High Level Of Diversity Research Articles

Examining the impact of board gender diversity and regional differentiation in the ESG‐corporate performance nexus: Evidence from financial service industry

AbstractThis study explores the impact of environmental, social, and governance (ESG) factors on corporations by investigating how board gender diversity moderates the relationship between ESG practices and corporate performance across different regions. Using traditional data envelopment analysis (DEA) and chance‐constrained DEA models, the study analyzes 225 financial service firms over an 11‐year period (2011–2021). Results indicate that high (low) board gender diversity levels significantly influence the connection between the environmental (social) aspects of ESG practices and corporate performance. Thus, the roles of stakeholder engagement and regional distinctions are highlighted in achieving sustainable development goals.

Diversity of Pleurostomatid Ciliates: Morphology, Taxonomy and Molecular Phylogeny of Freshwater Isolates Found in a Northern China Wetland, with a Description of Two New Species

Ciliates of the order Pleurostomatida play essential functions in microbial food webs from a variety of habitats and have been thought to possess a high level of diversity. Due to undersampling and often absent molecular data, the actual diversity and phylogenetic relationships within this group remain unclarified. To help address this deficiency, a survey of freshwater pleurostomatid ciliates was undertaken in Lake Weishan Wetland, northern China. Here, two new Amphileptus species, Amphileptus sinicus sp. nov. and Amphileptus piscinarius sp. nov., were investigated using modern morphological and molecular techniques. Amphileptus sinicus sp. nov. is characterized by possessing a comparatively large cell size of 330–490 μm, contractile vacuoles on both ventral and dorsal margins, and 8–10 left and 42–61 right kineties. Amphileptus piscinarius sp. nov. is characterized by possessing a cell size of 140–210 μm, a large distinctly developed apical extrusome group, 3–4 contractile vacuoles on the ventral margin, and 6–8 left and 24–28 right kineties. Phylogenetic results based on the 18S rRNA gene data of these two species group them with other congeners, with these data suggesting the genus Amphileptus is paraphyletic.

Multidrug-resistant Escherichia coli strains isolated from swine manure biofertilizer in Brazil.

Escherichia coli is one of the key bacteria responsible for a variety of diseases in humans and livestock-associated infections around the globe. It is the leading cause of mortality in neonatal and weaned piglets in pig husbandry, causing diarrhea and significant harm to the industry. Furthermore, the frequent and intensive use of antimicrobials for the prevention of diseases, particularly gastrointestinal diseases, may promote the selection of multidrug-resistant (MDR) strains. These resistant genotypes can be transmitted through the excrement of animals, including swine. It is common practice to use porcine manure processed by biodigesters as fertilizer. This study aimed to examine the antimicrobial susceptibility, the presence of virulence genes frequently associated with pathotypes of intestinal pathogenic E. coli (InPEC), and antimicrobial resistance genes (ARGs) of 28 E. coli isolates collected from swine manure fertilizers. In addition, the enterobacterial repetitive intergenic consensus-PCR (ERIC-PCR) technique was used to investigate the genetic relationship among the strains. Using disk diffusion, the antimicrobial susceptibility profiles of the strains were determined. Using polymerase chain reaction (PCR), 14 distinct virulence genes associated with the most prevalent diarrhea and intestinal pathogenic E. coli (DEC/InPEC) and five ARGs were analyzed. All isolates tested positive for multidrug resistance. There was no detection of any of the 14 virulence genes associated with InPECs, indicating the presence of an avirulent commensal microbiota. Molecular classification by ERIC-PCR revealed that the majority of isolates (27 isolates) coalesced into a larger cluster with a genetic similarity of 47.7%; only one strain did not cluster in this cluster, indicating a high level of genetic diversity among the analyzed isolates. Thus, it is of the utmost importance to conduct epidemiological surveillance of animal breeding facilities in order to determine their microbiota and formulate plans to reduce the use of antimicrobials and improve animal welfare.

Genetic Profile of Greek Indigenous Honey Bee Populations, Local Extinctions, Geographical Distinction, and Patterns, by Using mtDNA COI and Nuclear CSD Gene Analysis Markers

Evaluation and conservation of local genetic resources of the domestic honey bee populations is important, especially in regions with high diversity levels as well as high honey bee colony density. Greece is rich in honey bee biodiversity, hosting several subspecies, with the status of them being, though, doubtful. The purpose of the present study was to investigate the genetic relationships of both stationary and movable honey bee populations, originating from many location throughout Greece. Two molecular markers were utilized, namely, the conserved mitochondrial COI gene and the highly variable complementary sex determination (CSD) gene. Samples were collected from nine distant populations: eight populations from colonies that followed the traditional stationary beekeeping model and one following the modern migratory beekeeping model type, where the hives are transferred from place to place according to the season. Regardless the beekeeping model, all populations were characterized by sufficient genetic diversity indicating no signs of inbreeding or any bottleneck effects. Nevertheless, genetic differentiation and phylogenetic analysis in comparison with haplotypes obtained from GenBank revealed a genetic admixture pattern suggesting that movement causes genetic homogeneity, occasionally in the stable reared populations as well. Interestingly, two populations, namely, Kastoria and Protokklisi, belonging to A. m. macedonica population, were significantly differentiated, supporting the maintenance of their genetic integrity. Unfortunately, on the other hand, genetic structure of the populations from Crete (Sasalos population) provided evidence that the indigenous breed from the island, A. m. adami, has probably gone extinct. Future management strategies should focus on the conservation of the local genetic resources in which distinct genetic identity has been sustained.

Genomic analysis of inbreeding level, kinship and breed relationships in Creole cattle from South America.

The conservation of animal genetic resources refers to measures taken to prevent the loss of genetic diversity in livestock populations, including the protection of breeds from extinction. Creole cattle populations have suffered a drastic reduction in recent decades owing to absorbent crosses or replacement with commercial breeds of European or Indian origin. Genetic characterization can serve as a source of information for conservation strategies to maintain genetic variation. The objective of this work was to evaluate the levels of inbreeding and kinship through the use of genomic information. A total of 903 DNAs from 13 cattle populations from Argentina, Bolivia and Uruguay were genotyped using an SNP panel of 48 K. Also, a dataset of 76 K SNPs from Peruvian Creole was included. Two inbreeding indices (FROH and Fhat2) and kinship relationships were calculated. In addition, effective population size (Ne), linkage disequilibrium, population composition and phylogenetic relationships were estimated. In Creole cattle, FROH ranged from 0.14 to 0.03, and Fhat2 was close to zero. The inferred Ne trends exhibited a decline toward the present for all populations, whereas Creole cattle presented a lower magnitude of Ne than foreign breeds. Cluster analysis clearly differentiated the taurine and Zebu components (K2) and showed that Bolivian Creole cattle presented Zebu gene introgression. Despite the population reduction, Creole populations did not present extreme values of consanguinity and kinship and maintain high levels of genetic diversity. The information obtained in this work may be useful for planning conservation programmes for these valuable local animal genetic resources.

The Potential Role of Urinary Microbiota in Bladder Carcinogenesis: A Systematic Review.

The quantitative objective of the current systematic review was to identify the potential role of urinary microbiota in bladder cancer (BC) carcinogenesis, invasiveness, progression, and metastasis. The proposed systematic review was conducted in accordance with critical review according to the Preferred Reporting Items for Systematic Reviews and Meta-analyses (PRISMA) statement, and the Joanna Briggs Institute (JBI) methodology for systematic reviews. The search strategy aimed to find both published and unpublished studies up to the January 2024. A JBI appraisal checklist was used to assess possible biases. This systematic review was centered on 27 studies comprising 926 BC patients. Overall, 412 control individuals were compared with BC patients. The most common sampling method was midstream urine collection. Regarding microbial alpha diversity, there was no statistically significant difference between cancerous and healthy samples (n=8), recurrent and not recurrent (n=1), responders versus non-responders(n=1), tumor grades (n=1), and collection methods (n=1). However, five studies reported higher diversity in controls, and five other studies reported, conversely, high levels of alpha diversity in BC patients or recurrent cases. Furthermore, a responder (RE) to treatment and a non-muscle invasive bladder cancer (NMIBC) groups demonstrated significant difference with non-responder (NR) and muscle invasive bladder cancer (MIBC), respectively. In terms of beta-diversity, nine studies reported significant diversity between BC patients and controls, one article demonstrated difference between recurrent and not recurrent patients, a study reported significant difference in RE and NR groups whereas another showed opposite, and others (n=4) did not find any difference between BC, controls, MIBC and NMIBC patients, or between tumor grades. One study reported a difference between the collection method and beta-diversity in males and another reported the difference in females. The included studies demonstrate that the composition of urinary microbiota is altered in patients with BC. However, the differentially enriched genera in the urine of these patients vary between studies, and there is too much heterogeneity across studies to make any reliable and valid conclusions. Furthermore, well-designed research is necessary to assess the role of microbiota in the carcinogenesis and progression of BC.

Poor air quality at school and educational inequality by family socioeconomic status in Italy

This paper investigates social stratification in the context of poor air quality's impact on educational achievement in Italy, a country characterized by high levels of air pollution and significant geographical diversity. We address two primary questions: firstly, whether students from different socio-economic backgrounds vary in their exposure to high levels of particulate matter (PM2.5) at school, and secondly, if the effect of exposure to poor air quality on academic performance differs between children from high and low socio-economic status families. Utilizing a novel dataset comprising test scores in math and reading for 456,508 8th-grade students, collected nationally in Italy in 2019, we geocode the locations of 6882 schools based on their addresses and link the level of air pollution in the surrounding areas using PM2.5 data from the Atmospheric Composition Analysis Group. To address potential confounding factors, we estimate municipality and province fixed effects and control for indicators of school neighborhood characteristics and school quality. Our analysis yields three key findings. Firstly, students from higher socio-economic backgrounds tend to attend schools with higher PM2.5 levels. However, the positive association between SES and exposure to PM2.5 disappears when adding province and municipality fixed effects, suggesting that the positive association can be explained by selection into provinces and municipalities by SES. Secondly, we identify a small yet consistent negative effect of PM2.5 on math and reading test scores. Thirdly, this adverse impact is primarily observed among students from low socio-economic backgrounds. We conclude that the relationship between environmental risks and disparities in educational achievement based on social background in Italy is nuanced and critically influenced by the country's specific context.

Aspergillus flavus pangenome (AflaPan) uncovers novel aflatoxin and secondary metabolite associated gene clusters

BackgroundAspergillus flavus is an important agricultural and food safety threat due to its production of carcinogenic aflatoxins. It has high level of genetic diversity that is adapted to various environments. Recently, we reported two reference genomes of A. flavus isolates, AF13 (MAT1-2 and highly aflatoxigenic isolate) and NRRL3357 (MAT1-1 and moderate aflatoxin producer). Where, an insertion of 310 kb in AF13 included an aflatoxin producing gene bZIP transcription factor, named atfC. Observations of significant genomic variants between these isolates of contrasting phenotypes prompted an investigation into variation among other agricultural isolates of A. flavus with the goal of discovering novel genes potentially associated with aflatoxin production regulation. Present study was designed with three main objectives: (1) collection of large number of A. flavus isolates from diverse sources including maize plants and field soils; (2) whole genome sequencing of collected isolates and development of a pangenome; and (3) pangenome-wide association study (Pan-GWAS) to identify novel secondary metabolite cluster genes.ResultsPangenome analysis of 346 A. flavus isolates identified a total of 17,855 unique orthologous gene clusters, with mere 41% (7,315) core genes and 59% (10,540) accessory genes indicating accumulation of high genomic diversity during domestication. 5,994 orthologous gene clusters in accessory genome not annotated in either the A. flavus AF13 or NRRL3357 reference genomes. Pan-genome wide association analysis of the genomic variations identified 391 significant associated pan-genes associated with aflatoxin production. Interestingly, most of the significantly associated pan-genes (94%; 369 associations) belonged to accessory genome indicating that genome expansion has resulted in the incorporation of new genes associated with aflatoxin and other secondary metabolites.ConclusionIn summary, this study provides complete pangenome framework for the species of Aspergillus flavus along with associated genes for pathogen survival and aflatoxin production. The large accessory genome indicated large genome diversity in the species A. flavus, however AflaPan is a closed pangenome represents optimum diversity of species A. flavus. Most importantly, the newly identified aflatoxin producing gene clusters will be a new source for seeking aflatoxin mitigation strategies and needs new attention in research.

COVID-19 Hospitalization in Hawai'i and Patterns of Insurance Coverage, Race and Ethnicity, and Vaccination.

The people of Hawai'i have both high rates of health insurance and high levels of racial and ethnic diversity, but the degree to which insurance status and race and ethnicity contribute to health outcomes in COVID-19 remains unknown. To evaluate the associations of insurance coverage, race and ethnicity (using disaggregated race and ethnicity data), and vaccination with outcomes for COVID-19 hospitalization. This retrospective cohort study included hospitalized patients at a tertiary care medical center between March 2020 and March 2022. All patients hospitalized for acute COVID-19, identified based on diagnosis code or positive results on polymerase chain reaction-based assay for SARS-CoV-2, were included in analysis. Data were analyzed from May 2022 to May 2023. COVID-19 requiring hospitalization. Electronic medical record data were collected for all patients. Associations among race and ethnicity, insurance coverage, receipt of at least 1 COVID-19 vaccine, intensive care unit (ICU) transfer, in-hospital mortality, and COVID-19 variant wave (pre-Delta vs Delta and Omicron) were assessed using adjusted multivariable logistic regression. A total of 1176 patients (median [IQR] age of 58 [41-71] years; 630 [54%] male) were hospitalized with COVID-19, with a median (IQR) body mass index (BMI; calculated as weight in kilograms divided by height in meters squared) of 30 (25-36) and Sequential Organ Failure Assessment score of 1 (0-2). The sample included 16 American Indian or Alaska Native patients, 439 Asian (not otherwise specified) patients, 15 Black patients, 66 Chinese patients, 246 Filipino patients, 76 Hispanic patients, 107 Japanese patients, 10 Korean patients, 299 Native Hawaiian patients, 523 Pacific Islander (not otherwise specified) patients, 156 Samoan patients, 5 Vietnamese patients, and 311 White patients (patients were able to identify as >1 race or ethnicity). When adjusting for age, BMI, sex, medical comorbidities, and socioeconomic neighborhood status, there were no differences in either ICU transfer (eg, Medicare vs commercial insurance: odds ratio [OR], 0.84; 95% CI, 0.43-1.64) or in-hospital mortality (eg, Medicare vs commercial insurance: OR, 0.85; 95% CI, 0.36-2.03) as a function of insurance type. Disaggregation of race and ethnicity revealed that Filipino patients were more likely to die in the hospital (OR, 1.79; 95% CI, 1.04-3.03; P = .03). When considering variant waves, mortality among Filipino patients was highest during the pre-Delta time period (OR, 2.72; 95% CI, 1.02-7.14; P = .04), when mortality among Japanese patients was lowest (OR, 0.19; 95% CI, 0.03-0.78; P = .04); mortality among Native Hawaiian patients was lowest during the Delta and Omicron period (OR, 0.35; 95% CI, 0.13-0.79; P = .02). Patients with Medicare, compared with those with commercial insurance, were more likely to have received at least 1 COVID-19 vaccine (OR, 1.85; 95% CI, 1.07-3.21; P = .03), but all patients, regardless of insurance type, who received at least 1 COVID-19 vaccine had reduced ICU admission (OR, 0.40; 95% CI, 0.21-0.70; P = .002) and in-hospital mortality (OR, 0.42; 95% CI, 0.21-0.79; P = .01). In this cohort study of hospitalized patients with COVID-19, those with government-funded insurance coverage (Medicare or Medicaid) had similar outcomes compared with patients with commercial insurance, regardless of race or ethnicity. Disaggregation of race and ethnicity analysis revealed substantial outcome disparities and suggests opportunities for further study of the drivers underlying such disparities. Additionally, these findings illustrate that vaccination remains a critical tool to protect patients from COVID-19 mortality.

Peran Serangga Tanah dalam Budidaya Talas Beneng di Karangtanjung

Araceae is a plant family known as taro with a high level of diversity and is easily found by the public. Beneng taro (Xanthosoma undipes) is a plant in the Araceae family that is included in the local food commodities originating from Banten Province, especially in the Mount Karang. Soil insects are a type of insects that have an essential role in the food cycle, which supports the weathering process of organic material to have a positive influence on the physical and chemical properties of soil. The diversity of soil insects on taro beneng plants in Cinyurup Village is essential to be known to open up new opportunities for understanding their ecological benefits related to agricultural sustainability and biodiversity conservation. This research aims to determine soil insects and their role in the beneng taro cultivation area and to determine the diversity index of soil insects in the area. This research was carried out in February-March in Cinyurup Village, Karang Tanjung District, Pandeglang Regency. This research includes quantitative descriptive research with an exploratory method. Sampling was carried out by purposive sampling using the pitfall trap technique. The samples in this research are all ground insects trapped in pitfall traps. Trapped samples were identified based on their role and the calculated diversity index of the Shannon-Wiener method, which can facilitate the analysis of information about the type of individual and the number in an area. The identification results showed that there were 252 insects belonging to 6 families, namely Formicidae, Gryllidae, Tetrigidae, Scarabaeidae, Anisolabidae, and Muscidae. Formicidae and Scarabaeidae are land insects found in abundance due to the farming system based on the cultivation of wire that supports their survival. The diversity index value was obtained at 1.03064 which is included in the medium category. The insects found have varied roles, namely predators (Formicidae, Anisolabidae), herbivores (Gryllidae, Tetrigidae), pollinators (Formicidae, Muscidae), and decomposers (Scarabaeidae).

Detection of pathogenic bacteria in ticks from Isiolo and Kwale counties of Kenya using metagenomics.

Ticks are arachnid ectoparasites that rank second only to mosquitoes in the transmission of human diseases including bacteria responsible for anaplasmosis, ehrlichiosis, spotted fevers, and Lyme disease among other febrile illnesses. Due to the paucity of data on bacteria transmitted by ticks in Kenya, this study undertook a bacterial metagenomic-based characterization of ticks collected from Isiolo, a semi-arid pastoralist County in Eastern Kenya, and Kwale, a coastal County with a monsoon climate in the southern Kenyan border with Tanzania. A total of 2,918 ticks belonging to 3 genera and 10 species were pooled and screened in this study. Tick identification was confirmed through the sequencing of the Cytochrome C Oxidase Subunit 1 (COI) gene. Bacterial 16S rRNA gene PCR amplicons obtained from the above samples were sequenced using the MinION (Oxford Nanopore Technologies) platform. The resulting reads were demultiplexed in Porechop, followed by trimming and filtering in Trimmomatic before clustering using Qiime2-VSearch. A SILVA database pretrained naïve Bayes classifier was used to classify the Operational Taxonomic Units (OTUs) taxonomically. The bacteria of clinical interest detected in pooled tick assays were as follows: Rickettsia spp. 59.43% of pools, Coxiella burnetii 37.88%, Proteus mirabilis 5.08%, Cutibacterium acnes 6.08%, and Corynebacterium ulcerans 2.43%. These bacteria are responsible for spotted fevers, query fever (Q-fever), urinary tract infections, skin and soft tissue infections, eye infections, and diphtheria-like infections in humans, respectively. P. mirabilis, C. acnes, and C. ulcerans were detected only in Isiolo. Additionally, COI sequences allowed for the identification of Rickettsia and Coxiella species to strain levels in some of the pools. Diversity analysis revealed that the tick genera had high levels of Alpha diversity but the differences between the microbiomes of the three tick genera studied were not significant. The detection of C. acnes, commonly associated with human skin flora suggests that the ticks may have contact with humans potentially exposing them to bacterial infections. The findings in this study highlight the need for further investigation into the viability of these bacteria and the competency of ticks to transmit them. Clinicians in these high-risk areas also need to be appraised for them to include Rickettsial diseases and Q-fever as part of their differential diagnosis.

Applicability of SCoT markers in unraveling genetic variation and population structure among sugar beet (Beta vulgaris L.) germplasm.

Sugar beet (Beta vulgaris L.) holds significant importance as a crop globally cultivated for sugar production. The genetic diversity present in sugar beet accessions plays a crucial role in crop improvement programs. During the present study, we collected 96 sugar beet accessions from different regions and extracted DNA from their leaves. Genomic DNA was amplified using SCoT primers, and the resulting fragments were separated by gel electrophoresis. The data were analyzed using various genetic diversity indices, and constructed a population STRUCTURE, applied the unweighted pair-group method with arithmetic mean (UPGMA), and conducted Principle Coordinate Analysis (PCoA). The results revealed a high level of genetic diversity among the sugar beet accessions, with 265 bands produced by the 10 SCoT primers used. The percentage of polymorphic bands was 97.60%, indicating substantial genetic variation. The study uncovered significant genetic variation, leading to higher values for overall gene diversity (0.21), genetic distance (0.517), number of effective alleles (1.36), Shannon's information index (0.33), and polymorphism information contents (0.239). The analysis of molecular variance suggested a considerable amount of genetic variation, with 89% existing within the population. Using STRUCTURE and UPGMA analysis, the sugar beet germplasm was divided into two major populations. Structure analysis partitioned the germplasm based on the origin and domestication history of sugar beet, resulting in neighboring countries clustering together. The utilization of SCoT markers unveiled a noteworthy degree of genetic variation within the sugar beet germplasm in this study. These findings can be used in future breeding programs with the objective of enhancing both sugar beet yield and quality.

Within-Host Influenza Viral Diversity in the Pediatric Population as a Function of Age, Vaccine and Health Status

Abstract Seasonal influenza virus predominantly evolves through antigenic drift, marked by the accumulation of mutations at antigenic sites. Because of antigenic drift, influenza vaccines are frequently updated, though their efficacy may still be limited due to strain mismatches. Despite the high levels of viral diversity observed across populations, most human studies reveal limited intrahost diversity, leaving the origin of population-level viral diversity unclear. Previous studies show host characteristics, such as immunity, might affect within-host viral evolution. Here we investigate influenza A viral diversity in children aged between 6 months and 18 years. Influenza virus evolution in children is less well characterized than in adults, yet may be associated with higher levels of viral diversity given the lower level of pre-existing immunity and longer durations of infection in children. We obtained influenza isolates from banked influenza A-positive nasopharyngeal swabs collected at the Children’s Hospital of Philadelphia during the 2017-2018 influenza season. Using next-generation sequencing, we evaluated the population of influenza viruses present in each sample. We characterized within-host viral diversity using the number and frequency of intrahost single nucleotide variants detected in each sample. We related viral diversity to clinical metadata, including subjects’ age, vaccination status, and comorbid conditions, as well as sample metadata such as virus strain and cycle threshold. Consistent with previous studies, most samples contained low levels of diversity with no clear association between the subjects’ age, vaccine status or health status. Further, there was no enrichment of iSNVs near known antigenic sites. Taken together, these findings are consistent with previous observations that the majority of intrahost influenza virus infection is characterized by low viral diversity without evidence of diversifying selection.

Comparative karyotype analysis of the red brocket deer (M. americana sensu lato and M. rufa) complex: evidence of drastic chromosomal evolution and implications on speciation process.

Chromosomal rearrangements are often associated with playing a role in the speciation process. However, the underlying mechanism that favors the genetic isolation associated with chromosomal changes remains elusive. In this sense, the genus Mazama is recognized by its high level of karyotype diversity among species with similar morphology. A cryptic species complex has been identified within the genus, with the red brocket deer (Mazama americana and Mazama rufa) being the most impressive example. The chromosome variation was clustered in cytotypes with diploid numbers ranging from 42 to 53 and was correlated with geographical location. We conducted an analysis of chromosome evolution of the red brocket deer complex using comparative chromosome painting and Bacterial Artificial Chromosome (BAC) clones among different cytotypes. The aim was to deepen our understanding of the karyotypic relationships within the red brocket, thereby elucidating the significant chromosome variation among closely related species. This underscores the significance of chromosome changes as a key evolutionary process shaping their genomes. The results revealed the presence of three distinct cytogenetic lineages characterized by significant karyotypic divergence, suggesting the existence of efficient post-zygotic barriers. Tandem fusions constitute the main mechanism driving karyotype evolution, following a few centric fusions, inversion X-autosomal fusions. The BAC mapping has improved our comprehension of the karyotypic relationships within the red brocket deer complex, prompting questions regarding the role of these changes in the speciation process. We propose the red brocket as a model group to investigate how chromosomal changes contribute to isolation and explore the implications of these changes in taxonomy and conservation.

SNP‐based analysis of European Thymallus spp. (Salmonidae) reveals extensive mito‐nuclear discordance relevant for biogeographic inferences, taxonomy and conservation

AbstractAimPaleohydrological dynamics are well‐documented for European river systems, promoting shifting phases of isolation and connectivity of their aquatic fauna. These conditions coupled with high rates of hybridisation found in freshwater fishes may introduce considerable complexity and potential mito‐nuclear discordance of phylogenetic patterns. We evaluate this hypothesis using the first large‐scale analysis of nuclear SNPs in European species of grayling (Thymallus) compared to mtDNA data with the aim of reassessing the evolutionary history of this group of rheophilic fishes.LocationFreshwater systems in Europe.MethodsBased on mitochondrial (mitogenomes, control region) and nuclear (ddRADseq) data, we applied population‐genetic, phylogenetic, and biogeographic tools to evaluate lineage diversity in the context of paleohydrological alterations.ResultsThe results corroborated previously recognised high levels of lineage diversity, but revealed several cases of mito‐nuclear discordance and signals of both historical (natural) and human‐mediated introgression among major inter‐ and intraspecific lineages of Thymallus in Europe. A time‐calibrated phylogeny and ancestral area estimation, based on nuclear SNP data, supported a late Pliocene diversification of the genus in Europe and suggested an early colonisation of the Black Sea basin with subsequent dispersal into Central and Western Europe.Main ConclusionsThe genetic structure of Thymallus in Europe recovered by nuclear SNPs contrasts considerably with that supported by mtDNA. Several instances of mito‐nuclear discordance underscore frequent contact of allopatric lineages in a dynamic paleohydrological landscape and reveal the weakness of basing both taxonomic and conservation decisions on inferences based on mtDNA alone. The Danube and Rhine drainages were inferred as important zones of contact between divergent phylogeographic lineages. Additionally, our data cast doubt on the genetic integrity of the endangered T. aeliani. Its divergence from T. thymallus, using nuclear SNPs, appears minimal as samples of T. aeliani group within Danubian lineages, despite carrying highly divergent reciprocally monophyletic mtDNA.

Multiple dimensions of phyllostomid bat biodiversity across ecosystems of the Orinoco Llanos

AbstractUnderstanding the impacts of habitat conversion on species assemblages across multiple biodiversity dimensions (taxonomic, functional, and phylogenetic) and spatial scales is pivotal for implementing effective conservation strategies. Here, we surveyed phyllostomid bats using mist nets in riparian and unflooded forests, flooded savannahs, and conventional rice fields to investigate how changes in habitat quality affect multifaceted diversity from two Colombian farming systems in the Orinoco Llanos: traditional farmlands with high‐intensity agriculture (mainly rice production) and Civil Society Nature Reserves with greater ecosystem protection. We used a unified framework based on Hill numbers for quantifying bat taxonomic, functional, and phylogenetic diversity and modeled the relationship of these diversity facets with landscape variables (habitat cover and patch density) across three spatial scales (0.5, 1.5, 3 km) using Bayesian generalized linear mixed‐effect models. Our results indicate that increasing human activity toward rice monocultures representative of traditional farmlands negatively affected all diversity facets. In contrast, forested habitats associated mainly with riparian forests within private reserves contained higher taxonomic, functional, and phylogenetic diversity than savannahs and rice fields. However, the differences between riparian forests and rice crops were significant only for phylogenetic diversity, indicating loss of evolutionary history after habitat conversion. At the landscape scale, forest cover was a significant predictor for functional (0.5‐ and 3‐km scale) and phylogenetic diversity (0.5 km), and bats responded negatively at the 3‐km scale to rice patch density from a functional diversity perspective. Increasing habitat quality through preserving forest cover and patches should minimize the harmful effects of habitat conversion on multidimensional bat biodiversity. Furthermore, the conservation of riparian forests and the creation of more wildlife‐friendly farming, as practiced in the reserves, should be prioritized to ensure high levels of bat taxonomic, functional, and phylogenetic diversity across Orinoco countryside landscapes.

Association of Acidotolerant Cyanobacteria to Microbial Mats below pH 1 in Acidic Mineral Precipitates in Río Tinto River in Spain.

This report describes acidic microbial mats containing cyanobacteria that are strongly associated to precipitated minerals in the source area of Río Tinto. Río Tinto (Huelva, Southwestern Spain) is an extreme acidic environment where iron and sulfur cycles play a fundamental role in sustaining the extremely low pH and the high concentration of heavy metals, while maintaining a high level of microbial diversity. These multi-layered mineral deposits are stable all year round and are characterized by a succession of thick greenish-blue and brownish layers mainly composed of natrojarosite. The temperature and absorbance above and below the mineral precipitates were followed and stable conditions were detected inside the mineral precipitates. Different methodologies, scanning and transmission electron microscopy, immunological detection, fluorescence in situ hybridization, and metagenomic analysis were used to describe the biodiversity existing in these microbial mats, demonstrating, for the first time, the existence of acid-tolerant cyanobacteria in a hyperacidic environment of below pH 1. Up to 0.46% of the classified sequences belong to cyanobacterial microorganisms, and 1.47% of the aligned DNA reads belong to the Cyanobacteria clade.

Low genetic variability and high isolation of a post-harvest South American pinniped population as revealed by genome-wide single nucleotide polymorphisms

Abstract Otaria flavescens has been one of the most heavily exploited pinnipeds during the last 200 years, with depletion of ~90% in some colonies. After the prohibition on sealing in South America, populations stabilized except for the Uruguayan population, which showed a constant decrease. The underlying causes of its decline are unknown. This study used genome-wide single nucleotide polymorphisms to assess the variability and connectivity of some of the most overexploited sea lion colonies in the Atlantic Ocean. Our results revealed low allelic richness, nucleotide diversity, and heterozygosity in the Uruguayan population and evidence of complete isolation from the Argentinean populations under study. In contrast, the Patagonian populations showed a high degree of connectivity, which could explain their recovery and high levels of diversity at present. Our study highlights the critical situation of the Uruguayan sea lion population, emphasizing the need for maintaining continuous conservation efforts in the region.

Genomic Diversity and Demographic History of the Endangered Sichuan hill-partridge (Arborophila rufipectus).

Species conservation can be improved by knowledge of genetic diversity and demographic history. The Sichuan hill-partridge (Arborophila rufipectus, SP) is an endangered species endemic to the mountains in southwestern China. However, little is known about this species' genomic variation and demographic history. Here, we present a comprehensive whole-genome analysis of six SP individuals from the Laojunshan National Nature Reserve in Sichuan Province, China. We observe a relatively high genetic diversity and low level of recent inbreeding in the studied SP individuals. This suggests that the current population carries genetic variability that may benefit the long-term survival of this species, and that the present population may be larger than currently recognized. Analyses of demographic history showed that fluctuations in the effective population size of SP are inconsistent with changes of the historical climate. Strikingly, evidence from demographic modeling suggests SPs population decreased dramatically 15,100 years ago after the Last Glacial Maximum (LGM), possibly due to refugial isolation and later human interference. These results provide the first detailed and comprehensive genomic insights into genetic diversity, genomic inbreeding levels, and demographic history of the Sichuan hill-partridge, which are crucial for the conservation and management of this endangered species.

Genetic insights into Cyphocharax magdalenae (Characiformes: Curimatidae): Microsatellite loci development and population analysis in the Cauca River, Colombia.

Cyphocharax magdalenae, a Colombian freshwater fish species, plays a vital role in nutrients distribution and serves as a significant food source for other fish species and local fishing communities. Considered a short-distance migratory species, C. magdalenae populations face substantial extinction risk due to human activities impacting their habitats. To address the lack of knowledge on genetic diversity and population structure, this study used next-generation sequencing technology to develop species-specific microsatellite loci and conducted a population genetics analysis of C. magdalenae in the middle and lower sections of the Cauca River, Colombia. Out of 30 pairs of microsatellite primers evaluated in 324 individuals, 14 loci were found to be polymorphic, at linkage equilibrium and, in at least one population, their genotypic frequencies were in Hardy-Weinberg equilibrium. Results showed high genetic diversity levels compared to other neotropical Characiformes, with inbreeding coefficients similar to those reported for phylogenetically related species. Moreover, C. magdalenae exhibits seasonal population structure (rainy-dry) consisting of two genetic stocks showing bottleneck signals and high effective population sizes. This information is essential for understanding the current species genetics and developing future management programs for this fishery resource.