Early Evolution Research Articles

Volatile atmospheres of lava worlds

Context. A magma ocean (MO) is thought to be a ubiquitous stage in the early evolution of rocky planets and exoplanets. During the lifetime of the MO, exchanges between the interior and exterior envelopes of the planet are very efficient. In particular, volatile elements that initially are contained in the solid part of the planet can be released and form a secondary outgassed atmosphere. Aims. We determine trends in the H–C–N–O–S composition and thickness of these secondary atmospheres for varying planetary sizes and MO extents, and the oxygen fugacity of MOs, which provides the main control for the atmospheric chemistry. Methods. We used a model with coupled chemical gas-gas and silicate melt-gas equilibria and mass conservation to predict the composition of an atmosphere at equilibrium with the MO depending on the planet size and the extent and redox state of the MO. We used a self-consistent mass–radius model for the rocky core to inform the structure of the planet, which we combined with an atmosphere model to predict the transit radius of lava worlds. Results. The resulting MOs have potential temperatures ranging from 1415 to 4229 K, and their outgassed atmospheres have total pressures from 3.3 to 768 bar. We find that MOs (especially the shallow ones) on small planets are generally more reduced, and are thus dominated by H2-rich atmospheres (whose outgassing is strengthened at low planetary mass), while larger planets and deeper MOs vary from CO to CO2–N2–SO2 atmospheres, with increasing $\[f_{\mathrm{O}_2}\]$. In the former case, the low molecular mass of the atmosphere combined with the low gravity of the planets yields a large vertical extension of the atmosphere, while in the latter cases, secondary outgassed atmospheres on super-Earths are likely significantly shrunk. Both N and C are largely outgassed regardless of the conditions, while the S and H outgassing is strongly dependent on the $\[f_{\mathrm{O}_2}\]$, as well as on the planetary mass and MO extent for the latter. We further use these results to assess how much a secondary outgassed atmosphere may alter the mass–radius relations of rocky exoplanets.

New data on the crown proteid Bishara backa from the Upper Cretaceous (Bostobe Formation) of Kazakhstan: implications for early evolution and palaeobiogeography of proteidae

ABSTRACT We provide a detailed redescription of all available material for the geologically oldest proteid salamander Bishara backa from the Upper Cretaceous (Santonian – lower Campanian) Bostobe Formation in Kazakhstan, consisting an atlantal centrum (neotype of Bishara backa) and a trunk vertebra. Bishara backa is characterised by the following combination of characters: large, dorsoventrally compressed and almost flat anterior cotyles of atlas enclosing an angle about 230°; anterior cotylar surfaces are continuous medially across lateral surfaces of small, dorsally placed intercotylar tubercle; ventrolateral ridges are alar-like; atlantal transverse processes are bicipitate; oblique anterior alar processes and lateral fossae on atlas present; transverse processes on trunk vertebra are bicipitate and divergent; alar processes on trunk vertebra are prominent; anterodorsal ridge on trunk vertebra is present; neural arch of trunk vertebra with high neural spine and grooves on its posterior face; two large subcentral foramina on ventral surface of the centrum. Our phylogenetic analyses finds Bishara backa as a crown proteid and a basal member of Eurasian clade of crown proteids (Bishara+Proteus+Mioproteus). We propose a model of proteid evolution that includes three main episodes of radiations with the last two taking place during the Late Cretaceous and the Palaeocene – Eocene thermal maximum.

A new dichobunoid artiodactyl from the middle Eocene of Yunnan, China

Dichobunoids were the most basal artiodactyl group, widely distributed throughout the Eocene of Eurasia and North America, but were rarely reported from southern China. In this paper, we report the first dichobunoid artiodactyl, Shilinhyus chowi n. gen. n. sp., from the middle Eocene of Lunan Basin (Shilin County), China. Shilinhyus is characterized by its relatively large size, bunoselenodont tooth morphology with a highly developed p4 metaconid, and a mesially interrupted paracristid formed by a weak premetacristid and a strong preprotocristid. This morphology distinguishes Shilinhyus from all known dichobunoid artiodactyls. Within dichobunoids, Shilinhyus resembles Pakkokuhyus from the Eocene of Southeast Asia and “Gobiohyus” yuanchuensis from the Eocene of Shanxi, China, by the relatively large size, the absence of the paraconid, and the well-development of the hypolophid. However, Shilinhyus still differs from Pakkokuhyus and “Gobiohyus” yuanchuensis in the complete interruption of the paracristid and in the alignment of the entoconid and hypoconid as well as the protoconid and metaconiod. Shilinhyus, Pakkokuhyus, and “Gobiohyus” yuanchuensis might have derived from the Eocene Gobiohyus from northern China, constituting a distinct group. The discovery of Shilinhyus chowi enhances our understanding of the early evolution of dichobunoid artiodactyls, especially in southern China.

Chemical Antiquity in Metabolism.

ConspectusLife is an exergonic chemical reaction. The same was true when the very first cells emerged at life's origin. In order to live, all cells need a source of carbon, energy, and electrons to drive their overall reaction network (metabolism). In most cells, these are separate pathways. There is only one biochemical pathway that serves all three needs simultaneously: the acetyl-CoA pathway of CO2 fixation. In the acetyl-CoA pathway, electrons from H2 reduce CO2 to pyruvate for carbon supply, while methane or acetate synthesis are coupled to energy conservation as ATP. This simplicity and thermodynamic favorability prompted Georg Fuchs and Erhard Stupperich to propose in 1985 that the acetyl-CoA pathway might mark the origin of metabolism, at the same time that Steve Ragsdale and Harland Wood were uncovering catalytic roles for Fe, Co, and Ni in the enzymes of the pathway. Subsequent work has provided strong support for those proposals.In the presence of Fe, Co, and Ni in their native metallic state as catalysts, aqueous H2 and CO2 react specifically to formate, acetate, methane, and pyruvate overnight at 100 °C. These metals (and their alloys) thus replace the function of over 120 enzymes required for the conversion of H2 and CO2 to pyruvate via the pathway and its cofactors, an unprecedented set of findings in the study of biochemical evolution. The reactions require alkaline conditions, which promote hydrogen oxidation by proton removal and are naturally generated in serpentinizing (H2-producing) hydrothermal vents. Serpentinizing hydrothermal vents furthermore produce natural deposits of native Fe, Co, Ni, and their alloys. These are precisely the metals that reduce CO2 with H2 in the laboratory; they are also the metals found at the active sites of enzymes in the acetyl-CoA pathway. Iron, cobalt and nickel are relicts of the environments in which metabolism arose, environments that still harbor ancient methane- and acetate-producing autotrophs today. This convergence indicates bedrock-level antiquity for the acetyl-CoA pathway. In acetogens and methanogens growing on H2 as reductant, the acetyl-CoA pathway requires flavin-based electron bifurcation as a source of reduced ferredoxin (a 4Fe4S cluster-containing protein) in order to function. Recent findings show that H2 can reduce the 4Fe4S clusters of ferredoxin in the presence of native iron, uncovering an evolutionary precursor of flavin-based electron bifurcation and suggesting an origin of FeS-dependent electron transfer in proteins. Traditionally discussed as catalysts in early evolution, the most common function of FeS clusters in metabolism is one-electron transfer, also in radical SAM enzymes, a large and ancient enzyme family. The cofactors and active sites in enzymes of the acetyl-CoA pathway uncover chemical antiquity in metabolism involving metals, methyl groups, methyl transfer reactions, cobamides, pterins, GTP, S-adenosylmethionine, radical SAM enzymes, and carbon-metal bonds. The reaction sequence from H2 and CO2 to pyruvate on naturally deposited native metals is maximally simple. It requires neither nitrogen, sulfur, phosphorus, RNA, ion gradients, nor light. Solid-state metal catalysts tether the origin of metabolism to a H2-producing, serpentinizing hydrothermal vent.

The European earwig: a model species for studying the (early) evolution of social life

The European earwig: a model species for studying the (early) evolution of social life

The gas hydrate system of the western Black Sea Basin

The basin-scale distribution of gas hydrates and methane migration pathways in the western Black Sea remains enigmatic, owing to the region's complex geological history. Characterizing the abundant gas hydrate accumulations across temporal scales poses significant challenges. In this study, we developed and applied a 3D large-scale numerical model to study the formation, development, and fate of natural gas hydrate systems in the western Black Sea sub-basin. Our model enables us to simulate the dynamic evolution of basin geometry and facies distribution over the last 98 million years and under dynamically changing boundary conditions, e.g. due to sea-level changes. Our study estimates the total volume of gas hydrates stored within western Black Sea sediments at ∼14,607 MtC, equivalent to ∼30,073 × 1011 m3 of CH4 (at STP conditions) which is about 5 times higher than average gas hydrate density at continental margins. Our findings reveal three distinct mechanisms driving gas hydrate reservoir formation within the reconstructed sub-basin: gas hydrate recycling zones, chimney-like structure formation, and gas hydrate deposits associated with paleo-deep sea fans. We identified and simulated key controlling parameters, related to methane migration pathways and regional geomorphology, governing each type of hydrate formation. Subsequently, we conduct a detailed analysis of regional gas hydrate systems, focusing on the Dniepr paleo-fan system, the Danube paleo-fan region, multiple offshore locations near Turkey, and the central Black Sea area. Furthermore, we investigate various biogenic methane formation kinetics and their impact on basin-scale methane generation. Our sensitivity studies enable us to predict the optimal temperature range for microbial activity driving methanogenesis in the Black Sea sediments at 30 °C–40 °C. Overall, our study provides a novel understanding and quantitative correlation between methane generation, migration, and storage in the form of gas hydrates on a basin-scale in the western Black Sea.

An overview of Upper Pleistocene coastal deposits on Mallorca island

This review paper delves into the geological history of Mallorca, focusing on the Middle to Late Pleistocene period and its impact on the landscape and climate of the island. The Quaternary, particularly, the Last Interglacial, represents a relatively short timeframe on the global chronological scale, yet it is notable for its climatic instability and complex alternation of glacial and interglacial phases, leading to fluctuations in sea levels. During the last interglacial, millennial-scale fluctuations, known as Dansgaard–Oeschger and Heinrich events, occurred. Aeolianites are thought to have formed during periods of sparse vegetation cover and abundant sediment availability from the sea bed or platform (Heinrich events), while colluvial deposits and paleosols are believed to represent periods of reduced sediment supply and enhanced pedogenesis (Dansgaard–Oeschger events). These different deposits reflect climatic shifts and sea-level changes, offering insights into the environmental history of the island. Fossil evidence, including Strombus bubonius (currently known as Thetystrombus lauts) or “Senegalese hosts,” reveals past warm climatic fluctuations, particularly during the Last Interglacial. Myotragus balearicus exemplifies evolutionary adaptation and isolation on the island, offering a unique perspective on its paleontological legacy. The integration of stratigraphic characteristics and literature research on Optically Stimulated Luminescence (OSL) dating techniques provides a comprehensive temporal framework, spanning from Marine Isotope Stage 6 (MIS 6) to Marine Isotope Stage 2 (MIS 2), enabling the precise dating of geological events and a stratigraphic correlation.

Uranium oxidation states in zircon and other accessory phases

Zircon and other U-bearing accessory phases are important time-capsules for studying the evolution of Earth and other planetary bodies as these minerals can record both temporal and compositional information regarding their host rocks. In silicate melts, uranium can occur in either the UIV, UV, or UVI valence state and its redox sensitive nature could, in principle, allow for information on magma oxygen fugacity (ƒO2) to be gleaned from U-bearing phases provided they can incorporate multivalent U during crystallization. Currently, however, little is known regarding the details of how U is speciated in these minerals.In this study, we conducted conventional X-ray absorption near-edge structure (XANES) spectroscopy at the U M4-edge on a set of natural zircon (n = 140), titanite (n = 9), apatite (n = 7), baddeleyite (n = 7), and garnet (n = 2) samples to determine the oxidation state of U in these crystals. We also collected U L3-edge spectra for select zircon samples to investigate the bonding environment of U using extended X-ray absorption fine structure (EXAFS) analysis. The effects of crystallographic orientation and radiation damage on zircon U M4-edge spectra are found to be minimal compared to the magnitude of the peak shifts associated with U oxidation state. We find that titanite and garnet contain only tetravalent U, while zircon, apatite, and baddeleyite can contain U of variable valence. Of these phases, zircon shows the greatest variability, with white-line energy, Ewl (i.e., peak absorbance) covering a range of >2.0 eV between grains: i.e., the entire energy range expected between pure UIV and pure UVI species. Moreover, a correlation is observed between the Ewl of zircon U M4-edge spectra (i.e., relative proportions of UIV, UV, UVI) and the ƒO2 of their host rocks. Our results thus establish U oxidation states in zircon as a powerful new tracer of magma redox. Since XANES is non-destructive and can be performed in situ, this technique can be utilized alongside other microanalytical methods (e.g., LA-ICPMS, SIMS) to further expand the breadth of information that can be extracted from single mineral grains.

Short Communication: Calcareous nannofossil assemblages and age determination in Leuwi Kenit, Ciletuh Palabuhanratu Geopark, Indonesia

Abstract. Pratiwi SD, Nurdrajat, Pratiwy FM, Chiyonobu S. 2024. Short Communication: Calcareous nannofossil assemblages and age determination in Leuwi Kenit, Ciletuh Palabuhanratu Geopark, Indonesia. Biodiversitas 25: 3200-3207. Our meticulous and comprehensive investigation of nannofossil diversity in Leuwi Kenit, Sukabumi District, West Java Province, Indonesia, a part of the Ciletuh Palabuhanratu UGG, where the study of nannofossils is limited, is of significant importance their implications for age determination and clarifying the geological history of the region. The initial documentation of calcareous nannofossils in the Leuwi Kenit traverse of the Cikarang Member within the Jampang Formation resulted in the identification of thirty-three species from 62 samples. The studied section reveals seven nannofossil biozones, arranged from oldest to youngest as follows: LO Sphenolithus ciperoensis; LO Cyclicargolithus abisectus; FO Sp. disbelemnos; FCO Helicosphaera carteri; FO Sp. belemnos; LCO Sp. belemnos; LO Sp. conicus and FCO Sp. heteromorphus. Notably, the abundance of Coccolithus pelagicus, Cyclicargolithus floridanus, Reticulofenestra spp., and Sphenolithus spp. characterized their occurrence throughout the section. The diversity and preservation of nannofossils were found to be good, and based on nannofossil biohorizons, the age of Leuwi Kenit spans from 24.3 million years ago to around 17.7 million years ago at Paleogene (Oligocene age) to Neogen Periode (Early Miocene age). Based on the nannofossils assemblages, results show that the area has many important indicator species, making it essential for future research on ancient ocean conditions and past climate changes within this geopark.

A gene-rich mitochondrion with a unique ancestral protein transport system

Mitochondria originated from an ancient endosymbiosis involving an alphaproteobacterium.1,2,3 Over time, these organelles reduced their gene content massively, with most genes being transferred to the host nucleus before the last eukaryotic common ancestor (LECA).4 This process has yielded varying gene compositions in modern mitogenomes, including the complete loss of this organellar genome in some extreme cases.5,6,7,8,9,10,11,12,13,14 At the other end of the spectrum, jakobids harbor the most gene-rich mitogenomes, encoding 60-66 proteins.8 Here, we introduce the mitogenome of Mantamonas sphyraenae, a protist from the deep-branching CRuMs supergroup.15,16 Remarkably, it boasts the most gene-rich mitogenome outside of jakobids, by housing 91 genes, including 62 protein-coding ones. These include rare homologs of the four subunits of the bacterial-type cytochrome c maturation system I (CcmA, CcmB, CcmC, and CcmF) alongside a unique ribosomal protein S6. During the early evolution of mitochondria, gene transfer from the proto-mitochondrial endosymbiont to the nucleus became possible thanks to systems facilitating the transport of proteins synthesized in the host cytoplasm back to the mitochondrion. In addition to the universally found eukaryotic protein import systems, jakobid mitogenomes were reported to uniquely encode the SecY transmembrane protein of the Sec general secretory pathway, whose evolutionary origin was however unclear. The Mantamonas mitogenome not only encodes SecY but also SecA, SecE, and SecG, making it the sole eukaryote known to house a complete mitochondrial Sec translocation system. Furthermore, our phylogenetic and comparative genomic analyses provide compelling evidence for the alphaproteobacterial origin of this system, establishing its presence in LECA.

Zircon U‐Pb provenance analysis of impact melt and target rocks from the Rochechouart impact structure, France

AbstractThe Rochechouart impact structure in the northwestern part of the French Massif Central (FMC) has a great diversity of impactites, including monomict impact breccias, suevite, and impact melt rocks (IMRs). The structure is strongly eroded, which allows the study of impactites of the crater fill and the transition into the crater floor. The FMC has had a multistage geological evolution from the late Neoproterozoic to the Ordovician (600–450 Ma) until the later stages of the Variscan orogeny (~300 Ma). Previous geochronological work on Rochechouart has been focused mainly on the impactites and constraining the impact age, and scarce work has been done on the FMC‐related target rocks. Here, U‐Pb isotope analysis by LA‐MC‐ICP‐MS has been conducted on zircon from two IMRs from the Recoudert and Montoume localities, and from a monzodiorite, a paragneiss, and two amphibolite samples of the basement to the impact structure. Zircon from the target rocks yielded mainly Neoproterozoic to Carboniferous ages (~924 to ~301 Ma) that can mostly be correlated to different stages of the geological evolution of the FMC. The monzodiorite also yielded a Permian age of 272 ± 12 Ma. Zircon from the IMRs, and especially from the Montoume sample, gave a comparatively higher diversity of Neoproterozoic to Jurassic ages (~552 to ~195 Ma). Provenance analysis for the zircon age populations of the impactites compared to those of the basement rocks shows overall poor correlation between the two age groups. This suggests that other target lithologies were involved in the formation of these impact melts as well. Post‐Variscan and preimpact ages (281–226 Ma) obtained for both melt rocks probably reflect a previously unconstrained event in the evolution of the regional geological history. Ages similar to the currently most widely accepted impact age of ~204–206 Ma were obtained from both IMR samples. In addition, the Montoume melt rock yielded several post‐204 Ma ages, which might reflect a to date unconstrained, about 194 Ma postimpact thermal/hydrothermal event.

Evolution of magma compositions and phosphorus availability in early Earth’s crust: New constraints from zircon-melt partitioning experiments

Abstract Zircons are the oldest remaining witnesses of Earth’s near-surface processes, and conditions in the Hadean and Archaean crust are derived predominantly from their trace element and isotopic compositions. However, quantitative assessment of element and isotope partitioning between zircon and melt remains incomplete. We experimentally determined the effect of phosphorus (P) abundance on zircon-melt partition coefficients of Al (DAl), Li (DLi), and P (DP). Results indicate that P content has opposite effects on DAl and DLi, whereas the partitioning of P itself and other trace elements is independent of P abundance. Parametrization of our results yields new assessments of the aluminum saturation index (ASI) and P and Li contents of Hadean magmas. Magma ASI values are ~0.5 lower than previously thought and consistently remain below 1 during the first ~1 Ga of Earth evolution, suggesting involvement of only igneous protoliths. First peraluminous (ASI > 1) melts do not appear until ca. 3.6 Ga, supporting the hypothesis that a transition from a tectonic style dominated by vertical motion to horizontal tectonics accompanied by partial melting of sediments did not occur before that time. New calculated magma Li concentrations for young zircons are in much better agreement with the continental crust Li abundance. Average calculated Archaean and Hadean magma Li concentrations are unrealistically large (>1000 ppm), suggesting that Li in zircons formed before 2 Ga is not primary. Calculated magma P abundances are uniform (~1900 ± 400 ppm) throughout Earth history, suggesting sufficient crustal P was available throughout the Hadean to support the origin of life.

The Culprit of Bias for Paleointensity Estimation in the Shaw‐Type Protocol and an Innovative Calculation Method

AbstractPaleointensity records are vital for understanding the Earth's evolution, but obtaining accurate paleointensity is a challenging task. The Shaw‐type method, a widely‐used paleointensity protocol, produces biased results occasionally despite strict selection criteria. By examining the relationships between paleointensities and rock magnetic parameters from a pseudo‐Tsunakawa‐Shaw experiment, we ascertain that changes in the ratio of thermal to anhysteretic remanent magnetization (R) are proportional to bias in paleointensity, especially prominent in samples with hundred‐nanometer‐scale magnetic grains, and thus proved to be the culprit for the bias. Furthermore, we develop a method exploiting the Linear regression of R with Diverse cut‐off coercivity intervals for estimating Shaw‐type paleointensities (LoRD‐Shaw). Combined with a curve fit technique for samples with “folding" phenomenon, the LoRD‐Shaw method yields high‐accuracy results in all tested samples, demonstrating its efficiency in mitigating paleointensity bias from thermal alteration. The new method will enhance acquisition of high‐precision paleointensities for constraining the geodynamo evolution.

Robotic exploration of Martian caves: Evaluating operational concepts through analog experiments in lava tubes

Caves on Mars are a tantalizing target for exploration, as they could harbor evidence of extinct or extant life, clues to the planet’s geological history, and even potential future human habitation. However, the inherent challenges of navigating unknown and challenging terrain, coupled with limited communication capabilities, pose significant obstacles for robotic exploration in these caves. This paper presents the results of an effort to evaluate different operational concepts for a mission dedicated to exploration of caves on Mars. We conducted a series of analog exploration experiments in lava tubes on Earth, testing two hypotheses: (1) that two robots are more effective than one, and (2) that high levels of autonomy are more effective than low levels of autonomy. Our findings suggest that two robots are indeed more effective, except in low autonomy cases, where more operational resources are required. We also found that full autonomy is more efficient than low autonomy, as it enables quicker exploration and detection of targets of interest. However, the low autonomy cases benefited from the operator input to acquire higher quality data, an area of autonomy requiring further development. This paper provides insight into the design of our experiments, as well as detailing the results and implications for the design of future missions to explore caves on Mars. By shedding light on the operational concepts tested and their corresponding outcomes, we contribute to the knowledge base required to formulate optimal strategies for the realization of successful cave exploration missions on the Red Planet.

Far–field tectonic controls on deposition in the Appalachian Basin – A case study of Late Cambrian–Late Ordovician strata in Morrow County, Ohio

Far–field tectonics can often be overlooked when studying orogens, particularly when much of the deformation occurs near the loading loci. As stresses are propagated further from the loading into the craton, whether compressional, extensional, or shear, faults and fractures within the basement often act as pathways for stress transmission, traveling along these pre-existing planes of weakness, or creating new. The Appalachian Basin in the eastern United States is a classic foreland basin example that showcases far-field tectonic influence on deposition and structure. This study characterizes the structural architecture of the basement along the western Appalachian Basin margin by analyzing well log data from 2,662 wells to create structure, isopach, trend surface, and residual maps of Late Cambrian through Upper Ordovician strata (Knox through Black River). Fourteen lineaments interpreted as faults were delineated, creating two series of horsts and grabens. The northeast–southwest faults are related to structures that formed during Keweenawan extension, and the northwest–southeast faults are related to structures that formed during the Grenville Orogeny. Both sets of faults stem from the Precambrian basement and are shown to have been reactivated during the Blountian Tectophase of the Taconian Orogeny (Black Riverian deposition), creating localized thinning and thinning adjacent to the lineaments. Furthermore, these faults appear to have undergone additional reactivation since the deposition of these strata in a transtensional regime to create the observed horst and graben structures. Overall, far–field tectonics plays an important role in understanding the geologic history of a basin.

Early Diversification of Membrane Intrinsic Proteins (MIPs) in Eukaryotes.

Membrane intrinsic proteins (MIPs), including aquaporins (AQPs) and aquaglyceroporins (GLPs), form an ancient family of transporters for water and small solutes across biological membranes. The evolutionary history and functions of MIPs have been extensively studied in vertebrates and land plants, but their widespread presence across the eukaryotic tree of life suggests both a more complex evolutionary history and a broader set of functions than previously thought. That said, the early evolution of MIPs remains obscure. The presence of one GLP and four AQP clades across both bacteria and archaea suggests that the first eukaryotes could have possessed up to five MIPs. Here, we report on a previously unknown richness in MIP diversity across all major eukaryotic lineages, including unicellular eukaryotes, which make up the bulk of eukaryotic diversity. Three MIP clades have likely deep evolutionary origins, dating back to the last eukaryotic common ancestor (LECA), and support the presence of a complex MIP repertoire in early eukaryotes. Overall, our findings highlight the growing complexity of the reconstructed LECA genome: the dynamic evolutionary history of MIPs was set in motion when eukaryotes were in their infancy followed by radiative bursts across all main eukaryotic lineages.

Superior detection of low-allele burden Janus kinase 2 V617F mutation and monitoring clonal evolution in myeloproliferative neoplasms using chip-based digital PCR

The JAK2 V617F is a prevalent driver mutation in Philadelphia chromosome-negative myeloproliferative neoplasms (Ph−MPNs), significantly affecting disease progression, immunophenotype, and patient outcomes. The World Health Organization (WHO) guidelines highlight the JAK2 V617F mutation as one of the key diagnostic criterions for Ph−MPNs. In this study, we analyzed 283 MPN samples with the JAK2 V617F mutation to assess the effectiveness of three detection technologies: chip-based digital PCR (cdPCR), real-time quantitative PCR (qPCR), and next-generation sequencing (NGS). Additionally, we investigated the relationship between JAK2 V617F mutant allele burden (% JAK2 V617F) and various laboratory characteristics to elucidate potential implications in MPN diagnosis. Our findings demonstrated high conformance of cdPCR with qPCR/NGS for detecting % JAK2 V617F, but the mutant allele burdens detected by qPCR/NGS were lower than those detected by cdPCR. Moreover, the cdPCR exhibited high sensitivity with a limit of detection (LoD) of 0.08% and a limit of quantification (LoQ) of 0.2% for detecting % JAK2 V617F in MPNs. Clinical implications were explored by correlating % JAK2 V617F with various laboratory characteristics in MPN patients, revealing significant associations with white blood cell counts, lactate dehydrogenase levels, and particularly β2-microglobulin (β2-MG) levels. Finally, a case report illustrated the application of cdPCR in detecting low-allele burdens in a de novo chronic myeloid leukemia (CML) patient with a hidden JAK2 V617F subclone, which expanded during tyrosine kinase inhibitor (TKI) treatment. Our findings underscore the superior sensitivity and accuracy of cdPCR, making it a valuable tool for early diagnosis and monitoring clonal evolution.

Comprehensive genetic analysis reveals the genetic structure and diversity of Calanthe hoshii (Orchidaceae), an endemic species of the Ogasawara Islands: Implications for appropriate conservation of a critically endangered species

AbstractThe Ogasawara Islands, isolated from the continent throughout their geological history, harbor abundant endemic species. However, 32% of the native plant species are on the Japanese Red List, signaling their endangered status. Among these endangered species, Calanthe hoshii stands out as highly susceptible to extinction. Two wild and 89 ex situ individuals were alive in 2020, but the last known wild individual died in October 2021, indicating this species may have become extinct in the wild. Despite the conservation efforts under the Act for the Conservation of Endangered Species of Wild Fauna and Flora, the lack of essential information regarding genetic diversity and population structure among the remaining individuals poses a significant obstacle to developing effective conservation measures. In this research, we conducted a genetic analysis of the wild and ex situ individuals, which revealed notably reduced genetic diversity between individuals, with individual heterozygosity levels (1.0 × 10−5) measuring one‐ninth of those observed within a closely related species Calanthe triplicata (1.5 × 10−4). Comprehensive genetic analysis revealed that C. hoshii consisted of three genetic clusters of different sizes: cluster 1 comprised 95% of the total population, while clusters 2 and 3, with few individuals, were only found in the ex situ populations at Koishikawa Botanical Garden. Since extant C. hoshii maintains a remarkably low genetic diversity at both individual and population levels, it is necessary to consider future management strategies, such as artificial breeding among different clades identified in this study, to safeguard the stability and resilience of this species.

Exploring the Origins and Evolution of Oxygenic and Anoxygenic Photosynthesis in Deeply Branched Cyanobacteriota.

Cyanobacteriota, the sole prokaryotes capable of oxygenic photosynthesis (OxyP), occupy a unique and pivotal role in Earth's history. While the notion that OxyP may have originated from Cyanobacteriota is widely accepted, its early evolution remains elusive. Here, by using both metagenomics and metatranscriptomics, we explore 36 metagenome-assembled genomes from hot spring ecosystems, belonging to two deep-branching cyanobacterial orders: Thermostichales and Gloeomargaritales. Functional investigation reveals that Thermostichales encode the crucial thylakoid membrane biogenesis protein, vesicle-inducing protein in plastids 1 (Vipp1). Based on the phylogenetic results, we infer that the evolution of the thylakoid membrane predates the divergence of Thermostichales from other cyanobacterial groups and that Thermostichales may be the most ancient lineage known to date to have inherited this feature from their common ancestor. Apart from OxyP, both lineages are potentially capable of sulfide-driven AnoxyP by linking sulfide oxidation to the photosynthetic electron transport chain. Unexpectedly, this AnoxyP capacity appears to be an acquired feature, as the key gene sqr was horizontally transferred from later-evolved cyanobacterial lineages. The presence of two D1 protein variants in Thermostichales suggests the functional flexibility of photosystems, ensuring their survival in fluctuating redox environments. Furthermore, all MAGs feature streamlined phycobilisomes with a preference for capturing longer-wavelength light, implying a unique evolutionary trajectory. Collectively, these results reveal the photosynthetic flexibility in these early-diverging cyanobacterial lineages, shedding new light on the early evolution of Cyanobacteriota and their photosynthetic processes.

The Composition of Earth's Lower Mantle

Determining the composition of Earth's lower mantle, which constitutes almost half of its total volume, has been a central goal in the Earth sciences for more than a century given the constraints it places on Earth's origin and evolution. However, whether the major element chemistry of the lower mantle, in the form of, e.g., Mg/Si ratio, is similar to or different from the upper mantle remains debated. Here we use a multidisciplinary approach to address the question of the composition of Earth's lower mantle and, in turn, that of bulk silicate Earth (crust and mantle) by considering the evidence provided by geochemistry, geophysics, mineral physics, and geodynamics. Geochemical and geodynamical evidence largely agrees, indicating a lower-mantle molar Mg/Si of ≥1.12 (≥1.15 for bulk silicate Earth), consistent with the rock record and accumulating evidence for whole-mantle stirring. However, mineral physics–informed profiles of seismic properties, based on a lower mantle made of bridgmanite and ferropericlase, point to Mg/Si ∼ 0.9–1.0 when compared with radial seismic reference models. This highlights the importance of considering the presence of additional minerals (e.g., calcium-perovskite and stishovite) and possibly suggests a lower mantle varying compositionally with depth. In closing, we discuss how we can improve our understanding of lower-mantle and bulk silicate Earth composition, including its impact on the light element budget of the core. ▪The chemical composition of Earth's lower mantle is indispensable for understanding its origin and evolution.▪Earth's lower-mantle composition is reviewed from an integrated mineral physics, geophysical, geochemical, and geodynamical perspective.▪A lower-mantle molar Mg/Si of ≥1.12 is favored but not unique.▪New experiments investigating compositional effects of bridgmanite and ferropericlase elasticity are needed to further our insight.