carried out in the underexplored parts of Jordan and northern Saudi Arabia, as these places still hold a potential for new discoveries and are crucial for understating the biogeography of the Arabian herpetofauna.     

Review of subtribe Pterellina Rohdendorf, 1967 (Diptera: Sarcophagidae) of Middle East with descriptions of twelve new species

Summary

Based on a revision of large recent collections housed at the Natural History Museum (London), Tel Aviv University and in the private collection of Yu. Verves and L. Khrokalo (Kyiv, Ukraine), new distributional data and an updated list with comments of 28 species of Middle Eastern Sarcophagidae of the subtribe Pterellina are presented. Seventeen of them are recorded for Israel, 11 for Egypt, four for Iran, two each for the Palestinian Authority, Saudi Arabia and Turkey, and one each for Jordan and the UAE. No data are known for the territories of Bahrain, Cyprus, Iraq, Kuwait, Lebanon, Oman, Qatar, Syria and Yemen. Twelve species new to science are described, including nine from Israel (Chaetapodacra montana n. sp., Eremasiomyia bicolor n. sp., E. deserta n. sp., E. fuscata n. sp., Protomiltogramma bidentata n. sp., P. serrata n. sp., Pterella hermonica n. sp., P. indigens n. sp., P. zefatica n. sp.), two from Egypt (Chaetapodacra griseola n. sp., Eremasiomyia alba n. sp.) and one from Saudi Arabia (Protomiltogramma arabica n. sp.). The male of Eremasiomyia nigra Rohdendorf, 1935 is described for the first time. One new combination of specific name is proposed ? Protomiltogramma immunita (Villeneuve, 1923), n. comb. Original keys for the identification of genera and species are proposed. An annotated list of all world genera and species and compiled data on larval habits of Pterellina are included.     

Survey of the reptilian fauna of the Kingdom of Saudi Arabia. V. The lizard fauna of Turaif region

Turaif area located in the Northern border region of Saudi Arabia is one of the most important regions of the Kingdom. This work was proposed to throw light on the diversity of lizard fauna investigated through the collection and subsequent identification of specimens from different localities of Turaif region of Kingdom of Saudi Arabia. Sixteen species of lizards belonging to 5 families (Agamidae, Gekkonidae, Lacertidae, Scincidae and Varanidae) were recorded. Lacertidae was the most common family. Three species of lizards namely Acanthodactylus orientalis, Acanthodactylus scutellatus and Acanthodactylus grandis were reported for the first time in the Turaif region of Saudi Arabia. The geographical distribution of the collected species within this province was mapped.     

Amphibians distribution and habitats in the southwestern region of Saudi Arabia

This study surveyed 205 wetland sites in the Southwestern Saudi Arabia. We found seven species of amphibians (Anura), which belong to four families: Bufonidae; which includes four species, Sclerophrys tihamica; S. Arabica, Duttaphrynus dhufarensis, and Bufotes viridis; Hylidae, represented by only one species, the tree frog Hyla savignyi; Ranidae, which represented by one species, Pelophylax ridibundus and finally the Dicroglossidae, represented by one species, Euphlyctis ehrenbergii. The reasonable amount of rain received in southwest Arabia, and habitat diversity contribute to the relative abundance of amphibians in the region. Five types of wetland habitats were found in the study area. Valley streams, irrigated farms, seasonal ponds, dam reservoir and lagoons of treated sewage water. The current study revealed the wide spread of amphibians in southwestern Saudi Arabia than what had been reported earlier and confirmed the presence of the Bufotes viridis at three new sites in Asir Heights. It also showed the wide spread of S. arabica in all types of habitats in the southwestern region of Saudi Arabia. Habitat degradation was evident in the region, which might lead to species loss.     

Morphometeric criteria and partial sequence of the 18S rRNA gene of Ceratomyxa sultani n. sp. from the gallbladder of Upeneus margarethae in the Arabian Gulf,with a note on its seasonal prevalence

This paper describes a new coelozoic myxosporean parasite named Ceratomyxa sultani n. sp. isolated from the gallbladder of Upeneus margarethae sourced from the Arabian Gulf off Saudi Arabia. Of 104 U. margarethae specimens examined, 27 (26%) were infected, with the highest prevalence in winter and lowest in autumn. The pseudoplasmodia were disporous and irregularly elliptical in shape, with an average size of 22?×?17?μm. Mature spores were mostly elliptical with symmetrical valves and equal spherical polar capsules. Spores were 9?µm in length and 25?µm in thickness, while polar capsules were 4?µm wide with four filament coils. The paper further provides a morphological comparison with closely related Ceratomyxa spp. together with phylogenetic analysis based on the partial 18S rRNA sequence, which revealed that C. sultani n. sp. clustered within a robust clade of Ceratomyxa species from the Arabian Gulf and Red Sea or nearby geographic regions.     

Phytophagous and predaceous mites associated with vegetable crops from Riyadh,Saudi Arabia

This study was conducted to investigate phytophagous and predatory mites associated with vegetable plants in Riyadh, Saudi Arabia. Eight phytophagous and 10 predacious mites were collected from 14 species of vegetable crops covering five major production localities. Out of these 18 mite species, 13 species are new to the mite fauna of Saudi Arabia. In addition, the two species, Tenuipalpus punicae and Agistemus exsertus, are reported for the first time on vegetable crops in Saudi Arabia. For each mite species found, notes on host plant association and occurrence period are given. An illustrated key for the identification of the 18 mite species reported in this study is provided and this can be used to improve the IPM programs by applying the local natural predatory mites in controlling mite pests in Saudi Arabia.     

Tabanidae (Diptera) of Saudi Arabia

Samples were collected from southern, central and eastern regions of Saudi Arabia using Malaise traps and sweep nets. Nine species of Tabanidae were identified, two for the first time from Saudi Arabia, Hybomitra peculiaris (Szilády) and Atylotus pulchellus (Loew).Therefore, the total number of Tabanidae in Saudi Arabia is 31 species. Remarks of the species recorded in this study were given. A key to the genera of Tabanidae occurring in the Arabian Peninsula is also provided. Available literature for Saudi Arabian Tabanidae is summarized and provided. It is concluded that the tabanid fauna of Saudi Arabia is more similar to that of the Palaearctic region than to the Afrotropical region.     

Genetic diversity of populations of Old World screwworm fly, Chrysomya bezziana, causing traumatic myiasis of livestock in the Gulf region and implications for control by sterile insect technique

Abstract.  Fly larvae were collected from 181 cases of traumatic myiasis in livestock in 10 regions of four countries in the Middle East Gulf region: Iran, Iraq, Saudi Arabia and Oman. The predominant fly species responsible for cases was the Old World screwworm (OWS) fly, Chrysomya bezziana Villeneuve (Diptera: Calliphoridae). In cases from Iran and Oman, which included non-OWS fly species, OWS fly was found solely responsible for 67.6% of cases and jointly with other fly species for a further 12.7% of cases. The major hosts were sheep and goats, together comprising 84.6% of the total, which reflects their predominance among the livestock of these Gulf countries. The major site of wounding on sheep and goats was the tail (40.3%), followed by female genitalia (14.0%). The 3' terminal 715 nucleotides of the mitochondrial cytochrome b gene were sequenced for 178 larvae of OWS. Five haplotypes were identified: three had been recorded previously in the region (two were common throughout and one was unique to Oman), and two were newly identified, one from southern Iraq and the other from Saudi Arabia, both in regions sampled for the first time. The haplotypes varied from one another only at one or two nucleotide sites, equivalent to an intraspecific difference of 0.14–0.28% across the entire 715-bp fragment. There was a single statistically significant association between host species and haplotype in Saudi Arabia, a first such record for OWS fly. The small degree of genetic diversity between geographical populations of OWS fly within the Gulf region suggests that a single Gulf colony could be used to implement the sterile insect technique within an integrated control programme.     

First Record of the Myrmicine Ant Genus Meranoplus Smith, 1853 (Hymenoptera: Formicidae) from the Arabian Peninsula with Description of a New Species and Notes on the Zoogeography of Southwestern Kingdom Saudi Arabia

The ant genus Meranoplus is reported for the first time from the Arabian Peninsula (Kingdom of Saudi Arabia) by the new species M. pulcher sp. n., based on the worker caste. Specimens were collected from Al Sarawat and Asir Mountains of southwestern Kingdom of Saudi Arabia using pitfall traps. Meranoplus pulcher sp. n. is included in the Afrotropical M. magretii-group, with greatest similarity to M. magrettii André from Sudan. A key to the Afrotropical species of the M. magretii-group is presented. A brief review of the ant taxa with Afrotropical affinities in southwestern region of the Kingdom of Saudi Arabia is given.