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The Chagos archipelago in the British Indian Ocean Territory (BIOT) has been lacking in detailed genetic studies of its chondrichthyan populations. Chondrichthyes in Chagos continue to be endangered through illegal fishing operations, necessitating species distribution and abundance studies to facilitate urgent monitoring and conservation of the species. Here, we present a complete mitochondrial genome of the Silvertip Shark, Carcharhinus albimarginatus sampled in the Chagos archipelago. The mitochondrial genome of C. albimarginatus was 16,706 bp in length and consisted of 13 protein-coding genes, 22 tRNA genes, two rRNA genes, a replication origin and a D-loop region. GC content was at 38.7% and the control region was 1,065 bp in length. We expect that mitogenomes presented here will aid development of molecular assays for species distribution studies. Overall these studies will promote effective conservation of marine ecosystemes in the BIOT.

We present the first mitogenome sequence of the Smoothnose Wedgefish, Rhynchobatus laevis obtained through field sequencing on the MinION handheld sequencer. The mitochondrial genome of R. laevis is 16,560 bp in length and consisted of 13 protein-coding genes (PCGs), 22 tRNA genes, 2 rRNA genes, and a non-coding control region (D-loop). GC content was at 40.1%. The control region was 867 bp in length. Whole mitochondrial genome sequence of R. laevis will enable improved understanding of distribution, abundance, catch and trade rates of the Critically Endangered species.

Background Establishing the species limits and resolving phylogenetic relationships are primary goals of taxonomists and evolutionary biologists. At present, a controversial question is about interspecific phylogenetic information in morphological features. Are the interspecific relationships established based on genetic information consistent with the traditional classification system? To address these problems, this study analyzed the wing shape structure of 10 species of Libellulidae, explored the relationship between wing shape and dragonfly behavior and living habits, and established an interspecific morphological relationship tree based on wing shape data. By analyzing the sequences of mitochondrial COI gene and the nuclear genes 18S, 28S rRNA and ITS in 10 species of dragonflies, the interspecific relationship was established. Method The wing shape information of the male forewings and hindwings was obtained by the geometric morphometrics method. The inter-species wing shape relationship was obtained by principal component analysis (PCA) in MorphoJ1.06 software. The inter-species wing shape relationship tree was obtained by cluster analysis (UPGMA) using Mesquite 3.2 software. The COI, 18S, ITS and 28S genes of 10 species dragonfly were blasted and processed by BioEdit v6 software. The Maximum Likelihood(ML) tree was established by raxmlGUI1.5b2 software. The Bayes inference (BI) tree was established by MrBayes 3.2.6 in Geneious software. Results The main difference in forewings among the 10 species of dragonfly was the apical, radial and discoidal regions dominated by the wing nodus. In contrast, the main difference among the hindwings was the apical and anal regions dominated by the wing nodus. The change in wing shape was closely related to the ability of dragonfly to migrate. The interspecific relationship based on molecular data showed that the species of Orthetrum genus branched independently of the other species. Compared to the molecular tree of 10 species, the wing shape clustering showed some phylogenetic information on the forewing shape (with large differences on the forewing shape tree vs. molecular tree), and there was no interspecific phylogenetic information of the hindwing shape tree vs. molecular tree. Conclusion The dragonfly wing shape characteristics are closely related to its migration ability. Species with strong ability to migrate have the forewing shape that is longer and narrower, and have larger anal region, whereas the species that prefer short-distance hovering or standing still for a long time have forewing that are wider and shorter, and the anal region is smaller. Integrating morphological and molecular data to evaluate the relationship among dragonfly species shows there is some interspecific phylogenetic information in the forewing shape and none in the hindwing shape. The forewing and hindwing of dragonflies exhibit an inconsistent pattern of morphological changes in different species.

Half-fin anchovy (Setipinna tenuifilis) is one of the most important economic fishes around the world. In the present study, we determined the complete mitochondrial DNA sequence and organization of S. tenuifilis. The entire mitochondrial genome is a circular-molecule of 16,215 bp in length, which encodes 37 genes in all. These genes comprise 13 protein-coding genes (ATP6 and 8, COI–III, Cytb, ND1-6, and 4L), 22 transfer RNA genes (tRNAs), and two ribosomal RNA genes (12S and 16S rRNAs), with gene arrangement and content basically identical to those of other species of Engraulidae. The result of phylogenetic analysis strongly supported that S. tenuifilis was first clustered together with Setipinna melanochir and formed a monophyly in the genus Coilia, and then they constituted a sister-group relationship with two genus Engraulis, and Stolephorus. It concluded that the S. tenuifilis should be classified into the genus Setipinna. The present study also revealed the phylogenetic relationship of this genus at molecular levels. The complete mitochondrial genome sequence of S. tenuifilis can provide basic information for the studies on molecular taxonomy and phylogeny of teleost fishes.

Endophyte microorganisms have great biotechnological interest, with features applicable to different areas and are potentially useful in agriculture. The current study determines the biotechnological potential of endophytic fungi, isolated from leaves of Sapindus saponaria, to control phytopathogenic fungi and evaluate their enzyme production. Molecular taxonomy was performed by sequencing of the ITS1-5.8S-ITS2 ribosomal DNA region, identifying the genera Phomopsis, Sordariomycetes, Diaporthe, and Colletotrichum. In vitro antagonism against phytopathogens showed better results against Fusarium solani and provided inhibition indices between 41.8 % and 67.5 %. The endophytic strain SS81 (Diaporthe citri) presented the highest antagonism index against the pathogen. Against Glomerella sp. and Moniliophthora perniciosa, inhibition rates ranged between 18.7 % and 57.4 % and between 38.3 % and 64.8 %, respectively. Enzyme assays revealed that strain SS65 (Diaporthe sp.) produced 1.16 UI µmol/min of amylase; strain SS77 (Diaporthe sp.) produced 2.74 UI µmol/min of pectinase, and strain SS08 (Diaporthe sp.) produced 1.51 UI µmol/min of cellulase. Thus, the current study shows evidence the importance of isolated endophytes with phytoprotective properties of plants with medicinal properties as alternatives for biological control and natural sources of products with biotechnological interest.

It has been the aim of this study to molecular-taxonomically identify 15 Beauveria isolates collected from different geographical regions and insect hosts in Argentina and to investigate the levels of inter- and intra-specific diversity across this set of isolates. Based on phylogenetic analyses of EF1A-RPB1-RPB2 concatenated genes and BLOC markers, all Beauveria strains were identify as Beauveria bassiana. Within the B. bassiana clades of both phylogenies, isolates from Argentina were not clustered according to geographic origin or host. The 15 fungal isolates were further analyzed by PCR amplification of the intron insertion hot spot region of the nuclear 28S rRNA encoding sequence. By intron sequence and position, seven different group-I intron combinations termed variants A, B1, B2, C, D, E and F were found in the 15 isolates under study. Variants B1/B2 consisting of a single 28Si2 intron were found in ten isolates, whereas variant A occurred twice and variants C through F were unique across the set of isolates under study. The determination of the different introns and intron combinations in the 28S rRNA gene is a powerful tool for achieving infraspecific differentiation of B. bassiana isolates from Argentina., Competing Interests: Declaration of competing interest none., (Copyright © 2024 British Mycological Society. Published by Elsevier Ltd. All rights reserved.)

Octomeris is a chthamalid intertidal barnacle with eight shell plates. There are currently two species of such barnacles: O. brunnea Darwin, 1854 (type locality in the Philippines), common in the Indo-Pacific region, and O. angulosa Sowerby, 1825, only recorded in South Africa. Octomeris intermedia Nilsson- Cantell, 1921, identified from the Mergui Archipelago in Myanmar, was considered to be conspecific with O. brunnea by Hiro (1939) based on samples collected in Taiwan. The morphological differences in shell and opercular plates between O. brunnea and O. intermedia are believed to be intra-specific variations due to different degrees of shell erosion. In the present study, the genetic and morphological differentiations of Octomeris in the Indo-Pacific region were examined. This study found two molecular clades (with inter-specific differences) based on the divergence in the COI genes, and the species also have distinct geographical distributions. The Octomeris brunnea clade covers samples collected from the Philippines and Taiwan waters and the other clade, which we argue is O. intermedia, is distributed in Phuket and Krabi, Thailand and Langkawi, Malaysia. Phuket and Krabi are located approximately 300 km south of the Mergui Archipelago, the type locality of O. intermedia. The morphology of samples collected from Thailand fits the type description of O. intermedia in Nilsson-Cantell (1921). Our study concludes that O. intermedia is a valid species based on morphological and molecular evidence. [ABSTRACT FROM AUTHOR]

This study provides updated information on the distribution of the phlebotomine sand fly species and their genetic characterization in Sardinia, a Mediterranean island where leishmaniasis is endemic. From April to November 2017, sand flies were trapped in five different capture sites using sticky traps and light traps as collection methods, operated nearby sheep, poultry, cat, and dog shelters. Phlebotomine specimens (n = 513) collected were morphologically and molecularly identified as Phlebotomus perniciosus (249/513, 48.5%), Phlebotomus perfiliewi (236/513; 46%), and Sergentomyia minuta (28/513, 5.5%). Sand flies were collected from the second half of May to October confirming the well-defined seasonal activity, which peaks in August in Sardinia. Overall, correlation analyses indicated a significant positive association between the monthly number of sand flies collected and the mean temperature (r = 0.88, rho = 0.87, and tau = 0.69, P < 0.05), while there was non-significant, moderately negative correlation between the monthly number of sand flies collected and the monthly mean relative humidity and wind (r = − 0.22, rho = 0.02, and tau = 0.04, P > 0.05). This study provides the first data on the molecular characterization of phlebotomine sand flies in this region and confirms the presence of three sand fly species. Molecular results suggest that the morphological features used for analysis represent synapomorphic-derived characters which are shared among descendant taxa and the common ancestor. [ABSTRACT FROM AUTHOR]

Recent molecular and morphological data derived from members of the pollen-beetle subfamily Meligethinae suggest the need to separate the genus Sagittogethes Audisio & Cline, 2009, including species mostly distributed in Western Palaearctic areas, into two distinct (although related) genera, Sagittogethes and Teucriogethes gen. n. This new genus, comprising the Western European Meligethes obscurus Erichson, 1845 as its type species, includes less than ten species distributed between the Iberian Peninsula and North Africa westward, and China and Japan eastward. All inclusive species utilize members of the genus Teucrium L. (Lamiacaeae: Ajugoideae) as larval host-plants. Morphological and bionomical information, and molecular data clearly demonstrate the necessity for updating the taxonomic position of the two clades. Based on molecular evidence, the new genus represents the sister-group of Thymogethes Audisio & Cline, 2009, while the sister-group relationships of the remaining Sagittogethes taxa with other Lamiaceae-associated genera of Meligethinae remain uncertain. Within the new genus, the relictual and rare Western Mediterranean species T. minutus (C.N.F. Brisout de Barneville, 1863) seems to occupy an isolated position. [ABSTRACT FROM AUTHOR]

In order to test the congruence of genetic data to the morphologically defined Neotropical catfish genera Tympanopleura and Ageneiosus and explore species diversity, we generated 17 DNA barcodes from five of six species of Tympanopleura and 12 of 13 species of Ageneiosus. To discriminate limits between species, an automatic barcode gap discovery (ABGD), a generalised mixed yule‐coalescent model (GYMC) and fixed distance thresholds Kimura two‐parameter (K2P; 3%) were used to discriminate putative species limits from the DNA barcodes. The ABGD, GMYC and K2P methods agreed by each generating 13 clusters: six in Tympanopleura (five nominal plus one undescribed species) and seven in Ageneiosus. These clusters corresponded broadly to the described species, except in the case of the Ageneiosus ucayalensis group (A. akamai, A. dentatus, A. intrusus, A. ucayalensis, A. uranophthalmus and A. vittatus). Haplotype sharing and low divergences may have prevented molecular methods from distinguishing these species. We hypothesise that this is the result of a recent radiation of a sympatric species group distributed throughout the Amazon Basin. One putative new species of Tympanopleura was also supported by the molecular data. These results taken together highlight the utility of molecular methods such as DNA barcoding in understanding patterns of diversification across large geographic areas and in recognising overlooked diversity. [ABSTRACT FROM AUTHOR]

Three marine fish species of the Indo-Pacific genus Champsodon were reported as invasive species in the Eastern Mediterranean between 2009 and 2012; Champsodon nudivittis, C. vorax, and C. capensis. These are presumed to invade through the Suez Canal, but only C. nudivittis is known from the Red Sea, so the presence of C. vorax and C. capensis is surprising. To test the validity of the taxonomic identification of these two species, this study combined traditional morphology, genetic barcoding, and photography investigation. Our results demonstrate that only one species, C. nudivittis, has migrated into the Eastern Mediterranean. [ABSTRACT FROM AUTHOR]

Background: Species belonging to the genus Lernaea are cosmopolitan parasites that can infect many different freshwater fish hosts. Due to a high degree of morphological intraspecific variability and high levels of interspecific similarities, their classification is extremely difficult and controversial. Although the suitability of the shape of cephalic horns has been questioned decades ago by some experimental infection studies, this character still plays the central role in the identification of Lernaea spp. Methods: We used the nominal species Lernaea cyprinacea and Lernaea cruciata to test the hypothesis that the shape of the anchor can exhibit host-induced morphological variability, and that the two taxa may be synonymous. Results: We examined 517 wild or farmed specimens of five host fish species (four cyprinids and a mosquitofish), and found that all 16 parasite specimens collected from mosquitofish could be morphologically identified as L. cruciata, whereas the remaining 25 parasite specimens were all identified as L. cyprinacea. We experimentally infected goldfish and mosquitofish specimens with offspring (copepodids) of a single L. cyprinacea specimen: the adult parasites from goldfish were morphologically identified as L. cyprinacea, and those from mosquitofish as L. cruciata. We then used molecular data to corroborate that all these specimens are conspecific. Conclusions: Our results suggest that L. cyprinacea and L. cruciata may be synonyms, misidentified as different species as a result of host-induced morphological variation. Given the current shortage of molecular data for the genus Lernaea, in order to resolve the taxonomy of this genus (determine the exact number of species), future studies should aim to sequence as much molecular data as possible, and conduct further experimental infections. [ABSTRACT FROM AUTHOR]

The upside-down jellyfish Cassiopea is a benthic scyphozoan, considered a non-indigenous invasive species in the Mediterranean, forming large blooms in eutrophic areas. Taxonomy of the genus Cassiopea is extremely difficult because morphological/meristic characters used are variable within the same species, overlapping among different species, and cryptic species have been identified by molecular markers; nine Cassiopea species are recognized on the basis of molecular study. Mediterranean records of Cassiopea have been ascribed to andromeda species on the basis of a hypothesized invasion pathway from the Suez Canal. In the current study, an analysis of the main morphological characters of the sampled Cassiopea jellyfish from Palermo (Tyrrhenian Sea) was carried out and subsequently, molecular analyses were performed by using COI barcode in order to identify the species. Molecular data were compared with published information in GenBank. Morphological characters were highly variable, but molecular analyses confirmed that Mediterranean Cassiopea specimens belong to andromeda species. Moreover, high values of sequence divergence were found between Mediterranean Cassiopea and the other C. andromeda from the Red Sea, Hawaii and Florida. These results lead to a discussion of possible explanations linked to life history features of the species. Two different explanations are proposed; the first is that Mediterranean C. andromeda , finding a suitable ecological niche good for colonization and proliferation, could have been isolated in Palermo Harbour. The second considers the possibility of multiple introduction events by human transport as demonstrated for other non-indigenous jellyfish; in this case Cassiopea genetic differences increased in the invaded area. [ABSTRACT FROM AUTHOR]

The evolutionary process of adaptation to the cave environment leads to extreme genetic, morphological, and physiological modifications commonly known as stygomorphism. The cave-dwelling armored catfish Ancistrus cryptophthalmus is a good model to understand the evolutionary processes of stygomorphism in the Neotropics as its ecology and morphology have been studied in detail. Interestingly, it has been found a non-stygomorphic epigean population named Ancistrus sp. This population is morphologically distinct to the hypogean population of A. cryptophthalmus as they present better-developed ocular structures and intense pigmentation. Here we used Illumina sequencing technology to produce partial genome sequences for specimens of Ancistrus sp. and A. cryptophthalmus; we also genotyped molecular markers from individuals of both species. Based on the high level of mitogenome similarity and metapopulation connectivity between the surface and cave populations, we suggest that the evolution of stygomorphisms observed in A. cryptophthalmus may be the result of morphologic modification, by natural selection, of Ancistrus sp. surface population to colonize the harsh cave environment. [ABSTRACT FROM AUTHOR]

The taxonomy of genera Anabaena and Nostoc is very controversial. They are typically paraphyletic within phylogenetic trees and show similar morphological characters. The present study aimed to determine the taxonomic relationships among Anabaena and Nostoc strains of the Mosonmagyaróvár Algal Culture Collection (MACC) using 16S rRNA and rbcLX gene sequences. We concluded on the basis of the number of unsuccessful amplifications that more of the examined MACC Nostoc cultures are axenic than the Anabaena cultures. In agreement with previous studies we noticed that the applied phylogenetic algorithms gave congruent results in phylogenetic analyses. However, the genus Nostoc clearly was found not monophyletic in the present study and this finding differed from many of the previous studies. Molecular results contradicted the previous morphology-based classification of some MACC cyanobacteria strains, therefore polyphasic taxonomic approaches are required for the reliable identification of cyanobacterial species. Some strains seemed to be identical based on the alignment of 16S rRNA or rbcLX sequences. • Taxonomic relationships among Anabaena and Nostoc strains of the MACC were determined using 16S rRNA and rbcLX gene sequences. • More Nostoc cultures were found to be axenic than Anabaena cultures. • The genus Nostoc clearly was not found monophyletic in this study. • Molecular results contradicted the previous morphology-based classification of some MACC cyanobacteria strains. • Some strains seemed to be identical based on the alignment of 16S rRNA or rbcLX sequences. [ABSTRACT FROM AUTHOR]

Molecular species recognition and identification, based on the mitochondrial cox1 and on the nuclear ITS2, were performed on individuals of Torymus sinensis collected in Italy, on its close relative T. beneficus and on native torymids. The automatic-gap-discovery (ABGD) analyses correctly separate almost all morphospecies. On the basis of cox1 , individuals of late-spring T. beneficus clustered with T. sinensis, and those identified as early-spring T. beneficus were recognized as a separate entity. Whereas, T. beneficus ecotypes clustered with T. sinensis on the basis of ITS2. Coalescent tree-based methods confirmed these results. The cox1- based recognition of early-spring T. beneficus as a separate phylospecies led us to conclude that this taxon deserves to be treated as a valid species, whereas individuals identified as late-spring T. beneficus might be considered as part of T. sinensis. Morphological identification and BLAST analyses confirmed that no T. beneficus was imported into Italy to control Dryocosmus kuriphilus. [ABSTRACT FROM AUTHOR]

• Vineyard soil samples contained Beauveria spp. or Metarhizium spp. • Three Beauveria spp. were identified, B. australis , B. bassiana and B. pseudobassiana. • New B. australis sister clade within the B. bassiana clade was identified. • Two potentially new phylogenetic species within the B. australis clade were identified. • Six Metarhizium spp. were identified. Entomopathogenic Ascomycetes: Hypocreales fungi occur worldwide in the soil; however, the abundance and distribution of these fungi in a vineyard environment is unknown. A survey of Australian vineyards was carried out in order to isolate and identify entomopathogenic fungi. A total of 240 soil samples were taken from eight vineyards in two states (New South Wales and Victoria). Insect baiting (using Tenebrio molitor) and soil dilution methods were used to isolate Beauveria spp. and Metarhizium spp. from all soil samples. Of the 240 soil samples, 60% contained either Beauveria spp. (26%) or Metarhizium spp. (33%). Species of Beauveria and Metarhizium were identified by sequencing the B locus nuclear intergenic region (Bloc) and elongation factor-1 alpha (EFT1) regions, respectively. Three Beauveria species (B. bassiana , B. australis and B. pseudobassiana) and six Metarhizium species (M. guizhouense , M. robertsii , M. brunneum , M. flavoviride var. pemphigi , M. pingshaense and M. majus) were identified. A new sister clade made up of six isolates was identified within B. australis. Two potentially new phylogenetic species (six isolates each) were found within the B. bassiana clade. This study revealed a diverse community of entomopathogenic fungi in sampled Australian vineyard soils. [ABSTRACT FROM AUTHOR]

The white worm Enchytraeus albidus Henle, 1837 (Clitellata, Enchytraeidae) is easy to keep in laboratory cultures, and has therefore been employed as a model organism in basic and applied biological research. Its natural habitat includes terrestrial composts and wrack beds on seashores. However, the name E. albidus is currently used for a complex of morphologically similar and closely related species. We here revise the components of the E. albidus species complex based on a sample of 100 Enchytraeus specimens from 56 sites, most of which are across Europe. These samples were DNA-barcoded for the mitochondrial COI gene. A subset of them was sequenced for the nuclear ITS2 and H3 markers. Six species were delimited with strong support by the COI and ITS2 gene trees, as well as by a multi-locus species delimitation analysis. These species are identified morphologically and described as E. albidus s. str. (with designation of a neotype); Enchytraeus moebii(Michaelsen, 1885); Enchytraeus albellus Klinth, Erséus and Rota, sp. nov., E. cf. krumbachi (Čejka, 1913), E. sp. 1 (unnamed), and Enchytraeus polatdemiri Arslan and Timm, 2018. The last-mentioned species is a soda lake specialist, whereas E. albidus s. str. is both terrestrial and marine littoral; all other species occur only in seashores. The phylogeny of this group was estimated using the multi-species coalescent model. Monophyly of the E. albidus complex was recovered. Within this complex, three groups were recovered as monophyletic, but the relationship between them is unclear. One group comprises E. albidus s. str., E. albellus, and E. moebii; the second group E. cf. krumbachi and the unnamed E. sp. 1, and the third consists of only E. polatdemiri. This study serves as a framework for genetic identification of white worms used for experimental purposes. [ABSTRACT FROM AUTHOR]

This study contributes to knowledge of ash weevil (Stereonychus fraxini De Geer) molecular taxonomy, phylogeny and genetic diversity. Adult and larvae stages of insect were collected from several locations covering northern and central part of Serbia cojoined with homologous sequences with respect to their different geographic origin and hypothesis of their evolutionary relationships. Due to its slow rates of evolution the gene region that covers mitochondrial 16S rDNA, was choice for sequence profiling and phylogenetic reconstruction of ash weevil in correspondence with sequences of related tribes Cionini. Phylogenetic analyses demonstrating clear separation of the native weevil populations and the Cionini tribes. Even though bioinformatic tools confirm that all native specimens belong to species Stereonychus fraxini, different profile of the mitochondrial 16S rDNA in the clade of Serbian specimens indicate intraspecific genomic rearrangement in one specimen detached it to northern geographic position. Those particular specimens invade also different Fraxinus species. Genetic distinctness of other imagos from this particular individual proved by indels and point mutations found in their sequences. By screening the mitochondrial 16S rDNA, molecular evidence suggests the existence of the specimen with rearranged genome that indicate genetic variability in native populations of ash weevil species. [ABSTRACT FROM AUTHOR]

Entomopathogenic fungi from the genera Beauveria and Metarhizium , were isolated from soil using the Galleria mellonella baiting method, and from infected white grub larvae from a diversity of cropping systems in Puebla and Guanajuato, Mexico. Isolates were identified to species level using Bloc and Elongation Factor 1-α sequence information. Although widespread, Beauveria bassiana (41 isolates) was only isolated from soil and not from infected white grubs. In contrast, Beauveria pseudobassiana (six isolates) was predominantly isolated from white grub larvae (only one isolate from soil). Haplotype analysis of B. bassiana Bloc sequences identified 25 haplotypes indicating substantial genetic diversity; neither geographical origin nor crop type explained this genetic variation. Metarhizium brunneum (three isolates) and Metarhizium robertsii (17 isolates) were also only isolated from soil, while Metarhizium anisopliae (six isolates) and Metarhizium pingshaense (four isolates) were only isolated from white grub larvae. M. anisopliae was only found infecting Paranomala species while M. pingshaense was only found infecting Phyllophaga species. Species diversity in Metarhizium was influenced by crop type. Our results showed that entomopathogenic fungi species could co-exist in the same soil ecosystem but in separate niches. The potential ecological roles of these species are discussed. Image 1 • Beauveria and Metarhizium were isolated from soil and white grub larvae. • B. bassiana s.s., M. brunneum and M. robertsii were only isolated from soil. • B. pseudobassiana was predominantly isolated from white grub larvae. • M. anisopliae s.s. and M. pingshaense were only isolated from white grub larvae. • Niche separation was clear amongst species suggesting different ecological roles. [ABSTRACT FROM AUTHOR]

Torymus sinensis Kamijo was released into Europe to control the Asian chestnut gall wasp Dryocosmus kuriphilus Yasumatsu, proving to be an effective biocontrol agent.In Japan, hybrids between this exotic parasitoid and the native congeneric Torymus beneficus Yasumatsu and Kamijo have been recorded, whereas no case of hybridization with natives has been reported for Europe.The seasonal phenology of the Torymus species was investigated in north‐west Italy and 172 997 chestnut galls (Castanea spp.), 7866 oak galls (Quercus spp.), 29 wild rose galls (Rosa spp.) and 44 bramble galls (Rubus spp.) were collected over a 5‐year period.The seasonal flight activity was recorded for eight native Torymus species [Torymus affinis (Fonscolombe), Torymus auratus (Müller), Torymus bedeguaris (L.), Torymus calcaratus Nees, Torymus cyaneus Walker, Torymus flavipes (Walker), Torymus geranii (Walker) and Torymus notatus (Walker)] and five of them were found to overlap with T. sinensis flight, namely T. affinis, T. auratus, T. flavipes, T. geranii and T. notatus.Among the Torymus native species, T. notatus revealed to be morphologically and phylogenetically closely related to T. sinensis, thus suggesting hybridization potential. [ABSTRACT FROM AUTHOR]

Graphical abstract Highlights • Hydrocotyle tetragonocarpa is conspecific with H. sp. Hamelinensis. • Hydrocotyle tetragonocarpa is heterocarpic with winged and wingless fruit morphs. • Hydrocotyle scutellifera is conspecific with H. sp. Puberula. • Molecular phylogenies reveal Hydrocotyle is paraphyletic in respect to Neosciadium. • The basionym Hydrocotyle glochidiata Benth. is formally reinstated. Abstract Hydrocotyle L. is a cosmopolitan genus, with approximately 130 species, of mostly perennial herbs in the family Araliaceae. The genus includes around 95 perennial and 35 annual species, with all annual species endemic to Australia. In this study, I used sequences of a nDNA marker (ETS) and two cpDNA markers (psb A –trn H and trn L – t rn F) to reconstruct phylogenetic relationships among the annual species of Hydrocotyle. The final sampling included 21 species of Hydrocotyle and seven outgroup taxa. The phylogenetic analyses of the combined molecular dataset (i.e., ETS, psb A –trn H and trn L – t rn F) recovered three major clades within Hydrocotyle , defined by annual or perennial life histories, and the presence/absence of floral bracts. The topology reconstructed here indicates that there is insufficient molecular evidence for the formal recognition of two putative new species, Hydrocotyle sp. Hamelinensis and Hydrocotyle sp. Puberula, previously identified on the basis of morphology. More specifically, H. sp. Hamelinensis is conspecific with H. tetragonocarpa Bunge, while H. sp. Puberula is conspecific with H. scutellifera Benth. Morphological studies of H. tetragonocarpa revealed that this species is andromonoecious and has heterocarpic schizocarps. Fertile plants of H. tetragonocarpa bear fruit that are either ovoid and wingless or broadly obcordate and winged. A detailed re-examination of the schizocarp surfaces of H. scutellifera indicated that these schizocarps are either glabrous or papillate, with neither of these two character states co-varying with any other vegetative or reproductive traits. The phylogeny of the annual Hydrocotyle recovered a paraphyletic Hydrocotyle , with Neosciadium glochidiatum (Benth.) Domin nested within the genus. This study is the first to reconstruct a molecular phylogeny of Hydrocotyle using samples of both annual and perennial taxa. The findings from this study provide a phylogenetic framework for future systematic and taxonomic research within the genus. [ABSTRACT FROM AUTHOR]

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Diatoms are one of the most abundant and arguably the most species‐rich group of protists. Diatom species delimitation has often been based exclusively on the recognition of morphological discontinuities without investigation of other lines of evidence. Even though DNA sequences and reproductive experiments have revealed several examples of (pseudo)cryptic diversity, our understanding of diatom species boundaries and diversity remains limited. The cosmopolitan pennate raphid diatom genus Pinnularia represents one of the most taxon‐rich diatom genera. In this study, we focused on the delimitation of species in one of the major clades of the genus, the Pinnularia subgibba group, based on 105 strains from a worldwide origin. We compared genetic distances between the sequences of seven molecular markers and selected the most variable pair, the mitochondrial cox1 and nuclear encoded LSU rDNA, to formulate a primary hypothesis on the species limits using three single‐locus automated species delimitation methods. We compared the DNA‐based primary hypotheses with morphology and with other available lines of evidence. The results indicate that our data set comprised 15 species of the P. subgibba group. The vast majority of these taxa have an uncertain taxonomic identity, suggesting that several may be unknown to science and/or members of (pseudo)cryptic species complexes within the P. subgibba group. [ABSTRACT FROM AUTHOR]

Abstract Retortamonas spp. has been reported as an intestinal parasite among various host organisms, including humans; however, its intra-genus molecular diversity has not yet been elucidated. Haplotypes of the 18S small subunit ribosomal RNA locus (1836–1899 bp) of Retortamonas spp. from humans (n = 8), pigs (n = 6), dogs (n = 1), goats (n = 16), water buffalos (n = 23), cattle (n = 7), rats (n = 3), and chickens (n = 5) were analyzed with references isolated from non-human mammals, amphibians, and insects. Phylogenetic and network analyses revealed a statistically supported three cluster formation among the vertebrate-isolated haplotypes, while insect-isolated haplotypes were independently clustered with Chilomastix. In the clade of vertebrate isolates, assemblage A (amphibian genotype), which included the amphibian references, was addressed as an out-group of the other clusters. Assemblage B (mammalian and chicken genotype) included most haplotypes from various mammals including humans with the haplotypes isolated from a chicken. Human isolates were all classified into this assemblage, thus assemblage B might correspond to R. intestinalis. Assemblage C (bovine genotype), which included specific haplotypes from water buffalos and cattle, was addressed as a sister lineage of assemblage B. Among the diversified haplotypes of assemblage B, a specific haplotype, which was identified from multiple host mammals (humans, dogs, pigs, cattle, water buffalos, elks, goats, and rats), indicates the potential zoonotic transmission of the Retortamonas among them. The genotyping classification of retortamonads could contribute to a better understanding of its molecular epidemiology, especially among humans and related host organisms. Graphical abstract Unlabelled Image Highlights • The polyphyletic features of current Retortamonas spp. were confirmed as separated clusters. • Retortamonads from vertebrates were clustered with diplomonads, while the ones from insects were with Chilomastix. • Three cluster formation of genetic haplotypes of Retortamonas spp. isolated from vertebrates were confirmed. • Assemblage (ass.) A (amphibian genotype) and ass. C (bovine genotype) are host specific genotypes. • Ass. B [mammalian (including human) and avian genotype] might be correspond to Retortamonas intestinalis. [ABSTRACT FROM AUTHOR]

The molecular taxonomic study was performed on the microalgae of Al-Yahoudiyah rivulet, in the Babylon province in the middle of Iraq, is situated between 32° to 33.25° North latitude and 44° to 45° East longitude. It's opened from Shat Al-Hilla, it a source Euphrates river. Many pollutants in different amount and types were discharged in it, lead to increased pollutants synchronization with increase microalgae, fungi, bacteria and protozoa and reflect in bad influences against human, animal and nature. The aim of this study was to identify the microalgae based on microscopic and molecular characters and survey of fungal biodiversity in Al-Yahoudiyah rivulet. The results identified by many microalgae species: Desmodesmus armatus, Cyclotlla distinguenda, Nostoc verrucosum, Nitzschia linearis, Fistulifera aprophila and Chlorella spp., Micractinium sp. as new species were recorded for first time in Iraq based on sequence analysis of ITS region. Also many species were recorded in this study based on sequence analysis of 18S rDNA: Halamphora holsatica, Fistulifera saprophila, F. pelliculosa, F. solani and Amphora coffeaeformis. The main fungi shown high frequencies were: Aspergillus spp., Penicillium spp., Drechslera spp., Acrimonium sp, Fusarium spp and yeasts. [ABSTRACT FROM AUTHOR]

The brown algal genus Lobophora is widely reported from the Mediterranean Sea. Contrary to studies in the Indo-Pacific and Caribbean regions, little attention has been given to Lobophora in the Mediterranean Sea, at least using molecular tools. To address this knowledge gap, we sampled specimens across the Mediterranean Sea (Spanish coast, Balearic Islands, Greece and Israel), with an exhaustive effort in the Balearic Islands. Molecular analyses disclosed the presence of three species, none of them conspecific with the name L. variegata, as they were recorded up to now in the Mediterranean Sea. The most common species in the Mediterranean Sea is L. delicata. We here describe L. schneideri sp. nov., so far found only in Haifa Bay (Israel), where it forms large and dense populations. Similar to L. delicata, L. schneideri occurs across the North Atlantic Ocean. Though a recent range expansion or introduction cannot be ruled out, we regard the North Atlantic Ocean, including the Greater Caribbean and the Mediterranean Sea, as the natural range of both L. schneideri and L. delicata. A third species, described here as L. lessepsiana sp. nov., is found along the Israeli coast as well as in the Red Sea and is most probably a recent introduction through the Suez Canal. Further exploration along the North African coast, the Levantine Sea and the Aegean Sea, would probably increase the currently known species diversity for this group in the Mediterranean Sea. [ABSTRACT FROM AUTHOR]

• Nyssomyia antunesi and Psychodopygus davisi were the most abundant species;. • New records for Maranhão: Lu. evangelistai, Lu. sherlocki, Pr. equatorialis , and Pa. barrettoi ;. • Species delimitation analyses correctly delimited all species, except for Pressatia species;. • We sequenced for the first time COI barcodes of nine sand fly species;. • Detection of cryptic diversity for Pa. bigeniculata, Ps. davisi , and Sc. sordellii. The sand fly fauna and the usefulness of the DNA barcoding fragment of the cytochrome c oxidase subunit I (COI) gene were accessed in a forest fragment in the municipality of Governador Newton Bello, state of Maranhão, Brazil. We performed entomological collections in three independent campaigns in May and October 2021, and January 2023. Sand flies were morphologically-identified and then DNA barcoded. Sequences were deposited and analyzed in the BOLD System Database, and various species delimitation algorithms, to assess whether DNA sequences merge into taxonomic units in accordance with nominal species. In total, 1,524 sand flies were collected, comprising 32 nominal species. Nyssomyia antunesi was the most abundant species (31.5 %), followed by Psychodopygus davisi (27 %). We reported for the first time in the state of Maranhão, the presence of Lutzomyia evangelistai, Lutzomyia sherlocki, Pressatia equatorialis , and Psathyromyia barrettoi. We amplified and analyzed 67 COI barcodes of 23 species, which were merged with conspecific sequences extracted from GenBank. The maximum intraspecific p distances ranged from 0.0 % to 14.74 %, while the distances to the nearest neighbor varied from 1.67 % to 13.64 %. The phylogenetic gene tree and species delimitation tools clustered sequences into well-supported clades/clusters for each nominal species, except for Pressatia choti / Pr. equatorialis , which have the lowest interspecific genetic distance (1.67 %). We sequenced for the first time COI barcodes of Brumptomyia brumpti, Evandromyia monstruosa, Micropygomyia rorotaensis, Micropygomyia pilosa, Pintomyia christenseni, Pintomyia pacae, Pr. equatorialis, Pa. barrettoi , and Psathyromyia hermanlenti , which will be useful for further molecular identification and classification proposals of Neotropical species. This study updated the current list of the sand fly fauna for the state of Maranhão to 97, and demonstrated that COI barcodes are useful for specific identification. [ABSTRACT FROM AUTHOR]

We have investigated 59 Neobisium samples from 15 Georgian caves morphologically and morphometrically. Additionally, we sequenced two gene fragments (COI, 28S) of 38 specimens in order to assess the diversity of the Neobisium lineages in the caves of the Caucasus. Molecular species delimitation methods (ASAP, PTP, GMYC) were also implemented. We detected seven independent cavernicolous lineages in Georgia. A larger-scale analysis was also carried out by combining our data with publicly available sequence datasets from other localities in Europe. Recent synonymization of N. (Ommatoblothrus) BEIER, 1956 and N. (Heoblothrus) BROWNING, 1965 with N. (Neobisium) CHAMBERLIN, 1930 was subsequently supported by our preliminary molecular data. Our preliminary results suggest that the uniform troglobiont morphology of most cavernicolous species within the genus Neobisium from distinct geographical regions might be a result of convergent evolution. [ABSTRACT FROM AUTHOR]

Recent landmark publications from our research group outline a transformative approach to defining, studying and treating amyotrophic lateral sclerosis (ALS). Rather than approaching ALS as a single entity, we advocate targeting therapies to distinct “clusters” of patients based on their specific genomic and molecular features. Our findings point to the existence of a molecular taxonomy for ALS, bringing us a step closer to the establishment of a precision medicine approach in neurology practice.

Correct identification and classification of sponges is challenging due to ambiguous or misleading morphological features. A particular case is a blue keratose sponge occasionally referred to as the “Blue Photo Sponge” among aquarists, which appears frequently (and in several cases unintended) in private aquaria. This spicule-less species, occasionally specified as Collospongia auris Bergquist, Cambie & Kernan 1990, not only displays a high phenotypic plasticity in growth form and colour, it also proliferates in aquacultures under standard conditions unlike most other sponges. Therefore, this species is regarded as a pest for most aquarists. In turn, the ease of cultivation and propagation in aquacultures qualifies this species as a model organism for a wide array of scientific applications. For these purposes, correct identification and classification are indispensable. We reconstructed ribosomal gene trees and determined this species as Lendenfeldia chondrodes (De Laubenfels, 1954) (Phyllospongiinae), distant to Collospongia auris, and corroborated by skeletal features. Additionally, the resulting phylogeny corroborated major shortcomings of the current Phyllospongiinae classification—its consequences are discussed.

Migonemyia migonei (Franҫa, 1920) (Diptera: Psychodidae) belongs to the subfamily Phlebotominae, of epidemiological importance due to its role as a vector in leishmaniasis transmission cycles and its broad geographic distribution in South America. Few morphometric and genetic studies have demonstrated the existence of variability among geographically distant populations in Brazil. The aim of the study was to estimate the genetic distance within the morphospecies Mg. migonei through the analysis of cytochrome C oxidase subunit I (COI) sequences of specimens captured in Argentina and those available in online databases. The COI sequences from specimens collected in different localities of Argentina and sequences available in online databases were utilized. Genetic distances were analyzed and a median-joining haplotype network was constructed. Finally, phylogenetic reconstruction was performed according to Bayesian inference. The analyses led to the identification of at least two haplogroups: haplogroup I with sequences of specimens from Colombia, Brazil and Argentina, and haplogroup II with sequences of specimens from Argentina. Interestingly, specimens from Argentina whose haplotypes corresponded to both haplogroups, were collected in sympatry. The results suggest that Mg. migonei could be a species complex with at least two distinct members. This hypothesis could explain the known characteristics of adaptability and vector permissiveness of the species, as the putative cryptic species of the complex could differ in traits of epidemiological importance., (© 2023. Sociedade Entomológica do Brasil.)

Objective: A reliable taxonomic identification of species from molecular samples is the first step for many studies. For researchers unfamiliar with programming, running a BLAST analysis, filtering, and organizing results for hundreds of sequences through the BLAST web interface can be difficult. Additionally, sequences deposited in GenBank can have outdated taxonomic identification. The use of reliable Reference Sequences Library (RSL) containing accurate taxonomically-identified sequences facilitates this task. Pending the availability of a RSL with the user, we developed a tool that automates the molecular taxonomic identification of sequences., Results: We developed PARSID, a Python script running through the command-line that automates the routine workflow of blasting an input sequence file against the user's RSL, and retrieves the matches with the highest percentage of identity in five steps. PARSID accepts cut-off parameters and supplementary information in a.csv file for filtering the results. The final output is visualized in a spreadsheet. We tested its functioning using 10 input sequences simulating different situations of the molecular taxonomic identification of sequences against an example RSL containing 25 sequences. Step-by-step instructions and test files are publicly available at https://github.com/kokinide/PARSID.git ., (© 2024. The Author(s).)

Background: Strongyloidiasis is a neglected tropical disease (NTD) that is caused mainly by Strongyloides stercoralis, with an estimated 600 million people infected worldwide, and in fewer cases by Strongyloides fuelleborni fuelleborni and Strongyloides fuelleborni kellyi. A number of studies have been conducted on the genetic diversity of S. stercoralis in East and Southeast Asia; however, there is very limited corresponding information from West Asian countries, including Iran., Methods: For Strongyloides worms collected from patients in southwestern Iran, the hypervariable regions I (HVR-I) and IV (HVR-IV) of the nuclear 18S ribosomal DNA (rDNA) locus (SSU) and a fragment of the subunit 1 mitochondrial cytochrome c oxidase gene (cox-1) were sequenced. For a subset of the worms, whole-genome sequencing data were generated., Results: The cox-1 sequences of 136 worms isolated from 23 patients indicated that all isolates were S. stercoralis. Among the cox-1 sequences, 33 polymorphic sites and 13 haplotypes were found. The phylogenetic analysis demonstrated that some sequences clustered fairly closely with sequences from humans and dogs from other parts of the world, while others formed a separate, Iran-specific group. Among 64 S. stercoralis analyzed, we found three of the previously described SSU HVR-I haplotypes, with haplotype II being the most frequent haplotype. In contrast to Southeast Asia, where S. stercoralis heterozygous for different haplotypes at the HVR-I locus are rare, we found 20 worms to be heterozygous for two different HVR-I haplotypes, 18 of which fell into the Iran-specific cox-1 cluster. SSU-heterozygous worms also showed elevated heterozygosity at the whole-genome level., Conclusions: We conclude that the S. stercoralis population from the Khuzestan province shares much of the genetic diversity with the population in Southeast Asia, but there is an indication of additional genetic input. There appears to be some population structure with different subpopulations, which however do interbreed at least occasionally., (© 2024. The Author(s).)

We provide the incidental necropsy findings associated with anisakid nematode infections of black noddy terns, Anous minutus Boie, 1844 (Charadriiformes: Laridae), from offshore islands in the southern Great Barrier Reef, Queensland, Australia. Specimens collected from the proventriculi were identified morphologically as Contracaecum magnipapillatum Chapin, 1925 (Rhabditida: Anisakidae), using light and scanning electron microscopy (SEM). The entire nuclear ribosomal DNA internal transcribed spacer (ITS) region (ITS1-5.8S-ITS2) was amplified by polymerase chain reaction (PCR) and sequenced to provide reference sequences for morphologically well-identified voucher specimens. Interestingly, after an alignment with closely related taxa using BLAST, sequences of the ITS1 and ITS2 were 100% identical to the sequences assigned to Contracaecum septentrionale Kreis, 1955, from a razorbill, Alca torda Linnaeus, 1758 (Charadriiformes: Alcidae), from Spain. These results either raise questions about the ITS as a genetic marker for some members of Contracaecum, or the identity of the specimens assigned to C. septentrionale, given that no supporting morphological data was associated with them. We highlight the need for a combined morphological and molecular approach to parasite diagnostics and the use of multiple genetic loci to resolve the molecular taxonomy of cryptic species. Morphological identifications should be taxonomically robust, transparent and precede the deposition of molecular barcodes in public repositories. The gross and histopathological findings of our investigation concur with previous reports of widespread Contracaecum infections in black noddies and support the contention that Contracaecum spp. are an unlikely primary cause of mortality., (© 2024. The Author(s).)

The overall availability of user-friendly software tools tailored to the analysis of DNA barcodes is limited. Several obvious functions such as detecting and visualizing the DNA barcode gap, the calculation of matrices of pairwise distances at the level of species, or the filtering and decontaminating of sets of sequences based on comparisons with reference databases can typically be carried out only by complex procedures that involve various programs and/or a substantial manual work of formatting. The iTaxoTools project aims at contributing user-friendly software solutions to improve the speed and quality of the workflow of alpha-taxonomy. In this chapter, we provide detailed protocols for the use of a substantially improved version of the tool TaxI2 for distance-based exploration of DNA barcodes. The program calculates genetic distances from prealigned data sets, or based on pairwise alignments, or with an alignment-free approach. Sequence and metadata input can be formatted as tab-delimited files and TaxI2 then computes tables, matrices and graphs of distances, and distance summary statistics within and between species and genera. TaxI2 also includes modes to compare a set of sequences against one or two reference data sets and output lists of best matches or filter data according to thresholds or reciprocal matches. Here, detailed step-by-step protocols are provided for the use of TaxI2, as well as for the interpretation of the program's output., (© 2024. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.)

DNA barcoding plays an important role in exploring undescribed biodiversity and is increasingly used to delimit lineages at the species level (see Chap. 4 by Miralles et al.). Although several approaches and programs have been developed to perform species delimitation from datasets of single-locus DNA sequences, such as DNA barcodes, most of these were not initially provided as user-friendly GUI-driven executables. In spite of their differences, most of these tools share the same goal, i.e., inferring de novo a partition of subsets, potentially each representing a distinct species. More recently, a proposed common exchange format for the resulting species partitions (SPART) has been implemented by several of these tools, paving the way toward developing an interoperable digital environment entirely dedicated to integrative and comparative species delimitation. In this chapter, we provide detailed protocols for the use of two bioinformatic tools, one for single locus molecular species delimitation (ASAP) and one for statistical comparison of species partitions resulting from any kind of species delimitation analyses (LIMES)., (© 2024. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.)

Hydrophylax bahuvistara, a new species of fungoid frog, is described from peninsular India. It can be separated from its congeners based on a combination of characters including wider head, outline of snout in dorsal view truncated, finger and toe tips without lateroventral groove, foot moderately webbed, metatarsals of 4th and 5th toes closely set, outer metatarsal tubercle small, foot length less than or equal to half of snout vent length, dorsal parts of shank without glandular folds and sparse horny spinules, and heels touch each other when the legs are folded at right angles to the body. Genetically, H. bahuvistara forms a monophyletic group with H. malabaricus as a sister clade separated by a raw distance of 4.0 to 4.5% in the 16s rRNA gene. Morphometrically, H. bahuvistara forms a significantly different cluster from H. malabaricus and H. gracilis in Discriminant Analysis.