High Diversity Research Articles

High beta diversity of gaps contributes to plot-level tree diversity in a tropical forest.

Canopy gaps are widely recognized as being crucial for maintaining the diversity of forest tree communities. But empirical studies have found mixed results because the differences in diversity between individual gaps and non-gaps are often small and statistically undetectable. One overlooked factor, however, is how small individual gap versus non-gap differences may accumulate across sites and potentially have a large effect on forest diversity at the plot scale. Our study investigated sapling richness, density, and composition in 124 treefall gaps, and 200 non-gap sites in the 50-ha tropical forest plot at Barro Colorado Island (BCI), Panama. Additionally, we analyzed species accumulation curves to understand how species richness increases with increasing stem numbers. We observed that sapling richness and density were only slightly higher in gaps 7 years after formation and statistically indistinguishable from non-gaps after 12 years. However, species accumulation curves across multiple gaps were substantially higher than those across non-gaps. Species composition showed small differences between individual gaps and non-gaps but differed significantly between collections of gaps and non-gaps. Specifically, 55 species specialized in 7-year-old gaps compared with 24 in non-gaps; of these, 23 gap-specialized species and zero non-gap species were pioneers. Our results indicate that tree species richness is higher in gaps because of both higher stem density and the presence of gap-specialized species. Our study has finally provided compelling evidence to support the idea that gaps enhance the overall diversity of tropical forest tree communities.

The problem of ammonoid substantiation of the Artinskian–Kungurian boundary in Western Verkhoyanie

Kungurian ammonoids had high taxonomic diversity, but were distinguished by an extremely high level of endemism and sharp geographic differentiation. Therefore, outside the regions containing the most important conodont taxa, the Artinskian-Kungurian boundary based on ammonoids must be established through indirect evidence due to the lack of common species with potential global stratotypes of the lower boundary of the Kungurian. A long-term study of the reference sections of the Echian and Tumarian regional stages and their ammonoids made it possible to change the understanding of the bio- and lithostratigraphy of the Artinskian-Kungurian boundary deposits of the Kuranakh structural-facies zone of Western Verkhoyanie. Clarification of the upper boundary of the Khabakh Formation in the stratotype section led to the fact that the ammonoids previously belonging to this formation began to be considered in the lower part of the Orol formation. They characterize the Paratumaroceras? sp. nov. biostratigraphic beds of the lower part of the Tumarian Regional Stage. At the current level of knowledge, the ammonoid substantiation of the Artinskian–Kungurian boundary in Verkhoyanie is difficult due to the existing hiatus corresponding to the Khabakh formation and its age analogues. However, the appearance at the base of the Tumarian Regional Stage of the first paragastrioceratids with a ventral sinus in transverse sculpture (Paratumaroceras? sp. nov.) suggests that the boundary in question is located near the base of the indicated regional stage or even combined with it. For further clearer identification of the Kungurian lower boundary in Verkhoyanie, new studies of the Echian–Tumarian boundary deposits in typical sections, independent of paleontology, are necessary. Such research should primarily include isotope-stratigraphic subdivision and high-precision U-Pb dating.

Runs of Homozygosity decipher genetic diversity in cattle breed dwelling in the colder regions of the world.

Background Our study focuses on Yakutian cattle, a Siberian native breed, examining its inbreeding and diversity through genome-wide analysis of Runs of Homozygosity (ROH). Yakutian cattle are adapted to Siberia's harsh sub-arctic conditions, enduring temperatures below -70°C. However, the population genetics studies on this breed are scanty, to document the genetic uniqueness in this cattle. Results We analyzed 40 Yakutian cattle with strict quality control for ROH detection yielding 683 homozygous segments, averaging to 17 per individual with an average length of 9 Mb. ROH regions were found to be involved in important pathways pertaining to cold adaptation. Autozygosity ranged from 1% to 12% of the genome, with a relatively low average inbreeding coefficient (FROH) of 0.057309, as compared to other breeds. Also, the different diversity indicators namely, principal component analysis, heterozygosity and effective population size analysis revealed prevalence of genetic diversity within the breed. Conclusion Our findings on ROH are first of its kind in Yakutian cattle that support their adaptability to colder environments, as evidenced by low inbreeding and high genetic diversity.

Determining the Association Between MSP1/2 Variant and Multiplicity of Infection on Incidence of Severe Malaria in Sudanese Children in Gezira State, Sudan

The Almanagil province located in Gezira scheme, Gezira state, Sudan, represents a suitable environment for the breeding of malaria-carrying mosquitoes. An estimated 5.9% of Sudanese people suffer from malaria, with 87.6% of cases caused by Plasmodium falciparum and 12.4% by Plasmodium vivax. Clinical manifestation of malaria cases range from mild uncomplicated to severe and fatal complications and the genetic variants and multiplicity of falciparum infection can worsen the manifestations of malaria. The objective of this work is to determine the degree of genetic variation in P. falciparum infection in a high-transmission region of central Sudan by analyzing merozoite surface protein-1 (msp1) and merozoite surface protein-2 (msp2) variations. During the rainy season of 2022, Eighty-nine children with confirmed severe falciparum malaria whom admitted to Almanagil Pediatric Hospital were included in this study. Dry blood spots were used to extract the DNA and amplification of three msp1 and two of msp2 allelic subfamilies, namely K1, RO33 and MAD20 and FC27 and IC/3D7, respectively. The data was analyzed by using SPSS computer program (v 23.0). The three genetic subfamilies of msp1 (K1, RO33 and MAD20) and the two alleles of msp2 (FC27 and IC/3D7) were identified. Msp1 variants represent K1 (64/89, 71.9%), RO33 (56/89, 62.9%) and MAD20 (72/89, 80.9%), while msp2 diversity represents ICI/3D7 (52/89, 58.4%), FC27 (62/89, 69.6%) and ICI/3D7/FC27(33/89, 37.1%). The MAD20 and FC27 showed high genetic diversity among both genes respectively. RO33 allele shows a strong association with severity of falciparum malaria (OR 2.572, P 0.045 ), while the K1 was the lowest risk factor for malaria severity. The allele subfamily K1 and MAD20 of msp1 were associated with hypoglycemia (OR 4.21 and 2.91) respectively. Our study revealed high genetic polymorphisms of msp1 and msp2. Among Central Sudanese children with high MOI of P. falciparum isolates, there was a significant frequency of msp1, a strong association between the K1 allele and hypoglycemia, and a substantial association between the RO33 and MAD20 alleles with the severity of the infection. These findings could help develop malaria control strategies.

Genetic diversity and origin of Kazakh Tobet Dogs

The Kazakh Tobet is an indigenous Kazakh dog breed that has been used to guard livestock since ancient times. To understand the genetic structure and phylogenetic relationship of the Kazakh Tobet breed with other herding and livestock guarding dog breeds, we analysed short tandem repeat data of 107 Kazakh Tobet dogs from different regions of Kazakhstan and Mongolia, as well as whole genome sequencing data from two Kazakh Tobet dogs and 43 dogs from 24 working breeds. Our results indicate a high genetic diversity of the Kazakh Tobet, with the average number of alleles per locus ranging from 6.00 to 10.22 and observed heterozygosity ranging from 76 to 78%. The breed has a complex genetic structure characterised by seven different clusters. The neighbour-joining tree constructed based on 14,668,406 autosomal and the maximum likelihood tree based on mitochondrial D-loop sequences indicate a common genetic heritage between the Kazakh Tobet, the Central Asian Shepherd Dog and the Turkish Akbash. The presence of haplotype A18 in the Kazakh Tobets supports the hypothesis of the ancient origin of the breed, which was previously suggested by archaeological finds and written sources. These results provide an important genetic basis for the ongoing efforts to improve the Kazakh Tobet breed, to ensure its preservation as an independent genetic lineage and to recognise a breed on an international level.

Biodiversity of mudflat intertidal viromes along the Chinese coasts

Viruses constitute the most diverse and abundant biological entities on Earth. However, our understanding of this tiniest life form in complex ecosystems remains limited. Here, we recover 20,102 viral OTUs from twelve intertidal zones along the Chinese coasts. Our analysis demonstrates high viral diversity and functional potential in intertidal zones, encoding important functional genes that can be potentially transferred to microbial hosts and mediate elemental biogeochemical cycles, especially carbon, phosphate and sulfur. Virus-host abundance dynamics vary among different microbial lineages. Viral community composition is closely associated with environmental conditions, including dissolved organic matter. Concordant biogeographic patterns are observed for viruses and microbes. Viral communities are generally habitat specific with low overlaps between intertidal and other habitats. Environmental factors and geographic distance dominate the compositional variation of intertidal viromes. Overall, these findings expand our understanding of intertidal viromes within an ecological framework, providing insights into the virus-host coevolutionary arms race.

Whole-genome sequencing of Klebsiella pneumoniae MDR circulating in a pediatric hospital setting: a comprehensive genome analysis of isolates from Guayaquil, Ecuador

BackgroundKlebsiella pneumoniae is the major cause of nosocomial infections worldwide and is related to a worsening increase in Multidrug-Resistant Bacteria (MDR) and virulence genes that seriously affect immunosuppressed patients, long-stay intensive care patients, elderly individuals, and children. Whole-Genome Sequencing (WGS) has resulted in a useful strategy for characterizing the genomic components of clinically important bacteria, such as K. pneumoniae, enabling them to monitor genetic changes and understand transmission, highlighting the risk of dissemination of resistance and virulence associated genes in hospitals. In this study, we report on WGS 14 clinical isolates of K. pneumoniae from a pediatric hospital biobank of Guayaquil, Ecuador.ResultsThe main findings revealed pronounced genetic heterogeneity among the isolates. Multilocus sequencing type ST45 was the predominant lineage among non-KPC isolates, whereas ST629 was found more frequently among KPC isolates. Phylogenetic analysis suggested local transmission dynamics. Comparative genomic analysis revealed a core set of 3511 conserved genes and an open pangenome in neonatal isolates. The diversity of MLSTs and capsular types, and the high genetic diversity among these isolates indicate high intraspecific variability. In terms of virulence factors, we identified genes associated with adherence, biofilm formation, immune evasion, secretion systems, multidrug efflux pump transporters, and a notably high number of genes related to iron uptake. A large number of these genes were detected in the ST45 isolate, whereas iron uptake yersiniabactin genes were found exclusively in the non-KPC isolates. We observed high resistance to commonly used antibiotics and determined that these isolates exhibited multidrug resistance including β-lactams, aminoglycosides, fluoroquinolones, quinolones, trimetropins, fosfomycin and macrolides; additionally, resistance-associated point mutations and cross-resistance genes were identified in all the isolates. We also report the first K. pneumoniae KPC-3 gene producers in Ecuador.ConclusionsOur WGS results for clinical isolates highlight the importance of MDR in neonatal K. pneumoniae infections and their genetic diversity. WGS will be an imperative strategy for the surveillance of K. pneumoniae in Ecuador, and will contribute to identifying effective treatment strategies for K. pneumoniae infections in critical units in patients at stratified risk.

Upscaling biodiversity monitoring: Metabarcoding estimates 31,846 insect species from Malaise traps across Germany.

Mitigating ongoing losses of insects and their key functions (e.g. pollination) requires tracking large-scale and long-term community changes. However, doing so has been hindered by the high diversity of insect species that requires prohibitively high investments of time, funding and taxonomic expertise when addressed with conventional tools. Here, we show that these concerns can be addressed through a comprehensive, scalable and cost-efficient DNA metabarcoding workflow. We use 1815 samples from 75 Malaise traps across Germany from 2019 and 2020 to demonstrate how metabarcoding can be incorporated into large-scale insect monitoring networks for less than 50€ per sample, including supplies, labour and maintenance. We validated the detected species using two publicly available databases (GBOL and GBIF) and the judgement of taxonomic experts. With an average of 1.4 M sequence reads per sample we uncovered 10,803 validated insect species, of which 83.9% were represented by a single Operational Taxonomic Unit (OTU). We estimated another 21,043 plausible species, which we argue either lack a reference barcode or are undescribed. The total of 31,846 species is similar to the number of insect species known for Germany (~35,500). Because Malaise traps capture only a subset of insects, our approach identified many species likely unknown from Germany or new to science. Our reproducible workflow (~80% OTU-similarity among years) provides a blueprint for large-scale biodiversity monitoring of insects and other biodiversity components in near real time.

Comparative analysis of amphibian genomes: An emerging resource for basic and applied research.

Amphibians are the most threatened group of vertebrates and are in dire need of conservation intervention to ensure their continued survival. They exhibit unique features including a high diversity of reproductive strategies, permeable and specialized skin capable of producing toxins and antimicrobial compounds, multiple genetic mechanisms of sex determination and in some lineages, the ability to regenerate limbs and organs. Although genomic approaches would shed light on these unique traits and aid conservation, sequencing and assembly of amphibian genomes has lagged behind other taxa due to their comparatively large genome sizes. Fortunately, the development of long-read sequencing technologies and initiatives has led to a recent burst of new amphibian genome assemblies. Although growing, the field of amphibian genomics suffers from the lack of annotation resources, tools for working with challenging genomes and lack of high-quality assemblies in multiple clades of amphibians. Here, we analyse 51 publicly available amphibian genomes to evaluate their usefulness for functional genomics research. We report considerable variation in genome assembly quality and completeness and report some of the highest transposable element and repeat contents of any vertebrate. Additionally, we detected an association between transposable element content and climatic variables. Our analysis provides evidence of conserved genome synteny despite the long divergence times of this group, but we also highlight inconsistencies in chromosome naming and orientation across genome assemblies. We discuss sequencing gaps in the phylogeny and suggest key targets for future sequencing endeavours. Finally, we propose increased investment in amphibian genomics research to promote their conservation.

Four in one: An integrative taxonomic revision of the Microhyla berdmorei complex (Amphibia: Anura: Microhylidae) illustrates the tremendous amphibian diversity of Southeast Asia

Abstract Berdmore’s narrow-mouthed frog, Microhyla berdmorei (Blyth, 1856), is the largest member of the genus Microhyla and is distributed all over Southeast Asia, from Northeast India and southern China to Sumatra and Borneo in Indonesia. Here we demonstrate that M. berdmorei represents a complex of four species that are morphologically, acoustically, and genetically distinct from each other, and we implement taxonomic revisions. Phylogenetic analyses of three mitochondrial DNA (hereafter mtDNA, including COI, 12S, and 16S rRNA; 3119 bp) and one nuclear (BDNF; 716 bp) gene sequences are corroborated by phylogenomic analyses of 2700 ddRAD-seq loci (387,270 bp). All support that the M. berdmorei complex, which originates from the early Miocene (ca. 19.7 mya), consists of two clades that we date to the late Miocene (ca. 7.5 mya). The first clade, which regroups populations of large-sized individuals, is distributed in Indo-Burma and includes a lineage from Northeast India, Bangladesh, and Myanmar (M. berdmorei sensu stricto) and a lineage from West Malaysia, Thailand, Laos, Cambodia, and Vietnam (for which we propose to resurrect the species M. malcolmi Cochran, 1927). The second clade, which regroups populations of small-sized individuals, occurs in Sundaland and also includes two lineages for which we provide taxonomic descriptions on species rank. The first new species is widely distributed from Peninsular Malaysia to the islands of Borneo and Sumatra (described herein as M. sundaicasp. nov.), while the second one is restricted to the Malay Peninsula and occurs in extreme southern Thailand and adjacent Malaysia (M. peninsularissp. nov.). We further provide evidence for the synonymy of Callula natatrix Cope, 1867 with M. berdmorei sensu stricto, and M. fowleri Taylor, 1934 with M. malcolmi. Our study illustrates the high diversity of Southeast Asian amphibians, especially in the genus Microhyla, which presently totals 54 species.

Agro-morphological genetic diversity assessment of Amaranthus genotypes from Ethiopia based on qualitative traits

Amaranths are a promising plant in the family of Amaranthaceae because of their nutritional and functional properties, such as their high antioxidant content and dietary fiber content. However, it's being disregarded for several reasons, such as ignorance, a lack of in-depth research, and the plant's long-term genetic growth in Ethiopia, among other factors. In the current work, we described the genetic diversity of 120 amaranth genotypes using qualitative criteria. The experiment, which was configured with an alpha lattice design and duplicated twice, was run for two seasons in 2020 and 2021. Twenty qualitative descriptors were looked for in the gathered data. Among the 20 qualitative variables that were assessed, the chi-square test result indicated the presence of prevailing phenotypic variation. The results of the agro-morphological characterization also revealed a significant amount of variance. The overall mean of the Shannon diversity indices (H') was 0.61. The indices for germination rate, leaf margin, prominence of leaf veins, and the existence of auxiliary inflorescence varied from 0.12 to 0.99. The estimated diversity indices showed more intra-regional diversity (0.66) than inter-regional diversity (0.34), demonstrating the existence of gene flow between growing regions. Shannon–Weaver Diversity Index, ranged from 0.00 for auxiliary inflorescence to 1.94 for leaf coloration, with an overall mean of 19 characters (95%) that were found to have high diversity (> 0.76) while auxiliary inflorescence was invariant. Except for auxiliary inflorescence, all qualitative features showed a lot of variation. Additionally, Amaranthus hybridus L. subsp. cruentus (L.) Theil recorded the greatest Shannon diversity index (0.47) while Amaranthus spinosus L. recorded the lowest (0.00). The hierarchical clustering grouped all the genotypes into three clusters. The first cluster included the most genotypes (58), followed by the second (47), and the third cluster contained the fewest (15). Principal component analysis showed that the first six principal components with eigenvalues greater than one contributed 72% of the variability among genotypes. The study unequivocally demonstrated that, even when the genotypes were grouped into a small number of clusters, there was still enough divergence within the clusters to demonstrate the genotypes of amaranth to have a high genetic diversity. These results indicate that there is substantial genetic diversity among Ethiopian amaranth genotypes, which should be safeguarded and may be utilized in breeding in the future.

Connectivity and high genetic diversity in populations of the dog snapper Lutjanus jocu (Lutjanidae: Perciformes) from the South Western Atlantic, recovered with multilocus analysis

Connectivity and high genetic diversity in populations of the dog snapper Lutjanus jocu (Lutjanidae: Perciformes) from the South Western Atlantic, recovered with multilocus analysis

Spatio-temporal distribution and international context of bovine viral diarrhoea virus genetic diversity in France

Bovine viral diarrhoea (BVD) is one of the most economically damaging livestock enzootic diseases in the world. BVD aetiological agents are three pestiviruses (BVDV-1, -2 and HoBi-like pestivirus), which exhibit high genetic diversity and complex transmission cycles. This considerably hampers the management of the disease, which is why eradication plans have been implemented in several countries. In France, a national plan has been in place since 2019. Our understanding of its impact on the distribution of BVDV genotypes is limited by the availability of French genetic data. Here, we conducted a molecular epidemiology study to refine our knowledge of BVDV genetic diversity in France, characterise its international relationships, and analyse national spatio-temporal genotypic distribution. We collated 1037 BVDV-positive samples throughout France between 2011 and 2023, with a greater sampling effort in two major cattle production areas. We developed a high-throughput sequencing protocol which we used to complete the 5’UTR genotyping of this collection. We show that two main BVDV-1 genotypes, 1e and 1b, account for 88% of genotyped sequences. We also identified seven other BVDV-1 genotypes occurring at low frequencies and three BVDV-2 samples (genotype 2c). Phylogenetic analyses indicate different worldwide distribution patterns between the two main BVDV-1 genotypes. Their relative frequencies present no major changes in France since the 1990s and few variations at the national scale. We also found some degree of local spatial structuring in western France. Overall, our results demonstrate the potential of large-scale sequence-based surveillance to monitor changes in the epidemiological situation of enzootic diseases.

Multiple origins of dorsal ecdysial sutures in trilobites and their relatives

Euarthropods are an extremely diverse phylum in the modern, and have been since their origination in the early Palaeozoic. They grow through moulting the exoskeleton (ecdysis) facilitated by breaking along lines of weakness (sutures). Artiopodans, a group that includes trilobites and their non-biomineralizing relatives, dominated arthropod diversity in benthic communities during the Palaeozoic. Most trilobites – a hyperdiverse group of tens of thousands of species - moult by breaking the exoskeleton along cephalic sutures, a strategy that has contributed to their high diversity during the Palaeozoic. However, the recent description of similar sutures in early diverging non-trilobite artiopodans means that it is unclear whether these sutures evolved deep within Artiopoda, or convergently appeared multiple times within the group. Here, we describe new well-preserved material of Acanthomeridion, a putative early diverging artiopodan, including hitherto unknown details of its ventral anatomy and appendages revealed through CT scanning, highlighting additional possible homologous features between the ventral plates of this taxon and trilobite free cheeks. We used three coding strategies treating ventral plates as homologous to trilobite-free cheeks, to trilobite cephalic doublure, or independently derived. If ventral plates are considered homologous to free cheeks, Acanthomeridion is recovered sister to trilobites, however, dorsal ecdysial sutures are still recovered at many places within Artiopoda. If ventral plates are considered homologous to doublure or non-homologous, then Acanthomeridion is not recovered as sister to trilobites, and thus the ventral plates represent a distinct feature to trilobite doublure/free cheeks.

Multiple origins of dorsal ecdysial sutures in trilobites and their relatives.

Euarthropods are an extremely diverse phylum in the modern, and have been since their origination in the early Palaeozoic. They grow through moulting the exoskeleton (ecdysis) facilitated by breaking along lines of weakness (sutures). Artiopodans, a group that includes trilobites and their non-biomineralizing relatives, dominated arthropod diversity in benthic communities during the Palaeozoic. Most trilobites - a hyperdiverse group of tens of thousands of species - moult by breaking the exoskeleton along cephalic sutures, a strategy that has contributed to their high diversity during the Palaeozoic. However, the recent description of similar sutures in early diverging non-trilobite artiopodans means that it is unclear whether these sutures evolved deep within Artiopoda, or convergently appeared multiple times within the group. Here, we describe new well-preserved material of Acanthomeridion, a putative early diverging artiopodan, including hitherto unknown details of its ventral anatomy and appendages revealed through CT scanning, highlighting additional possible homologous features between the ventral plates of this taxon and trilobite free cheeks. We used three coding strategies treating ventral plates as homologous to trilobite-free cheeks, to trilobite cephalic doublure, or independently derived. If ventral plates are considered homologous to free cheeks, Acanthomeridion is recovered sister to trilobites, however, dorsal ecdysial sutures are still recovered at many places within Artiopoda. If ventral plates are considered homologous to doublure or non-homologous, then Acanthomeridion is not recovered as sister to trilobites, and thus the ventral plates represent a distinct feature to trilobite doublure/free cheeks.

Genetic Diversity of Local Chili (Capsicum annum L.) from West Sumatra Indonesia Based on Inter Simple Sequences Repeat (ISSR) Markers

Capsicum annum L. is the most widely cultivated species due to its economic importance and health benefits. West Sumatra is one of the largest chili pepper producers in Indonesia, so it has a lot of local chili genetic resources. There is inadequate information on the genetic diversity of local chilies in West Sumatra. The purpose of this research was to analyze the genetic diversity of 23 genotypes of chili pepper from West Sumatra amplified with 10 markers of ISSR. The material used was leaves from 23 genotypes of West Sumatra’s local chili which are collections of the Agriculture Faculty, Andalas University, Padang, West Sumatra. The results showed that ISSR markers (ISSR primer 12, ISSR UBC, and ISSR 3M) had produced 84 polymorphic DNA bands with a total polymorphic percentage of 61.45%. The dendrogram based on 10 ISSR markers showed that the 23 chili genotypes were retrieved into three main groups (I, II, III, IV) with genetic similarity coefficient values ranging from 0.67 to 0.97 or a diversity of features of 0.03–0.33 (30%). Group I consisted of 1 genotype, group II consisted of 3 genotypes, and group III consisted of 14 genotypes. Kopay chili (G20) has a large genetic distance compared to the other genotypes, while Lolai and Gero chilies have a very high similarity. This genetic diversity information can be used as a basis for generating crosses between genotypes in a breeding program. The farther the genetic distance will produce a high population diversity, the greater the chance of getting superior hybrids. Keywords: Capsicum annum, ISSR, local chili, West Sumatra

Higher abundance of disturbance‐favoured trees and shrubs in European temperate woodlands prior to the late‐quaternary extinction of megafauna

Abstract Large herbivorous mammals strongly influence vegetation structure by creating and maintaining open areas and causing disturbance within closed woody habitats. The herbivores alive today in Europe are only a small remnant of the large species that existed in high diversity and abundance before modern humans. The extinction of so many large herbivores during the last 50,000 years, and the loss of megaherbivores (body weight ≥1000 kg) from most of the continent before the Pleistocene–Holocene transition, is likely to have had cascading effects on vegetation structure and composition. To evaluate these effects within the European temperate forest biome, we examine the abundance change of three important European woody taxa (deciduous oaks, Quercus spp.; hazel, Corylus [mainly C. avellana]; and yew, Taxus baccata) before and after the late‐Quaternary downgrading of the region''s large herbivore fauna. These taxa are disturbance‐favoured, depend on canopy openings for regeneration, and tend to decline in closed dense forests. Quercus and Corylus may thrive in systems affected by megafauna herbivory or fire, whilst Taxus is fire‐sensitive but can thrive in grazed systems. Using pollen‐based reconstructions (REVEALS), we investigated the proportional cover of these three focal taxa in the Last Interglacial (129,000–116,000 before present [BP]) and early–mid‐Holocene (8700–5700 BP). We found that woodlands in the Last Interglacial exhibited higher cover of Corylus and Taxus relative to the Holocene, with the former reaching very high percentage cover; meanwhile, Quercus had a consistent, moderately high percentage cover in both periods. Furthermore, we found that the cover of Corylus and Taxus appeared to be influenced more by unmeasured, non‐climatic factors than Quercus. Synthesis: The abundance of Taxus suggests a limited role of fire; whilst the observed levels of Taxus, Corylus and Quercus align with the potential influence of megafauna herbivory; however, a direct quantitative link remains to be established. Our results suggest that vegetation was structurally and compositionally affected by differences in disturbance regimes between the Last Interglacial and early–mid‐Holocene, with the loss of diverse disturbance regimes likely contributing to the divergence of Holocene vegetation from long‐term ecological baselines.

Is development and persistence of multiple physical symptoms associated with coping? A longitudinal study over a decade

ObjectiveTo examine the development and persistence of multiple physical symptoms (MPS) over a decade including the associations with sociodemographics and coping strategies. MethodA longitudinal study of 16,405 individuals aged 20–64 years participating in the Danish Symptom Cohort (DaSC) was conducted in 2012 with follow-up data in 2022 (DaSC II). MPS were assessed according to the unifying diagnostic construct of bodily distress syndrome, and coping was measured with the Brief Approach/Avoidance Coping Questionnaire. Descriptive statistics and multivariable logistic regression analyses were performed. ResultsAmong individuals not having MPS in 2012, 17 % had developed MPS in 2022. Among individuals having MPS in 2012, 57 % had persistence of MPS in 2022. Individuals who developed or had persistence of MPS at follow-up were more likely to be female, have lower educational level, be immigrant, redeem antidepressants, have lower approach scores as well as higher diversion and resignation scores. ConclusionsIndividuals responding to stressful situations with low approach, high diversion, and high resignation may be at higher risk of developing MPS and have persistence of MPS. As coping can be targeted through psychotherapy, it is important to focus on maladaptive strategies, especially in high-risk groups for developing and maintaining MPS.

Transformer Based Pluralistic Image Completion With Reduced Information Loss.

Transformer based methods have achieved great success in image inpainting recently. However, we find that these solutions regard each pixel as a token, thus suffering from an information loss issue from two aspects: 1) They downsample the input image into much lower resolutions for efficiency consideration. 2) They quantize 2563 RGB values to a small number (such as 512) of quantized color values. The indices of quantized pixels are used as tokens for the inputs and prediction targets of the transformer. To mitigate these issues, we propose a new transformer based framework called "PUT". Specifically, to avoid input downsampling while maintaining computation efficiency, we design a patch-based auto-encoder P-VQVAE. The encoder converts the masked image into non-overlapped patch tokens and the decoder recovers the masked regions from the inpainted tokens while keeping the unmasked regions unchanged. To eliminate the information loss caused by input quantization, an Un-quantized Transformer is applied. It directly takes features from the P-VQVAE encoder as input without any quantization and only regards the quantized tokens as prediction targets. Furthermore, to make the inpainting process more controllable, we introduce semantic and structural conditions as extra guidance. Extensive experiments show that our method greatly outperforms existing transformer based methods on image fidelity and achieves much higher diversity and better fidelity than state-of-the-art pluralistic inpainting methods on complex large-scale datasets (e.g., ImageNet).

Using multilayer network analysis to detect the collaborative knowledge construction characteristics among learner groups with low, medium, and high levels of cognitive engagement

Collaborative knowledge construction (CKC) is advanced by group members’ cognitive engagement across three levels: individual-level knowledge processing and proposing, the peer-level social interactions and knowledge exchanges between two group members, and the group-level coordination and construction of knowledge across multiple group members. The interconnected and transformative relationship among three levels is an essential factor during the CKC process. Individual viewpoints can trigger peer feedback, which can be further refined by other group members; the group-level consensus can provide foundations for subsequent individual- or peer-level cognitive engagement. The group-level coordination of knowledge advancement involves the processing, synthesis, and reflection of knowledge from multiple members to reach a group consensus. However, previous analytical approaches have faced challenges in modeling distinct types of interconnections across the individual, peer, and group levels during the CKC process. To address this gap, this research employed multilayer network analysis (MNA) to model and quantify the multi-level and interconnected characteristics of CKC in a series of face-to-face, computer-supported CKC activities in China’s higher education. First, small groups were categorized into the high, medium, and low levels of cognitive engagement groups. Second, multilayer networks were constructed for each category, where students’ use of cognitive strategies were set as nodes, the interconnections between cognitive strategies were set as edges, and three levels (i.e., individual, peer, and group levels) were set as layers. The node-, layer-, and network-level metrics were calculated to quantify the overall characteristics of the networks, the interconnected characteristics within a level and across the three levels. The MNA results revealed that, compared to lower level of cognitive engagement groups, groups with higher cognitive engagement demonstrated (1) more influential moderate and deep cognitive strategies at group and peer levels; (2) interconnections between cognitive strategies with higher diversity, connectivity, and more balanced distribution across three levels, but relatively lower information exchanging efficiency; and (3) communities with more interconnections related to the moderate and deep cognitive strategies at peer and group levels. Based on the empirical findings, this research proposed pedagogical implications for CKC practices and analytical implications for using MNA to improve the understanding of computer-supported collaborative learning mechanisms.