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Thermophilic cyanobacteria thrive in extreme environments, making their thermoresistant enzymes valuable for industrial applications. Common habitats include hot springs, which act as evolutionary accelerators for speciation due to geographical isolation. The family Thermosynechococcaceae comprises thermophilic cyanobacteria known for their ability to thrive in high-temperature environments. These bacteria are notable for their photosynthetic capabilities, significantly contributing to primary production in extreme habitats. Members of Thermosynechococcaceae exhibit unique adaptations that allow them to perform photosynthesis efficiently at elevated temperatures, making them subjects of interest for studies on microbial ecology, evolution, and potential biotechnological applications. In this study, the genome of a thermophilic cyanobacterium, isolated from a hot spring near Okahandja in Namibia, was sequenced using a PacBio Sequel IIe long-read platform. Cultivations were performed at elevated temperatures of 40, 50, and 55°C, followed by proteome analyses based on the annotated genome. Phylogenetic investigations, informed by the 16S rRNA gene and aligned nucleotide identity (ANI), suggest that the novel cyanobacterium is a member of the family Thermosynechococcaceae. Furthermore, the new species was assigned to a separate branch, potentially representing a novel genus. Whole-genome alignments supported this finding, revealing few conserved regions and multiple genetic rearrangement events. Additionally, 129 proteins were identified as differentially expressed in a temperature-dependent manner. The results of this study broaden our understanding of cyanobacterial adaptation to extreme environments, providing a novel high-quality genome of Thermosynechococcaceae cyanobacterium sp. Okahandja and several promising candidate proteins for expression and characterization studies., (© 2024 The Author(s). MicrobiologyOpen published by John Wiley & Sons Ltd.)

Five Gram-stain-positive strains (M1-10 T , M1-13, M1-21 T , M2-14 T and S1-1 T ) were isolated from paper mulberry ( Broussonetia papyrifera ) in Taiwan. Cells were rod-shaped, non-motile, non-haemolytic, asporogenous, facultatively anaerobic, heterofermentative, and did not exhibit catalase and oxidase activities. Phylogenetic analysis of the 16S rRNA gene sequences revealed that these novel strains belonged to the genus Fructobacillus . On the basis of 16S rRNA gene sequence similarities, the type strains of Fructobacillus fructosus and Fructobacillus durionis were the closest neighbours to strains M1-10 T , M1-13, M1-21 T , M2-14 T and S1-1 T . Sequence analyses of concatenated two partial housekeeping genes, the RNA polymerase beta subunit ( rpoC ) and recombinase A ( recA ) also indicated that the novel strains belonged to the genus Fructobacillus . The 16S rRNA and concatenated rpoC and recA gene sequence similarities between strains M1-10 T and M1-13 were 100 %, respectively. The average nucleotide identity values of M1-10 T , M1-21 T , M2-14 T and S1-1 T with F. fructosus and F. durionis were 75.1-78.9% and 76.5-77.5 %, respectively. The digital DNA-DNA hybridization values were 19.7-21.5% and 19.6-20.4 %, respectively. Phenotypic and genotypic test results demonstrated that these strains represent four novel species of the genus Fructobacillus , for which the names Fructobacillus papyriferae sp. nov., Fructobacillus papyrifericola sp. nov., Fructobacillus broussonetiae sp. nov. and Fructobacillus parabroussonetiae sp. nov. are proposed with the type strains M1-10 T (=BCRC 81237 T =NBRC 114433 T ), M1-21 T (=BCRC 81239 T =NBRC 114435 T ), M2-14 T (=BCRC 81240 T =NBRC 114436 T ) and S1-1 T (=BCRC 81241 T =NBRC 114437 T ), respectively.

A novel, aerobic nitrogen-fixing methylotrophic bacterium, strain 29k T , was enriched and isolated from sludge generated during wastewater treatment at a paper mill in Baikal, Russian Federation. Cells were Gram-stain-variable. The cell wall was of the negative Gram-type. Cells were curved oval rod-shaped, 0.5-0.7×1.7-3.4 µm and formed yellow-coloured colonies. Cells tended to be pleomorphic if grown on media containing succinate or coccoid if grown in the presence of methyl alcohol as the sole carbon source. Cells were non-motile, non-spore-forming and contained retractile (polyphosphate) and lipid (poly-β-hydroxybutyrate) bodies. The major respiratory quinone was ubiquinone Q-10 and the predominant cellular fatty acids were C 18:1 ω7, C 19:0 cyclo and C 16:0 . The genomic DNA G+C content was 67.95 mol%. Strain 29k T was able to grow at 4-37 °C (optimum, 30 °C), at pH 6.0-8.5 (optimum, pH 6.5-7.0) and at salinities of 0-0.5% (w/v) NaCl (optimum, 0% NaCl). Catalase and oxidase were positive. Strain 29k T could grow chemolithoautotrophically in mineral media under an atmosphere of H 2 , O 2 and CO 2 as well as chemoorganoheterotrophically on methanol, ethanol, n-propanol, n-butanol and various organic acids. The carbohydrate utilization spectrum is limited by glucose and raffinose. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the newly isolated strain was a member of the genus Xanthobacter with Xanthobacter autotrophicus 7c T (99.9% similarity) and Xanthobacter viscosus 7d T (99.4 % similarity) as closest relatives among species with validly published names. The average nucleotide identity and digital DNA-DNA hybridization values of 92.7 and 44.9%, respectively, of the 29k T to the genome of the most closely related species, X. autotrophicus 7c T , were below the species cutoffs. Based on genotypic, phenotypic and chemotaxonomic characteristics, it is proposed that the isolate represents a novel species, Xanthobacter oligotrophicus sp. nov. The type strain is 29k T (=KCTC 72777 T =VKM B-3453 T ).

A novel cytorhabdovirus, tentatively named "paper mulberry mosaic-associated virus" (PMuMaV), was discovered and identified by transcriptome sequencing (RNA-seq), small RNA sequencing (sRNA-seq), and RT-PCR amplification. The whole-genome sequence of PMuMaV is 13,736 nucleotides (nt) in length and contains six open reading frames (ORFs) encoding a nucleocapsid protein (N), a phosphoprotein (P), a putative movement protein (P3), a matrix protein (M), a glycoprotein (G), and an RNA-dependent RNA polymerase (L). The coding sequences are flanked by a 194-nt leader and a 370-nt trailer sequence at the 3' terminus and 5' terminus, respectively. Pairwise sequence comparisons showed that PMuMaV is related to northern cereal mosaic virus (NCMV, 38.97%), barley yellow striate mosaic virus (BYSMV, 38.86%), and maize yellow striate virus (MYSV, 38.76%), and phylogenetic analysis also placed these viruses together into the same branch, thus suggesting that PMuMaV is a member of a new species in the genus Cytorhabdovirus.

A bacterial strain, designated NS31-3(T), was isolated from the wastewater of a paper mill. Cells of the isolate were obligately anaerobic, non-pigmented, non-motile, Gram-negative, short rods (0.7-1.0 × 1.4-2.5 µm). The isolate was able to grow on media containing 20% bile salts. API 20A tests showed that acid was produced from glucose, lactose, sucrose, maltose, D-xylose, L-arabinose, cellobiose, D-mannose, D-melezitose, D-raffinose, D-trehalose, D-mannitol, salicin and D-sorbitol. The main fermentation products from PYG broth were lactic acid, propionic acid, formic acid and acetic acid. Chemotaxonomic analysis showed that the major fatty acids were anteiso-C(15:0), C(15:0) and iso-C(17:0) 3-OH and the predominant respiratory quinones were MK-9 and MK-10. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain NS31-3(T) was related to members of genus Parabacteroides (91.2-93.2% sequence similarity); the isolate had the closest affinity with Parabacteroides merdae JCM 9497(T). The G+C content of the genomic DNA was 37.2 mol%. On the basis of phenotypic, chemotaxonomic and phylogenetic analysis, strain NS31-3(T) represents a novel species of the genus Parabacteroides, for which the name Parabacteroides chartae sp. nov. is proposed. The type strain is NS31-3(T) (=JCM 17797(T) =DSM 24967(T)).

The WOX (WUSCHEL-related homeobox) is a plant-specific transcription factor involved in plant development and stress response. However, few studies have been reported on the WOX gene in woody plants. In this study, 10 BpWOX genes were isolated from paper mulberry by RACE-PCR and categorized into three clades through phylogenetic analysis, ancient, intermediate and WUS clade. Among them, five members had the transcriptional activity detected by yeast one-hybrid and seven were uniquely localized to the nucleus through green fluorescent protein (GFP) observation. The expression patterns of BpWOX genes in different tissues and under diverse treatments were quantified by the qRT-PCR method. Results showed that BpWUS was expressed in the apical bud, stem and root, BpWOX5 and BpWOX7 functioned only in the root tip, and three BpWOXs regulated leaf development redundantly. BpWOX9 and BpWOX10 were induced by indole-3-acetic acid (IAA) or jasmonic acid (JA), while BpWOX2 was repressed by five phytohormones. Interestingly, most BpWOX genes were responsive to the abiotic stress stimuli of drought, salt, cold, and cadmium (CdCl₂). Together, our study revealed that BpWOXs were functionally divergent during paper mulberry development and environmental adaptation, which might be related to their evolutionary relationships. Our work will benefit the systematic understanding of the precise function of WOX in plant development and environmental stress responses., Competing Interests: The authors declare no conflict of interest.

Trees are a canonical structure for representing evolutionary histories. Many popular criteria used to infer optimal trees are computationally hard, and the number of possible tree shapes grows super-exponentially in the number of taxa. The underlying structure of the spaces of trees yields rich insights that can improve the search for optimal trees, both in accuracy and in running time, and the analysis and visualization of results. We review the past work on analyzing and comparing trees by their shape as well as recent work that incorporates trees with weighted branch lengths.

The trematode family Cyathocotylidae infects various hosts worldwide, including birds, mammals, reptiles, and fish. However, the lack of molecular data from adult worms hinders phylogenetic, epidemiological, and host association studies. This study aims to identify the common cyathocotylid trematodes infecting African catfish in Egypt using morphological and molecular evidence. Out of 142 Clarias gariepinus, 123 fish (86.6%) harbored cyathocotylid metacercariae, with a mean metacercarial intensity of 201 ± 38.5/g. Cyathocotylid metacercariae prevalence gradually rose as host size increased. Although there was no significant difference between groups, larger fish had a higher mean metacercarial intensity. The prevalence and intensity were unrelated to the fish gender. Histopathological examination of metacercariae-infected catfish revealed varying degrees of degenerative changes, including intermuscular edema leading to muscle fiber dispersion and atrophy, involving 11% to over 81% of muscle sections. We identified three cyathocotylid metacercariae and eight cyathocotylid adult species from experimental infection using morphometric and molecular data, including internal transcribed spacer (ITS) and/or mitochondrial cytochrome c oxidase subunit 1 (cox1) sequences. We determined the phylogenetic position of these cyathocotylid samples. The ITS sequence analysis linked the isolated Cyathocotylidae sp. 1 and 2 metacercariae to Prohemistomum vivax adults. Mesostephanus appendiculatoides and Paracoenogonimus ovatus were reported for the first time in Egypt. These findings may provide valuable genetic data for future molecular epidemiological and phylogenetic studies of cyathocotylid trematodes., (© 2024. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

Premise: Cladoxylopsids, one of the first lineages with complex organization to rise from the plexus of structurally simple plants that comprised the earliest euphyllophyte floras, are moniliformopsid euphyllophytes. They formed Earth's earliest forests by the Middle Devonian and are thought to have given rise to the equisetopsids and probably some fern lineages. The Lower Devonian (Emsian) Battery Point Formation (Quebec, Canada) contains previously unrecognized cladoxylopsids preserved anatomically. One of these provides new data on structural evolution among euphyllophytes and is described here., Methods: The anatomy and morphology of permineralized axes of the new plant were studied with light and electron microscopy on sections produced using the cellulose acetate peel technique. Morphological comparisons and phylogenetic analysis were used for taxonomic placement of the plant., Results: The plant represents a new species, Paracladoxylon kespekianum Chu et Tomescu, gen. et sp. nov., that has tracheids with modern-looking bordered pits and the complex cauline vascular architecture characteristic of the genus Cladoxylon. Its dissected ultimate appendages have complex regular taxis and a pattern of vascularization that suggests bilateral symmetry., Conclusions: Paracladoxylon kespekianum is one of the largest Early Devonian euphyllophytes, among the oldest representatives of the cladoxylopsid group, and older than any species of the closely related Cladoxylon by at least 35 million years. It is also one of the oldest anatomically preserved representatives of the cladoxylopsid group. Its anatomical organization pushes the rise of complex vascular architecture among moniliformopsid euphyllophytes deeper in time than previously recognized., (© 2024 Botanical Society of America.)

The Cretaceous period is the time of the first appearance of the diatoms in the fossil record. These fossils give us direct evidence of the age and early evolution of the diatom lineage. The fossil record, however, is incomplete and therefore often extrapolated through time-calibrated phylogenies. These two approaches offer different perspectives on the early evolution of diatoms, which is still poorly understood. We compiled the first comprehensive Cretaceous Diatom Database, a tool to investigate the taxonomy, diversity, and occurrence of the earliest known diatom lineages. To further aid the integration and use of the oldest diatom fossils in molecular clock analyses, we present a set of well-documented Cretaceous fossils that can be placed onto molecular phylogenetic trees of extant and extinct species, making them ideal candidates for the calibration of molecular clocks. The analysis of the fossil record and the Cretaceous Diatom Database revealed Cretaceous diversity is substantially greater than previously thought, yet considerable taxonomic work is still needed. The Cretaceous Diatom Database and the list of Cretaceous fossils for calibrating molecular clocks represent valuable resources for future evolutionary and taxonomic studies of modern and fossil diatoms., (© 2024 The Author(s). Journal of Phycology published by Wiley Periodicals LLC on behalf of Phycological Society of America.)

Fundamental aspects in the evolution of nematodes parasitizing woody plants are reviewed. (1) Nematode faunal lists of natural refugia are useful to predict the risks of opportunistic pathogens becoming true pathogens in the forest and park communities. (2) Nematode composition in natural refugia gives a chance to identify nematode antagonists of insect vectors of dangerous fungal and nematode infections, which can be potentially used as the biological agents for woody plants' protection. (3) Dauers in the ancestors of wood-inhabiting nematodes played a role as a survival stage in the detritus decomposition succession, and they later acquired the functions of dispersal and adaptations for transmission using insect vectors. (4) When inspecting wilted trees, it is necessary to use dauers for diagnostics, as sexually mature nematodes may be absent in tree tissues. (5) Plant parasitic nematodes originated from members of the detritus food web and retained a detritivorous phase in the life cycle as a part of the propagative generation. (6) Vectors in the life cycles of plant parasitic nematodes are inherited from the ancestral detritivorous nematode associations, rather than inserted in the dixenic life cycle of the 'nematode-fungus-plant' association. (7) Despite the significant difference in the duration of the nematode-tree and nematode-vector phases of the life cycle, the actual parasitic nematode specificity is dual: firstly to the vector and secondly to the natural host plant (as demonstrated in phytotests excluding a vector)., (© 2024. Pleiades Publishing, Ltd.)

A novel anaerobic, heterotrophic bacterium, designated strain Zn2(T), was isolated from the wastewater of a paper mill in Zhejiang, China. Cells were gram-type-positive rods, 0.5-0.8 µm wide and 2-4 µm long, and were motile by a lateral flagellum. The ranges of temperature and pH for growth were 10-50 °C and pH 6.0-9.5. Optimal growth occurred at 35 °C and pH 7.3-7.5. The strain did not require NaCl for growth, but its inclusion in the medium improved growth (optimum concentration 6 %). Substrates utilized as sole carbon sources were peptone, tryptone, Casamino acids, D-xylose, salicin, glycerol, formate, acetate and propionate. The main products of carbohydrate fermentation were acetate, formate, propionate and lactate. Elemental sulfur, thiosulfate and Fe(III) were used as electron acceptors, but sulfate, sulfite, nitrate, nitrite and Mn(IV) were not. Growth was inhibited by the addition of 10 µg ampicillin, penicillin, tetracycline or chloramphenicol ml(-1). iso-C15 : 0, C14 : 0, C16 : 0, C16 : 1 cis9 and C18 : 1 cis9 were the major fatty acids. Strain Zn2(T) did not contain any detectable menaquinones or ubiquinones. The main polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylserine, two unknown phospholipids and four unknown glycolipids. The genomic DNA G+C content was 37 mol%, as determined by HPLC. 16S rRNA gene sequence analysis revealed that strain Zn2(T) was a member of family Clostridiaceae, and was most closely related to the type strains of Geosporobacter subterraneus, Thermotalea metallivorans and Caminicella sporogenes, showing 91.2, 90.3 and 91.1 % sequence similarity, respectively. On the basis of its phenotypic and genotypic properties, strain Zn2(T) is suggested to represent a novel species of a new genus, for which the name Salimesophilobacter vulgaris gen. nov., sp. nov. is proposed. The type strain of Salimesophilobacter vulgaris is Zn2(T) ( = DSM 24770(T)  = JCM 17796(T)).

The global flora is thought to contain a large proportion of herbs, and understanding the general spatiotemporal processes that shaped the global distribution of these communities is one of the most difficult issues in biogeography. We explored patterns of world-wide biogeography in a species-rich herbaceous group, the paper daisy tribe Gnaphalieae (Asteraceae), based on the hitherto largest taxon sampling, a total of 835 terminal accessions representing 80% of the genera, and encompassing the global geographic range of the tribe, with nuclear internal transcribed spacer (ITS) and external transcribed spacer (ETS) sequences. Biogeographic analyses indicate that Gnaphalieae originated in southern Africa during the Oligocene, followed by repeated migrations into the rest of Africa and the Mediterranean region, with subsequent entries into other continents during various periods starting in the Miocene. Expansions in the late Miocene to Pliocene appear to have been the driving force that shaped the global distribution of the tribe as forests were progressively broken up by the mid-continent aridification and savannas and grasslands expanded into the interior of the major continents. This pattern of recent colonizations may explain the world-wide distribution of many other organisms in open ecosystems and it is highlighted here as an emerging pattern in the evolution of the global flora., (© 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.)

Rodents have received substantial attention in the study of olfaction. However, the rhinarium, the naked part of the nose, which plays an important role in chemical, tactile, and thermal perception, has been relatively overlooked. This study presents a comprehensive analysis of the rhinarium morphology and spatially associated structures (i.e., upper lip, and philtrum) in sigmodontines, a diverse group within the Cricetidae rodents. The research covers 483 specimens representing 145 species, accounting for 74% of genera in the clade, including all 13 recognized tribes, three incertae sedis genera, and the murid representatives Mus musculus and Rattus norvegicus. The inconsistent use of terminology in describing rhinarium traits across the literature poses a challenge for comparative analyzes. To address this issue, a standardized terminology was proposed to characterize the rhinarium. A paired complex protuberance typically with epidermal ridges (i.e., rhinoglyphics), termed here the tubercle of Hill, was identified as a distinctive feature in muroid rhinaria. Comparative assessments among tribes revealed unique sets of features defining each major clade, encompassing variations in hairiness, dorsum nasi complexity, size and positioning of the tubercle of Hill, and other key attributes. Two primary rhinarium configurations were discerned: one shared by Oryzomyalia and Sigmodontini and another specific to Ichthyomyini. The former groups display a ventrally positioned rhinarium prominently featuring the tubercle of Hill and sculptured areola circularis. In contrast, Ichthyomyini exhibit a frontally directed rhinarium characterized by an enlarged dorsum nasi fused to the tubercle of Hill, resulting in a distinctive "cherry" appearance. Convergent rhinarium structures observed in fossorial species, characterized by well-developed plica alaris and hair fringes, are presumed to mitigate potential damage during digging. Conversely, semiaquatic carnivorous sigmodontines showcase an integrated apical structure in their rhinarium, facilitating enhanced somatosensory capabilities crucial for predation activities during diving expeditions., (© 2024 Wiley Periodicals LLC.)

The tympanoperiotic complex of a blue whale Balaenoptera musculus is described and compared to the homologous structures in the other extant and fossil baleen whale species. The periotic and the tympanic bulla represent informative anatomical regions in both functional and phylogenetic studies and for this reason a micro-CT scan of the bones was performed in order to better characterize their external aspect and to reconstruct the inner structures. In particular, the cochlea, the semicircular canals and associated portions of the periotic are reconstructed so that these structures may be used in phylogenetic analyses. We observed that the blue whale periotic is characterized by the presence of a strong dorsal protrusion which is posteriorly bordered by a previously undescribed morphological character that we name the posterotransverse fossa. The peculiar shape of the anterior process and the en echelon organization of the posterior foramina of the pars cochlearis are also described and compared. From a phylogenetic perspective, the blue whale is confirmed to be closely related to the fin whale, Balaenoptera physalus, but it is suggested, based on ear bone characters only, that it diverged before the other balaenopterid species in the phylogeny of Balaenopteridae. This placement supports a series of morphological observations suggesting that the extant blue whale was an early-diverging member of Balaenoptera. Our results help to decipher the evolutionary origin of the blue whale, the largest living animal, by allowing new and more detailed morphological analyses of the balaenopterid fossil record., (© 2024 American Association for Anatomy.)

The Cenozoic topographic development of the Himalaya-Tibet orogen (HTO) substantially affected the paleoenvironment and biodiversity patterns of High Asia. However, concepts on the evolution and paleoenvironmental history of the HTO differ massively in timing, elevational increase and sequence of surface uplift of the different elements of the orogen. Using target enrichment of a large set of transcriptome-derived markers, ancestral range estimation and paleoclimatic niche modelling, we assess a recently proposed concept of a warm temperate paleo-Tibet in Asian spiny frogs of the tribe Paini and reconstruct their historical biogeography. That concept was previously developed in invertebrates. Because of their early evolutionary origin, low dispersal capacity, high degree of local endemism, and strict dependence on temperature and humidity, the cladogenesis of spiny frogs may echo the evolution of the HTO paleoenvironment. We show that diversification of main lineages occurred during the early to Mid-Miocene, while the evolution of alpine taxa started during the late Miocene/early Pliocene. Our distribution and niche modelling results indicate range shifts and niche stability that may explain the modern disjunct distributions of spiny frogs. They probably maintained their (sub)tropical or (warm)temperate preferences and moved out of the ancestral paleo-Tibetan area into the Himalaya as the climate shifted, as opposed to adapting in situ. Based on ancestral range estimation, we assume the existence of low-elevation, climatically suitable corridors across paleo-Tibet during the Miocene along the Kunlun, Qiangtang and/or Gangdese Shan. Our results contribute to a deeper understanding of the mechanisms and processes of faunal evolution in the HTO., (© 2024 The Author(s). Molecular Ecology published by John Wiley & Sons Ltd.)

The Ophidiidae is a group of more than 300 species of fishes characterized by elongated, snake-like bodies and continuous dorsal, anal, and caudal fins. While describing a new species in the genus Monomitopus, we discovered a bilaterally paired fenestra on the dorsomedial surface of the neurocranium. We surveyed the distribution of this fenestra across species of Monomitopus and previously hypothesized allies in the genera Dannevigia, Dicrolene, Homostolus, Neobythites, and Selachophidium, finding variation in its presence and size. We also found a prominent bilaterally paired lateral fenestra and a posterior expansion of the exoccipital in the neurocrania of M. americanus and S. guentheri, with soft tissue connecting the back of the neurocranium to the first epineural and pectoral girdle in S. guentheri. In this study, we describe the distribution of and variation in these features. We integrate morphological characters and DNA data to generate a phylogeny of Monomitopus and allies to understand their relationships and trace the evolutionary history of these novel features. Our results call the monophyly of Monomitopus into question. The presence of the lateral neurocranial fenestra and posterior expansion of the exoccipital support the reclassification of M. americanus as a species of Selachophidium., (© 2024 Wiley Periodicals LLC.)

The reproductive diversity of extant cartilaginous fishes (class Chondrichthyes) is extraordinarily broad, reflecting more than 400 million years of evolutionary history. Among their many notable reproductive specialisations are viviparity (live-bearing reproduction) and matrotrophy (maternal provision of nutrients during gestation). However, attempts to understand the evolution of these traits have yielded highly discrepant conclusions. Here, we compile and analyse the current knowledge on the evolution of reproductive diversity in Chondrichthyes with particular foci on the frequency, phylogenetic distribution, and directionality of evolutionary changes in their modes of reproduction. To characterise the evolutionary transformations, we amassed the largest empirical data set of reproductive parameters to date covering nearly 800 extant species and analysed it via a comprehensive molecular-based phylogeny. Our phylogenetic reconstructions indicated that the ancestral pattern for Chondrichthyes is 'short single oviparity' (as found in extant holocephalans) in which females lay successive clutches (broods) of one or two eggs. Viviparity has originated at least 12 times, with 10 origins among sharks, one in batoids, and (based on published evidence) another potential origin in a fossil holocephalan. Substantial matrotrophy has evolved at least six times, including one origin of placentotrophy, three separate origins of oophagy (egg ingestion), and two origins of histotrophy (uptake of uterine secretions). In two clades, placentation was replaced by histotrophy. Unlike past reconstructions, our analysis reveals no evidence that viviparity has ever reverted to oviparity in this group. Both viviparity and matrotrophy have arisen by a variety of evolutionary sequences. In addition, the ancestral pattern of oviparity has given rise to three distinct egg-laying patterns that increased clutch (brood) size and/or involved deposition of eggs at advanced stages of development. Geologically, the ancestral oviparous pattern arose in the Paleozoic. Most origins of viviparity and matrotrophy date to the Mesozoic, while a few that are represented at low taxonomic levels are of Cenozoic origin. Coupled with other recent work, this review points the way towards an emerging consensus on reproductive evolution in chondrichthyans while offering a basis for future functional and evolutionary analyses. This review also contributes to conservation efforts by highlighting taxa whose reproductive specialisations reflect distinctive evolutionary trajectories and that deserve special protection and further investigation., (© 2024 Cambridge Philosophical Society.)

Appropriate diagnoses of parasites of apex marine predators are crucial to understand their biodiversity, host specificity, biogeography, and life cycles. Such diagnoses are also informative of ecological and biological characteristics of both host and environment in which the hosts and their parasites live. We here (i) investigate the parasite fauna of a bluntnose sixgill shark Hexanchus griseus (Bonnaterre, 1788) obtained from the Gulf of Naples (Tyrrhenian Sea), (ii) characterize molecularly all its metazoan parasites, and (iii) resurrect and report the main morphological features and phylogenetic position of Grillotia acanthoscolex, a cestode species previously synonymized with Grillotia adenoplusia. A rich parasite fauna represented by eight different taxa was found, including two monogeneans (Protocotyle grisea and Protocotyle taschenbergi), one digenean (Otodistomum veliporum), four cestodes (Crossobothrium dohrnii, Clistobothrium sp., G. acanthoscolex, and G. adenoplusia), and one copepod (Protodactylina pamelae). Sequencing of these samples accounts for an important molecular baseline to widen the knowledge on the parasitic fauna of bluntnose sixgill sharks worldwide and to reconstruct their correct food chains. The bluntnose sixgill shark was found to be a definitive host for all endoparasites found here, confirming that it occupies an apex trophic level in the Mediterranean Sea. The taxa composition of the trophic parasite fauna confirms that the bluntnose sixgill shark mostly feeds on teleost fish species. However, the occurrence of two phillobothrid cestodes (C. dohrnii and Clistobothrium sp.) suggests that it also feeds on squids. Finally, we emphasize the importance of using integrative taxonomic approaches in the study of parasites from definitive and intermediate hosts to elucidate biology and ecology of taxa generally understudied in the Mediterranean Sea., (© 2024 Fisheries Society of the British Isles.)

Premise of the Study: Evolutionary significance of the Compositae capitulum and variation in its structure is poorly understood, although it may permit flexibility in sexual expression. Optimal sex ratio differs with life-history and reproductive strategy. We explore how the genus Ifloga and related members of southern African Gnaphalieae achieved different sex ratios, and the associations of these ratios with annual and perennial life history., Methods: Sex allocation was measured using the male to female ratio (M/F), a novel approximator of the pollen to ovule ratio (P/O). Life-history (annuality/perenniality), capitulum structure, capitular sexual system, and M/F were reconstructed on time-proportional phylogenies. Trait associations were examined using phylogenetically independent contrasts (PICs)., Key Results: Annual taxa have strongly female-biased capitula, as measured by M/F, and either gynomonoecious or monoecious sexual systems, while perennials have equal or male-biased capitula that are hermaphroditic or monoecious. These results are largely supported by PIC analysis. Different sexual systems afford differing flexibility in sex allocation, with hermaphrodites having the least, and monoecious taxa the greatest, range in M/F. Within Ifloga, the anomalous capitulum evolved in an annual, gynomonoecious ancestor, followed by two independent gains of monoecy. Two subsequent gains of perenniality occurred within a monoecious sublineage., Conclusions: Different life histories have divergent sex allocation optima and are strongly associated with different sexual systems in gnaphalioid daisies. An anomalous capitulum structure in Ifloga may have facilitated the evolution of monoecy, which in turn may be linked to the evolution of life-history diversity in the genus.

The large daisy tribe Gnaphalieae occurs in extra-tropical habitats worldwide, but is most diverse in southern Africa and in Australia. We explore the age and evolutionary history of the tribe by means of a phylogenetic hypothesis based on Bayesian analysis of plastid and nuclear DNA sequences, maximum likelihood reconstruction of ancestral areas, and relaxed Bayesian dating. Early diversification occurred in southern Africa in the Eocene-Oligocene, resulting in a grade of mostly Cape-centred lineages which subsequently began speciating in the Miocene, consistent with diversification times for many Cape groups. Gnaphalieae from other geographic regions are embedded within a southern African paraphylum, indicating multiple dispersals out of southern Africa since the Oligocene to Miocene which established the tribe in the rest of the world. Colonisation of Australia via direct long-distance trans-oceanic dispersal in the Miocene resulted in the radiation which produced the Australasian gnaphalioid flora. The similarly diverse regional gnaphalioid floras of Australasia and southern Africa thus exhibit very different temporal species accumulation histories. An examination of the timing and direction of trans-Indian Ocean dispersal events in other angiosperms suggests a role for the West Wind Drift in long-distance dispersal eastwards from southern Africa.

Phylogenetic studies are revealing that major ecological niches are more conserved through evolutionary history than expected, implying that adaptations to major climate changes have not readily been accomplished in all lineages. Phylogenetic niche conservatism has important consequences for the assembly of both local communities and the regional species pools from which these are drawn. If corridors for movement are available, newly emerging environments will tend to be filled by species that filter in from areas in which the relevant adaptations have already evolved, as opposed to being filled by in situ evolution of these adaptations. Examples include intercontinental disjunctions of tropical plants, the spread of plant lineages around the Northern Hemisphere after the evolution of cold tolerance, and the radiation of northern alpine plants into the Andes. These observations highlight the role of phylogenetic knowledge and historical biogeography in explanations of global biodiversity patterns. They also have implications for the future of biodiversity.

Phylogenies describe the origins and history of species. However, they can also help to predict species' fates and so can be useful tools for managing the future of biodiversity. This article starts by sketching how phylogenetic, geographic, and trait information can be combined to elucidate present mammalian diversity patterns and how they arose. Recent diversification rates and standing diversity show different geographic patterns, indicating that cradles of diversity have moved over time. Patterns in extinction risk reflect both biological differences among mammalian lineages and differences in threat intensity among regions. Phylogenetic comparative analyses indicate that for small-bodied mammals, extinction risk is governed mostly by where the species live and the intensity of the threats, whereas for large-bodied mammals, ecological differences also play an important role. This modeling approach identifies species whose intrinsic biology renders them particularly vulnerable to increased human pressure. We outline how the approach might be extended to consider future trends in anthropogenic drivers, to identify likely future battlegrounds of mammalian conservation, and the likely casualties. This framework could help to highlight consequences of choosing among different future climatic and socioeconomic scenarios. We end by discussing priority-setting, showing how alternative currencies for diversity can suggest very different priorities. We argue that aiming to maximize long-term evolutionary responses is inappropriate, that conservation planning needs to consider costs as well as benefits, and that proactive conservation of largely intact systems should be part of a balanced strategy.

The field of molecular genetics has many roles in biodiversity assessment and conservation. I summarize three of those standard roles and propose logical extensions of each. First, many biologists suppose that a comprehensive picture of the Tree of Life will soon emerge from multilocus DNA sequence data interpreted in concert with fossils and other evidence. If nonreticulate trees are indeed valid metaphors for life's history, then a well dated global phylogeny will offer an opportunity to erect a universally standardized scheme of biological classification. If life's history proves to be somewhat reticulate, a web-like phylogenetic pattern should become evident and will offer opportunities to reevaluate the fundamental nature of evolutionary processes. Second, extensive networks of wildlife sanctuaries offer some hope for shepherding appreciable biodiversity through the ongoing extinction crisis, and molecular genetics can assist in park design by helping to identify key species, historically important biotic areas, and biodiversity hotspots. An opportunity centers on the concept of Pleistocene Parks that could protect "legacy biotas" in much the same way that traditional national parks preserve special geological features and historical landmarks honor legacy events in human affairs. Third, genetic perspectives have become an integral part of many focused conservation efforts by unveiling ecological, behavioral, or evolutionary phenomena relevant to population management. They also can open opportunities to educate the public about the many intellectual gifts and aesthetic marvels of the natural world.

Canine piroplasmosis is an emerging disease worldwide, with multiple species of piroplasm now recognised to infect dogs. A nested polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) assay was developed for the detection and differentiation of each of the piroplasm species currently known to infect dogs on the basis of the 18S ribosomal RNA gene. The assay can potentially amplify and discriminate between Theileria annae, Theileria equi, Babesia conradae, Babesia gibsoni, Babesia sp. (Coco) and each of the Babesia canis subspecies. Non-canine piroplasm species can also potentially be detected using the described assay, however amplification of Neospora caninum was also observed. The PCR was found to have a high detection limit, capable of detecting a 2.7x10(-7)% parasitaemia or the equivalent of 1.2 molecules of target DNA when using DNA extracted from whole EDTA blood and detected a parasitaemia of 2.7x10(-5)% using blood applied to both Flinders Technology Associates (FTA) cards and IsoCodetrade mark Stix. The application of blood samples to filter paper may greatly assist in piroplasm identification in regions of the world where local technologies for molecular characterisation are limited. The assay reported here has the potential to be standardised for routine screening of dogs for piroplasmosis.

The arguments by Pavlinov against my critical analysis of the concept of the "phylogenetic presumptions" proposed by Rasnitsyn are briefly discussed. It is proved that these arguments are invalid because they are based on the substitution of terms. Instead of the term "phylogenetic presumption" introduced by Rasnitsyn just as an analogue of the presumption of innocence in jurisprudence, Pavlinov considers the presumption in the wider understanding, i.e. as a "preliminary statement".

Under brief consideration is the uses of presumptions, as a kind of a priori judgments, in phylogenetics in light of their critics by Pesenko (2005). It is shown that the concept of presumption is fully compatible with the hypothetic-deductive argumentation scheme allowing to realize the parsimony principle in its epistemic interpretation. System of phylogenetic presumptions deserves future development in the framework of construing phylogenetics as a kind of the informal axiomatics.

Anthropogenic rapid warming has caused decreases in richness and body mass of birds following the metabolic theory of ecology; yet, the pervasiveness of these shifts remains controversial among different taxa. Here, by combining phylogenetic methods and fossil data, we synthesized spatial patterns of richness and body mass for 328 seabird species belonging to two groups: Procellariimorphae (PM) and non-Procellariimorphae (NPM). We found that the relationship between body mass and richness, as well as diversification rate, exhibits distinct patterns in these two groups. Ancestral state reconstruction analyses indicate that smaller PM, as opposed to NPM seabirds, evolved in warmer waters from larger ancestors and exhibited a slower diversification rate. Different ancestral climatic origins explain the reduced influence of environmental factors on richness patterns among PM compared to NPM seabirds. Furthermore, whereas NPM seabirds in high latitudes face a high extinction risk, warmer sea temperatures positively correlate with a high extinction risk among PM seabirds. Our results indicate that PM seabirds, evolving from cold waters, have reduced body mass and diversification rate, making them more vulnerable to warmer temperature., (© 2024 John Wiley & Sons Ltd.)

Coniferous forests are under severe threat of the rapid anthropogenic climate warming. Abies (firs), the fourth-largest conifer genus, is a keystone component of the boreal and temperate dark-coniferous forests and harbors a remarkably large number of relict taxa. However, the uncertainty of the phylogenetic and biogeographic history of Abies significantly impedes our prediction of future dynamics and efficient conservation of firs. In this study, using 1,533 nuclear genes generated from transcriptome sequencing and a complete sampling of all widely recognized species, we have successfully reconstructed a robust phylogeny of global firs, in which four clades are strongly supported and all intersectional relationships are resolved, although phylogenetic discordance caused mainly by incomplete lineage sorting and hybridization was detected. Molecular dating and ancestral area reconstruction suggest a Northern Hemisphere high-latitude origin of Abies during the Late Cretaceous, but all extant firs diversified during the Miocene to the Pleistocene, and multiple continental and intercontinental dispersals took place in response to the late Neogene climate cooling and orogenic movements. Notably, four critically endangered firs endemic to subtropical mountains of China, including A. beshanzuensis, A. ziyuanensis, A. fanjingshanensis and A. yuanbaoshanensis from east to west, have different origins and evolutionary histories. Moreover, three hotspots of species richness, including western North America, central Japan, and the Hengduan Mountains, were identified in Abies. Elevation and precipitation, particularly precipitation of the coldest quarter, are the most significant environmental factors driving the global distribution pattern of fir species diversity. Some morphological traits are evolutionarily constrained, and those linked to elevational variation (e.g., purple cone) and cold resistance (e.g., pubescent branch and resinous bud) may have contributed to the diversification of global firs. Our study sheds new light on the spatiotemporal evolution of global firs, which will be of great help to forest management and species conservation in a warming world., (© 2024 Institute of Botany, Chinese Academy of Sciences.)

Sixteen isolates of bacteria obtained from the entomopathogenic nematode (Heterorhabditis sp.) infected cadavers of Galleria mellonella larvae were identified following phenotypic characterization and molecular analysis of 16S rRNA. Two isolates were identified as the symbiotic bacterium, Photothabdus luminescens, while 14 other isolates were represented by nine species of nonsymbiotic bacteria viz., Stenotrophomonas maltophilia, Alcaligenes aquatilis, Brevundimonas diminuta, Brucella pseudointermedia, Ochrobactrum sp., Brucella pseudogrignonensis, Brucella anthropic, Pseudomonas azatoformans and Pseudomonas lactis. The phylogenetic analysis confirmed the evolutionary relationship between P. luminescens and Pseudomonas spp. The study also found a close relationship among the nonsymbiotic bacteria such as A. aquatilis, B. diminuta, Ochrobactrum sp., and Brucella spp. P. luminescens has been documented for its insecticidal effects against a wide range of insects. The two local isolates obtained in this study may be explored for their biocontrol potential against major pests of the region. Further, the association of nonsymbiotic bacteria with the EPN may be investigated., (© 2024 Wiley‐VCH GmbH.)

The humerus is central for locomotion in turtles as quadrupedal animals. Osteological variation across testudine clades remains poorly documented. Here, we systematically describe the humerus anatomy for all major extant turtle clades based on 38 species representing the phylogenetic and ecological diversity of crown turtles. Three Late Triassic species of shelled stem turtles (Testudindata) are included to establish the plesiomorphic humerus morphology. Our work is based on 3D models, establishing a publicly available digital database. Previously defined terms for anatomical sides of the humerus (e.g., dorsal, ventral) are often not aligned with the respective body sides in turtles and other quadrupedal animals with sprawling gait. We propose alternative anatomical directional terms to simplify communication: radial and ulnar (the sides articulating with the radius/ulna), capitular (the side bearing the humeral head), and intertubercular (opposite to capitular surface). Turtle humeri show low morphological variation with exceptions concentrated in locomotory specialists. We propose 15 discrete characters to summarize osteological variation for future phylogenetic studies. Disparity analyses comparing non-shelled and shelled turtles indicate that the presence of the shell constrains humerus variation. Flippered aquatic turtles are released from this constraint and significantly increase overall disparity. Ontogenetic changes of turtle humeri are related to increased ossification and pronunciation of the proximal processes, the distal articulation areas, and the closure of the ectepicondylar groove to a foramen. Some turtle species retain juvenile features into adulthood and provide evidence for paedomorphic evolution. We review major changes of turtle humerus morphology throughout the evolution of its stem group., (© 2024 The Authors. The Anatomical Record published by Wiley Periodicals LLC on behalf of American Association for Anatomy.)

This study presents a comprehensive investigation into the evolutionary trajectories of Rhipicephalus ticks (Ixodidae) through the interpretation of molecular phylogenetics, elucidating their chromatographic spectrum. The use of advanced chromatographic tools in this study explored the dynamics chemical profiling, providing valuable insights into the evolutionary history and ecological adaptations. Prevalence of Rhipicephalus ticks was 4.5% in sheep and 3.9% in goats. The ITS2 sequence of the Rhipicephalus sanguineus (OK642408) and Rhipicephalus microplus (OK642409) form a distinct clade with sequences from other countries. The 16S rRNA sequences of R. sanguineus (OK560870) clustered with sequences form three lineages, tropical, temperate, and south-eastern. The Cox I gene-identified Rhipicephalus turanicus (OK623472) and R. microplus (OK623463) form separate clades with sequences. The HPLC chromatogram of tick samples reveals a diverse array of identified hydrocarbons, explained the complex chemical composition of their exoskeletons. This analytical approach provides valuable insights into the specific hydrocarbon profiles, allowing for potential applications in species differentiation, ecological studies, and a deeper understanding of the functional roles played by hydrocarbon compounds in tick physiology. The findings revealed the potential of applying molecular phylogenetics tools with chromatography not only to enhance our understanding of tick evolution but also to inform strategies for disease control and management in regions where Rhipicephalus ticks (Ixodidae) are endemic. RESEARCH HIGHLIGHTS: Chemical mapping utilizing advanced chromatographic techniques. Scanning microscopic insights high-resolution scanning tool to observe structural and morphological features of ticks at a molecular level. Molecular phylogeny data elucidate the evolutionary relationships among tick species., (© 2024 Wiley Periodicals LLC.)

Intracellular parasites of the genus Glugea Thélohan, 1891 (Microsporidia) comprise about 34 putative species capable of causing high morbidity and mortality in freshwater and marine teleost fishes. In this study, we report on the first mass mortality event associated with Glugea sp. infecting free-ranging round sardinella Sardinella aurita in the southern Tyrrhenian Sea (Italy). Here, we describe the ultrastructure of mature spores of this microsporidian and characterize it molecularly, as well as report its phylogenetic position. Most of the affected fish showed an irregular swelling of its abdomen. At necropsy, a variable number of xenomas, spherical to ellipsoidal in shape, were found in the peritoneal cavity strongly attached to the viscera of all fish. Histological analysis revealed varying severity of chronic inflammation along with occasional necrosis in visceral organs associated with multiple xenoma proliferation. These pathological findings were considered the main cause of this mass mortality event. Morphologically, the present material was closely related to G. sardinellesis and G. thunni. The phylogenetically closest taxa to the newly SSU rDNA sequence were G. thunni and an erroneusly identified  G. plecoglossi, which were very closely related to each other, also suggesting that all these sequences might belong to the same species., (© 2024 John Wiley & Sons Ltd.)

We describe a new species in the Australopapuan pelodryadid frog genus Litoria from upper hill forest (940 m a.s.l.) on the northern slopes of Papua New Guinea’s central cordillera. The new species is moderately small (male body length = 31.9–35.1 mm) and slender (head width/body length = 0.29–0.30), with extensive golden-yellow markings ventrally. It is most similar to Litoria iris, L. majikthise, L. ollauro, and L. verae but differs from them by a suite of morphological and colour features. The advertisement call is a series of short buzzes and clicks reminiscent of calls produced by both L. iris and L. ollauro. Phylogenetic analysis of mitochondrial ND4 nucleotide sequences shows that the new species is closest to L. iris and L. majikthise but shows a net sequence divergence of 14–15% from both of these taxa. The new species is unusual in being found calling from forest on limestone substrate where free-standing water is rarely encountered.