Early-diverging Lineages Research Articles

Comparative case study of evolutionary insights and floral complexity in key early-diverging eudicot Ranunculales models

Famously referred to as “Darwin’s abominable mystery,” the rapid diversification of angiosperms over the last ~140 million years presents a fascinating enigma. This diversification is underpinned by complex genetic pathways that evolve and rewire to produce diverse and sometimes novel floral forms. Morphological innovations in flowers are shaped not only by genetics but also by evolutionary constraints and ecological dynamics. The importance of model organisms in addressing the long-standing scientific questions related to diverse floral forms cannot be overstated. In plant biology, Arabidopsis thaliana, a core eudicot, has emerged as a premier model system, with its genome being the first plant genome to be fully sequenced. Similarly, model systems derived from crop plants such as Oryza sativa (rice) and Zea mays (maize) have been invaluable, particularly for crop improvement. However, despite their substantial utility, these model systems have limitations, especially when it comes to exploring the evolution of diverse and novel floral forms. The order Ranunculales is the earliest-diverging lineage of eudicots, situated phylogenetically between core eudicots and monocots. This group is characterized by its exceptional floral diversity, showcasing a wide range of floral morphologies and adaptations that offer valuable insights into the evolutionary processes of flowering plants. Over the past two decades, the development of at least five model systems including, Aquilegia, Thalictrum, Nigella, Delphinium and Eschscholzia within the Ranunculales order has significantly advanced our understanding of floral evolution. This review highlights the conservation and divergence of floral organ identity programs observed among these models and discusses their importance in advancing research within the field. The review also delves into elaborate petal morphology observed in Aquilegia, Nigella, and Delphinium genera, and further discusses the contributions, limitations, and future research directions for Ranunculales model systems. Integrating these diverse models from the early-diverging eudicot order has enhanced our understanding of the complex evolutionary pathways that shape floral diversity in angiosperms, bridging the knowledge gaps essential for a comprehensive understanding of floral evolution.

Mitochondrial phylogenomics reveals the sister relationship between the endogean Mediterranean raymondionymine weevils and the remaining 51,000+ Curculionidae (Coleoptera)

The tribe Raymondionymini has long been neglected in phylogenetic studies. The tribe is characterized by uncertain monophyly, fluctuating taxonomic status, and a composition prone to instability. All raymondionymine weevils are wingless and have eyes either completely absent or, rarely, consisting of a single ommatidium. With body lengths predominantly below three millimeters, they inhabit deep soil environments and are infrequently collected. The core of this tribe comprises nine genera distributed in Europe and around the Mediterranean region and encompassing 76 species, while six additional genera include 17 species distributed in USA (California), Mexico, Ecuador, Venezuela, Russian Far East, and Madagascar. Here, we present eight new mitogenomes, complemented by one publicly available, encompassing all but two Mediterranean genera of raymondionymine weevils. We used publicly available Curculionoidea mitogenomes to compile an all-inclusive dataset with 391 terminals and a reduced dataset with 61 terminals representing main families of Curculionoidea and subfamilies within Curculionidae. Our maximum likelihood and Bayesian phylogenetic analyses, employing both DNA and amino acids datasets under alternative partition schemes, consistently produced congruent phylogenies. Our results show that the Mediterranean raymondionymines form a strongly supported clade, and their easternmost and morphologically distinct genus Ubychia is sister to the rest of them. Most notably, our results consistently recover a sister relationship between the clade of Mediterranean raymondionymine weevils and a clade encompassing all remaining Curculionidae. Consequently, we propose a revision of weevil taxonomy: (i) Our target group is removed from the non-monophyletic subfamily Brachycerinae; (ii) this clade is resurrected to its former subfamily level within Curculionidae, as the subfamily Raymondionyminaestat. rev; (iii) the nine Mediterranean genera Alaocephala, Alaocyba, Coiffaitiella, Derosasius, Ferreria, Raymondiellus, Raymondionymus, Tarattostichus, and Ubychia compose Raymondionyminaestat. rev; (iv) and non-Mediterranean genera Alaocybites, Bordoniola, Gilbertiola, Homosomus, Neoubychia, and Schizomicrus are considered as “incertae sedis” pending further phylogenetic corroboration. We hypothesize that the remaining Brachycerinae and the non-Mediterranean representatives within Raymondionyminae constitute a series of species-poor early-diverging lineages representing currently unrecognized subfamilies of Curculionidae.

Comprehensive analysis of the Lycopodium japonicum mitogenome reveals abundant tRNA genes and cis-spliced introns in Lycopodiaceae species.

Lycophytes and ferns represent one of the earliest-diverging lineages of vascular plants, with the Lycopodiaceae family constituting the basal clade among lycophytes. In this research, we successfully assembled and annotated the complete Lycopodium japonicum Thunb. (L. japonicum) mitochondrial genome (mitogenome) utilizing PacBio HiFi sequencing data, resulting in a single circular molecule with a size of 454,458 bp. 64 unique genes were annotated altogether, including 34 protein-coding genes, 27 tRNAs and 3 rRNAs. It also contains 32 group II introns, all of which undergo cis-splicing. We identified 195 simple sequence repeats, 1,948 dispersed repeats, and 92 tandem repeats in the L. japonicum mitogenome. Collinear analysis indicated that the mitogenomes of Lycopodiaceae are remarkably conserved compared to those of other vascular plants. We totally identified 326 RNA editing sites in 31 unique protein-coding genes with 299 sites converting cytosine to uracil and 27 sites the reverse. Notably, the L. japonicum mitogenome has small amounts foreign DNA from plastid or nuclear origin, accounting for only 2.81% of the mitogenome. The maximum likelihood phylogenetic analysis based on 23 diverse land plant mitogenomes and plastid genomes supports the basal position of lycophytes within vascular plants and they form a sister clade to all other vascular lineages, which is consistent with the PPG I classification system. As the first reported mitogenome of Lycopodioideae subfamily, this study enriches our understanding of Lycopodium mitogenomes, and sets the stage for future research on mitochondrial diversity and evolution within the lycophytes and ferns.

Phylogenetic and phylogeographic evidence for the colonization success of the diplochorous Astydamia latifolia across the Canary Islands.

Astydamia latifolia is the only species of the genus Astydamia, which forms an early-diverging lineage of Apiaceae, subfamily Apioideae. This species is subendemic to the Canary Islands and one of the most representative species of the coastal environments of this archipelago. Astydamia displays diplochory, that is, diaspores with two long-distance dispersal (LDD) syndromes. In particular, A. latifolia has both anemochorous and thalassochorous fruit traits (corky and winged mericarps). Although we expect this species to have a high dispersal capacity, there is no genetic study addressing it. The divergence time of this species from its sister taxon is also unknown. In this study, we aimed (i) to unveil the phylogenetic relationships and divergence times of A. latifolia; (ii) to reconstruct its phylogeographic structure across the Canary Islands; and (iii) to estimate the number of inter-island colonization events. To these ends, we first sequenced the internal transcribed spacer (ITS) region for A. latifolia, reconstructed the phylogenetic relationships of Astydamia and Apiaceae relatives and estimated divergence times. Then, two plastid DNA regions (psaI-aacD and psbK-trnS) were sequenced for 158 individuals (from 36 Canarian population and one NW African population) to reconstruct a haplotype network. The recently developed method Phylogeographic Analysis of Island Colonization Events (PAICE) was used to estimate the number of inter-island colonization events. Results show that A. latifolia is a phylogenetically isolated lineage that diverged from the most closely related genus (Molopospermum) in the Eocene-Miocene. It displays a low plastid DNA diversity (only four haplotypes detected), which is accompanied by a high degree of haplotype sharing between islands and highly linear rarefaction curves of colonization obtained in PAICE. These findings suggest a high colonization ability for this species, most likely related to the availability of two LDD syndromes.

Marine Fungal Diversity and Dynamics in the Gulf of Trieste (Northern Adriatic Sea)

Fungi contribute to different important ecological processes, including decomposition of organic matter and nutrient cycling, but in the marine environment the main factors influencing their diversity and dynamics at the spatial and temporal levels are still largely unclear. In this study, we performed DNA metabarcoding on seawater sampled monthly over a year and a half in the Gulf of Trieste (northern Adriatic Sea), targeting the internal transcribed spacer (ITS) and the 18S rRNA gene regions. The fungal communities were diverse, very dynamic, and belonged predominantly to marine taxa. Samples could be clustered in two groups, mainly based on the high (> 30%) or low relative proportion of the ascomycetes Parengyodontium album, which emerged as a key taxon in this area. Dissolved and particulate organic C:N ratio played important roles in shaping the mycoplankton assemblages, suggesting that differently bioavailable organic matter pools may be utilized by different consortia. The proportion of fungal over total reads was 31% for ITS and 0.7% for 18S. ITS had the highest taxonomic resolution but low power to detect early divergent fungal lineages. Our results on composition, distribution, and environmental drivers extended our knowledge of the structure and function of the mycobiome of coastal waters.

Sphaerocrystals in seeds of Euphorbia subgenus Esula (Euphorbiaceae): morphology, occurrence, and relationship with phylogeny

Abstract The term ‘sphaerocrystals’ (also sphaerites) in classic plant morphology was usually applied to spherical bodies visible in polarized light with a characteristic ‘Maltese cross’ and consisting of both inorganic and organic compounds. Initially sphaerocrystals were found in algal cells but were later also discovered in various organs of vascular plants (including seeds). Several authors noticed spherical particles on the seed surface and in testa cells of some Euphorbia species but a comprehensive study of this character in the genus (including the morphological origin of such particles) has not been carried out. We studied 72 species belonging to all 21 sections of Euphorbia subgenus Esula for presence of spherical particles on seed surface and in the testa using scanning, transmission, confocal laser electron microscopy, and light microscopy; histochemical and element analyses were also involved. We found that these particles have the same morphological features (including the demonstration of ‘Maltese cross’ in polarized light) as the ‘classic’ sphaerocrystals. We have recorded sphaerocrystals in 53 sampled species belonging to 20 sections of Euphorbia subgenus Esula; they are localized mostly in mesotesta cells and in some species are exuded onto the seed surface where they are often aggregated into clusters. Sphaerocrystals were absent in the sampled species (with one exception) of one of the major clades of the subgenus, formed by E. sect. Helioscopia and E. sect. Holophyllum. The absence of sphaerocrystals in this early divergent lineage of E. subgen. Esula may be related with adaptation of species of this lineage to more mesic habitats.

Armillaria korhonenii, the sixteenth biological species of Armillaria from China

Armillaria korhonenii, designated as Chinese biological species Q (CBSQ) here, is described as a new species based on phylogenetic and morphological evidence as well as the results of mating tests. This species is the sixteenth biological species of Armillaria reported from China following the discovery of 15 previously known biological species. Phylogenetically, A. korhonenii is the earliest divergent lineage of the genus Armillaria as inferred from the nucleotide sequences of the Elongation Factor 1-Alpha (EF1a). Morphologically, it is characterized by its ellipsoid to elongate basidiospores, yellowish orange to honey yellow pileus with fibrillose squamules. Mating tests indicated that A. korhonenii is a tetrapolar heterogeneous species and is inter-sterile with all the tested species except partial compatibility with CBSH.

Foraminifera as a model of eukaryotic genome dynamism.

In contrast to the canonical view that genomes cycle only between haploid and diploid states, many eukaryotes have dynamic genomes that change content throughout an individual's life cycle. However, the few detailed studies of microeukaryotic life cycles render our understanding of eukaryotic genome dynamism incomplete. Foraminifera (Rhizaria) are an ecologically important, yet understudied, clade of microbial eukaryotes with complex life cycles that include changes in ploidy and genome organization. Here, we apply fluorescence microscopy and image analysis techniques to over 2,800 nuclei in 110 cells to characterize the life cycle of Allogromia laticollaris strain Cold Spring Harbor (CSH), one of few cultivable foraminifera species. We show that haploidy and diploidy are brief moments in the A. laticollaris life cycle and that A. laticollaris nuclei endoreplicate up to 12,000 times the haploid genome size. We find that A. laticollaris reorganizes a highly endoreplicated nucleus into thousands of haploid genomes through a non-canonical mechanism called Zerfall, in which the nuclear envelope degrades and extrudes chromatin into the cytoplasm. Based on these findings, along with changes in nuclear architecture across the life cycle, we believe that A. laticollaris uses spatio-temporal mechanisms to delineate germline and somatic DNA within a single nucleus. The analyses here extend our understanding of the genome dynamics across the eukaryotic tree of life.IMPORTANCEIn traditional depictions of eukaryotes (i.e., cells with nuclei), life cycles alternate only between haploid and diploid phases, overlooking studies of diverse microeukaryotic lineages (e.g., amoebae, ciliates, and flagellates) that show dramatic variation in DNA content throughout their life cycles. Endoreplication of genomes enables cells to grow to large sizes and perhaps to also respond to changes in their environments. Few microeukaryotic life cycles have been studied in detail, which limits our understanding of how eukaryotes regulate and transmit their DNA across generations. Here, we use microscopy to study the life cycle of Allogromia laticollaris strain CSH, an early-diverging lineage within the Foraminifera (an ancient clade of predominantly marine amoebae). We show that DNA content changes significantly throughout their life cycle and further describe an unusual process called Zerfall, by which this species reorganizes a large nucleus with up to 12,000 genome copies into hundreds of small gametic nuclei, each with a single haploid genome. Our results are consistent with the idea that all eukaryotes demarcate germline DNA to pass on to offspring amidst more flexible somatic DNA and extend the known diversity of eukaryotic life cycles.

Both-strand gene coding in a plastome-like mitogenome of an enoplid nematode.

The phylum Nematoda remains very poorly sampled for mtDNA, with a strong bias toward parasitic, economically important or model species of the Chromadoria lineage. Most chromadorian mitogenomes share a specific order of genes encoded on one mtDNA strand. However, the few sequenced representatives of the Dorylaimia lineage exhibit a variable order of mtDNA genes encoded on both strands. While the ancestral arrangement of nematode mitogenome remains undefined, no evidence has been reported for Enoplia, the phylum's third early divergent major lineage. We describe the first mitogenome of an enoplian nematode, Campydora demonstrans, and contend that the complete 37-gene repertoire and both-strand gene encoding are ancestral states preserved in Enoplia and Dorylaimia versus the derived mitogenome arrangement in some Chromadoria. The C. demonstrans mitogenome is 17,018 bp in size and contains a noncoding perfect inverted repeat with 2013 bp-long arms, subdividing the mitogenome into two coding regions. This mtDNA arrangement is very rare among animals and instead resembles that of chloroplast genomes in land plants. Our report broadens mtDNA taxonomic sampling of the phylum Nematoda and adds support to the applicability of cox1 gene as a phylogenetic marker for establishing nematode relationships within higher taxa.

Stem chewing lice on Cretaceous feathers preserved in amber

Phthirapteran lice (true lice or parasitic lice) are a major group of ectoparasitic insects living on their bird or mammal hosts during their entire life cycle.1 Due to their highly specialized lifestyles, they are extremely poorly represented in fossil records.2 Molecular clock estimations have speculated extensively about the origin time of parasitic lice,3,4 yet none have been confirmed unequivocally. Herein, we report a new family of stem chewing lice, based on two adult insects associated with several semiplume feathers preserved within a piece of Kachin amber from the mid-Cretaceous. They display some defining characteristics of the Amblycera, an early-diverging lineage of the crown lice group. These features include a wingless body, chewing mouthparts, narrow and small thorax, and short tarsus with elongated euplantulae. Our phylogenetic analysis places the new taxa in the Amblycera, and the discovery thus pushes back the lice fossil records by at least 55 million years. Furthermore, the new specimens show primitive characters such as compressed and club-shaped terminal segments of antennae, maxillary and labial palps, and unmodified femora of hind legs, providing key information for the evolutionary relationship between free-living booklice and parasitic lice. This suggests that some ectoparasitic characters defining the crown lice group might have evolved among amblyceran and non-amblyceran lice in parallel. These newly described fossil specimens imply at least a Cretaceous age of Phthiraptera.

Silica-associated proteins from hexactinellid sponges support an alternative evolutionary scenario for biomineralization in Porifera

Metazoans use silicon traces but rarely develop extensive silica skeletons, except for the early-diverging lineage of sponges. The mechanisms underlying metazoan silicification remain incompletely understood, despite significant biotechnological and evolutionary implications. Here, the characterization of two proteins identified from hexactinellid sponge silica, hexaxilin and perisilin, supports that the three classes of siliceous sponges (Hexactinellida, Demospongiae, and Homoscleromorpha) use independent protein machineries to build their skeletons, which become non-homologous structures. Hexaxilin forms the axial filament to intracellularly pattern the main symmetry of the skeletal parts, while perisilin appears to operate in their thickening, guiding extracellular deposition of peripheral silica, as does glassin, a previously characterized hexactinellid silicifying protein. Distant hexaxilin homologs occur in some bilaterians with siliceous parts, suggesting putative conserved silicifying activity along metazoan evolution. The findings also support that ancestral Porifera were non-skeletonized, acquiring silica skeletons only after diverging into major classes, what reconciles molecular-clock dating and the fossil record.

New nephridiophagid genera (Fungi, Chytridiomycota) in a mallow beetle and an earwig.

Nephridiophagids are unicellular fungi (Chytridiomycota) that infect the Malpighian tubules of insects. Most species have been found in cockroach hosts and belong to the genus Nephridiophaga. Three additional genera have been described from beetles and an earwig. Here, we characterise morphologically and molecular phylogenetically the nephridiophagids of the European earwig Forficulaauricularia and the mallow beetle Podagricamalvae. Their morphology and life cycle stages resemble those of other nephridiophagids, but their rRNA gene sequences support the existence of two additional genera. Whereas the earwig nephridiophagid (Nephridiochytriumforficulaegen. nov. et sp. nov.) forms a sister lineage of the Nephridiophaga cluster, the mallow beetle nephridiophagid (Malpighivincopodagricaegen. nov. et sp. nov.) represents the earliest divergent lineage within the nephridiophagids, being sister to all other species. Our results corroborate the hypothesis that different insect groups harbour distinct nephridiophagid lineages.

Ducellierialesord. nov. and evidence for a novel clade of endobiotic pollen-infecting "lagenidiaceous" Peronosporomycetes.

The genus Ducellieria (Ducellieriaceae) contains three species (D. chodatii, D. tricuspidata, D. corcontica), and a single variety (D. chodatii var. armata) of obligate endobiotic pollen parasites. These organisms have been first assigned to the green alga genus Coelastrum, as they form very similar spherical structures, but the observation of heterokont zoospores has led to their reclassification to the phylum Oomycota. However, despite their widespread nature, these organisms are only known from their descriptive morphology, and life cycle traits of some species still remain incompletely known. Only the type species, D. chodatii, has been rediscovered several times, but the phylogeny of the genus remains unresolved, since none of its species has been studied for their molecular phylogeny. At present the genus is still included in some algal databases. To clarify the evolutionary affiliation of Ducellieria, efforts were undertaken to isolate D. chodatii from pollen grains, to infer its phylogenetic placement based on nrSSU sequences. By targeted isolation, the pollen endoparasitoid was rediscovered from three lakes in Germany (Mummelsee, Okertalsperre, Knappensee). Apart from the typical coelastrum-like spheroids, oomycetes sporulating directly from pollen grains in a lagenidium-like fashion were observed, and molecular sequences of both types of oomycetes were obtained. Phylogenetic reconstruction revealed that coelastrum-like and lagenidium-like forms are unrelated, with the former embedded within the deep branching early-diverging lineages, and the later stage forming a distinct clade in Peronosporales. Consequently, the life cycle of D. chodatii needs careful revision using single-spore isolates of the species, to infer if previous lifecycle reconstructions that involve various different thallus types are stages of a single species or potentially of several ones. Citation: Buaya AT, Thines M (2023). Ducellieriales ord. nov. and evidence for a novel clade of endobiotic pollen-infecting "lagenidiaceous" Peronosporomycetes. Fungal Systematics and Evolution 12: 247-254. doi: 10.3114/fuse.2023.12.12.

Evolution of Seed Dispersal Modes in the Orchidaceae: Has the Vanilla Mystery Been Solved?

Orchid seeds are predominantly wind-dispersed, often developed within dry, dehiscent fruits that typically release millions of dust-like seeds into the air. Animal-mediated seed dispersal is a lesser-known phenomenon in the family and predominantly occurs in groups belonging to early-diverging lineages bearing indehiscent, fleshy fruits with hard, rounded, dark seeds. In this review, we explore the evolutionary trends of seed dispersal mechanisms in Orchidaceae, focusing on the pantropical genus Vanilla. Notably, certain Neotropical species of Vanilla produce vanillin-aromatic compounds synthesized naturally in their fruits, which plays a pivotal role in seed dispersal. Ectozoochory occurs in dry, dehiscent fruits, whose seeds are dispersed by (i) male euglossine bees collecting the fruit’s vanillin aromatic compounds and (ii) female stingless bees collecting the fruit’s mesocarp. Endozoochory occurs in (iii) highly nutritious, indehiscent fruits consumed by terrestrial mammals or (iv) fleshy, dehiscent fruits whose mesocarp is consumed by arboreal mammals. Wind dispersal appears to be a derived state in Orchidaceae and, given its predominance, a trait likely associated with enhanced speciation rates. Zoochory primarily occurs in groups derived from early-diverging lineages; occasional reversions suggest a link between dispersal mode and fruit and seed traits. Interestingly, fruit dehiscence and fleshiness in Vanilla lack phylogenetic signal despite their role in determining dispersal modes, suggesting potential environmental adaptability.

Distinct hybridization modes in wide- and narrow-ranged lineages of Causonis (Vitaceae)

BackgroundExplaining contrasting patterns of distribution between related species is crucial for understanding the dynamics of biodiversity. Despite instances where hybridization and whole genome duplication (WGD) can yield detrimental outcomes, a role in facilitating the expansion of distribution range has been proposed. The Vitaceae genus Causonis exhibits great variations in species’ distribution ranges, with most species in the derived lineages having a much wider range than those in the early-diverged lineages. Hybridization and WGD events have been suggested to occur in Causonis based on evidence of phylogenetic discordance. The genus, therefore, provides us with an opportunity to for explore different hybridization and polyploidization modes in lineages with contrasting species’ distribution ranges. However, the evolutionary history of Causonis incorporating potential hybridization and WGD events remains to be explored.ResultsWith plastid and nuclear data from dense sampling, this study resolved the phylogenetic relationships within Causonis and revealed significant cyto-nuclear discordance. Nuclear gene tree conflicts were detected across the genus, especially in the japonica-corniculata clade, which were mainly attributed to gene flow. This study also inferred the allopolyploid origin of the core Causonis species, which promoted the accumulation of stress-related genes. Causonis was estimated to have originated in continental Asia in the early Eocene, and experienced glaciation in the early Oligocene, shortly after the divergence of the early-divergent lineages. The japonica-corniculata clade mainly diversified in the Miocene, followed by temperature declines that may have facilitated secondary contact. Species distribution modeling based on current climate change predicted that the widespread C. japonica tends to be more invasive, while the endemic C. ciliifera may be at risk of extinction.ConclusionsThis study presents Causonis, a genus with complex reticulate evolutionary history, as a model of how hybridization and WGD modes differ in lineages of contrasting species’ geographic ranges. It is important to consider specific evolutionary histories and genetic properties of the focal species within conservation strategies.

Independent wing reductions and losses among stick and leaf insects (Phasmatodea), supported by new Cretaceous fossils in amber

BackgroundPhasmatodea (stick and leaf insects) play a central role on the debate regarding wing reduction and loss, and its wings are putative reacquisition from secondarily wingless ancestors based solely on extant species. A pivotal taxon in this respect is the species-poor Timematodea, consisting of approximately 21 wingless extant species, which form the sister group of all remaining winged or wingless stick and leaf insects, the Euphasmatodea.ResultsHerein, the new fossils of Timematodea from mid-Cretaceous Kachin amber are reported, with winged and wingless species co-occurring. The palaeogeographic distributions of all fossils of Holophasmatodea are summarized, showing their wide paleo-distributions. The phylogenetic analysis based on morphological characters confirms the earliest-diverging lineage of winged Breviala cretacea gen. et sp. nov. in Timematodea, and the possible relationships among all families of Holophasmatodea. These are critical for the reconstruction of patterns of wing evolution in early Phasmatodea.ConclusionsThe new fossils suggest that Timematodea once had wings, at least during the mid-Cretaceous. The palaeogeographic occurrences imply that Timematodea probably have been widely distributed since at least the Jurassic. The phylogenetic analysis with the ancestral-state reconstruction of wings indicates that the common ancestors of Holophasmatodea were winged, the reductions and losses of wings among Timematodea and Euphasmatodea have occurred independently since at least the Cretaceous, and the reduction or loss of the forewing earlier than the hind wings.

Genome and transcriptome reveal lithophilic adaptation of Cladophialophora brunneola, a new rock-inhabiting fungus

ABSTRACT Rock-inhabiting fungi (RIF) are slow-growing microorganisms that inhabit rocks and exhibit exceptional stress tolerance owing to their thick melanised cell walls. This study reports the identification of a novel rock-inhabiting fungus, Cladophialophora brunneola sp. nov. which was isolated from a karst landform in Guizhou, China, using a combination of morphological and phylogenetic analyses. The genome of C. brunneola was sequenced and assembled, with a total size of approximately 33.8 Mb, encoding 14,168 proteins and yielding an N50 length of 1.88 Mb. C. brunneola possessed a larger proportion of species-specific genes, and phylogenomic analysis positioned it in an early diverged lineage within Chaetothyriales. In comparison to non-RIF, C. brunneola displayed reduction in carbohydrate-active enzyme families (CAZymes) and secondary metabolite biosynthetic gene clusters (BGCs). Transcriptome analysis conducted under PEG-induced drought stress revealed elevated expression levels of genes associated with melanin synthesis pathways, cell wall biosynthesis, and lipid metabolism. This study contributes to our understanding of the genomic evolution and polyextremotolerance exhibited by rock-inhabiting fungi.

Gene expression in the liver of the hagfish (Eptatretus burgeri) belonging to the Cyclostomata is ancestral to that of mammals.

Although the liver of the hagfish, an earliest diverged lineage among vertebrates, has a histological architecture similar to that of mammals, its gene expression has not been explored yet. The present study was undertaken to comparatively characterize gene expression in the liver of the hagfish with that of the mouse, using in situ hybridization technique. Expression of alb (albumin) was detectable in all hepatocytes of the hagfish liver, but was negative in intrahepatic bile ducts. Their expression in abundant periportal ductules was weak. The expression pattern basically resembled that in mammalian livers, indicating that the differential expression of hepatocyte markers in hepatocytes and biliary cells may have been acquired in ancestral vertebrates. alb expression was almost homogeneous in the hagfish liver, whereas that in the mouse liver lobule was zonal. The glul (glutamate-ammonia ligase) expression was also homogeneously detectable in hepatocytes without zonation, and weakly so in biliary cells of the hagfish, which contrasted with its restricted pericentral expression in mouse livers. These findings indicated that the hagfish liver did not have mammalian-type zonation. Whereas tetrapods had Hnf (hepatocyte nuclear factor) 1a and Hnf1b genes encoding the transcription factors, the hagfish had a single gene of their orthologue hnf1. Although HNF1α and HNF1β were immunohistochemically detected in hepatocytes and biliary cells of the mouse, respectively, hnf1 was expressed in both hepatocytes and biliary cells of the hagfish. These data indicate that gene expression of hnf1 in the hagfish liver may be ancestral with that of alb and glul during vertebrate evolution.

New reptile shows dinosaurs and pterosaurs evolved among diverse precursors.

Dinosaurs and pterosaurs have remarkable diversity and disparity through most of the Mesozoic Era1-3. Soon after their origins, these reptiles diversified into a number of long-lived lineages, evolved unprecedented ecologies (for example, flying, large herbivorous forms) and spread across Pangaea4,5. Recent discoveries of dinosaur and pterosaur precursors6-10 demonstrated that these animals were also speciose and widespread, but those precursors have few if any well-preserved skulls, hands and associated skeletons11,12. Here we present a well-preserved partial skeleton (Upper Triassic, Brazil) of the new lagerpetid Venetoraptor gassenae gen. et sp. nov. that offers a more comprehensive look into the skull and ecology of one of these precursors. Its skull has a sharp, raptorial-like beak, preceding that of dinosaurs by around 80 million years, and a large hand with long, trenchant claws that firmly establishes the loss of obligatory quadrupedalism in these precursor lineages. Combining anatomical information of the new species with other dinosaur and pterosaur precursors shows that morphological disparity of precursors resembles that of Triassic pterosaurs and exceeds that of Triassic dinosaurs. Thus, the 'success' of pterosaurs and dinosaurs was a result of differential survival among a broader pool of ecomorphological variation. Our results show that the morphological diversity of ornithodirans started to flourish among early-diverging lineages and not only after the origins of dinosaurs and pterosaurs.

Changes of biliary cilia, smooth muscle tissue distribution, innervation and extracellular matrices during morphological evolution of hepatic architectures in vertebrates

BackgroundThe liver architecture of vertebrates can be classified into two types, the portal triad type (having periportal bile ducts) and the non-portal triad type (having bile ducts independent of the course of portal veins). The former is typically detectable in livers of tetrapods and cartilaginous fish, and its ancestral state is found in the hagfish, an earliest diverged lineage among vertebrates. Teleosts other than osteoglossomorphs have the latter. The aim of the present study is to reveal the changes of the hepatic innervation, biliary cilia and smooth muscle distribution, and extracellular matrices along vertebrate evolution with attention to the two types of liver architectures. MethodsThe hepatic innervation, biliary cilia and smooth muscle distribution, and collagen deposition were immunohistochemically and histochemically compared among livers of various vertebrates, using anti-acetylated tubulin and anti-α-smooth muscle actin antibodies, and Sirius red staining. These were also ultrastructurally examined. ResultsAlthough the hagfish liver had periportal intrahepatic bile ducts and ductules as detected in mammalian livers, it lacked smooth muscles around bile ducts and portal veins. Extracellular matrices in their connective tissues had thick collagen fibers. Its innervation was restricted to intrahepatic bile ducts and portal veins in the hilum. In livers of other vertebrates, including teleosts, the innervation was broadly detectable, especially around bile ducts, hepatic arteries and portal veins (afferent vessels), but not around central veins (efferent vessels). The chondrichthyans ultrastructurally had smooth muscle tissue around bile ducts. Cilia distribution was confirmed in intrahepatic bile ducts of tetrapods and basal actinopterygians. Teleosts other than osteoglossomorphs lacked cilia in their intrahepatic bile ducts. ConclusionsThe liver architecture of the hagfish may be unique for innervation and extracellular matrices. Hepatic innervation may not have occurred in vertebrate ancestors. Hepatic innervation in bile ducts, hepatic arteries and portal veins may have been conserved among the extant jawed vertebrates. Cilia distribution in bile ducts may have changed during evolution of actinopterygians.