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".

Elongatibacter sediminis gen. nov., sp. nov., isolated from intertidal sediment, and genomic comparison with all genera in the family Wenzhouxiangellaceae.

A novel slightly halophilic, aerobic, and Gram-stain-negative strain, designated as CH-27T, was isolated during a bacterial resource investigation of intertidal sediment collected from Xiaoshi Island in Weihai, PR China. Cells of strain CH-27T were rod-shaped with widths of 0.3-0.6 µm and lengths of 2.0-11.0 µm. Strain CH-27T grew optimally at 37 °C, pH 7.0 and with 2.0 % (w/v) NaCl. Catalase activity was weakly positive and oxidase activity was positive. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain CH-27T was most related to Marinihelvus fidelis KCTC 92639T (93.6 %), followed by Wenzhouxiangella marina MCCC 1K00261T (92.0 %). Based on genome comparisons between strain CH-27T and M. fidelis KCTC 92639T, the average amino acid identity was 63.6 % and the percentage of conserved proteins was 48.3 %. The major cellular fatty acid of strain CH-27T (≥10 %) was iso-C15 : 0 and the sole respiratory quinone was quinone-8. The polar lipids were phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, and aminophospholipid. The DNA G+C content was 62.7 mol%. Based on comprehensive analysis of its phylogenetic, physiological, biochemical, and chemotaxonomic characteristics, strain CH-27T represents a novel species in a novel genus, for which the name Elongatibacter sediminis gen. nov., sp.nov. is proposed. The type strain is CH-27T (=MCCC 1H00480T=KCTC 8011T).

Three novel woody litter inhabiting fungi in Didymosphaeriaceae, Phaeoseptaceae and Synnemasporellaceae from Zhujiangyuan Nature Reserve, Yunnan Province, P.R. China.

Zhujiangyuan Nature Reserve, located in Qujing City, Yunnan Province, China, is reported with high fauna and floral diversity, while the fungal diversity of the region is poorly documented. During the summer season in 2023, decaying wood-inhabiting microfungi were collected from different microhabitats. The novel species were identified based on morphological characteristics and phylogenetic analyses (based on combined datasets of ITS, LSU, SSU, tef1-α, and rpb2 regions). Two species belong to Dothideomycetes (viz., Spegazziniazhujiangyuanensis sp. nov. and Phaeoseptumzhujiangyuanense sp. nov. in Pleosporales) while the other one resides in Sordariomycetes (Synnemasporellafanii sp. nov. in Diaporthales). The results are in conformity with the earlier studies that predicted higher fungal diversity in this region.

Multi-gene phylogenetic analyses revealed two novel species and one new record of Trichobotrys (Pleosporales, Dictyosporiaceae) from China.

The rotting wood in freshwater is a unique eco-environment favoring various fungi. During our investigation of freshwater fungi on decaying wood, three hyphomycetes were collected from Jiangxi and Guangxi Provinces, China. Based on the morphological observations and phylogenetic analysis of a combined DNA data containing ITS, LSU, SSU and tef1-α sequences, two new Trichobotrys species, T.meilingensis and T.yunjushanensis, as well as a new record of T.effusa, were introduced. Additionally, a comprehensive description of the genus with both morphological and molecular data was first provided.

Thioclava litoralis sp. nov., a novel species of alphaproteobacterium, isolated from surface seawater.

A Gram-negative, aerobic, rod-shaped, non-motile bacterium, designated as FTW29T, was isolated from surface seawater sampled in Futian district, Shenzhen, China. Growth of strain FTW29T was observed at 15-42 ℃ (optimum, 28-30 ℃), pH 4.0-9.0 (optimum, pH 5.5-7.5) and in the presence of 0.5-10% NaCl (optimum, 3.0% NaCl). Strain FTW29T showed 95.0-96.8% 16 S rRNA gene sequence similarity to various type strains of the genera Thioclava, Sinirhodobacter, Rhodobacter, Haematobacter and Frigidibacter of the family Paracoccaceae, and its most closely related strains were Thioclava pacifica DSM 10,166T (96.8%) and Thioclava marina 11.10-0-13T (96.7%). The phylogenomic tree constructed on the bac120 gene set showed that strain FTW29T formed a clade with the genus Thioclava, with a bootstrap value of 100%. The evolutionary distance values between FTW29T and type strains of the genus Thioclava were 0.17-0.19, which are below the recommended standard (0.21-0.23) for defining a novel genus in the family Paracoccaceae. In strain FTW29T, the major fatty acids identified were summed feature 8 (C18:1ω7c) and C16:0, and the predominant respiratory quinones were ubiquinone-10 and ubiquinone-9. The composition of polar lipids in strain FTW29T included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, an unidentified phospholipid, an unidentified aminolipid, two unidentified glycolipids and an unidentified lipid. The genome of strain FTW29T comprised one circle chromosome and six plasmids, with a G + C content of 61.4%. The average nucleotide identity, average amino acid identity, and digital DNA-DNA hybridization values between strain FTW29T and seven type strains of the genus Thioclava were 76.6-78.4%, 53.2-56.4% and 19.3-20.4%, respectively. Altogether, the phenotypic, phylogenetic and chemotaxonomic evidence illustrated in this study suggested that strain FTW29T represents a novel species of the genus Thioclava, with the proposed name Thioclava litoralis sp. nov. The type strain is FTW29T (= KCTC 82,841T = MCCC 1K08523T).

Novel powdery mildew of cotton (Gossypium hirsutum) caused by Phyllactinia gossypina sp. nov. in Brazil.

Cotton (Gossypium hirsutum, Malvaceae) is the most important fiber crop in the world. There are published records of many fungal pathogens attacking Gossypium spp., causing numerous diseases, including powdery mildews. Recently, in 2022, non-cultivated spontaneous G. hirsutum plants bearing powdery mildews symptoms were found at roadsides in two municipalities of the state of Minas Gerais (Brazil): Varginha and Ubá. Such localities are situated ca. 260 km apart, suggesting a broader distribution of this fungus-host association in Brazil. Samples were taken to the laboratory, and an Ovulariopsis-like, asexual stage of Phyllactinia, was identified forming amphigenous colonies, that were more evident, white and cottony, abaxially. Morphological and molecular data- of the ITS and LSU regions- have shown that colonies from those two samples were of the same fungus species, belonging to a previously unknown species of Erysiphaceae (Ascomycota). The fungus fits into the Phyllactinia clade and is described herein as the new species Phyllactinia gossypina sp. nov. This new species belongs to the 'basal Phyllactinia group', a lineage that includes species known only from the Americas. This report expands the list of pathogenic fungi on cotton. It is early to anticipate whether this new powdery mildew represents a threat to cultivated cotton, which is a major crop in Brazil. Nevertheless, further studies about its infectivity to commercial cotton varieties are recommended, since all known Erysiphaceae are specialized obligate plant parasites and several species cause major losses to important crops.

Wing mechanics and acoustic communication of a new genus of sylvan katydid (Orthoptera: Tettigoniidae: Pseudophyllinae) from the Central Cordillera cloud forest of Colombia.

Stridulation is used by male katydids to produce sound via the rubbing together of their specialised forewings, either by sustained or interrupted sweeps of the file producing different tones and call structures. There are many species of Orthoptera that remain undescribed and their acoustic signals are unknown. This study aims to measure and quantify the mechanics of wing vibration, sound production and acoustic properties of the hearing system in a new genus of Pseudophyllinae with taxonomic descriptions of two new species. The calling behaviour and wing mechanics of males were measured using micro-scanning laser Doppler vibrometry, microscopy, and ultrasound sensitive equipment. The resonant properties of the acoustic pinnae of the ears were obtained via µ-CT scanning and 3D printed experimentation, and numerical modelling was used to validate the results. Analysis of sound recordings and wing vibrations revealed that the stridulatory areas of the right tegmen exhibit relatively narrow frequency responses and produce narrowband calls between 12 and 20 kHz. As in most Pseudophyllinae, only the right mirror is activated for sound production. The acoustic pinnae of all species were found to provide a broadband increased acoustic gain from ~40-120 kHz by up to 25 dB, peaking at almost 90 kHz which coincides with the echolocation frequency of sympatric bats. The new genus, named Satizabalus n. gen., is here derived as a new polytypic genus from the existing genus Gnathoclita, based on morphological and acoustic evidence from one described (S. sodalis n. comb.) and two new species (S. jorgevargasi n. sp. and S. hauca n. sp.). Unlike most Tettigoniidae, Satizabalus exhibits a particular form of sexual dimorphism whereby the heads and mandibles of the males are greatly enlarged compared to the females. We suggest that Satizabalus is related to the genus Trichotettix, also found in cloud forests in Colombia, and not to Gnathoclita.

A new Mexican species of the Cryptopygus complex (Collembola, Isotomidae) associated with the hermit crab Coenobitaclypeatus (Crustacea, Coenobitidae).

A new species of Cryptopygus Willem, 1901 associated with hermit crabs living on seashores of Quintana Roo State, Mexico, is described and illustrated. It is blind, with 9-11 postlabial setae, unguis with a pair of lateral teeth, empodial appendix lanceolate and almost as long as unguis, tenaculum with 4 + 4 teeth and 3-4 setae on corpus, manubrium with 11-14 pairs of manubrial setae on anterior surface and 17-18 pairs on posterior surface, and mucro bidentate. An updated key for the identification of 29 American species of Cryptopygus complex is included.

Ooceraeahainingensis sp. nov.: A new Chinese Ooceraea (Hymenoptera, Formicidae, Dorylinae) species with a dealate queen, closely allied to the queenless clonal raider ant O.biroi.

The clonal raider ant, Ooceraeabiroi, is a queenless species that reproduces asexually, and these traits make it an attractive model system for laboratory research. However, it is unclear where on the ant phylogeny these traits evolved, partly because few closely related species have been described and studied. Here, we describe a new raider ant species, Ooceraeahainingensis sp. nov., from Zhejiang, China. This species is closely related to O.biroi but can be distinguished by the following features: 1) workers of O.hainingensis sp. nov. have an obvious promesonotal suture and a metanotal groove, whereas these characters are ambiguous in O.biroi; and 2) the subpetiolar process of O.hainingensis is prominent and anteroventrally directed like a thumb with sublinear posteroventral margin, while in O.biroi, it is anteroventrally directed but slightly backward-bent. Molecular phylogenetic analyses confirm that O.hainingensis is genetically distinct from O.biroi. Importantly, unlike O.biroi, O.hainingensis has a queen caste with wings and well-developed eyes. This suggests that the loss of the queen caste and transition to asexual reproduction by workers is specific to O.biroi and occurred after that species diverged from closely related congeneric species.

Revision of Trigastrotheca Cameron (Hymenoptera, Braconidae, Braconinae) with descriptions of 13 new species.

The Old World braconine wasp genus Trigastrotheca Cameron is revised. The genus is recorded from the island of Madagascar for the first time based on two new species, T.christianhenrichi Quicke & Butcher, sp. nov. and T.formosa Quicke & Friedman, sp. nov. Trigastrothecagriffini Quicke, sp. nov. is described from Australia; T.aethiopica Quicke & Friedman, sp. nov. is described from Ethiopia; T.braeti Quicke & Butcher, sp. nov. is described from Congo; T.simba van Noort, sp. nov. is described from Tanzania; T.freidbergi Quicke & Friedman, sp. nov., T.carinata Ranjith, sp. nov., T.flava Ranjith, sp. nov. and T.similidentata Ranjith, sp. nov. are described from India; T.khaoyaiensis Quicke & Butcher, sp. nov., T.naniensis Quicke & Butcher, sp. nov., and T.sublobata Quicke & Butcher, sp. nov. are described from Thailand. Trigastrothecatridentata is recorded from Thailand for the first time. A putative female of T.sureeratae is described for the first time. Acroceriliatricolor Quicke & Ingram, 1993 is transferred into Trigastrotheca, as T.acroceropsis nom. nov. A key is provided for the identification of species.

Diversity of Orbiniella (Orbiniidae, Annelida) in the North Atlantic and the Arctic.

In this work, the diversity of the genus Orbiniella in the Nordic Seas and the North Atlantic waters south of Iceland is studied based on the analyses of molecular markers (mitochondrial COI, 16S rDNA and nuclear ITS2) and morphological characters. Our results showed the presence of at least five genetic lineages in the studied material which could also be morphologically identified by their segmental annulation patterns, the number and the shape of acicular spines, and the length and the shape of pygidial lobes. The species name Orbiniellapetersenae is assigned to one of the lineages restricting its geographical and vertical distribution to the deep-sea areas north of Iceland and Jan Mayen, and three lineages are described as new species (i.e., Orbiniellagriegi Meca & Budaeva, sp. nov., Orbiniellamayhemi Meca & Budaeva, sp. nov., and Orbiniellaparapari Meca & Budaeva, sp. nov.) elevating the number of known species in the genus to 25. Three deep-sea species of Orbiniella in our study are reported only north of the Greenland-Iceland-Scotland Ridge, one deep-sea species found south of the ridge. A single shallow-water species is distributed along the ridge and on the Norwegian shelf.

Lappulaeffusa (Boraginaceae), a new species from Xinjiang, China.

Lappulaeffusa D.H.Liu & W.J.Li, a new species of Boraginaceae from Xinjiang, China, is described and illustrated in this study. The new species is morphologically similar to Lappulahimalayensis and L.tadshikorum. However, it can be distinguished from the compared species by several characteristics, such as: stem single, erect, frequently branched at middle and above, densely spreading hispid, hairs discoid at base; corolla white or blue; fruit compressed, heteromorphic nutlets with two rows of marginal glochids, nutlets acute ovoid, disc narrowly ovate-triangular. The diagnosis of the new species is supported with comprehensive investigation including photographs, detailed description, notes on etymology, distribution and habitat, conservation status, as well as comparisons with morphologically similar species.

Revisiting the infrageneric classification of Garcinia L. (Clusiaceae): an updated sectional name and new, legitimate names in Garcinia for Allanblackiagabonensis (Pellegr.) Bamps and A.parviflora A.Chev.

In a recent publication dealing with the sectional-level taxonomy of Garcinia, an illegitimate superfluous sectional name and two illegitimate homonyms were published. Herein we choose a legitimate sectional name, GarciniasectionRheediopsis Pierre, for the superfluous name GarciniasectionRheedia (L.) S.W.Jones ex P.W.Sweeney; and create two new legitimate names in Garcinia for Allanblackiagabonensis (Pellegr.) Bamps and A.parviflora A.Chev.

To what extent are ephippia of Mexican Anomopoda (Crustacea, Cladocera) identifiable?

Diapausing embryos encased within cladoceran ephippia result from sexual reproduction and increase genetic diversity. They are also important means by which species bypass harsh environmental conditions and disperse in space and time. Once released, ephippia usually sink to the benthos and remain there until hatching. Using the Sars' method (incubating sediments to identify cladoceran hatchlings), ephippial egg bank biodiversity can be evaluated. Yet, even when samples are incubated under a variety of conditions, it is not possible to warrant that all have hatched. Few keys are available that facilitate the identification of cladocerans by using only ephippial morphology. Our goal was to analyze some cladoceran ephippia from Mexico, to develop a means to identify them using easily recognizable characteristics. Ephippia of 23 cladoceran species from waters in Aguascalientes (México) in 11 genera (Alona, Biapertura, Ceriodaphnia, Chydorus, Daphnia, Dunhevedia, Ilyocryptus, Macrothrix, Moina, Pleuroxus, and Simocephalus) were analyzed. In our analysis six morphological features were selected that permitted the identification of ephippia to species(-group) level. The results demonstrate that with a proper catalog of features, some ephippia can be identified.

An updated review of the genus Toxorhina Loew, 1850 (Diptera, Limoniidae) from Yunnan, China with a description of a new species.

Seven species of the genus Toxorhina Loew, 1850 have been recorded from China, of which three are known to occur in Yunnan Province. Herein, all known species from Yunnan, China are reviewed with more detailed descriptions and illustrations of the male hypopygium. A species of Toxorhina belonging to the subgenus Ceratocheilus Wesché, 1910 from Yunnan, T. (C.) pianmicasp. nov., is described and illustrated as new to science.

Paragoniastreavariabilis Kishi, Nomura & Fukami, sp. nov. (Cnidaria, Anthozoa, Scleractinia), a new coral species previously considered as a variant of Paragoniastreadeformis, from Japan and northern Taiwan.

A new zooxanthellate scleractinian coral, Paragoniastreavariabilis Kishi, Nomura & Fukami, sp. nov. (Scleractinia, Merulinidae), is described from non-coral reef regions of Japan and northern Taiwan. This new species was previously recognized as a morphological variant of Paragoniastreadeformis (Veron, 1990) and can be morphologically distinguished from that species by lacking groove-and-tube structures on corallite wall joints, and by having larger calices, numerous septa, and up to three corallites in one valley. The new species also formed an independent clade from its congeners, P.australensis (Milne Edwards & Haime, 1857), P.deformis and P.russelli (Wells, 1954), in the molecular phylogeny based on the mitochondrial intergenic region and nuclear ribosomal internal transcribed spacers.

ICTV Virus Taxonomy Profile: Phasmaviridae 2024.

Phasmaviridae is a family for negative-sense RNA viruses with genomes of about 9.7-15.8 kb. These viruses are maintained in and/or transmitted by insects. Phasmavirids produce enveloped virions containing three single-stranded RNA segments that encode a nucleoprotein (N), a glycoprotein precursor (GPC), and a large (L) protein containing an RNA-directed RNA polymerase (RdRP) domain. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family Phasmaviridae, which is available at ictv.global/report/phasmaviridae.

ICTV Virus Taxonomy Profile: Turriviridae 2024.

The family Turriviridae includes viruses with a dsDNA genome of 16-17 kbp. Virions are spherical with a diameter of approximately 75 nm and comprise a host-derived internal lipid membrane surrounded by a proteinaceous capsid shell. Members of the family Turriviridae infect extremophilic archaea of the genera Sulfolobus and Saccharolobus. Viral infection results in cell lysis for Sulfolobus turreted icosahedral virus 1 infection but other members of the family can be temperate. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family Turriviridae, which is available at ictv.global/report/turriviridae.

Pinibarreniales, a new order of Sordariomycetes from pine barrens ecosystem.

Pinibarrenia chlamydospora, sp. nov. isolated from the roots of highbush blueberry in the New Jersey Pine Barrens, is described and illustrated. Based on multigene phylogenetic analysis, as well as morphological and ecological characteristics, Pinibarreniales and Pinibarreniaceae are established to accommodate this novel lineage in Sordariomycetidae, Sordariomycetes. Pinibarreniales, Tracyllalales, and Vermiculariopsiellales are proposed to be included in the subclass Sordariomycetidae. Pinibarreniales likely have a wide distribution and forms association with Ericaceae plants that live in acidic and oligotrophic environments because its DNA barcode matches with environmental sequences from other independent ecological studies. The plant-fungal interaction experiment revealed negative impacts on Arabidopsis, indicating its pathogenicity. This uncovered new fungal lineage will contribute to a better understanding of the diversity and systematics of Sordariomycetes.

Metabarcoding expands knowledge on diversity and ecology of rare actinobacteria in the Brazilian Cerrado.

Rare and unknown actinobacteria from unexplored environments have the potential to produce new bioactive molecules. This study aimed to use 16 s rRNA metabarcoding to determine the composition of the actinobacterial community, particularly focusing on rare and undescribed species, in a nature reserve within the Brazilian Cerrado called Sete Cidades National Park. Since this is an inaccessible area without due legal authorization, it is understudied, and, therefore, its diversity and biotechnological potential are not yet fully understood, and it may harbor species with groundbreaking genetic potential. In total, 543 operational taxonomic units (OTUs) across 14 phyla were detected, with Actinobacteria (41.2%), Proteobacteria (26.5%), and Acidobacteria (14.3%) being the most abundant. Within Actinobacteria, 107 OTUs were found, primarily from the families Mycobacteriaceae, Pseudonocardiaceae, and Streptomycetaceae. Mycobacterium and Streptomyces were the predominant genera across all samples. Seventeen rare OTUs with relative abundance < 0.1% were identified, with 82.3% found in only one sample yet 25.5% detected in all units. Notable rare and transient genera included Salinibacterium, Nocardia, Actinomycetospora_01, Saccharopolyspora, Sporichthya, and Nonomuraea. The high diversity and distribution of Actinobacteria OTUs indicate the area's potential for discovering new rare species. Intensified prospection on underexplored environments and characterization of their actinobacterial diversity could lead to the discovery of new species capable of generating innovative natural products.