Phylogenetic relationships of the Mangrove Hummingbird, "Amazilia" boucardi (Apodiformes: Trochilidae) of Costa Rica / Relaciones filogenéticas del Colibrí manglero "Amazilia" boucardi (Apodiformes: Trochilidae) de Costa Rica

Abstract Introduction: A recent revision of the generic classification of the Trochilidae based on DNA sequences revealed many inconsistencies with the current generic classification, largely based on plumage characters subject to homoplasy, especially in the Trochilini, the largest tribe. A thorough generic reorganization brought the classification into accord with the phylogeny, but due to lack of genetic data, two species remained unclassified. One of these was the Mangrove Hummingbird, "Amazilia" boucardi, endemic to Costa Rica and included in the IUCN red list of threatened species. Objective: To obtain molecular evidence to clarify the generic relationships of "A." boucardi. Methods: We isolated DNA from tissues of this species and amplified 4 nuclear and 4 mitochondrial fragments and compared these with homologous fragments from 56 species in the Trochilini, constructing phylogenetic trees with maximum likelihood and Bayesian methods. Results: Our phylogenetic analyses confirmed the placement of boucardi in the Trochilini and definitely excluded it from Amazilia but placed it with high confidence in the genus Chrysuronia Bonaparte, 1850, within which its closest relative is C. coeruleogularis, which also inhabits mangroves. Conclusions: Our genetic data based on nuclear and mitochondrial regions clearly indicate the relationship of A. boucardi and L. coeruleogularis. Moreover, it is also supported by their habitat distribution in the mangroves of the Pacific coast of Costa Rica and Western Panama. Therefore, we suggested to exclude A. boucardi as "incertae sedis".

Resumen Introducción: Una revisión reciente de la clasificación de la familia Trochilidae con base en secuencias de ADN demostró muchas incongruencias con la clasificación genérica previa, que había sido hecho con base en caracteres del plumaje muy sujetos a homoplasia, especialmente en la tribu más grande, Trochillini. Una reorganización de los géneros logró llevar su clasificación genérica a la concordancia con la filogenia, pero debido a la ausencia de datos genéticos, dos especies permanecieron sin clasificar. Una de estas fue el colibrí de manglar Amazilia boucardi, una especie endémica de Costa Rica, considerada como amenazada en la lista roja de la UICN. Objetivo: Obtener evidencia molecular para esclarecer las relaciones genéricas de A. boucardi. Métodos: Se aisló ADN de tejidos de esta especie y se amplificaron 4 fragmentos de ADN del núcleo y 5 de la mitocondria, y se compararon con fragmentos homólogos de 56 especies en la tribu Trochillini, generando árboles filogenéticos con métodos de máxima verosimilitud y bayesiano. Resultados: Los análisis filogénticos obtenidos confirmaron la ubicación de boucardi en Trochilini y definitivamente la excluyó del género Amazilia, pero la ubicó con un alto grado de confianza en el género Chrysuronia Bonaparte, 1850, dentro los cuales su pariente más cercano es C. coeruleogularis, que también habita manglares. Conclusiones: Nuestros datos genéticos basados en regiones nucleares y mitocondriales indican claramente la relación entre A. boucardi and L. coeruleogularis. Es más, lo anterior se sustenta por su distribución en los manglares de la costa Pacífica de Costa Rica y oeste de Panamá. Por lo tanto, sugerimos excluir a A. boucardi como "incertae sedis".

Description and Molecular Characterization of a New Dorylaimid Nematode, Mesodorylaimus pini n. sp. (Nematoda: Dorylaimidae) from Korea.

Mesodorylaimus pini n. sp., a new species isolated from the bark and cambium layer of a dead black pine tree is characterized herein using integrative taxonomy, considering both morphological and molecular phylogenetic analyses of the 18S- and 28S-rRNA genes. Mesodorylaimus pini n. sp. is characterized by having a medium-sized body 1.50-1.89 mm long; lip region angular and offset by a depression; a relatively long odontostyle (17.0-19.0 µm); vulval opening a transverse slit, positioned slightly posteriorly; pars refringens vaginae with two elongated drop-shaped to spindle-shaped sclerotizations; an intestine-prerectum junction with a long anteriorly directed conical or tongue-like projection; a relatively long female tail (115-187 µm); spicules 48.0-57.0 µm long; and regularly spaced 7-8 ventromedian supplements. It is closest to M. subtilis, especially in having similar body length and number of ventromedian supplements but can be differentiated from M. subtilis by the longer odontostyle, tongue-like projection, and longer spicules. The phylogenies based on the 18S- and 28S-rRNA sequences showed a well-supported sister relation of M. pini n. sp. with M. subtilis, M. japonicus, M. bastiani, M. pseudobastiani, Calcaridorylaimus castaneae, C. heynsi, and other member species of the group.

Specific amino acid changes correlate with pathogenic flavobacteria.

Flavobacterium is a genus of microorganisms living in a variety of hosts and habitats across the globe. Some species are found in fish organs, and only a few, such as Flavobacterium psychrophilum and Flavobacterium columnare, cause severe disease and losses in fish farms. The evolution of flavobacteria that are pathogenic to fish is unknown, and the protein changes accountable for the selection of their colonization to fish have yet to be determined. A phylogenetic tree was constructed with the complete genomic sequences of 208 species of the Flavobacterium genus using 861 softcore genes. This phylogenetic analysis revealed clade CII comprising nine species, including five pathogenic species, and containing the most species that colonize fish. Thirteen specific amino acid changes were found to be conserved across 11 proteins within the CII clade compared with other clades, and these proteins were enriched in functions related to replication, recombination, and repair. Several of these proteins are known to be involved in pathogenicity and fitness adaptation in other bacteria. Some of the observed amino acid changes can be explained by preferential selection for certain codons and tRNA frequency. These results could help explain how species belonging to the CII clade adapt to fish environments.

Refurbishing the marine parasitoid order Pirsoniales with newly (re)described marine and freshwater free-living predators.

Pirsoniales is a stramenopile order composed of marine parasitoids of diatoms with unique life cycle. Until recently, a single genus, Pirsonia, uniting six species, was known. The recent identification of new free-living eukaryotrophic Pirsoniales Pirsonia chemainus, Feodosia pseudopoda, and Koktebelia satura changed our understanding of this group as exclusively parasitic. However, their cell ultrastructure and feeding preferences were not fully studied due to the death of the cultures. In this study, we re-isolated some of these Pirsoniales and established six new strains exhibiting predatory behavior, including a first freshwater representative. This allowed us to describe five new genera and species, as well as to emend the diagnosis of the order Pirsoniales. The 18S rRNA gene phylogenetic analysis revealed the position of new strains within Pirsoniales and their relationships with parasitoid relatives and environmental sequence lineages. Feeding experiments on novel Pirsoniales strains using diverse algal prey showed that they were not able to form trophosomes and auxosomes. The ability of cell aggregation in Pirsoniales was observed for the first time. One of the studied strains contained intracellular gammaproteobacteria distantly related to Coxiella. Ultrastructural analyses revealed a more complex cytoskeleton structure in Pirsoniales than previously thought and supported the monophyly of Bigyromonadea and Pseudofungi.

A comprehensive molecular survey of vector-borne blood parasites in cattle in Kyrgyzstan with a note of the first molecular detection of Anaplasma bovis and Candidatus Anaplasma Camelii.

Vector-borne pathogens continue to increase their impact on the livestock industry worldwide. To protect animals against these pathogens, it is very important to identify the species that cause the disease and understand their prevalence. This study aimed to investigate the presence and prevalence of vector-borne pathogens in apparently healthy cattle in different parts of Kyrgyzstan using molecular diagnostic techniques. For this purpose, 531 blood samples were collected from the Osh, Jalal-Abad, and Batken oblasts of Kyrgyzstan. The blood samples were investigated for vector-borne pathogens using PCR, RLB, and RFLP. Moreover, DNA sequence analyses were used to confirm the results of molecular techniques and phylogenetic analyses of these pathogens. 359 (67.61%) out of 531 samples were found to be infected with at least one pathogen, whereas 172 (32.39%) were detected to be negative. Thirteen vector-borne pathogens were detected in cattle blood samples, and the prevalence of these pathogens was as follows: Theileria orientalis (47.83%), T. annulata (25.61%), Babesia major (0.19%), B. occultans (0.38%), Anaplasma phagocytophilum-like 1 (3.20%), A. capra (3.01%), A. centrale (2.82%), A. bovis (1.13%), (A) ovis (0.19%), Candidatus Anaplasma camelii (0.94%), Trypanosoma theileri (19.21%), Mycoplasma wenyonii (6.03%), and Ca. Mycoplasma haemobos (2.64%). Among the positive samples, one pathogen was identified in 189 cattle (35.59%), and co-infections (two or more pathogens) were determined in 170 (32.01%) animals. Theileria parva, T. mutans, (B) bigemina, B. bovis, B. divergens, and A. marginale could not be detected in the study. Anaplasma bovis and Ca. Anaplasma camelii were detected for the first time in the country. This molecular survey provides important epidemiological and genetic data for the vector-borne pathogens in cattle. The results of the study showed that vector-borne pathogens have a significant spread and distribution in cattle in Kyrgyzstan.

Characterization of the complete mitochondrial genome of Loxocephala sichuanensis (Hemiptera: Eurybrachidae) with the phylogenetic analyses of Fulgoromorpha.

Little is known about the mitochondrial genome of the family Eurybrachidae, with only two species sequenced. This study added one more mitogenome of Loxocephala sichuanensis in this family. The mitochondrial genome length of this species was 15,605 bp, consisting of 37 genes: 13 PCGs, 2 rRNAs, 22 tRNAs, and a control region. An unusually high A + T content, reaching 94.3% at the third codon position of 13 PCGs in Loxocephala, was found in Eurybrachidae, which was the highest among all planthoppers, especially on N-strand. Three tandem repeat regions were detected in the control region. Phylogenetic analyses based on complete mitochondrial genome sequences from 145 species (encompassing 18 planthopper families and 135 species in Fulgoromorpha as ingroup, and 6 other non-planthopper families in Auchenorrhyncha as outgroup) were conducted. Six datasets (PCG123R24, PCG123R2, PCG123, PCG12R24, PCG12R2, PCG12) were established to investigate the influence of 22 tRNAs and the third codon of the 13 PCGs of mitogenome for phylogeny analyses. Both Maximum likelihood and Bayesian trees supported the monophyly of the superfamilies Delphacoidea and Fulgoroidea. Delphacoidea, consisting of Cixiidae and Delphacidae as sister group, was in the basal position of Fulgoromorpha. In Fulgoroidea, the families Meenoplidae and Kinnaridae, Dictyopharidae and Fulgoridae, Acanaloniidae and Tropiduchidae were sister groups which were strongly supported. Caliscelidae was close to the sister group Lophopidae with Eurybrachidae. The four families Flatidae, Nogodinidae, Ricaniidae and Issidae were closely related. The position of Tettigometridae was uncertain. Derbidae and Achilidae form a sister group when 22 tRNAs were included in the phylogeny. The joining of the tRNA sequences of mitochondrial genome enhanced the stability of family-level nodes and adjusted some phylogenetic positions, highlighting the significant role of joining tRNAs in phylogenetic analyses. Including or excluding the third codon position of 13 PCGs generally did not affect the overall phylogenetic structures of Fulgoromorpha.

Description and circadian rhythms of Chandlerella sinensis Li, 1933 (Nematoda; Onchocercidae), with remarks of microfilariae effects on the host health.

During investigation of common linnet (Linaria cannabina) blood using the buffy coat method one bird with microfilariae in the blood was found. The morphometric description of adult worms corresponded to the Chandlerella sinensis. This species was found for the first time in common linnets. DNA sequences of cox1 and 28S gene fragments of adult worm recovered during necropsy was identical to that from the microfilariae in the bird blood. Phylogenetic analysis of the cox1 gene fragment clustered this parasite with Chandlerella quiscali. Histological examination revealed the presence of microfilariae in the lumen of small capillaries and other blood vessels in different organs, but no inflammations were notice. The greatest number of microfilariae was in the lungs. Even if there was no inflammation, but vessels associated with the lungs were markedly distended with blood, parabronchial walls were thickened and, in some cases, almost completely obstructing the lumen. The large number of microfilariae in lungs indicates possible disturbance of gas exchange in the lungs adversely affected the ability of the bird to exercise and made breathing difficult at rest. The investigation of circadian rhythm of the microfilariae showed that C. sinensis microfilariae in blood of common linnet were more numerous at night and morning and less numerous at midday. The survival rate of mosquitoes infected with C. sinensis microfilariae was significantly lower than that of uninfected mosquitoes.

How life became colourful: colour vision, aposematism, sexual selection, flowers, and fruits.

Plants and animals are often adorned with potentially conspicuous colours (e.g. red, yellow, orange, blue, purple). These include the dazzling colours of fruits and flowers, the brilliant warning colours of frogs, snakes, and invertebrates, and the spectacular sexually selected colours of insects, fish, birds, and lizards. Such signals are often thought to utilize pre-existing sensitivities in the receiver's visual systems. This raises the question: what was the initial function of conspicuous colouration and colour vision? Here, we review the origins of colour vision, fruit, flowers, and aposematic and sexually selected colouration. We find that aposematic colouration is widely distributed across animals but relatively young, evolving only in the last ~150 million years (Myr). Sexually selected colouration in animals appears confined to arthropods and chordates, and is also relatively young (generally <100 Myr). Colourful flowers likely evolved ~200 million years ago (Mya), whereas colourful fruits/seeds likely evolved ~300 Mya. Colour vision (sensu lato) appears to be substantially older, and likely originated ~400-500 Mya in both arthropods and chordates. Thus, colour vision may have evolved long before extant lineages with fruit, flowers, aposematism, and sexual colour signals. We also find that there appears to have been an explosion of colour within the last ~100 Myr, including >200 origins of aposematic colouration across nine animal phyla and >100 origins of sexually selected colouration among arthropods and chordates.

Earthworm (Oligochaeta, Lumbricidae) intraspecific genetic variation and polyploidy.

Earthworms are known for their intricate systematics and a diverse range of reproduction modes, including outcrossing, self-fertilization, parthenogenesis, and some other modes, which can occasionally coexist in a single species. Moreover, they exhibit considerable intraspecific karyotype diversity, with ploidy levels varying from di- to decaploid, as well as high genetic variation. In some cases, a single species may exhibit significant morphological variation, contain several races of different ploidy, and harbor multiple genetic lineages that display significant divergence in both nuclear and mitochondrial DNA. However, the relationship between ploidy races and genetic lineages in earthworms remains largely unexplored. To address this question, we conducted a comprehensive review of available data on earthworm genetic diversity and karyotypes. Our analysis revealed that in many cases, a single genetic lineage appears to encompass populations with different ploidy levels, indicating recent polyploidization. On the other hand, some other cases like Octolasion tyrtaeum and Dendrobaena schmidti/D. tellermanica demonstrate pronounced genetic boundaries between ploidy races, implying that they diverged long ago. Certain cases like the Eisenia nordenskioldi complex represent a complex picture with ancient divergence between lineages and both ancient and recent polyploidization. The comparison of phylogenetic and cytological data suggests that some ploidy races have arisen independently multiple times, which supports the early findings by T.S. Vsevolodova-Perel and T.V. Malinina. The key to such a complex picture is probably the plasticity of reproductive modes in earthworms, which encompass diverse modes of sexual and asexual reproduction; also, it has been demonstrated that even high-ploidy forms can retain amphimixis.

Phylogenomics of Bivalvia Using Ultraconserved Elements (UCEs) Reveal New Topologies for Pteriomorphia and Imparidentia.

Despite significant advances in phylogenetics over the past decades, the deep relationships within Bivalvia (phylum Mollusca) remain inconclusive. Previous efforts based on morphology or several genes have failed to resolve many key nodes in the phylogeny of Bivalvia. Advances have been made recently using transcriptome data, but the phylogenetic relationships within Bivalvia historically lacked consensus, especially within Pteriomorphia and Imparidentia. Here, we inferred the relationships of key lineages within Bivalvia using matrices generated from specifically designed ultraconserved elements (UCEs) with 16 available genomic resources and 85 newly sequenced specimens from 55 families. Our new probes (Bivalve UCE 2k v.1) for target sequencing captured an average of 849 UCEs with 1085-bp in mean length from in vitro experiments. Our results introduced novel schemes from six major clades (Protobranchina, Pteriomorphia, Palaeoheterodonta, Archiheterodonta, Anomalodesmata and Imparidentia), though some inner nodes were poorly resolved, such as paraphyletic Heterodonta in some topologies potentially due to insufficient taxon sampling. The resolution increased when analyzing specific matrices for Pteriomorphia and Imparidentia. We recovered three Pteriomorphia topologies different from previously published trees, with the strongest support for ((Ostreida + (Arcida + Mytilida)) + (Pectinida + (Limida + Pectinida))). Limida were nested within Pectinida, warranting further studies. For Imparidentia, our results strongly supported the new hypothesis of (Galeommatida + (Adapedonta + Cardiida)), while the possible non-monophyly of Lucinida was inferred but poorly supported. Overall, our results provide important insights into the phylogeny of Bivalvia and show that target enrichment sequencing of UCEs can be broadly applied to study both deep and shallow phylogenetic relationships.

Genetic relationships of three species of black flies (Diptera: Simuliidae) in Taiwan.

As an island about 150 km from the mainland, Taiwan would be expected to have endemic species. About 64 % of its 36 species of black flies are considered endemic, more than twice the level of endemicity that has been recorded for all insects on the island. To begin assessing the validity of the high level of endemism for the Simuliidae, we used giant chromosome banding patterns and cytochrome c oxidase I (COI) sequences, against a well-defined morphological backdrop, to evaluate three of Taiwan's black flies, Simulium chungi Takaoka & Huang, S. pingtungense Huang & Takaoka, and S. sakishimaense Takaoka. Molecular data revealed high similarity of populations of S. sakishimaense in Taiwan and at the type locality on Ishigaki Island, Japan, about 180 km to the east. Thus, populations referred to as S. sakishimaense in Taiwan are conspecific with typical S. sakishimaense in Japan, confirming their non-endemicity in Taiwan. Simulium sakishimaense might have reached Ishigaki by island hopping via Taiwan from the Chinese mainland. Chromosomes and the COI gene agree with morphology that S. sakishimaense is a member of the S. multistriatum species group although the chromosomal banding patterns do not indicate that it is distinct from S. fenestratum Edwards on the mainland. Although molecular sequences indicate S. sakishimaense is monophyletic, this taxon falls within the same Operational Taxonomic Unit as nine other members of the S. multistriatum group, including S. fenestratum. Simulium pingtungense, in agreement with morphology, is molecularly distinct from the 10 other analyzed members of the S. striatum species group, tentatively suggesting that it is endemic to Taiwan, pending analysis of samples from mainland China. Simulium chungi in Taiwan is chromosomally and molecularly unique, with larvae resembling those of S. saskishimaense. It is not, however, a member of either the S. multistriatum or S. striatum species groups. For now, the S. chungi species group remains a legitimate taxon consisting of two species. Strengthening the case for endemic taxa in Taiwan awaits analysis of key samples from the Chinese mainland.

The evolution of tenascins.

BACKGROUND: The evolution of extracellular matrix is tightly linked to the evolution of organogenesis in metazoans. Tenascins are extracellular matrix glycoproteins of chordates that participate in integrin-signaling and morphogenetic events. Single tenascins are encoded by invertebrate chordates, and multiple tenascin paralogs are found in vertebrates (designated tenascin-C, tenascin-R, tenascin-W and tenascin-X) yet, overall, the evolution of this family has remained unclear. RESULTS: This study examines the genomes of hemichordates, cephalochordates, tunicates, agnathans, cartilaginous fishes, lobe-finned fishes, ray-finned fishes and representative tetrapods to identify predicted tenascin proteins. We comprehensively assess their evolutionary relationships by sequence conservation, molecular phylogeny and examination of conservation of synteny of the encoding genes. The resulting new evolutionary model posits the origin of tenascin in an ancestral chordate, with tenascin-C-like and tenascin-R-like paralogs emerging after a whole genome duplication event in an ancestral vertebrate. Tenascin-X appeared following a second round of whole genome duplication in an ancestral gnathostome, most likely from duplication of the gene encoding the tenascin-R homolog. The fourth gene, encoding tenascin-W (also known as tenascin-N), apparently arose from a local duplication of tenascin-R. CONCLUSIONS: The diversity of tenascin paralogs observed in agnathans and gnathostomes has evolved through selective retention of novel genes that arose from a combination of whole genome and local duplication events. The evolutionary appearance of specific tenascin paralogs coincides with the appearance of vertebrate-specific cell and tissue types where the paralogs are abundantly expressed, such as the endocranium and facial skeleton (tenascin-C), an expanded central nervous system (tenascin-R), and bone (tenascin-W).

The assembly and comparative analysis of the first complete mitogenome of Lindera aggregata.

Lindera aggregata, a member belongs to the genus Lindera of Lauraceae family. Its roots and leaves have been used as traditional Chinese medicine or functional food for thousands of years. However, its mitochondrial genome has not been explored. Our aim is to sequence and assemble the mitogenome of L. aggregata to elucidate the genetic mechanism and evolutionary pathway. The results had shown that the mitogenome was extremely complex and had a unique multi-branched conformation with total size of 912,473 bp. Comprehensive analysis of protein coding genes of 7 related species showed that there were 40 common genes in their mitogenome. Interestingly, positive selection had become an important factor in the evolution of ccmB, ccmFC, rps10, rps11 and rps7 genes. Furthermore, our data highlighted the repeated trend of homologous fragment migrations between chloroplast and mitochondrial organelles, and 38 homologous fragments were identified. Phylogenetic analysis identified a tree that was basically consistent with the phylogeny of Laurales species described in the APG IV system. To sum up, this study will be helpful to the study of population genetics and evolution of Lindera species.

The complete mitochondrial genome and phylogenetic analysis of Rattus tanezumi (Niethammer, 1975), captured from North China.

Rattus tanezumi (Niethammer, 1975) is one of the commensal rodent species in South China. With the development of transportation and climate change, R. tanezumi has gradually migrated north and become the dominant rat species for the past few years. In this study, we assembled a complete mitochondrial genome of R. tanezumi, captured from North China. The mitogenome contains 16,307 nucleotide pairs, including 13 protein-coding genes, 2 ribosomal RNA genes, and 22 transfer RNA genes, as well as one non-coding control region. Based on whole mitogenome phylogenetical analysis showed that R. tanezumi captured from North China had a close phylogenetic relationship with that from Japan and South Korea. These findings are valuable for further studies on the evolution, genetic diversity, and taxonomy of Asian commensal rodent.

The complete chloroplast genome sequence of Lilium saccatum S. Yun Liang (Liliaceae, Lilieae) and its phylogenetic analysis.

Lilium saccatum is a species of ornamental plant found in southeastern Xizang, China. In the present study, the complete chloroplast (cp) genome of L. saccatum was sequenced using next-generation sequencing (NGS). The de novo assembled cp genome was 151,839 bp in length, including a pair of inverted repeat regions (IRs; 26,421 bp), a small single-copy region (SSC; 17,528 bp), and a large single-copy region (LSC; 81,469 bp). The cp genome encodes 113 unique genes, including 79 protein-coding genes (PCGs), 30 tRNA genes, and four rRNA genes. The total GC content of the cp genome was 37.0%. Phylogenetic analysis of 24 cp genomes revealed that L. saccatum was closely related to L. souliei. This study could provide fundamental information for the phylogenomics and utilization of Lilium.

The complete mitochondrial genome data of Argania spinosa (L.) Skeels.

Argania spinosa (L.) Skeels, an endemic Moroccan plant species from the Sapotaceae family, holds significant ecological, pharmaceutical, and socioeconomic value in the arid mid-western region. However, it is facing rapid degradation. Therefore, understanding its genetic diversity is critical for preserving this national heritage. We sequenced, assembled, and annotated the mitochondrial genome of A. spinosa and compared it to other plants in the Ericales order. Mitochondrial-like sequences from the A. spinosa genome were assembled using GetOrganelle, resulting in a 707,441 base pair mitochondrial genome with 45.75 % GC content. Annotation identified 32 protein-coding genes, 16 transfer RNAs, and 2 ribosomal RNA genes. Phylogenetic analysis of 15 Ericales species affirms that A. spinosa is closely related to the Theaceae family, which is in accordance with results from the chloroplast genome.

New insights into the phylogeny of Carasobarbus Karaman, 1971 (Actinopterygii, Cyprinidae) with the description of three new species.

Fishes from the genus Carasobarbus, widely distributed throughout the river systems of North Africa and West Asia, are commonly referred to as Himris. In the Persian Gulf basin, they are widespread and are also found in fast-flowing rivers or the deeper regions of lakes. In this region, representation of these fishes in scientific collections is scarce, and except for C. luteus, the other species are very poorly documented and frequently misidentified due to their similarities. In this study we analysed the relationships among Carasobarbus species using mitochondrial genes (Cyt b, COI) and present morphological characters based on examinations. Our results revealed three new species which we describe here. Carasobarbus doadrioi, new species, is distinguished by 40-44 scales on the lateral line and a prominent black blotch on end of caudal peduncle in specimens < 85 mm SL. Carasobarbus hajhosseini, new species is distinguished by 32-34 scales on the lateral line and long head length (20-24% SL). Carasobarbus saadatii, new species, is distinguished by 38-40 scales on the lateral line and short head length (19-20% HL). In the Persian Gulf basin, Carasobarbus species exhibit uncorrected genetic distances of 1.6 to 5.5% in the COI barcode region and 2.6% to 9.9% in the Cyt b gene. This study highlights the importance of investigating the unexplored diversity that exists within poorly sampled and understudied freshwater fish group. Such investigations are essential for developing a comprehensive understanding of the true extent of biodiversity, which is critical for informing effective conservation and protection strategies.

Structural and Evolutionary Analysis of Proteins Endowed with a Nucleotidyltransferase, or Non-canonical Palm, Catalytic Domain.

Many polymerases and other proteins are endowed with a catalytic domain belonging to the nucleotidyltransferase fold, which has also been deemed the non-canonical palm domain, in which three conserved acidic residues coordinate two divalent metal ions. Tertiary structure-based evolutionary analyses provide valuable information when the phylogenetic signal contained in the primary structure is blurry or has been lost, as is the case with these proteins. Pairwise structural comparisons of proteins with a nucleotidyltransferase fold were performed in the PDBefold web server: the RMSD, the number of superimposed residues, and the Qscore were obtained. The structural alignment score (RMSD × 100/number of superimposed residues) and the 1-Qscore were calculated, and distance matrices were constructed, from which a dendogram and a phylogenetic network were drawn for each score. The dendograms and the phylogenetic networks display well-defined clades, reflecting high levels of structural conservation within each clade, not mirrored by primary sequence. The conserved structural core between all these proteins consists of the catalytic nucleotidyltransferase fold, which is surrounded by different functional domains. Hence, many of the clades include proteins that bind different substrates or partake in non-related functions. Enzymes endowed with a nucleotidyltransferase fold are present in all domains of life, and participate in essential cellular and viral functions, which suggests that this domain is very ancient. Despite the loss of evolutionary traces in their primary structure, tertiary structure-based analyses allow us to delve into the evolution and functional diversification of the NT fold.

An unusual Cretaceous beetle with affinity to Anamorphidae (Coleoptera: Coccinelloidea).

Coccinelloid beetles have a sparse fossil record in the Mesozoic. Here, we describe and illustrate an unusual coccinelloid beetle, Yassibum yoshitomii gen. et sp. nov., from mid-Cretaceous Kachin amber. Yassibum stands out within the Coccinelloidea due to its notched profemora and the presence of antennal grooves on the elytral epipleura. Based on our phylogenetic analyses, we suggest that Yassibum is most likely related to the family Anamorphidae. The alternative placements are critically evaluated based on our comparison of the morphology.

Unraveling the mystery of a myxozoan parasite of the trout: redescription of Chloromyxum schurovi.

Myxozoans are microscopical parasites widely distributed in fish, with over 2,600 described species, but their actual diversity is still underestimated. Among salmonids, more than 70 myxozoan species have been identified. This study focuses on species of Chloromyxum Mingazzini, 1890 that infect salmonid kidneys, particularly C. majori Yasutake et Wood, 1957 and C. schurovi Shulman et Ieshko, 2003. Despite their similar spore morphology, they exhibit distinct host preferences, tissue affinities and geographical distributions. Chloromyxum schurovi predominantly infects the renal tubules of Salmo salar Linnaues and S. trutta Linnaeus in Europe, while C. majori targets the glomeruli of Oncorhynchus mykiss (Walbaum) and O. tshawytscha (Walbaum) in North America. The sequence data for C. majori and C. schurovi have been either missing or questionable. In our study, we examined the kidneys of two salmonid species for chloromyxid infections, using both morphological and molecular data to characterise Chloromyxum species in salmonids. The sequence of C. schurovi obtained in our study did not match the previously published parasite data. Instead, it clustered as an independent lineage sister to the Paramyxidium Freeman et Kristmundsson, 2018 clade gathering the species from various fish organs, including the urinary tract. Our findings clarified the taxonomic origin of the previous C. schurovi sequence as Myxidium giardi Cépède, 1906, highlighting the risks associated with the presence of myxozoan blood stages in the bloodstream of their fish host and the challenges of non-specific PCR amplification. We redescribe C. schurovi, thus contributing to a better understanding of the diversity and phylogeny of kidney-infecting species of Chloromyxum.