Redescription of Cyprinion muscatense (Teleostei: Cyprinidae) with the first phylogenetic analysis of the genus.

Members of the genus Cyprinion (Cypriniformes: Cyprinidae) are found in the Indus River basin west to the Arabian Peninsula and the Tigris-Euphrates River drainages (Persian Gulf basin). The taxonomic status of Cyprinion including Cyprinion muscatense is poorly understood when compared to other cyprinid genera. C. muscatense has been considered as a member of the Cyprinion watsoni-microphthalmum group and a valid species endemic to the Arabian Peninsula. Here, we redescribe C. muscatense based on an integrative morphological and molecular approach and freshly sampled material from several localities in the Oman Mountains ecoregion. The results showed that C. muscatense is distinguished from the other Cyprinion species in the Arabian Peninsula by having a short, thin, and slightly serrated last unbranched dorsal fin ray; the lower number of circumpeduncular scales; lateral line scales; and also scales between the lateral line and the dorsal-fin origin. Subterminal mouth, presence of one pair of small barbels at the mouth corner, 3-4 unbranched and 9½-10½ dorsal-fin branched rays, 12-14 pectoral-fin rays, 7-8 pelvic-fin rays, 2-3 unbranched and 6½-7½ branched anal-fin rays, and 37-40 lateral line scales are other morphological characteristics of C. muscatense. C. muscatense is also well distinguished by molecular characters among its congeners. The first molecular phylogenetic analysis of the genus, covering all currently recognized Cyprinion species except for C. watsoni, is also presented. C. muscatense is resolved as the sister species to another endemic fish of the Arabian Peninsula Cyprinion mhalense, with a Kimura-2-Parameter model distance of 5.3%.

Otoliths of Caspian gobies (Teleostei: Gobiidae): Morphological diversity and phylogenetic implications.

Otoliths (ear stones) of the inner ears of teleost fishes, which develop independently from the skeleton and are functionally associated with hearing and the sense of equilibrium, have significantly contributed to contemporary understanding of teleost fish systematics and evolutionary diversity. The sagittal otolith is of particular interest, since it often possesses distinctive morphological features that differ significantly among species, and have been shown to be species- and genus-specific, making it an informative taxonomic tool for ichthyologists. The otolith morphology of the Caspian Sea gobiids has not been thoroughly studied yet, with data available for only a few species. The aim of the present paper is to examine the qualitative and quantitative taxonomic and phylogenetic information in the sagittal otoliths of these species. A total of 118 otoliths representing 30 gobiid species (including 53.5% of the Caspian gobiofauna) in three gobiid lineages (i.e., Gobius, Pomatoschistus, and Acanthogobius) and 11 genera (i.e., all Ponto-Caspian gobiid genera except Babka) were analysed at taxonomic levels using an integrated descriptive and morphometric approach. The results indicated high taxonomic efficiency of otolith morphology and morphometry at taxonomic levels for the Ponto-Caspian gobiids. Our qualitative and quantitative otolith data also (i) support the monophyly of neogobiin gobies, (ii) along with other morphological and ecological data, offer a new perspective on the systematics of Neogobius bathybius, (iii) suggest the reassignment of Hyrcanogobius bergi to the genus Knipowitschia, and (iv) question the phylogenetic integrity of the four phenotypic groups previously defined in the tadpole-goby genus Benthophilus; however, more studies are needed to complete these evaluations and confirm our otolith study findings.

Morphological and molecular characterization of the Makran Glossogobius cf. giuris (Teleostei: Gobiidae) and the Glossogobius giuris species complex taxonomy.

The Indo-West Pacific Glossogobius giuris(Hamilton, 1822) species complex has four spatially circumscribed independent lineages, partially taxonomically resolved. A sample of gobies from the G. giurisspecies complex was recently collected from the Makran River System, south-eastern Iran, which drains into the northern Oman Sea. The taxonomic status of thispopulation was clarified using a molecular and morphological framework. Molecular and morphological data both revealed that the examined sample from the Makran River System is conspecific with G. giurisB which is widely distributed in the coastal habitats and basins of the Indian Ocean. In addition, consensus from different molecular species delimitations, K2P genetic distance, and tree topologies confirmed the four lineages of the G. giuris species complex as distinct taxonomic entities, hereby highlighting the necessity of an integrative morphological and molecular approach to complete the clarification of taxonomic diversity within this group. Glossogobius giuris species complex taxonomy is discussed and solution recommended.

An integrative insight into the diversity, distribution, and biogeography of the freshwater endemic clade of the Ponticola syrman group (Teleostei: Gobiidae) in the Caucasus biodiversity hotspot.

Freshwater habitats of the Caucasus biodiversity hotspot represent a center of endemism for the gobiid genus Ponticola Iljin, 1927. Hitherto, large-scale molecular studies, owing to restricted taxon and geographical sampling, have failed to give an elaborate picture of diversity and evolutionary history of these species. Here, to contribute to filling this gap, we assessed taxonomic diversity, phylogeography and evolutionary history for the south Caspian populations of Ponticola presently classified as P. iranicus and P. patimari, using an integrative taxonomic approach comprising an entire geographic range sampling, and analyses of mitochondrial DNA haplotypes, the head lateral line system, otolith shape, and meristic and morphometric variation. All freshwater samples of the P. syrman group belong to a monophyletic clade with two main subclades: a small subclade confined to the upper Sefidroud sub-basin including the type locality of P. iranicus and a large subclade with three geographically constrained haplogroups (Hg1, Hg2, and Hg3), comprising the rest of the distribution. Hg1 showed an eastern distribution including the type locality of P. patimari, while Hg2 and Hg3 are sister groups with central and western-central distributions, respectively. The freshwater clade diverged from P. syrman during the Tyurkyanian low stand (~150 m b.s.l. lasting ~0.1 Myr), while the divergence of P. iranicus and P. patimari and radiations within P. patimari took place during the Bakunian high stand (up to 50 m a.s.l. lasting ~378-480 kya). Species delimitation analyses indicated two distinct species, corresponding to each main subclade. Although the otolith shape and lateral line analyses did not reflect with phylogeographic pattern, PCA and DFA plots of meristic and morphometric data showed a clear separation of the two major subclades corresponding to P. iranicus and P. patimari, suggesting the presence of significant morphological variation meriting formal taxonomic recognition. Overall, our findings (i) reveal the presence of two freshwater endemic species in the P. syrman group, and pending further investigation, hypothesize the presence of a third cryptic species; (ii) revise and document a narrow distributional range and low diversity for P. iranicus, in contrast to a wider distributional range and high diversity for P. patimari; (iii) suggest that the climatic oscillations of the Pleistocene were associated with the cladogenesis within the P. syrman group; and (iv) allowed for the recognition of conservation units and proposition of management measures.

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

Oman, a country in Southwest Asia, situated on the southeastern quarter of the Arabian Peninsula presents a high level of biological diversity especially marine elements. Although arid habitats cover most parts of Oman (82%), the region has several freshwater systems that are vital for the survival of people as well as for different groups of animals and plants. Research works on Oman biodiversity including terrestrial and marine, have been steadily increasing over the last few decades, but freshwater ecosystems have not been well investigated. Oman comprises parts of three freshwater ecoregions including the Oman Mountains, Southwestern Arabian Coast, and Arabian Interior having xeric freshwaters and endorheic (closed) basins which support a variety of inland fishes. The current checklist provides for each species of inland waters of Oman all recognized and named taxa, documenting recent changes and controversies in nomenclature, its records, taxonomic status, synonyms, etymology, common English name, short description, range expansion, and detailed distribution map based on several field surveys throughout the country. We also provide native, endemic, and introduced species. The diversity of inland fishes of Oman included in this annotated checklist consists of 23 recognized species in 15 genera, 10 families, seven orders, and a class. Also, for the first time, we report and confirm the presence of four species in the inland waters of Oman. The most diverse order is Cypriniformes (nine species, 39.13%), followed by Gobiiformes (six species, 26.09%), Cyprinodontiformes (three species, 13.04%), Cichliformes (two species, 8.69%), and Centrarchiformes, Gonorynchiformes and Mugiliformes (one species, 4.35% each). 21 native species (91.3%) in nine families and two exotic species (8.7%) in two families are listed here. Out of 21 native species, eight species (16.8%) in two families are endemic elements that are restricted to the Oman territory only. Identification of all recognized species was confirmed by DNA barcoding (mitochondrial COI). Oman Mountains Ecoregion (OME), Southwestern Arabian Coast Ecoregion (SACE), and Arabian Interior Ecoregion (AIE) harbor 15, 12, and one species, respectively. The provided data will be necessary for increasing the fish knowledge, the development of competent and pragmatic management plans and effective conservation policies.

Ponticola hircaniaensis sp. nov., a new and critically endangered gobiid species (Teleostei: Gobiidae) from the southern Caspian Sea basin.

Ponticola hircaniaensis sp. nov. is described as a new gobiid species from the Kaboudval Stream, southern Caspian Sea basin. The new species is diagnosed among Caspian Sea basin Ponticola species by the following combination of characters: second dorsal-fin branched rays 1416, anal-fin branched rays 1012, scales in lateral series 5259; lower jaw slightly, if at all, prognathous; head and body yellowish brown showing a reticulate brown pattern on a yellow background, first dorsal fin with a marginal bright orangish-yellow band and a dark anterior spot, upper part of pectoral-fin base with a distinct dark brown stripe; length of third spine in first dorsal fin 13.418.3 % of standard length (SL), second dorsal-fin spine length 11.113.8 % SL, caudal peduncle length and depth 16.420.1 % and 11.112.8 % SL, respectively, head depth at nape 70.981.0 % of head length (HL), and at eye 52.566.0 % HL; sagittal otolith dorsal rim with a broad concavity in the middle, dorsal depression absent or indistinct, sulcus length/sulcus height and sulcus height/otolith height ratios 1.471.82 and 0.340.40, respectively. It is also characterised by a K2P nearest neighbour distance of 5% to P. kessleri in the mtDNA COI barcode region. Mitochondrial and nuclear DNA analyses suggested extensive hybridization between P. hircaniaensis sp. nov. and P. gorlap at Kaboudval, providing evidence for the first record of hybridization in the Ponto-Caspian gobiids. Based on narrow geographic range isolated above the Zarrin Gol Dam (< 2 km2), extensive hybridization with P. gorlap, and other threats, the new species should be considered Critically Endangered.

Oxyurichthys omanensis sp. nov., a new Eyebrow Goby (Teleostei: Gobiidae) from Oman.

Oxyurichthys omanensis sp. nov. is described as a new gobiid species from a mudflat/estuary habitat in northern Oman. The new species is diagnosed among all currently recognised congeners by the following combination of character states: elongate tentacle on dorsoposterior surface of the eye; nape with well-developed membranous crest; nape scaled to above anterior half of opercle along sides with naked median along membranous crest, scales never reaching to above preopercle; opercle and pectoral base naked; scales ctenoid laterally on trunk posterior to base of second dorsal fin 3rd element; lateral scale rows 5158, usually 5156; transverse forward scale rows 2329, usually 2428; transverse rearward scale rows 1416, usually 1415; upper lip usually constricted at premaxillary symphysis; infraorbital transverse papillae row 2 reaching eye margin dorsally and markedly short of longitudinal row d ventrally; additional short transverse papillae rows between rows 2 and 3i present; dark saddle present over caudal peduncle; snout length 34.945.4% HL; second dorsal-fin longest ray 1.11.6 head depth; pelvic fin always reaching or passing anal-fin origin. The K2P genetic distances (%) in the mtDNA COI barcode region between O. omanensis and the other Oxyurichthys species were all high (11.230.6%) with the K2P nearest neighbor distance of 11.2% to O. cornutus and O. ophthalmonema.

Mystus cyrusi, a new species of bagrid catfish (Teleostei: Bagridae) from Middle East.

Mystus cyrusi, new species, is described from the Kol River drainage which flows to the Straits of Hormuz in southern Iran. It is distinguished from its closest relative, Mystus pelusius from the Tigris-Euphrates River system by a combination of characters: The maxillary barbel short, not reaching to beyond pelvic fin (vs. extends as far as anal fin in some female M. pelusius), shorter adipose fin (30.837.4% SL) and with a steeper sloping at its origin vs. longer (37.645.6% SL) and with a more gently sloping in M. pelusius), greater head depth (16.6421.9% SL vs. 12.616.59% SL in M. pelusius), greater caudal-peduncle depth (10.312.5% SL vs. 8.710.5% SL in M. pelusius) and fewer total gill rakers (1214, mode 12) vs. (1417 in M. pelusius). Mystus cyrusi is also well distinguished by molecular characters. Genetically, M. cyrusi shows the lowest genetic distance with M. pelusius (4.6%), and then with M. singaringan (11.6%), M. wolffii (13.1%), and M. bleekeri (13.4%) among the 21 studied species in their mtDNA sequences. Mystus cyrusi shows the highest genetic distance with M. montanus (26.5%).

Gobies (Teleostei: Gobiidae) of the oldest and deepest Caspian Sea sub-basin: an evidence-based annotated checklist and a key for species identification.

An evidence-based annotated checklist of gobiid species (Teleostei: Gobiidae) inhabiting the South Caspian Sea and its catchment area (i.e., the South Caspian Sea sub-basin) is compiled. The South Caspian Sea sub-basin gobiofauna currently comprises 38 confirmed species in 11 genera (i.e., 88.4% of the Caspian gobiofauna); the most diverse genus is Benthophilus (16 species, 42.1%), followed by Ponticola (seven species, 18.4%), and Neogobius (four species, 10.5%). Ten species (26.3%) are endemic to the South Caspian Sea sub-basin, another 21 species (55.3%) are endemic in the Caspian Sea basin as a whole, six (15.8%) are native to the Ponto-Caspian region, and one species (2.6%) is exotic. According to the current IUCN Red List, 24 species (64.9%) are listed as being of "Least Concern", eight species (21.6%) are "Data Deficient", and five species (13.5%) as "Not Evaluated". Similar numbers of species are confirmed to inhabit the South Caspian Sea sub-basin waters of the three countries that border it: Iran harbors 25 species (nine genera), Azerbaijan has 28 species (10 genera), and Turkmenistan has 26 species (10 genera). The greatest known diversity of Benthophilus in South Caspian waters occurs in Azerbaijan and Turkmenistan (11 species each), whereas Iranian waters harbor seven species. In comparison, Iran, with six out of eight species (75%), has the greatest diversity of Ponticola known from the Caspian Sea basin. Species richness and endemism of the Caspian Sea gobiid-fauna varies considerably with latitude: the North, Middle and South sub-basins respectively harbor 21, 31, and 37 native species, of which 0, 3, and 10 species are endemic in that sub-basin alone. The high species diversity and endemism of Gobiidae in the South Caspian Sea sub-basin may have resulted from: (i) greater ecological diversity compared to the northern Caspian Sea marine areas (e.g., water depths) that may have led to differential niche adaptation and adaptive radiation in the Benthophilus-Anatirostrum species flock, (ii) lower historical extinction rate compared to Caspian higher latitudes, which had greater exposure to the Pleistocene's extreme climatic changes, (iii) geological history of freshwater habitats in the South Caspian Sea sub-basin that set the speciation and evolutionary stage for the genus Ponticola during these Pleistocene climatic oscillations, (iv) presently less limiting conditions compared to the North Caspian Sea, i.e., higher present winter minimum of water temperature and higher salinity, and (v) Iranian freshwater abundance, variability and habitat diversity. Contemporary gobiid diversity and endemism in the Caspian Sea basin suggests two higher-priority conservation areas: (i) freshwater habitats of the South Caspian Sea region in Iran and Azerbaijan, and (ii) shallow coastal and deep waters of the South and Middle Caspian Sea sub-basins. An identification key is provided for the updated gobiid species from the South Caspian Sea sub-basin.

A new species of tadpole-goby, Benthophilus persicus sp. nov. (Teleostei: Gobiidae) from the southern Caspian Sea.

A new gobiid species, Benthophilus persicus sp. nov., is described from the southern Caspian Sea, Iran. The new species is diagnosed by the following character states: dermal fold on cheek well-developed, large, rectangular; chin barbel 1/32/3 of eye diameter; maximum body width 15.122.9% of standard length; mouth width, 36.355.8% of head length; second dorsal fin I+78; origin of anal fin in front of vertical through origin of second dorsal fin; dermal tubercles present on body, clearly larger than granules, with two posterior rows of spinules forming an acute angle, always less than right angle; dorsal row of tubercles complete, 2229; ventral row of tubercles 2225; ventrolateral row of tubercles absent; tubercles not present on temporal and occipital head regions; granules not present on flanks; transversal suborbital row 6i below posterior end of row b; anterior interorbital transversal row pa with one or two papillae and anterior interorbital transversal papilla row pp with two or three papillae; body with 2022 transversal ltm rows starting anteriorly behind pectoral axilla and alternating anteriorly with three longitudinal llm rows.

DNA barcoding and species delimitation of the Old World tooth-carps, family Aphaniidae Hoedeman, 1949 (Teleostei: Cyprinodontiformes).

The fishes, which have currently named Aphanius Nardo, 1827 are the relict of the ancient ichthyofauna of the Tethys Sea. For a long time since 1827, the genus name has been subjected to revision by several researchers using mainly morphological features. Until recently, no comprehensive single- or multi-locus DNA barcoding study has been conducted on whole members of the family Aphaniidae. In the present study, by applying four conceptually different molecular species delimitation methods, including one distance-based method, one network-based and two topology-based methods, we examined a single-locus DNA barcode library (COI) diversity for the 268 sequences within the family Aphaniidae from the Old World (57 sequences are new in the present study and 211 sequences were retrieved from NCBI database). The molecular analyses revealed a clearer picture of intra-family relationships and allowed us to clarify the generic names, and also describe a new genus for the family Aphaniidae. Results supported distinction of three major clades related to three genera within this family: i) the first clade includes the A. mento group which are placed in a new genus, Paraphanius gen. nov., found in the Orontes (= Asi) and Tigris-Euphrates River drainage, the Levant in coastal waters and the Dead Sea basin, western Jordan, and in southern Turkey in the Mediterranean basins as well as in central Turkey. This clade positioned at the base of the phylogenetic tree, (ii) the second clade contains the A. dispar-like brackish water tooth-carps which are transferred to the genus Aphaniops Hoedeman, 1951 (type species, Lebias dispar), distributed in the coastal waters around the Red Sea and the Persian Gulf basins; and (iii) the third clade, the genus Aphanius Nardo, 1827 (type species Aphanius nanus = A. fasciatus) contains all the inland and inland-related tooth-carps, which are mainly distributed in the inland waters in Turkey and Iran and also in the inland-related drainages around the Mediterranean basin.

Scale morphology and phylogenetic character mapping of scale-surface microstructures in sixteen Aphanius species (Teleostei: Aphaniidae).

Recent studies on the analysis of the evolutionary relationships between the various taxa of the teleost fishes are based on the evaluation of the efficacy of different approaches, verifying the taxonomical congruence between the hypotheses inferred from molecular data and those from morphological data. The first objective of this study was to investigate the macro- and microscopic characterization of the body key scales for the sixteen Aphanius species, and to discuss their taxonomic significance. In addition, to reveal the phylogenetic origins of particular adaptations and to identify a possible cases of convergent evolution in scales of Aphanius species, we used a phylogenetic character mapping procedure that uses an independent data source, namely molecular data that is presumed to be functionally independent of the scale traits. Comparison of the resulted phylogenetic trees and scale data dendrogram implied that neither scale shape/scale surface morphology, nor scale surface microstructure can be used for the species identification and inferring phylogenetic relationships in the genus Aphanius. This conclusion confirms previous studies, indicating that the scale shape and ornamentations varies with habitat, age and size of the fish. We also concluded that the polygonal state in the scales of Aphanius species was a primitive shared character state.

Genetic Diversity and Phylogenetic Analysis of the Iranian Leishmania Parasites Based on HSP70 Gene PCR-RFLP and Sequence Analysis.

Despite the broad distribution of leishmaniasis among Iranians and animals across the country, little is known about the genetic characteristics of the causative agents. Applying both HSP70 PCR-RFLP and sequence analyses, this study aimed to evaluate the genetic diversity and phylogenetic relationships among Leishmania spp. isolated from Iranian endemic foci and available reference strains. A total of 36 Leishmania isolates from almost all districts across the country were genetically analyzed for the HSP70 gene using both PCR-RFLP and sequence analysis. The original HSP70 gene sequences were aligned along with homologous Leishmania sequences retrieved from NCBI, and subjected to the phylogenetic analysis. Basic parameters of genetic diversity were also estimated. The HSP70 PCR-RFLP presented 3 different electrophoretic patterns, with no further intraspecific variation, corresponding to 3 Leishmania species available in the country, L. tropica, L. major, and L. infantum. Phylogenetic analyses presented 5 major clades, corresponding to 5 species complexes. Iranian lineages, including L. major, L. tropica, and L. infantum, were distributed among 3 complexes L. major, L. tropica, and L. donovani. However, within the L. major and L. donovani species complexes, the HSP70 phylogeny was not able to distinguish clearly between the L. major and L. turanica isolates, and between the L. infantum, L. donovani, and L. chagasi isolates, respectively. Our results indicated that both HSP70 PCR-RFLP and sequence analyses are medically applicable tools for identification of Leishmania species in Iranian patients. However, the reduced genetic diversity of the target gene makes it inevitable that its phylogeny only resolves the major groups, namely, the species complexes.

Phylogeography, genetic diversity and demographic history of the Iranian Kurdish groups based on mtDNA sequences.

Throughout the history of modern humans, the current Kurdish-inhabited area has served as part of a tricontinental crossroad for major human migrations. Also, a significant body of archaeological evidence points to this area as the site of Neolithic transition. To investigate the phylogeography, origins and demographic history, mtDNA D-loop region of individuals representing four Kurdish groups from Iran were analysed. Our data indicated that most of the Kurds mtDNA lineages belong to branches of the haplogroups with the Western Eurasian origin; with small fractions of the Eastern Eurasian and sub-Saharan African lineages. The low level of mtDNA diversity observed in the Havrami group presented a bias towards isolation or increased drift due to small population size; while in the Kurmanji group it indicated a bias towards drift or mass migration events during the 5-18th century AD. The Mantel test showed strong isolation by distance, and AMOVA results for global and regional scales confirmed that the geography had acted as the main driving force in shaping the current pattern of mtDNA diversity, rather than linguistic similarity. The results of demographic analyses, in agreement with archaeological data, revealed a recent expansion of the Kurds (~9,500 years before present) related to the Neolithic transition from hunting and gathering, to farming and cattle breeding in the Near East. Further, the high frequencies of typical haplogroups for early farmers (H; 37.1%) and hunter-gatherers (U; 13.8%) in the Kurds may testify the earlier hunter-gatherers in the Kurdish-inhabited area that adopted and admixed the Kurds ancestors following the Neolithic transition.

Mitochondrial DNA variation, genetic structure and demographic history of Iranian populations.

In order to survey the evolutionary history and impact of historical events on the genetic structure of Iranian people, the HV2 region of 141 mtDNA sequences related to six Iranian populations were analyzed. Slight and non-significant FST distances among the Central-western Persian speaking populations of Iran testify to the common origin of these populations from one proto-population. Mismatch distribution suggests that this proto-Iranian population started to colonize Iran about 30000 years ago which is almost consistent with the timing of arrival and colonization of western Asia by the anatomically modern human. Star-like haplotype network structures, significant and negative Tajima's D (D=-2.08, P<0.05) and unimodal mismatch distributions support the genetic effects of this expansion. Iranian populations presented mtDNA lineages that clearly belong to the European gene pool (i.e. H and U), while the Mashhad population was characterized by the presence of eastern and central Asian mtDNA lineages (i.e. M, B and D). Furthermore, the low diversity (h=0.428) observed in Mashhad may indicated the presence of inbreeding, drift or bottleneck events. The application of Monmonier's maximum differences algorithm revealed a geographic zone of genetic discontinuity between the Arab people of Khuzestan and rest of Iranian populations. Geographical factors, in cooperation with cultural/linguistic differences, are the main reasons for this differentiation. The lack of a sharp geographical or ethno-linguistic structure for mtDNA HV2 sequence diversity was statistically supported by AMOVA and Mantel (r=0.19, P<0.05) tests.