Search Results (402)

Pleurotus tuoliensis is a unique species discovered in Xinjiang, China, which is recognized for its significant edible, medicinal, and economic value. It has been successfully incorporated into industrial production. Controversy has emerged concerning the evolution and environmental adaptability of this species due to inadequate interspecific ecology and molecular data. This study examines the germplasm resources of P. tuoliensis in the Xinjiang region. A total of 225 wild and cultivated strains of P. tuoliensis were gathered from seven representative regions. Phylogenetic analysis revealed that seven populations were notably segregated into three distinct groups, primarily attributed to environmental factors as the underlying cause for this differentiation. Population historical size data indicate that P. tuoliensis underwent two expansion events, one between 2 and 0.9 Mya (Miocene) and the other between 15 and 4 Mya (Early Pleistocene). The ancient climate fluctuations in the Xinjiang region might have contributed to the comparatively modest population size during the Pliocene epoch. Moreover, through the integration of biogeography and ancestral state reconstruction, it was determined that group C of P. tuoliensis emerged initially and subsequently dispersed to groups D and B, in that order. Subsequently, group D underwent independent evolution, whereas group B continued to diversify into groups A and EFG. The primary factor influencing this mode of transmission route is related to the geographical conditions and prevailing wind direction of each group. Subsequent research endeavors focused on assessing the domestication adaptability of P. tuoliensis to different substrates. It was found that the metabolic processes adapted during the domestication process were mainly related to energy metabolism, DNA repair, and environmental adaptability. Processes adapted to the host adaptability include responses to the host (meiosis, cell cycle, etc.) and stress in the growth environment (cysteine and methionine metabolism, sulfur metabolism, etc.). This study analyzed the systematic evolution and genetic differentiation of P. tuoliensis in Xinjiang. The identified loci and genes provide a theoretical basis for the subsequent improvement of germplasm resources and conducting molecular breeding. Full article

Cynanchum belongs to the Apocynaceae family and is a morphologically diverse genus that includes around 200 shrub or perennial herb species. Despite the utilization of CPGs, few molecular phylogenetic studies have endeavored to elucidate infrafamilial relationships within Cynanchum through extensive taxon sampling. In this research, we constructed a phylogeny and estimated divergence time based on the chloroplast genomes (CPGs) of nine Cynanchum species. We sequenced and annotated nine chloroplast (CP) genomes in this study. The comparative analysis of these genomes from these Cynanchum species revealed a typical quadripartite structure, with a total sequence length ranging from 158,283 to 161,241 base pairs (bp). The CP genome (CPG) was highly conserved and moderately differentiated. Through annotation, we identified a total of 129–132 genes. Analysis of the boundaries of inverted repeat (IR) regions showed consistent positioning: the rps19 gene was located in the IRb region, varying from 46 to 50 bp. IRb/SSC junctions were located between the trnN and ndhF genes. We did not detect major expansions or contractions in the IR region or rearrangements or insertions in the CPGs of the nine Cynanchum species. The results of SSR analysis revealed a variation in the number of SSRs, ranging from 112 to 150. In five types of SSRs, the largest number was mononucleotide repeats, and the smallest number was hexanucleotide repeats. The number of long repeats in the cp genomes of nine Cynanchum species was from 35 to 80. In nine species of Cynanchum, the GC3s values ranged from 26.80% to 27.00%, indicating a strong bias towards A/U-ending codons. Comparative analyses revealed four hotspot regions in the CPG, ndhA-ndhH, trnI-GAU-rrn16, psbI-trnS-GCU, and rps7-ndhB, which could potentially serve as molecular markers. In addition, phylogenetic tree construction based on the CPG indicated that the nine Cynanchum species formed a monophyletic group. Molecular dating suggested that Cynanchum diverged from its sister genus approximately 18.87 million years ago (Mya) and species diversification within the Cynanchum species primarily occurred during the recent Miocene epoch. The divergence time estimation presented in this study will facilitate future research on Cynanchum, aid in species differentiation, and facilitate diverse investigations into this economically and ecologically important genus. Full article

The Osumi Granodiorite, located on the Osumi Peninsula in southwest Japan, is an example of outer zone granites that were formed during a limited period (13–15 Ma) in response to the subduction of the Philippine Sea Plate. This event, which is linked to the separation of southwest Japan from continental Asia, resulted in unique igneous activity. The Osumi Granodiorite is the largest Miocene granite body in the region. It intrudes into the Mesozoic to Paleogene accretionary complex of the Shimanto Belt and affects contact metamorphism. Despite considerable research on the Osumi Granodiorite, limited geochemical studies, especially on trace and rare earth element (REE) analyses, have been conducted. Furthermore, there are insufficient data on the Rb–Sr isotopic system, leaving the formation process unclear. This study presents whole-rock geochemical and Rb-Sr isotopic data to investigate the petrogenesis of the Osumi Granodiorite. The results suggest a common magma origin for this pluton, as indicated by linear trends on the Harker diagrams and similar REE patterns. The presence of a relatively large Eu anomaly implies formation under a reducing environment. The AKF diagram indicates predominant contamination by pelitic rocks of the Shimanto Belt during magma formation. The Rb–Sr whole-rock isochron diagram and SrI–1000/Sr diagram suggest that the Osumi Granodiorite body was formed by heterogeneous assimilation of magma into the Shimanto Belt. Furthermore, the whole-rock isochron age is 64.3 Ma, which differs by approximately 50 My from the previously reported biotite K–Ar age (14–22 Ma). This age is considered to be a pseudo-isochron age, rather than the consolidation age. During the middle Miocene, the compressive stress field in the outer zone south of the Butsuzo Tectonic Line made it difficult for magma to rise. As a result, it reacted with the sedimentary rocks of the Shimanto Belt to various degrees. The Osumi Granodiorite underwent magma differentiation upon intrusion into the Shimanto Belt. It subsequently ascended, cooled, and interacted with pelitic rocks under stable geological conditions. Full article

This paper focuses on the structural and finite strain analysis of the Pelagonian nappe, the HP/LT Ampelakia unit, and the Olympos-Ossa unit in the Olympos-Ossa mountainous area in order to better understand the exhumation history of the Ampelakia unit and the underlain Olympos-Ossa unit. Two main stages of Tertiary deformation were revealed, related to nappe stacking and exhumation processes. During the Paleocene–Eocene crustal subduction, HP/LT metamorphism, compression, and nappe stacking were developed progressively. This D₁ stage was terminated with the final SW-ward emplacement of the Ampelakia and Pelagonian nappe on the Olympos-Ossa unit during the Eocene–Early Oligocene. The next stage of deformation, D₂, was developed during the Oligocene–Miocene following the orogenic nappes stacking. D₂ was considered an extensional event, related to metamorphic isothermal decompression, nappes tectonic denudation, crustal uplift, and final exhumation of the Ampelakia unit and the Olympos-Ossa unit as a tectonic window. The calculated finite strain ellipsoids indicate a main flattening type strain geometry and middle strain intensity, increasing along the nappe contacts. The quartz C-axes diagrams also reveal a flattening type of deformation and non-coaxial flow towards the southwest and northeast at the western and eastern flanks of Olympos-Ossa Mountain, respectively. The calculated W_k vorticity number ranges from 0.23 to 0.93. Full article

SE Anatolia is witnessing the final stage of the Wilson Cycle, where a continental collision between the Tauride–Anatolide block and Arabian platform occurred, and a 1.5 km Eastern Tauride mountain chain formed. We present new low-temperature thermochronology (LTT) ages, including eight apatite fission track (AFT) and seven apatite and zircon U-Th-Sm/He (AHe, ZHe) ages, for the metamorphic rocks from the Nappe Zone of the Southeast Anatolian Orogenic Belt. The ZHe ages vary from 51.2 ± 0.7 Ma to 30.4 ± 0.6 Ma, the AFT ages range from 33.1 ± 1.6 Ma to 18.1 ± 0.9 Ma, and the AHe ages range from 23.6 ± 2.5 Ma to 6 ± 1.9 Ma. The LTT data show a continuous slow uplift of the region. However, the thermal modeling results suggest an Eocene and middle–late Miocene fast uplift of the region. Similar to our results, the LTT studies along the SAOB show that the vertical movements initiated during the Eocene period have continued in a steady-state regime to recent times. The Eocene epoch is identified by arc–back-arc setting in the region, whereas the Miocene epoch is marked by the continental collision. Within this tectonic framework, vertical movements on the overriding plate are controlled by both extensional and compressional tectonics. The LTT data obtained along the SAOB show fingerprints of thrust propagation from north to south. Full article

The mountainous regions of southwest China are recognized as pivotal centers for the origin and evolution of Osmanthus species. Baoxing Osmanthus (Osmanthus serrulatus Rehder), a rare and endemic species known for its spring blooms, is sparsely distributed within the high altitude evergreen broad-leaved forests surrounding the southwestern Sichuan Basin. However, persistent anthropogenic disturbances and habitat fragmentation have precipitated a significant decline in its natural population size, leading to the erosion of genetic resources. To assess the genetic status of O. serrulatus and formulate effective conservation strategies, we conducted sampling across ten wild populations, totaling 148 individuals in their natural habitats. We employed two cpDNA fragments (matK and trnS-trnG) to elucidate the phylogeographic structure and historical population dynamics. The results revealed low species-level genetic diversity, alongside pronounced regional differentiation among populations (F_ST = 0.812, p < 0.05) and a notable phylogeographic structure (N_ST = 0.698 > G_ST = 0.396, p < 0.05). Notably, genetic variation was predominantly observed among populations (81.23%), with no evidence of recent demographic expansion across the O. serrulatus distribution range. Furthermore, divergence dating indicated a timeline of approximately 4.85 Mya, corresponding to the late Miocene to early Pleistocene. This temporal correlation coincided with localized uplift events in the southwestern mountains and heightened Asian monsoons, suggesting pivotal roles for these factors in shaping the current phylogeographic pattern of O. serrulatus. These findings support the effective conservation of O. serrulatus germplasm and offer insights into the impact of Quaternary climate oscillations on companion species within evergreen broad-leaved forests. They also enhance our understanding of the origin and evolution of these forests in the southwestern mountains, aiding biodiversity conservation efforts in the region. Full article

The Upper Miocene–Pliocene Kampungbaru Formation crops out in the easternmost part of the Lower Kutai Basin, Indonesia. The sedimentological analysis of seven outcrops was carried out, and a total of twenty-five samples from these outcrops was analyzed for bulk geochemistry, organic petrography, and bulk and clay mineralogy to assess the effect of the climate and depositional environment on organic matter enrichment. The Kampungbaru Formation consists of interbedded sandstone, siltstone, claystone, and thick coal beds, which were classified into eleven lithofacies. Subsequently, seven facies associations were identified, namely the fluvial-dominated distributary channel, sheet-like sandstone, tide-influenced distributary channel, mouth bar, crevasse splay, delta plain, and delta front. The coal facies generally have a high amount of total organic carbon (TOC, 5.1–16.9; avg. 10.11 wt.%), and non-coal layers range from 0.03 to 4.22 wt.% (avg. 1.54 wt.%). The dominant maceral is vitrinite, while liptinite occurs only rarely in the samples. Organic matter is inferred to have originated from terrestrial plants growing in mangrove swamps. Identified clay minerals include varying proportions of kaolinite, illite, chlorite, and mixed layer illite/smectite (I/S). Kaolinite, which commonly constitutes up to 30% of the clay volume, indicates intensive chemical weathering during a warm and humid climate. In accordance with the Köppen climate classification, the paleoclimate during the deposition of the Kampungbaru Formation is classified as type Af, which is a tropical rainforest. Tropical climate was favorable for the growth of higher plants and deposition of organic matter under anoxic conditions and led to higher amounts of TOC in the Kampungbaru Formation. Full article

The Old-World quails, Coturnix coturnix (common quail) and Coturnix japonica (Japanese quail), are morphologically similar yet occupy distinct geographic ranges. This study aimed to elucidate their evolutionary trajectory and ancestral distribution patterns through a thorough analysis of their mitochondrial genomes. Mitogenomic analysis revealed high structural conservation, identical translational mechanisms, and similar evolutionary pressures in both species. Selection analysis revealed significant evidence of positive selection across the Coturnix lineage for the nad4 gene tree owing to environmental changes and acclimatization requirements during its evolutionary history. Divergence time estimations imply that diversification among Coturnix species occurred in the mid-Miocene (13.89 Ma), and their current distributions were primarily shaped by dispersal rather than global vicariance events. Phylogenetic analysis indicates a close relationship between C. coturnix and C. japonica, with divergence estimated at 2.25 Ma during the Pleistocene epoch. Ancestral range reconstructions indicate that the ancestors of the Coturnix clade were distributed over the Oriental region. C. coturnix subsequently dispersed to Eurasia and Africa, and C. japonica to eastern Asia. We hypothesize that the current geographic distributions of C. coturnix and C. japonica result from their unique dispersal strategies, developed to evade interspecific territoriality and influenced by the Tibetan Plateau’s geographic constraints. This study advances our understanding of the biogeographic and evolutionary processes leading to the diversification of C. coturnix and C. japonica, laying important groundwork for further research on this genus. Full article

The Indo-Australian Archipelago (IAA) today exhibits the highest marine biodiversity, which has been evolving since the early Miocene. The existence of this high palaeobiodiversity is attested to by the presence of many fossil invertebrates; however, the region’s fossil fish record is sparse and understudied, which is also the case for cartilaginous fishes. Elasmobranch fossils are dominantly represented by shark and ray teeth in the geological record and can give a quick overview of the composition of the fauna. The first IAA elasmo fossils, shark teeth were described from Java (Indonesia) at the end of the 19th century, and until today, most of the publications are known from this island. In the early and middle of the 20th century, remarkable fossils were also reported from the islands of Madura (NE Java) and Sulawesi, some with detailed taxonomical descriptions. In addition, only sporadic reports on fossil occurrences exist elsewhere from the IAA, but these lack any detailed taxonomic accounts. In 2019 our research group reported a late Miocene elasmobranch fauna from Brunei (Borneo), which is now the most diverse known shallow water fossil assemblage from the entire IAA. This fauna was described from a single fossiliferous outcrop, called Ambug Hill. However, several new localities have been discovered and studied over the years, as a result the number of fossils increased, and their age range extended. Here we provide an overview of these new sites and their elasmobranch fossils, and describe remains from ten taxa among, of which eight are new to the IAA fossil record (Chiloscyllium sp., cf. Hemitriakis sp., Paragaleus sp., Carcharhinus borneensis, C. limbatus, Lamiopsis sp., Scoliodon sp., Rhinobatos sp.). The overall north Bornean elasmo assemblage is then compared with other IAA occurrences. An extended fauna list is given based on literature review and preliminary investigation of the Naturalis Biodiversity Centre collection in Leiden (The Netherlands) where most of the fossil fishes of the early explorations are stored. These assemblages are also briefly summarized, and attention is drawn to some of the unique and thus far unreported taxa (e.g., Dalatias licha). Full article

Fossils can document the morphological diversification through time and date lineages, providing relevant characters are preserved. Primascena Klimaszewsi, 1997 was erected for P. subita Klimaszewsi, 1997 on the basis of a single, partly damaged male from Dominican amber. Originally assigned to Rhinocolidae: Paurocephalinae, the genus was subsequently transferred to Psyllidae: Aphalaroidinae. Recently, two undescribed species resembling the fossil species were discovered in Brazil (Mato Grosso do Sul), allowing a detailed morphological study of adults and immatures. Based on the morphological study, a revised diagnosis of the genus is provided, including the previously unknown female and fifth instar immatures. Primascena subita is redescribed and P. empsycha n. spec. and P. ruprechtiae n. spec. are formally described and illustrated. An identification key is provided for the species of Primascena. A cladistic morphological analysis supports the placement of the two new species in Primascena, and of this genus in the Aphalaroidinae. It is sister to all but Aphalaroida, though with little support. The two Brazilian species develop on Ruprechtia spp. (Polygonaceae: Eriogonoideae), an unusual psyllid host. Immatures of P. ruprechtiae are free-living on the lower leaf face and do not induce galls. Full article

Eolian sediments are extensively distributed across the Earth’s surface, and their formation is intricately linked to climate change, tectonic activity, and topographic features. Consequently, the investigation of eolian sediments bears great geological significance. The northwest region of China is renowned for hosting the most extensive and thickest Late Miocene–Pliocene red clay deposits globally. Nonetheless, scholars have yet to reach a consensus regarding the precise formation processes of these red clays. The identification of the source region of the red clays is crucial for comprehending their formation mechanism. The correlation of zircon U-Pb age spectra is a frequently utilized method for determining the provenance of eolian sediments. In this study, we compared the previously published zircon U-Pb ages (n = 12,918) of the Late Miocene–Pliocene red clays in the Ordos Plateau with those from the potential provenance regions (n = 24,280). The analysis, supported by the tectonic and climatic background of the region, revealed that the Late Miocene–Pliocene red clay in the Ordos Plateau originates predominantly from the Yellow and Wei rivers, with a minor contribution from the weathering of bedrock in the western North China Craton. The transport of these detrital materials by the East Asian winter monsoon is impeded by the presence of the Qinling and Taihang Shan, resulting in their deposition on the flat surface of the Ordos Plateau. This development of red clay is consistent with the proximal accumulation model, illustrating how the hydrosphere, atmosphere, and lithosphere interacted to shape the red clay deposits during the Late Miocene and Pliocene periods in the Ordos Plateau. Full article

Sinojackia Hu. comprises five to eight Chinese endemic species with high ornamental and medicinal value. However, the generic limits, interspecific relationships and evolutionary history of the genus remain unresolved. In this study, we newly sequenced three plastomes of S. oblongicarpa and compared them with those of the other congeneric species to explore the taxonomic delimitation of the species and the evolutionary history of the genus. The plastome structure of Sinojackia species was extremely conserved in terms of number of genes, sequence length, and GC content. The codon usage patterns revealed that natural selection may be the main factor shaping codon usage bias. Our phylogenetic tree shows that Sinojackia is monophyletic and can be divided into two clades. Sinojackia oblongicarpa as a distinct species is supported for it is distantly related to S. sarcocarpa. The evolutionary analysis of morphological features indicates that the woody mesocarp is an ancestral feature. Sinojackia originated in central Southeast China during the early Miocene. In this period, it experienced elevated diversification and migrated from central Southeast China to the Hunan Province and the Sichuan Province with the development of the Asian monsoon and East Asian flora. Glacial–interglacial interactions with the monsoon climate may provide favorable expansion conditions for Sinojackia on a small scale. Full article

Potamanthidae belongs to the superfamily Ephemeroidea but has no complete mt genome released in the NCBI (except for two unchecked and one partial mt genome). Since the sister clade to Potamanthidae has always been controversial, we sequenced seven mt genomes of Potamanthidae (two species from Rhoenanthus and five species from Potamanthus) in order to rebuild the phylogenetic relationships of Potamanthidae in this study. The divergence time of Potamanthidae was also investigated by utilizing five fossil calibration points because of the indeterminate origin time. In addition, because Rhoenanthus coreanus and Potamanthus luteus are always in low-temperature environments, we aimed to explore whether these two species were under positive selection at the mt genome level. Amongst the 13 PCGs, CGA was used as the start codon in COX1, whereas other genes conformed to initiating with an ATN start codon. From this analysis, UUA (L), AUU (I), and UUU (F) had the highest usage. Furthermore, the DHU arm was absent in the secondary structure of S1 in all species. By combining the 13 PCGs and 2 rRNAs, we reconstructed the phylogenetic relationship of Potamanthidae within Ephemeroptera. The monophyly of Potamanthidae and the monophyly of Rhoenanthus and Potamanthus were supported in the results. The phylogenetic relationship of Potamanthidae + (Ephemeridae + Polymitarcyidae) was also recovered with a high prior probability. The divergence times of Potamanthidae were traced to be 90.44 Mya (95% HPD, 62.80–121.74 Mya), and the divergence times of Rhoenanthus and Potamanthus originated at approximately 64.77 Mya (95% HPD, 43.82–88.68 Mya), thus belonging to the late Pliocene Epoch or early Miocene Epoch. In addition, the data indicated that R. coreanus was under negative selection and that ATP8 and ND2 in Potamanthidae had a high evolutionary rate. Full article

The 2012 satellite ASTER geoscience maps of Australia were designed to provide public, web-accessible, and spatially comprehensive surface mineralogy for improved mapping and solutions to geoscience challenges. However, a number of the 2012 products were clearly compromised by variable green and/or dry vegetation cover. Here, we show a strategy to first estimate and then unmix the contributions of both these vegetation components to leave, as residual, the target surface mineralogy. The success of this unmixing process is validated by (i) visual suppression/removal of the regional climate and/or local fire-scar vegetation patterns; and (ii) pixel values more closely matching field sample data. In this process, we also found that the 2012 spectral indices used to gauge the AlOH content, AlOH composition, and water content can be improved. The updated (new indices and vegetation unmixed) maps reveal new geoscience information, including: (i) regional “wet” and “dry” zones that appear to express “deep” geological characters often expressed through thick regolith cover, with one zone over the Yilgarn Craton spatially anti-correlated with Archaean gold deposits; (ii) a ~1000 km wide circular feature over the Lake Eyre region defined by a rim of abundant “muscovite” that appears to coincide with opal deposits; (iii) a N–S zonation across the western half of the continent defined by abundant muscovite in the south and kaolinite in the north, which appears to reflect opposing E ↔ W aeolian sediment transport directions across the high-pressure belt; (iv) various paleo-drainage networks, including those over aeolian sand covered the “lowlands” of the Canning Basin, which are characterized by low AlOH content, as well as those over eroding “uplands”, such as the Yilgarn Craton, which have complicated compositional patterns; and (v) a chronological history of Miocene barrier shorelines, back-beach lagoons, and alluvial fans across the Eucla Basin, which, to date, had proved elusive to map using other techniques, with potential implications for heavy mineral sand exploration. Here, we explore the latter three issues. Full article

Agate veins and nodules occur in the Lece Volcanic Complex (Oligocene-Miocene) situated in the south of Serbia and occupying an area of 700 km². This volcanic complex is composed predominantly of andesites, with sporadic occurrences of andesite-basalts, dacites and latites, and features agate formations that have been very little investigated. This study focuses on five selected agate occurrences within the Lece Volcanic Complex, employing optical microscopy, scanning electron microscopy (SEM), X-ray powder diffraction analysis, inductively coupled plasma mass spectrometry (ICP-MS), and Fourier transform infrared spectroscopy (FTIR). In three localities (Rasovača, Mehane, and Ždraljevići), agate mineralization is directly related to distinct fault zones with strong local brecciation. In the other two localities (Vlasovo and Sokolov Vis), the agate is found in nodular form and does not show any connection with fracture zones. The silica phases of the Lece volcanic agates consist of cristobalite and tridymite, length-fast chalcedony, quartzine (length-slow chalcedony), and macrocrystalline quartz. Vein agates show a frequent alternation between length-fast chalcedony and quartz bands. Nodular agates consist primarily of length-fast chalcedony, occasionally containing notable quantities of opal-CT, absent in vein agates. Microtextures present in vein agates include crustiform, colloform, comb, mosaic, flamboyant, and pseudo-bladed. Jigsaw puzzle quartz microtexture supports the recrystallization of previously deposited silica in the form of opal or chalcedony from hydrothermal fluids. Growth lines in euhedral quartz (Bambauer quartz) point to agate formations in varying physicochemical conditions. These features indicate epithermal conditions during the formation of hydrothermal vein agates. Due to intense hydrothermal activity, vein agate host rocks are intensively silicified. Vein agates are also enriched with typical ore metallic elements (especially Pb, Co, As, Sb, and W), indicating genetic relation with the formation of polymetallic ore deposits of the Lece Volcanic Complex. In contrast, nodular agates have a higher content of major elements of host rocks (Al₂O₃, MgO, CaO, Na₂O, and K₂O), most probably mobilized from volcanic host rocks. Organic matter, present in both vein and nodular agate with filamentous forms found only in nodular agate, suggests formation in near-surface conditions. Full article