Farshad Nejat

To aid in the empirical evaluation of species hypotheses / concepts we present a strategy that uses NGS whole nuclear genome assemblies to identify novel single-copy universal PCR targets whose sequences discriminate species-scale clades. Our approach begins by identifying UCEs within partial Illumina genome assemblies across a strategically-chosen taxa set and culminates with experimental validation of appropriate single-copy nuclear DNA regions for PCR/Sanger sequencing. The highly diverse (~ 35 K species) group of eupulmonate gastropods was used as proof-of-concept. Among the ~ 24 K ultraconserved elements identified across 14 de novo and publicly-available genome assemblies spanning eupulmonate phylogeny, 61 informative universal PCR targets were ultimately identified. These allow for targeted sequence recovery from loci known to contain useful phylogenetic signal and permit efficient scaling to larger sample sizes, something that is immensely important when working with issues as complex as evolution and biodiversity.

Shell morphology in terrestrial gastropods is widely assumed to reflect climatic adaptation, yet empirical support for body size-climate relationships remains inconsistent across scales. We investigated how shell morphology is associated with large-scale climatic gradients in nine rock-dwelling Pyramidula species across 228 sites in the Western Palearctic. We hypothesised that climatic conditions linked to high solar radiation and low precipitation are associated primarily with shell traits potentially mediating conductive heat exchange with sun-exposed limestone substrates rather than with overall body size. For 519 adult shells, we analysed shell width, height, width/height ratio and a novel composite shell geometry index ( SGI ) using linear mixed-effects models with species and locality as random factors. Shell width showed the strongest and most consistent climatic associations, decreasing with increasing solar radiation and decreasing precipitation. In contrast, shell height and body volume exhibited weak or no independent climatic relationships. The SGI displayed intermediate but consistent responses, particularly to precipitation of the driest month. An additive model combining solar radiation and low precipitation explained nearly 19% of shell width variation. Responses were directionally consistent across species, suggesting shared morphological responses to similar climatic conditions. Observed patterns indicate that shell geometry, particularly shell width, is more closely associated with climatic gradients related to heat and drought stress than is overall body size.

The genus Pyramidula (Gastropoda: Pupilloidea) has represented one of the most taxonomically puzzling groups of Western Palaearctic micro land snails owing to a high level of morphological conservatism and shell convergence. We reconstructed Pyramidula phylogeny across the entire Western Palaearctic, using both mitochondrial (COI) and nuclear (ITS1 + ITS2) markers, based on 123 individuals from 89 localities. Unlike earlier efforts, we treated each distinct ITS indel area as a separate binary presence/absence variable that could be used as a genetic character state. Quantitative and qualitative shell features were also coded from 355 individuals sourced from genetically verified populations. Bayesian analysis and maximum likelihood both generated trees with nine well-supported species-level clades, with ITS1 + ITS2 tree resolution being notably improved at shallow phylogenetic levels through formal inclusion of indel information. Each of these clades was also found to possess distinct shell morphology and biogeography. Two are described as new species: Pyramidula koshka Horsák & Leonov sp. nov. and Pyramidula pygmaea Horsák & Kafimola sp. nov. Our results establish the first comprehensive phylogenetic framework for the genus across the Western Palaearctic. We document how indels can affect phylogenetic inference at multiple evolutionary scales and provide practical guidelines for incorporating them into Bayesian inference and maximum likelihood analyses.

Aim: This study investigates the diversity and phylogeny of Dactylogyrus species in the Middle East, as well as uncovers the historical dispersal routes and biogeographical contacts of cyprinoid host species using their host‐specific parasites. Location: The Middle East. Taxon: Dactylogyrus (Dactylogyridae: Monogenea), Cyprinoidei (Cypriniformes). Methods: More than 1040 cyprinoid fish and their host‐specific parasites were sampled in the Middle East. Phylogenetic analyses were conducted using the partial 18S rDNA, 28S rDNA, and complete ITS1 regions for the parasite species from the Middle Eastern species and those retrieved from GenBank, and the biogeographical analysis was performed. The mapping of the morphological characters of the attachment organ (haptor) onto the phylogeny was performed to reveal the patterns of morphological evolution and adaptation. Results: Phylogenetic analyses of Middle Eastern species and those retrieved from GenBank revealed seven major clades of Dactylogyrus parasites. Dactylogyrus species from the Middle East were present in five of these clades, alongside species from Europe, North Africa, and East Asia, emphasising the role of the Middle East, a crossroad of the historical dispersal of cyprinoids, in Dactylogyrus diversification. The deep nodal split of lineages suggests at least two independent dispersion events involving Dactylogyrus parasites from Asia to Europe and Africa. Additionally, mapping the morphological characters illustrated that the evolutionary patterns of haptor adaptation do not fully follow the evolutionary novelty.

The freshwaters of Iraq harbour a high diversity of endemic and phylogenetically unique species. One of the most diversified fish groups in this region is cyprinoids, and although their distribution is relatively well known, their monogenean parasites have only rarely been investigated. Herein, we applied an integrative approach, combining morphology with molecular data, to assess the diversity and phylogeny of cyprinoid-associated monogenean parasites. A total of 33 monogenean species were collected and identified from 13 endemic cyprinoid species. The highest species diversity was recorded for Dactylogyrus (Dactylogyridae, 16 species) and Gyrodactylus (Gyrodactylidae, 12 species). Four species of Dactylogyrus and 12 species of Gyrodactylus were identified as new to science and described. Two other genera, Dogielius (Dactylogyridae) and Paradiplozoon (Diplozoidae), were represented only by 4 and 1 species, respectively. Phylogenetic analyses of the Dactylogyrus and Gyrodactylus species revealed that the local congeners do not form a monophyletic group and are phylogenetically closely related to species from other regions (i.e. Europe, North Africa and Eastern Asia). These findings support the assumption that the Middle East served as an important historical crossroads for the interchange of fauna between these 3 geographic regions.

Diplozoidae are common monogenean ectoparasites of cyprinoid fish, with the genus Paradiplozoon being the most diversified. Despite recent studies on Diplozoidae from Europe, Africa and Asia, the diversity, distribution and phylogeny of this parasite group appears to be still underestimated in the Middle East. The objective of this study was to investigate the diversity, endemism and host specificity of diplozoids parasitizing cyprinoid fish from the Middle East, considering this region as an important historical interchange of fish fauna, and to elucidate the phylogenetic position of Middle Eastern Paradiplozoon species within Diplozoidae. Four Paradiplozoon species were collected from 48 out of 94 investigated cyprinoid species. Three known species, Paradiplozoon homoion, Paradiplozoon bliccae and Paradiplozoon bingolensis, were recorded on new cyprinoid host species, and a new species, Paradiplozoon koubkovae n. sp., was recorded on Luciobarbus capito and Capoeta capoeta from the Caspian Sea basin in Iran and Turkey. Paradiplozoon bliccae, exhibiting a wide host range in the Middle East, expressed both morphological and genetic intraspecific variabilities. The four Paradiplozoon species collected in the Middle East were placed in divergent clades, showing the rich evolutionary history of diplozoid parasites in the Middle East. Our study also revealed that two lineages of African diplozoids have a Middle Eastern origin. We stress the importance of applying an integrative approach combining morphological, ecological and molecular methods to reveal the real diversity of diplozoids.

Combining morphological and molecular data in an integrative approach, three new mayfly species of Epeorus (Caucasiron) are described. These include Epeorus (Caucasiron) alborzicus Hrivniak & Sroka, sp. nov. and Epeorus (Caucasiron) shargi Hrivniak & Sroka, sp. nov. from northern Iran, and Epeorus (Caucasiron) zagrosicus Hrivniak & Sroka, sp. nov. from central Iran. They are unambiguously delimited using both distance-based and likelihood-based approaches in the analyses of barcode COI sequences. Each new species is compared with other species of the subgenus and morphological diagnostic characters are provided. Based on extensive sampling of streams throughout the country, the distribution and habitat preferences of all Caucasiron species in Iran are assessed. Altogether, there are now six species recorded, among them also E. (C.) nigripilosus Sinitshenkova, 1976 is reported for the first time in Iran. Five species are distributed in the Alborz Mts. in northern Iran, one species was found in the Zagros Mts. in central Iran.

The present contribution gives a faunistic overview on the distribution of Caenidae in Iran. Four species have so far been reported, of which Caenis macrura Stephens, 1835 Stephens, J.F . (1835), ‘Illustrations of British Entomology; or, a Synopsis of Indigenous Insects’, Mandibulata, 6, 60. [Google Scholar] by far is the most abundant and most widely spread species. Caenis kopetdagi Kluge, 1985 was previously only known from three localities in the Kopet Dag Mountain range, which stretches along the border between Turkmenistan and Iran. We report this species from three further localities at the western border of the Zagros Mountains in southwest Iran, thus considerably expanding its distribution. The nymph of Caenis kopetdagi is re-described, its validity is confirmed, and modern diagnostic characters are added. Its CO1 sequence is provided and compared with sequences of other species of Caenis Stephens, 1835 Stephens, J.F . (1835), ‘Illustrations of British Entomology; or, a Synopsis of Indigenous Insects’, Mandibulata, 6, 60. [Google Scholar] occurring in the Middle East. The habitat of C. kopetdagi as well as the distribution of Caenidae in Iran and of Caenis in the Middle East is also discussed.

The simultaneous use of the scale and otolith morphometry was assessed as a potential tool for the identification of Persian brown trout Salmo trutta stocks of the Lar Lake and five rivers from Lar Basin, Iran. Fourier coefficients (FC) and circularity, rectangularity, roundness, ellipticity and form factor shape indices (SI) were calculated for otolith and scale. Several SIs were significantly different among sites for both structures. Permutational multivariate analysis of variance revealed significant differences between several pairwise comparisons for otolith and scale (FCs and indices separately). Discriminant analysis showed otolith FCs (cross‐classification rates: 25–86%) and SI (20–45%) appear to be a relatively acceptable tool to discriminate between several locations. Comparatively, the scale morphometry showed lower discriminatory power (FC = 3–65%; SI = 15–34%), with the exception of SI for Elarm River (60%), Kamardasht River (56%) and Lar Lake (75%). Cross‐classification rates improved up to 100% when discriminate analysis incorporating all variables for otolith and scale was performed. The results showed a potential segregation between some water bodies, suggesting that the otolith and scale morphometry could be a useful tool to delimit S. trutta populations in relatively close freshwater environments.