Low Levels Of Variation Research Articles

Genetic Diversity Among Independent Isolates of the Dolichocephalovirinae Subfamily

Members of the Dolichocephalovirinae subfamily are giant viruses with an elongated head and a flexible tail that is used to infect Caulobacter strains. In this paper, we describe the isolation and characterization of nine newly isolated phages and present evidence that seven of these phages represent a new Dolichocephalovirinae genus that has significant differences from the four previously described Dolichocephalovirinae genera. In addition, since these new phages were isolated from a single sampling site over the course of three years, a comparison of their genome sequences reveals a low level of within-population diversity resulting from both single-nucleotide polymorphisms and insertions or deletions. A comparison of the host ranges of these phages suggests that differences in host susceptibility may be an important factor in maintaining this diversity.

The genomic landscape of short tandem repeats in cattle.

Short tandem repeats (STRs) are abundant and have high mutation rates across cattle genomes; however, comprehensive exploration of cattle STRs is needed. Here, we constructed a comprehensive map of 467 553 polymorphic STRs (pSTRs) constructed from 423 cattle genomes representing 59 breeds worldwide. We observed that pSTRs in coding sequences and 5'UTRs (Untranslated Regions) were under strong selective constraints and exhibited a relatively low level of diversity. Furthermore, we found that these pSTRs underwent more contraction than expansion. Population analysis showed a strong positive correlation (R = 1) between pSTR diversity and single nucleotide polymorphic heterozygosity. We also investigated STR differences between taurine and indicine cattle and detected 2301 highly divergent STRs, which might relate to immune, endocrine and neurodevelopmental pathways. In summary, our large-scale study characterizes the spectrum of STRs in cattle, expands the scale of known cattle STR variation and provides novel insights into differences among various cattle subspecies.

Diversity-productivity relationships of savanna ecosystems in the Cerrado-Pantanal transition of southern Mato Grosso, Brazil

Productivity and ecosystem carbon (C) storage are often positively associated with species and/or structural diversity; however, positive relationships in tropical forests and woodlands are not universal and the strength of this relationship may be affected by climate. Diversity-productivity relationships were evaluated in upland and seasonally flooded savanna (Cerrado) of the Cuiaba Basin and Northern Pantanal in southern Mato Grosso, Brazil. Data on wood C increment, tree species composition, and alpha diversity were measured over a 10-year period in nine communities located in the Cerrado-Pantanal transition zone. Communities were composed of a wide spectrum of tropical savanna physiognomies, including mixed grassland (campo sujo), typical wooded savanna (stricto sensu), dense wooded savanna (cerrado denso), seasonal forest (mata seca and mata ciliar), and riparian forest (mata de galeria). We hypothesized that tree species richness and diversity would increase from grassland to forest. We further hypothesized that there would be a positive relationship between woody C storage and diversity, but the strength of this relationship would be higher in wet years and wetter environments, such as the Pantanal, due to an increase in water availability. We found that tree species richness and diversity did not increase from mixed grasslands to forests, as mixed grasslands and riparian forests had similarly low levels of tree species richness and diversity compared to the other physiognomies. However, the rate of annual aboveground wood C increment was positively related to species richness and alpha diversity, and the positive relationship was primarily observed during wet years when the annual precipitation was at, or above, the long-term average for the region. Presumably, the impact of structural and species diversity on productivity declines during dry years when water availability becomes a more important control on stem C increment for tree species in the Cerrado-Pantanal transition. These data suggest that maintenance of diversity in these Cerrado woodlands and forests is important for maximizing aboveground C gain. However, climate change, which is causing warming and drying for the region, may limit the importance of diversity on wood C storage.

Population genetics of Salvator merianae (Reptilia, Teiidae) in its southernmost distribution

The black and white tegu (Salvator merianae, Duméril and Bibron, 1839) is the most widespread lizard species in the southern part of South America. This is an important species as a natural resource, traditionally used for food and traded as leather and pets, and this intensive exploitation can be important for regional economies in their range. We analyzed their genetic diversity, structure, and mating system in Argentina using the mitochondrial ND4 locus and 10 microsatellite loci. We hypothesized low genetic diversity, high levels of interpopulation structure, and multiple paternal contribution to clutches. Our results support our hypotheses, detecting two divergent mitochondrial haplogroups, low levels of allelic diversity and low to medium population structure values using microsatellites, and that S. merianae is both polygynous and has multiple paternal contributions to the clutches we analyzed. These results are informative for the on-going sustainable use-based management of S. merianae, ensuring the sustainability of its commercially exploited populations and the habitats on which they depend.

Evolution of the subtropical surface wind in the north-east Atlantic under climate change

The climate of western Europe and northwest Africa strongly depends on the Azores anticyclone strength, location, and shape and, locally, also on the characteristics of the Iberia and Sahara summer thermal lows. EC-EARTH3 global simulations are here used to assess the predicted behaviour of these two relevant surface pressure systems and associated surface wind, by the end of XXI century (2071–2100), considering two climate change scenarios. Additionally, a high-resolution Weather Research and Forecasting (WRF) simulation centred on Madeira Island is used to assess the influence of climate change on the surface wind at smaller scales, in a region well known for its perturbed flows. Results indicate a general mean wind speed decrease over a sector of the North-Atlantic, associated with a flatter Azores anticyclone. However, the predicted intensification of the Iberia and Sahara thermal lows imposes an increasing surface wind speed near west Iberia and northwest Africa, in summer. Southwest of Iberia, Madeira Island is also predicted to experience a summer intensification of its tip-jets. The projected changes in low-level wind speed and variability will impact on different sectors of activity, either directly as are the cases of aeronautical operation and offshore renewable energy, or indirectly through changes in the ocean circulation.

Expanding the boundaries: investigating the integration of contextual information across a spectrum of inter-trial variability.

It is well-documented that feature integration across perception and action creates a retrievable episodic representation, known as a stimulus-response episode or an event file. Previous studies have demonstrated that a task-irrelevant stimulus, which functions as contextual information, can be integrated in various ways. In some cases, the context modulated the binding between a stimulus and a response, resulting in a configural binding structure. In other cases, the context was found to be directly bound with the response in a binary fashion. The current study examined the integration of context within a stimulus-response (S-R) episode, with a focus on the role of inter-trial variability. Specifically, the context variability was manipulated across five experimental groups, ranging from the minimum to the maximum level. The minimum-variability group maintained a consistent pattern of two context tones per block, while the maximum-variability group used a uniformly random order of eight different context tones. Intermediate groups progressively employed greater degrees of variability in the presentation of contextual stimuli. Results showed that the integration of context changed as a function of its variability level: The contextual stimuli with minimal to low level of variability did not exhibit a pattern of integration, while those with moderate to high variability were involved in a configural binding with another stimulus and the response. Only when the context exhibited maximal variability did it become directly bound with the response in a binary fashion. The current findings extend previous assumptions about saliency thresholds for stimulus integration into the realm of inter-trial variability and underscore the role of stimulus uncertainty in shaping context integration. Possible underlying mechanisms are discussed.

Weed Community Changes Due To Herbicide Treatment In Mature Oil Palm Plantations

Stenochlaena palustris, commonly known as pakisan weed, poses significant challenges in oil palm plantations due to its highly invasive nature, which can lead to reduced agricultural productivity. Management of this weed is critical, as effective control measures can inhibit its dominance and promote the proliferation of alternative weed species, thereby enhancing biodiversity within the ecosystem. This study aimed to 1) assess the effectiveness of the herbicide ammonium glufosinate, in combination with an adjuvant, for controlling S. palustris in oil palm plantations, and 2) investigate the subsequent alterations in the weed community structure following herbicide application. We employed a randomised group design (RAK), incorporating the herbicide with added adjuvants. Results showed a clear change from S. palustris to Asystasia sp. as the dominant species. Treatments K and H had the most Asystasia sp., while treatment L had the least. Furthermore, we clearly compared treatments L, K, and S to the control treatment, emphasizing the emergence of diverse species within the treatment plots. However, low levels of diversity and evenness suggest a stressed weed community, indicating that the herbicide application can disrupt existing ecological balances. This study emphasizes the importance of assessing herbicide impacts not only on targeted weed species but also on broader community dynamics, revealing a significant research gap in understanding the long-term ecological consequences of herbicide use in oil palm plantations.

Structured, Inbred and Plastic: the Genome and Population Genetics of the weed False cleavers (Galium spurium)

Abstract False cleavers (Galium spurium L.) is an aggressive weed from the Rubiaceae. Here we assemble a chromosome scale draft of its genome, laying the foundations for determining the genetic basis of auxinic herbicide resistance and for systematic research into its polyphyletic genus. We use the genome to examine the population genetics in material from the Canadian Prairies and, in concert with a common greenhouse experiment, to examine whether the phenotypic variation observed in the field results primarily from genetic or environmental factors. The genome assembly covers approximately 85% of G. spurium’s expected 360Mbp genome size with 94% of BUSCO genes complete and most single copy (89%). Approximately 37% of the genome is repetitive elements and 35,540 genes were annotated using RNA-Seq data, including 100 homologs for genes involved or, potentially involved in, herbicide resistance. The genome shows strong synteny with other members of the Rubiaceae including smooth bedstraw (Cruciata laevipes Opiz) and robusta coffee [Coffea canephora (Pierre ex Froehner]. Double digested RADseq data for the 19 populations from the Canadian Prairies indicated that G. spurium has high levels of population structure (FST = 0.54) and inbreeding (FIS =0.86) with low levels of hetrozygosity (HO = 0.02) and nucleotide diversity (π = 0.0003). Variation in flowering time and seed weight largely overlapped among populations grown in the greenhouse. A redundancy analysis investigating genotype-phenotype associations showed few associations between SNP variation and these characteristics. In contrast, the majority of SNPs under selection were associated with mericarp hook density. This suggests that for most traits, environmental variation rather than genetic variation likely underlies phenotypic differences observed in the field. Several genes of interest including several homologs involved in the assembly of the Skp1-Culliun-F-Box IR1/AFB E3 ubiquitin ligase complex (e.g. CAND1, ECR1) are located in areas of the genome with evidence of selection and are targets for further investigation.

A-173 Evaluation of Artificial Intelligence (AI)-assisted Flow Cytometry Analysis for Plasma Cell Neoplasms

Abstract Background Flow cytometry plays a critical role in diagnosing hematologic disorders, yet manual analysis is time-consuming and prone to variability. Significant advancements in artificial intelligence (AI) within healthcare have occurred in recent years. Previously, we developed and evaluated an AI-assisted automated system for diagnosing acute leukemia. This study aims to assess the effectiveness of the AI system in diagnosing plasma cell neoplasms. Methods A total of 76 bone marrow samples were analyzed using a panel of antibodies (CD38, CD56, CD138, Kappa, and Lambda) to determine plasma cell percentages and immunophenotype. All samples were used for initial diagnosis of plasma cell neoplasm or therapeutic monitoring. Manual analysis using Kaluza™ software served as the gold standard. The same flow cytometry data was processed by the AI software (DeepFlow™) for comparison. Pearson correlation coefficients were used to compare AI and manual analysis for diagnosis and plasma cell count. Results Among the 76 cases, manual analysis identified 57 positive cases for monoclonal plasma cells (36 cases of CD38+/CD138+/Kappa+ and 21 cases of CD38+/CD138+/Lambda+), with 89% showing aberrant CD56 expression. AI identified 49 monoclonal cases, missing 8 cases with low plasma cell levels (<0.07%) or brighter fluorescence. AI accurately matched 97% of immunophenotypes with manual analysis. Pearson correlation coefficients demonstrated excellent correlation (r=1.0) between manual and AI plasma cell percentages. Furthermore, AI has also enhanced laboratory efficiency, reducing analysis time per case from 10 minutes with manual methods to just 3 minutes with AI analysis. Conclusions This study shows promise for AI-assisted flow software in diagnosing plasma cell neoplasms. AI has enhanced operational efficiency by reducing the manual processing and analysis time. Further training is needed to improve the identification of variations in fluorescence intensity and low plasma cell levels.

Resequencing reveals population structure and genetic diversity in Tibetan sheep

BackgroundThe Tibetan sheep is one of the three major primitive sheep breeds in China, representing a unique and high-quality genetic resource in the Qinghai-Tibet Plateau and neighboring high-altitude regions, exhibiting exceptional adaptability to high-altitude climatic environments. However, research on the genetic relationships among different populations of Tibetan sheep at the whole-genome level remains insufficient. This study aims to explore the population structure and historical dynamics among 11 Tibetan sheep populations, accurately assess the genetic diversity within the populations, and providing a theoretical basis for the development of targeted genetic breeding strategies for Tibetan sheep.ResultsIn this study, a total of 10,884,454 high-quality SNPs were obtained. All Tibetan sheep populations exhibited varying degrees of linkage disequilibrium, with similar decay rates; among them, the WT population showed the fastest decay, while the TS population exhibited the slowest decay rate. Analyses using Tajima’s D and π indicated that the genetic diversity levels of the Tibetan sheep populations are generally low. Fst results revealed that most populations exhibited moderate to low levels of genetic differentiation. The effective population size among Tibetan sheep populations showed an increasing trend over time. The evolutionary relationships among Tibetan sheep populations reflect the correlation between their geographical locations and genomic genetic distances, while also indirectly confirming the impact of historical activities such as early human migration, admixture, fusion, and expansion on the population sizes and distributions of Tibetan sheep.ConclusionsThe results indicate that the genetic diversity levels and genetic differentiation among Tibetan sheep populations are relatively low. In this study, we identified the genetic characteristics of Tibetan sheep populations, which exhibit low levels of diversity, genetic differentiation, and a strong population structure. A deeper genomic exploration of the population structure and diversity status of Tibetan sheep populations will provide theoretical support for subsequent genetic breeding and diversity conservation efforts.

Genetic diversity of populations of East Siberian ende

Based on nucleotide polymorphism of cpDNA intergenic spacers psbA-trnH, trnL-trnF, and trnS-trnG, we studied the genetic diversity and population structure of a mountain species Oxytropis vasskovskyi Jurtz., endemic to East Siberia. The populations were characterized by medium and high haplotype (0.524–1.000) and low nucleotide (0.0003–0.0008) diversity. Variability distribution analysis showed a moderate level of diff erentiation; the interpopulation component accounted for about 44% of the total genetic variation in O. vasskovskyi. We observed demographic expansion for three of fi ve O. vasskovskyi populations. The haplotypes of the fi ve studied populations form a single complex in the genealogical network, which is probably due to their common origin, relatively recent divergence and incomplete lineage sorting, as well as the existing gene exchange between populations. Thus, in four of the fi ve studied populations, a low level of nucleotide diversity and the absence of nucleotide substitutions were determined, which indicates the need to use certain measures to protect all known habitats, conduct regular monitoring of their state and search for new locations of the species.

Ecological connectivity of the Qiongzhou Strait: a case form Orangefin Ponyfish (Photopectoralis bindus) haplotype diversity and genetic structure

Grasping the genetic structure of marine fish populations is vital for comprehending species connectivity patterns and determining the appropriate spatiotemporal scales for conservation management strategies. Here, we analyzed the population genetics of the Orangefin Ponyfish (Photopectoralis bindus Valenciennes, 1835) by examining a portion of the gene coding for the mitochondrial cytochrome c oxidase subunit I. The aim was to evaluate the haplotype pattern, genetic structure, demographic history, as well as the influence of ecological connectivity through the Qiongzhou Strait on the distribution patterns of this species in the northern South China Sea and the Beibu Gulf. In total, 257 specimens yielded only 13 haplotypes, with the predominant haplotype present at all sampling locations. The analysis revealed a “star-like” haplotype pattern, indicating low levels of both haplotype and nucleotide diversity. Additionally, a small but significant genetic structure was observed between the coastal regions flanking the Leizhou Peninsula. These patterns in the haplotype network and genetic structure may be significantly influenced by contemporary currents, particularly through the connectivity of the Qiongzhou Strait. Tajima’s D and Fu’s Fs demonstrated pronouncedly negative values, along with a unimodal mismatch distribution, suggested a recent demographic expansion of Photopectoralis bindus during the late Pleistocene, likely influenced by fluctuations in sea levels.

Analysis of Mangrove Vegetation in Mesjid Raya Sub-District, Aceh Besar District

Mangrove ecosystems, characterized by their unique adaptation to intertidal zones along coastlines and river estuaries, play a crucial role in coastal ecology. This study investigated the composition and diversity of mangrove vegetation in Mesjid Raya District, Aceh Besar Regency. Employing a quantitative approach with purposive sampling, nine plots measuring 10x10 meters were established across three stations with varying physical environmental conditions, totaling 90 plots. Vegetation analysis revealed the presence of nine mangrove species belonging to five families. The Shannon diversity index (Ĥ) indicated a low level of species diversity within the studied mangrove communities.

Quantifying Western Discourses about Technology

In this article, we explore the social impact of technology in contemporary societies using a dataset of multilingual newspapers in English, French, Spanish, Italian, and German. Our observational time covers twenty years (1999-2018). We filter documents using four technological key terms: nuclear, oil, internet, and automation, that we consider as proxies reflecting Smil 2006 taxonomy of technology. Our methodology is formed by a five-step pipeline: Topic modelling (Pachinko Allocation), word embeddings, Ward’s hierarchical cluster analysis, network analysis, and sentiment analysis. We analyze information stability (which we define as low levels of semantic diversity in our data outcomes over time at the individual key term level) and information homogeneity (which we understand as low levels of semantic diversity in our data outcomes across our selection of key terms). We seek to observe to what extent our selection of key terms permeates into press discourses similarly or differently, and whether those discourses fall into semantic categories that could be considered as essential elements of the fabric of contemporary societies (such as finance, education, or politics). Results show, firstly, a consistent overlap of content across newspapers’ semantic fields that could be considered as pillars of society. Secondly, we notice a progressive simplification of information historically, reflecting less polarizing views across countries and, therefore, demonstrating an increasing agreement on technologically related discourses. We interpret these results as an indicator of the rising intrusion of technology in Western, industrialized countries.

Diversity, functional redundancy, and vulnerability of reef fish communities of the Saudi Arabian coast, in the northern Red Sea

Diversity, functional redundancy, and vulnerability of reef fish communities of the Saudi Arabian coast, in the northern Red Sea

Genetic diversity of Spotted scat (Scatophagus argus) based on 16s rRNA gene markers in WPP 573 Western part as management basis

Abstract Spotted scat (Scatophagus argus) is one of the demersal fish that has important economic value, this fish is used as a consumption fish and ornamental fish. It is also an active migratory fish that allows genetic transfer from different waters. This study aims to analyze the genetic diversity of Spotted scat in WPP 573 West Part based on 16s rRNA gene markers as a sustainable resource management. Amplification results show amplicon with single strand band but there are still smears due to the presence of contaminants. The BLASTn sequencing and validation results showed that all Spotted scat samples belonged to the Scatophagus argus species with a percent identification of 99.51 until 100%. The results showed that the Spotted scat samples had a very close kinship relationship, but the population of spotted scat was classified into the unfavorable category because of the low level of diversity.

Infection Rates and Characterisation of Rickettsia africae (Rickettsiaceae) Detected in Amblyomma Species from Southern Africa.

Tick-borne rickettsioses are considered among the oldest known vector-borne zoonotic diseases. Among the rickettsiae, Rickettsia africae is the most reported and important in Africa, as it is the aetiological agent of African tick bite fever (ATBF). Studies describing the prevalence of R. africae in southern Africa are fragmented, as they are limited to small geographical areas and focused on Amblyomma hebraeum and Amblyomma variegatum as vectors. Amblyomma spp. ticks were collected in Angola, Mozambique, South Africa, Zambia and Zimbabwe during the sampling period from March 2020 to September 2022. Rickettsia africae was detected using the ompA gene, while characterisation was conducted using omp, ompA, ompB and gltA genes. In total, 7734 Amblyomma spp. ticks were collected and were morphologically and molecularly identified as Amblyomma eburneum, A. hebraeum, Amblyomma pomposum and A. variegatum. Low levels of variability were observed in the phylogenetic analysis of the R. africae concatenated genes. The prevalence of R. africae ranged from 11.7% in South Africa to 35.7% in Zambia. This is one of the largest studies on R. africae prevalence in southern Africa and highlights the need for the inclusion of ATBF as a differential diagnosis when inhabitants and travellers present with flu-like symptoms in the documented countries.

What we know and do not know after the first decade of Homo naledi.

It has been just over 10 years since the first fossils attributed to Homo naledi were recovered from the Rising Star Cave system in South Africa's Cradle of Humankind. The hominin fossil evidence for H. naledi displays a distinctive combination of primitive and derived morphology, yet for a time-averaged fossil sample it is remarkable for its relatively low level of variation. Thus-unusually for palaeoanthropology-there has been little pushback against the decision to recognize a single novel taxon for all of the material recovered from the Rising Star Cave system. However, almost everything else claimed about H. naledi-its age, burial context and behaviour-has been controversial. Here we examine the strength of the evidence for these claims.

Impact of Model Resolution and Initial/Boundary Conditions in Forecasting Low-Level Atmospheric Fields over the Incheon International Airport

Abstract This study investigates the impact of initial conditions/boundary conditions (ICs/BCs) and horizontal resolutions on forecast for average weather conditions, focusing on low-level weather variables such as 2-m temperature (T2m), 2-m water vapor mixing ratio (Q2m), and 10-m wind speed (WS10). A Weather Research and Forecasting (WRF) Model is used for regional mesoscale model simulations and large-eddy simulations (LESs). The 6-h-interval forecast fields generated by the Global Forecast System of the National Centers for Environmental Prediction and the Korean Integrated Model of the Korea Meteorological Administration are utilized as ICs/BCs for the regional models. Numerical experiments are performed for 24 h starting at 0000 UTC on each day in April 2021 when the average monthly wind speed was strongest during 10 years (2011–20). A comparison of model simulations with observations obtained around the Yeongjong Island, where Incheon International Airport is situated, shows that the regional models capture the time series of T2m, Q2m, and WS10 more effectively than the global model forecasts. Moreover, the LES experiments with a 100-m horizontal grid spacing simulate higher Q2m and lower WS10 during the daytime compared to the 1-km WRF. This results in a deterioration of their time-series correlation with the observations. Meanwhile, the 100-m LES forecasts time series of T2m over ocean stations and Q2m over land stations, as well as probability density functions of low-level weather variables, more accurately than that of the 1-km WRF. Our study also emphasizes the need for caution when comparing high-resolution model results with observation values at specific stations due to the high spatial variability in low-level meteorological fields.

Plant species richness and legume presence increase microbial necromass carbon accumulation

Plant species richness and legume presence increase microbial necromass carbon accumulation