Ichthyodiversity in southeastern Arabian Peninsula: Annotated checklist, taxonomy, short description and distribution of Inland fishes of Oman.

The Arabian Peninsula comprises the seven countries of Bahrain, Kuwait, Oman, Qatar, Saudi Arabia, the United Arab Emirates, and Yemen (including the Socotra archipelago), covering an area of more than 3 million km). Although arid habitats cover most parts of the Arabian Peninsula, the region has several freshwater systems and comprises all or parts of four freshwater ecoregions basins that support a variety of inland aquatics including fishes. The current checklist provides all fish species in inland waters of the Arabian Peninsula including all recognized and named taxa, documenting recent changes and controversies in nomenclature, records, taxonomic status, occurrence, synonyms, common English name, range distribution, and conservation status based on several field surveys throughout the area and available articles. The confirmed inland ichthyodiversity of the Arabian Peninsula comprise 48 species belonging to 25 genera, 14 families, nine orders, and a class. Among these, 10 species (20.8%) are alien, and 21 species (52.3%) are considered endemic to the Arabian Peninsula. Favonigobius reichei is a new record for inland waters of the Arabian Peninsula. The most diverse order is Cypriniformes (19 species, 39.6%), followed by Cyprinodontiformes and Gobiiformes (eight species, 16.7% in each), Cichliformes (four species, 8.33%), Mugiliformes (three species, 6.25%), Anguilliformes and Siluriformes (two species, 4.17% in each), and Centrarchiformes and Gonorynchiformes (one species, 4.2% each). Saudi Arabia and Oman with 23 species (47.9% each) rank first in fish diversity (both native and exotic), followed by Yemen (15 species, 31.25%), UAE (seven species, 14.58%), Bahrain (two species, 4.17%), and Qatar and Kuwait (one species, 2.1% each). Of 21 endemic species of the Arabian Peninsula, six, six, and four species are restricted to the territories of Oman, Saudi Arabia and Yemen, respectively. No endemic fish have been reported from Bahrain, Kuwait, Qatar, and the United Arab Emirates. The list also includes two subterranean species belonging to the genus Garra. The provided data will be necessary to take action for effective conservation management strategies and policies.

In this paper, an atmospheric investigation of frontal dust storms in southwest Asia is presented. Atmospheric analysis is done on six severe frontal dust storms which occurred on the Tigris and Euphrates alluvial plain dust sources in non-summer seasons during the last two decades. NCEP-NCAR Reanalysis Data were used for synoptic analysis, and the Aerosol Optical Depth (AOD) data were used to identify the dusty days, dust plumes, and estimation of the dust load over the area. Atmospheric analysis results demonstrated that in non-summer seasons, the high pressure system over the southeastern Arabian Peninsula and neighboring areas with the low pressure system over the east of the Mediterranean Sea and neighboring areas are responsible for noticeable frontal dust storms over the Tigris and Euphrates rivers valley dust sources. These circulation systems provide a favorable condition for southeastward, northeastward, and eastward transport of the dust plumes. An investigation on the affected area by the dust plumes demonstrated that southern Iraq, Kuwait and the Khuzestan province in Iran have the highest AODs and dust load during the investigated dust events. Central Iraq, western and southwestern Iran, and northeastern Saudi Arabia are the regions which were affected by frontal dust storms dust plumes more than the other areas in the Middle East. Studies have shown that the most severe frontal dust storms occurred during March and April and the analysis of the MODIS (Moderate Resolution Imaging Spectroradiometer) AODs data demonstrated that the maximum dust load over the area exceeded 5 g m−2.

Our purpose in this study was to gather all previously published data and our own data of extensive field expeditions and camera trapping to present a general view of the Fars mammals. The mammals of Fars Province, southern Iran, comprise of 72 species in 53 genera, 28 families and seven orders. The most diverse order is Chiroptera with 23 species or 31.9% of the mammalian fauna, followed by Carnivora and Rodentia (each with 18 species, 25%). The most diverse family is Vespertilionidae with nine species or 12.5% of the mammalian fauna, followed by Rhinopomatidae and Muridae, each with eight species or 11.1% of the mammalian fauna, Felidae and Canidae (each with five species, 6.9%), respectively. Sixteen families have only one species each. The Fars Province is the type locality of Triaenops persicus Dobson, 1871, Eptesicus serotinus shiraziensis (Dobson, 1871), Microtus irani Thomas, 1921, and Apodemus witherbyi (Thomas, 1902). Five species are listed in the Appendix I, eight species in the Appendix II, and eight species in the Appendix III of the Convention on International Trade in Endangered Species (CITES). In addition, three species are considered as endangered and nine species as protected species based on the rules and regulations/laws of the Iranian Department of the Environment (DOE). The Asiatic Lion Panthera leo persica Meyer, 1826 is extirpated in Iran. Among the reported species, 60 species (83.3%) are considered as Least Concern (LC), two species as Not Evaluated (2.7%), one species as Data Deficient (1.4%), six species (8.3%) as Vulnerable (VU), and three species (4.2%) as Near Threatened (NT) in the IUCN Red List of Threatened Species. The current checklist shows that the mammalian fauna of Fars Province is rich and taxonomically diverse, and the provided information will be necessary for the development of competent and pragmatic management plans and effective conservation policies.

DNA barcoding, the use of standard segments of DNA to assign specimens to a species, has emerged as a major field of biodiversity research over the last 20 years. Large-scale global initiatives are building DNA barcode reference libraries for animals, fungi, and plants, while pipelines are being developed for metabarcoding-based biomonitoring. The effectiveness of these approaches rests on the premise that much less variation exists within species than between them. While exceptions occur, this principle has been demonstrated to apply in the many animal taxa where the barcode region of the COI gene is effective in species discrimination. Sawflies are an exception to this general pattern because DNA barcodes often fail to distinguish congeneric species, an observation which prompted us to search for an explanation. Using high-throughput single-molecule DNA sequencing to recover COI sequences from thousands of sawflies, we found that single individuals often possess multiple, seemingly functional, full-length DNA barcodes – a phenomenon not documented at similar prevalence in any animal taxon. While the evolutionary causes of multiple variants require further investigation, our observation is remarkable as it violates the one-barcode-one-specimen assumption. The presence of multiple variants of barcodes within individuals does not jeopardize the concept, but its occurrence does introduce a complexity for species inventories based on metabarcoding. They will overestimate the species count when barcode-based operational species units are used as species proxies. Similarly, reference libraries must consider how best to deal with the high frequency of multiple variants in sawflies and any other groups of organisms.Significance StatementDNA barcoding is revolutionizing biodiversity science by enabling the accurate identification of organisms, accelerating taxonomic workflows, and permitting DNA-based biomonitoring. The DNA barcode region for the animal kingdom, mitochondrial COI, is highly effective in discriminating species in almost all studied animal groups. However, the use DNA barcoding is sometimes complicated by the presence of nuclear pseudogenes (NUMTs) or by variants of the mitogenome itself (heteroplasmy) within individuals. By using high-throughput sequencing (HTS) to analyze thou-sands of specimens, we demonstrate that multiple, seemingly functional, full-length variants of the COI barcode region are frequent in North European sawflies. Since these variants are sometimes very divergent, it is important to consider the impact of this within-individual variability on studies based on DNA barcodes.

Major part of our planet includes the marine habitat which faces severe threat due to overexploitation of its bio resources. Assessment of biodiversity in the massive and diverse marine ecosystem is a challenging task. In this introductory chapter, we give a brief description of the marine habitat and types of marine organisms, followed by the concept of DNA barcoding. We also describe the applications and different initiatives of DNA barcoding in the marine ecosystem. A brief account of DNA barcoding in marine fungi, different groups of animals and plants is also elucidated. This chapter gives a bird’s eye view on the DNA barcoding in the marine perspective.

Pleistocene hominin dispersals out of, and back into, Africa necessarily involved traversing the diverse and often challenging environments of Southwest Asia1–4. Archaeological and palaeontological records from the Levantine woodland zone document major biological and cultural shifts, such as alternating occupations by Homo sapiens and Neanderthals. However, Late Quaternary cultural, biological and environmental records from the vast arid zone that constitutes most of Southwest Asia remain scarce, limiting regional-scale insights into changes in hominin demography and behaviour1,2,5. Here we report a series of dated palaeolake sequences, associated with stone tool assemblages and vertebrate fossils, from the Khall Amayshan 4 and Jubbah basins in the Nefud Desert. These findings, including the oldest dated hominin occupations in Arabia, reveal at least five hominin expansions into the Arabian interior, coinciding with brief ‘green’ windows of reduced aridity approximately 400, 300, 200, 130–75 and 55 thousand years ago. Each occupation phase is characterized by a distinct form of material culture, indicating colonization by diverse hominin groups, and a lack of long-term Southwest Asian population continuity. Within a general pattern of African and Eurasian hominin groups being separated by Pleistocene Saharo-Arabian aridity, our findings reveal the tempo and character of climatically modulated windows for dispersal and admixture.

Palaeohydrological corridors for hominin dispersals in the Middle East ∼250–70,000 years ago

The North American fauna of Drymeia Meigen was studied. Four new species are described (Drymeia huckettisp. nov., Drymeia pontisp. nov., Drymeia vockerothisp. nov., Drymeia woodorumsp. nov.), and three new synonymies are proposed: Drymeia amnicola (Huckett, 1966) (= Drymeia rivalis (Huckett, 1966), syn. nov.); Drymeia glacialis (Rondani, 1866) (= Drymeia alpicola (Rondani, 1871), syn. nov.); and Drymeia spinitarsis (Aldrich, 1918) (= Drymeia longiseta Sorokina & Pont, 2015, syn. nov.). An annotated checklist, DNA barcodes (when available), and keys for each sex of the 24 named species of North American Drymeia are provided. The utility of DNA barcodes for the identification of Drymeia species across a wide geographical range was explored using sequences from five countries. A match between morphology and DNA barcodes was found for 71% (22/31) of species studied (including three unnamed taxa). The remaining nine species clustered into two groups of taxa with very little interspecific variation within clusters (groups of two and seven species). Caution is advised against using DNA barcoding as the only determination tool for Drymeia material without prior knowledge of its limitations for certain species groups.

This checklist aims to reviews and summarize the results of the systematic and zoogeographical research on the Iranian inland ichthyofauna that has been carried out for more than 200 years. Since the work of J.J. Heckel (1846-1849), the number of valid species has increased significantly and the systematic status of many of the species has changed, and reorganization and updating of the published information has become essential. Here we take the opportunity to provide a new and updated checklist of freshwater fishes of Iran based on literature and taxon occurrence data obtained from natural history and new fish collections. This article lists 288 species in 107 genera, 28 families, 22 orders and 3 classes reported from different Iranian basins. However, presence of 23 reported species in Iranian waters needs confirmation by specimens. The most diverse order is Cypriniformes (171 species, 59.40%), followed by Gobiiformes (42 species, 14.60%), Cyprinodontiformes (17 species, 5.90%), and Clupeiformes (11 species, 3.82%). Eighty-eight endemic species (30.56%) in 7 families and 26 exotic species (9.03%) in 9 families are listed here. Among 288 reported species, 163 (56.6%) species are Not Evaluated (NE), 93 (32.3%) Least Concern (LC), 11 (3.8%) Vulnerable (VU), 8 (2.8%) Data Deficient (DD), 7 (2.4%) Critically Endangered (CR), 3 (1%) Near Threatened (NT), 1 (0.3%) is Endangered (EN) and 1 (0.3%) Extinct in the Wild (EW) of the red list of IUCN. The only reason for this high number of not listed and least concern species in the IUCN Red List is lack of information about the species at national and global levels. This shows the necessity of reconsideration of global categories and application of the IUCN Red List criteria at the national level. Considering the number of endemic fishes (88, 30.56%) in Iran, the first step should be preparing an endemic national assessment for inclusion on the IUCN Red List. Over the last ten years, some native and exotic fishes have been translocated or introduced into natural water bodies. Aquaculture, sport fishing, control of malaria, ornamental purposes, research activities, demonstration in national fairs and accidental introduction are the main reasons for these introductions. Here, we report presence of the Alligator gar, Atractosteus spatula , as an introduced predatory fish from Marivan Lake which seems to have been released from an aquarium. In this checklist, additional, problematic species are also listed, the English/common name of each species is provided, the etymology of each genus is given, the conservation status of each species is given and the bibliographic list of most of published literature on the systematics of inland fishes is mentioned. The provided information will be necessary for the development of competent and pragmatic management plans and effective conservation policies.

With 400 K described species, beetles (Insecta: Coleoptera) represent the most diverse order in the animal kingdom. Although the study of their diversity currently represents a major challenge, DNA barcodes may provide a functional, standardized tool for their identification. To evaluate this possibility, we performed the first comprehensive test of the effectiveness of DNA barcodes as a tool for beetle identification by sequencing the COI barcode region from 1872 North European species. We examined intraspecific divergences, identification success and the effects of sample size on variation observed within and between species. A high proportion (98.3%) of these species possessed distinctive barcode sequence arrays. Moreover, the sequence divergences between nearest neighbor species were considerably higher than those reported for the only other insect order, Lepidoptera, which has seen intensive analysis (11.99% vs up to 5.80% mean NN divergence). Although maximum intraspecific divergence increased and average divergence between nearest neighbors decreased with increasing sampling effort, these trends rarely hampered identification by DNA barcodes due to deep sequence divergences between most species. The Barcode Index Number system in BOLD coincided strongly with known species boundaries with perfect matches between species and BINs in 92.1% of all cases. In addition, DNA barcode analysis revealed the likely occurrence of about 20 overlooked species. The current results indicate that DNA barcodes distinguish species of beetles remarkably well, establishing their potential to provide an effective identification tool for this order and to accelerate the discovery of new beetle species.

DNA sequence data enable not only the inference of phylogenetic relationships but also provide an efficient method for species-level identifications under the terms DNA barcoding or DNA taxonomy. In this study, we have sequenced partial sequences of mitochondrial COI and 16S rRNA genes from 63 specimens of 8 species of Pectinidae to assess whether DNA barcodes can efficiently distinguish these species. Sequences from homologous regions of four other species of this family were gathered from GenBank. Comparisons of within and between species levels of sequence divergence showed that genetic variation between species exceeds variation within species. When using neighbour-joining clustering based on COI and 16S genes, all species fell into reciprocally monophyletic clades with high bootstrap values. These evidenced that these scallop species can be efficiently identified by DNA barcoding. Evolutionary relationships of Pectinidae were also examined using the two mitochondrial genes. The results are almost consistent with Waller's classification, which was proposed on the basis of shell microstructure and the morphological characteristics of juveniles.

The need for multi-gene analysis in evolutionary and taxonomic studies is generally accepted. However, the sequencing of multiple genes is not always possible. For various reasons, short mitochondrial DNA barcodes are the only source of molecular information for some species in many genera, although multi-locus data are available for other species of the same genera. In particular, such situation exists in the species-rich butterfly subgenus Polyommatus (Agrodiaetus). Here, we analyzed the partitioning of this subgenus into species groups by using three data sets. The first data set was represented by short mitochondrial DNA barcodes for all analyzed samples. The second and third data sets were represented by a combination of short mitochondrial DNA barcodes for part of the taxa with longer mitochondrial sequences COI + tRNA-Leu + COII (data set 2) and with longer mitochondrial COI + tRNA-Leu + COII and nuclear 5.8S rDNA + ITS2 + 28S rDNA sequences (data set 3) for the remaining species. We showed that the DNA barcoding approach (data set 1) failed to reveal the phylogenetic structure, resulting in numerous polytomies in the tree obtained. Combined analysis of the mitochondrial and nuclear sequences (data sets 2 and 3) revealed the species groups and the position within these species groups, even for the taxa for which only short DNA barcodes were available.

Butterfly monitoring and Red List programs in Switzerland rely on a combination of observations and collection records to document changes in species distributions through time. While most butterflies can be identified using morphology, some taxa remain challenging, making it difficult to accurately map their distributions and develop appropriate conservation measures. In this paper, we explore the use of the DNA barcode (a fragment of the mitochondrial gene COI) as a tool for the identification of Swiss butterflies and forester moths (Rhopalocera and Zygaenidae). We present a national DNA barcode reference library including 868 sequences representing 217 out of 224 resident species, or 96.9% of Swiss fauna. DNA barcodes were diagnostic for nearly 90% of Swiss species. The remaining 10% represent cases of para- and polyphyly likely involving introgression or incomplete lineage sorting among closely related taxa. We demonstrate that integrative taxonomic methods incorporating a combination of morphological and genetic techniques result in a rate of species identification of over 96% in females and over 98% in males, higher than either morphology or DNA barcodes alone. We explore the use of the DNA barcode for exploring boundaries among taxa, understanding the geographical distribution of cryptic diversity and evaluating the status of purportedly endemic taxa. Finally, we discuss how DNA barcodes may be used to improve field practices and ultimately enhance conservation strategies.

This is an annotated checklist of all the recognized and named taxa of freshwater fishes in Iran. It documents recent changes and controversies in the nomenclature and includes primary synonyms updated from the Jouladeh-Roudbar et al. (2015b) checklist. We provide an updated comprehensive listing of taxonomy, diagnostic and meristic characters, names, and conservation status, including detailed distribution maps. We strive to record the most recent justified taxonomic assignment in a hierarchical framework, providing annotations, including alternative possible arrangements, for some proposed changes. We provide common English and Persian names, and detail distributional data for all taxa, listing occurrence by basins, including indications of native, endemic, and translocated populations. We used the IUCN Red List Categories and Criteria for classifying species at high risk of global extinction. This checklist consists of 274 recognized species in 100 genera, 33 families, 20 orders and 3 classes. We also report and confirm for the first time the presence of seven species from Iran's basins: Aphanius kruppi, Capoeta kaput, Luciobarbus conocephalus, Oxynoemacheilus veyselorum, O. gyndes, O. hanae and Squalius latus. The confirmed freshwater fishes of Iran comprise 264 species in 97 genera, 33 families, 20 orders and 3 classes. The 241 endemic and native fish species can be divided into the following conservation statuses: 1 Extinct in the Wild (EW), 17 Critically Endangered (CR), 12 Endangered (EN), 15 Vulnerable (VU), 9 Near Threatened (NT), 148 Least Concern (LC) and 39 Data Deficient (DD). Forty-four fish species (18.3% of the 241 species listed) are officially regarded as globally Threatened (Critically Endangered [CR], Endangered [EN], or Vulnerable [VU]). These numbers and percentages of Threatened species have increased since the last checklist.

Simple SummaryDNA barcoding identified 28 species from larvae collected from the Dongta spawning ground. Six invasive species were identified in the larval pool, implying that these species had successfully colonized the middle Pearl River. Several migratory species common in the lower Pearl River were rare or absent in the Dongta spawning ground, suggesting that adverse effects of dam construction posed on these migratory species. Our study provided important reference data for fishery management and conservation in the Pearl River.Resolving the species composition of a larval pool in a spawning ground can provide novel insights into regional fish stocks and can support the development of effective monitoring and conservation policies. However, it is challenging to identify fish larvae to species due to their high diversity and dramatic phenotypic changes over development. In this study, we collected fish larvae in the Dongta spawning ground (Guiping City, Guangxi Province, China) in the middle reaches of the Pearl River between May and August 2018. We used a DNA barcoding approach to determine the species composition of the larval pool. A total of 905 larvae were chosen for molecular identification, of which 750 yielded high-quality barcoding sequences. Of these, 597 (≈79.6%), 151 (≈20.1%)/and 2 (≈0.3%) were assigned to 28 species, 8 genera, and 1 subfamily using the Barcode of Life Data System and GenBank nucleotide databases, respectively. Among the 28 identified species, 21 were cyprinids. Two species (Mugilogobius myxodermus and Pseudolaubuca engraulis) that were present only infrequently in previous adult surveys were abundant in the larval pool. Six invasive species were identified in the larval pool, implying that these species had successfully colonized the studied river section. Several migratory species common in the lower Pearl River were rare or absent in the investigated region, suggesting that dam construction in the Pearl River has had adverse effects on these migratory species. In summary, our study confirmed the applicability of DNA barcoding to studies of fish larval ecology and provided important reference data for fishery management and conservation in the Pearl River.