Intraspecific Variation Research Articles

Impacts of land use and abiotic factors on fruit, seed, and leaf morphology of the desert date Balanites aegyptiaca in Benin: Implications for management

Preserving intraspecific phenotypic variation within socio-economically important but declining species is fundamental in the current context of rapid change in land use and environmental conditions. Balanites aegyptiaca (L.) Delile is a valuable seed oil tree species native to the arid and semi-arid regions of Africa. Notable morphological variations within the species are recognized by local communities, who often select trees with preferred traits for preservation in croplands. This study compared phenotypic variation in B. aegyptiaca based on sixteen phenotypic traits of fruits, seeds, and leaflets between trees in a strictly protected area and those in croplands. Furthermore, the relative role of land use, soil characteristics, bioclimatic variables, elevation, and slope in the observed variation was analysed. Student t-test, principal component analysis, redundancy analysis, and variance partitioning were used for data analysis in R software. Results showed that, after accounting for tree variation, significant differences were observed in only two traits: seed ratio, and leaflet dry weight, with mean values in cropland being 1.470 (higher), and 0.943 (lower) times that of wild trees, respectively. Furthermore, principal component analysis showed great overlap between ellipses of cropland and wild trees. The variance partitioning analysis showed that bioclimatic variables explained 18 % of the total variation followed by soil characteristics (11 %), and land use (9 %). These findings collectively suggest weak impacts of croplands and a lack of domestication syndrome in B. aegyptiaca in Benin, potentially due to persisting gene flow between wild and cropland trees, inadvertent species management, or low intensity of selection pressures. Future studies should explore organoleptic properties, physico-chemical characteristics of the pulp and seed oil and discern the extent to which observed differences are attributable to genetic factors and biotic factors (pest attacks, plant-plant interactions, etc.).

A new species of the pill millipede genus Rhopalomeris Verhoeff, 1906 (Diplopoda, Glomerida, Glomeridae) from Myanmar, and notes on Rhopalomeriscarnifex (Pocock, 1889).

The taxonomy of the pill millipede genus Rhopalomeris Verhoeff, 1906, which is restricted to Indochina and currently comprises six described species, is refined and updated. An integrative taxonomic approach was employed that combines morphological examination with DNA barcoding using the cytochrome c oxidase subunit I (COI) gene for species identification and delineation. The first objective was to confirm the identity of Rhopalomeriscarnifex (Pocock, 1889), a charismatic species known as the "candy pill millipede" due to its vivid coloration, based on specimens collected near the type locality in Myanmar. The second objective was to describe a new species, Rhopalomerisnigroflava Likhitrakarn, sp. nov., discovered in Linno Gu, Kayin State, Myanmar. This new species is distinguished by its small body size (5.1-9.7 mm long) and yellow body with contrasting brown to blackish markings on certain terga. In addition, the position of the telopod syncoxital lobe relative to the lateral syncoxite horns separates it from other Rhopalomeris species. The interspecific divergence between R.nigroflava Likhitrakarn, sp. nov. and other congeners ranges from 10.85% to 16.13%, based on uncorrected COI p-distances, while the intraspecific divergence was 0%-7.44%. A distribution map of and a revised identification key to all known species of Rhopalomeris are also provided.

Differential Effects of Chewing Lice on Body Condition across Host Age and Sex in Rough-legged Hawks (Buteo lagopus).

Chewing lice infesting avian hosts can significantly affect host health and fitness. Here, we present quantitative data on host body condition and louse abundance observed from 121 Rough-legged Hawks (Buteo lagopus) sampled across the North American nonbreeding range. Among hawks examined, louse prevalence was 71%, with a mean abundance and intensity of 9.1 and 12.8 lice, respectively. We identified lice as Craspedorrhynchus sp., either Craspedorrhynchus dilatatus or Craspedorrhynchus taurocephalus, dependent on future taxonomic revision of the genus. Female and juvenile hawks had greater louse intensity and prevalence compared with male and adult hawks, respectively. Host body condition, measured as a breast muscle score (keel score), was negatively correlated with louse abundance after controlling for host age and sex. Possible explanations for these patterns include the following: sex-biased louse transfer between adults and nestlings, when female nestlings experience increased transfer loads; body size differences between males and females, when females are larger than males in each life stage; and preening limitations in females and juveniles, when both spend more time hunting and less time preening relative to adult males. Our results corroborate previous studies suggesting that the primary sources of intraspecific variation in louse abundance are host body size and preening limitations.

Molecular and morphological data provide evidence for only one alien species of pearl oyster in the Mediterranean Sea

Taxonomic identification of alien bivalve species in the Mediterranean Sea can be challenging because of high morphological variability and the occurrence of cryptic species complexes, as in the case of pearl oysters. While the presence of the Lessepsian species Pinctada radiata is well-established in the eastern Mediterranean Sea, the presence of P. fucata was recently suggested based on morphological data. In this study we performed an integrative assessment based on morphological and genetic data on pearl oysters collected across the Mediterranean Basin. Molecular species delimitation and phylogenetic analyses allowed a straightforward taxonomic assignment of all collected specimens to P. radiata. These specimens show the entire suite of morphological character states considered diagnostic of either P. fucata or P. radiata by previous studies. This finding clearly demonstrates that these morphological characters have no taxonomic value, and their variability observed in specimens from the Mediterranean Sea represents (part of) the intraspecific variability of P. radiata. While no evidence has been found for the presence of P. fucata, the earlier occurrences of P. radiata from the eastern and southern Mediterranean Sea are complemented with verified occurrence in the western and northern regions, demonstrating a further spreading of this non-native species throughout the Mediterranean Sea. This study clarifies the taxonomic identification and geographical distribution of pearl oysters in the Mediterranean Sea and substantiates the importance of molecular identification of alien bivalves characterized by extensive variation in shell characters.

Migratory strategies across an ecological barrier: is the answer blowing in the wind?

BackgroundEcological barriers can shape the movement strategies of migratory animals that navigate around or across them, creating migratory divides. Wind plays a large role in facilitating aerial migrations and can temporally or spatially change the challenge posed by an ecological barrier, with beneficial winds potentially converting a barrier into a corridor. Here, we explore the role wind plays in shaping initial southbound migration strategy among individuals breeding at two sites along an ecological barrier.MethodsUsing GPS satellite transmitters, we tracked the southbound migrations of Short-billed Dowitchers (Limnodromus griseus caurinus) from two breeding sites in Alaska to nonbreeding sites in coastal Mexico. The breeding sites were positioned in distinct regions along an ecological barrier – the Gulf of Alaska. We investigated potential differences in migratory timing, wind availability, and tailwind support en route across the Gulf of Alaska between individuals breeding at the two sites.ResultsRoute choice and arrival timing to wintering sites differed markedly between the two breeding sites: individuals departing from the more westerly site left at the same time as those from further east but crossed the Gulf of Alaska farther west and arrived along the Pacific coast of Mexico an average of 19 days earlier than their counterparts. Dowitchers from both sites departed with slight tailwinds, but once aloft over the Gulf of Alaska, birds from the more westerly site had up to twelve times more tailwind assistance than birds from the more easterly one.ConclusionsThe distinct migration strategies and degree of wind assistance experienced by birds at these two breeding sites demonstrates how differences in wind availability along migratory routes can form the basis for intraspecific variation in migration strategies with potential carryover effects. Future changes in wind regimes may therefore interact with changes in habitat availability to influence migration patterns and migratory bird conservation.

Anomalous latitudinal gradients in parasitoid wasp diversity-Hotspots in regions with larger temperature range.

Knowledge of global patterns of genetic diversity is essential for biodiversity conservation as this parameter describes the ability of a species to respond to environmental changes. Ichneumonoids parasitoid wasps are among the few taxa showing an anomalous latitudinal diversity gradient. Using the largest georeferenced molecular dataset for this group, we used a macrogenetics approach to examine latitudinal patterns and predictors of intraspecific genetic diversity. We calculated the mean nucleotide diversity of mitochondrial DNA barcode sequences at three geographic levels: grid cells, latitudinal bands and climatic zones. Nucleotide diversity values were consistently higher at northern temperate latitudes, peaking at 50°. We found a positive but weak relationship between intraspecific diversity and the latitude, between intra- and interspecific diversity, and a positive effect of the temperature range. Examining the spatial relationship between different levels of biodiversity and its drivers is particularly relevant considering climate change and its impact on species distribution. Yet, in insects, it has been challenging to integrate ecological, evolutionary and geographical components when analysing the processes leading to species richness gradients.

The interplay between host-specificity and habitat-filtering influences sea cucumber microbiota across an environmental gradient of pollution

Environmental gradients can influence morpho-physiological and life-history differences in natural populations. It is unclear, however, to what extent such gradients can also modulate phenotypic differences in other organismal characteristics such as the structure and function of host-associated microbial communities. In this work, we addressed this question by assessing intra-specific variation in the diversity, structure and function of environmental-associated (sediment and water) and animal-associated (skin and gut) microbiota along an environmental gradient of pollution in one of the most urbanized coastal areas in the world. Using the tropical sea cucumber Holothuria leucospilota, we tested the interplay between deterministic (e.g., environmental/host filtering) and stochastic (e.g., random microbial dispersal) processes underpinning host-microbiome interactions and microbial assemblages. Overall, our results indicate that microbial communities are complex and vary in structure and function between the environment and the animal hosts. However, these differences are modulated by the level of pollution across the gradient with marked clines in alpha and beta diversity. Yet, such clines and overall differences showed opposite directions when comparing environmental- and animal-associated microbial communities. In the sea cucumbers, intrinsic characteristics (e.g., body compartments, biochemistry composition, immune systems), may underpin the observed intra-individual differences in the associated microbiomes, and their divergence from the environmental source. Such regulation favours specific microbial functional pathways that may play an important role in the survival and physiology of the animal host, particularly in high polluted areas. These findings suggest that the interplay between both, environmental and host filtering underpins microbial community assembly in H. leucospilota along the pollution gradient in Hong Kong.

Application of otolith morphometrics in delineating population structure of Aphaniops stoliczkanus (Teleostei: Aphaniidae) in southern Iranian waters

AbstractWidely distributed Species in different geological and ecological environments often exhibit great intraspecific diversity. Aphaniops stoliczkanus (Day, 1872) is an endemic species of Middle East occurring over a vast geographic range in different basins. This species has been observed in freshwater, brackish water and hot sulphur springs; therefore, its populations are known to exhibit considerable morphological variation. In the present study, we have investigated the poorly studied populations of A. stoliczkanus of the Hormuz and Makran basins of Iran in terms of otolith morphology and morphometrics. According to the results, these populations can be divided into two distinct groups including east and west of the Strait of Hormuz. Our results also provide evidence that there is a relationship between otolith morphology and the environment, serving as environmental factors that may influence the formation of specific regions in the otolith shape. Despite the remarkable morphological similarities among otoliths in geographically close populations of Charak and Chiruyeh, our data purposed that geographically these populations have different dorsal tip shapes in their otolith. In comparison to the data from other studies, the otoliths of Qeshm Island appear to resemble the overall shape of otolith found in Oman very closely. However, it is believed that Qeshm Island population was separated from the Hormuz basin populations during the Holocene Sea level rise. Also, the outcomes of this study provide insights into the potential role of environmental factors in shaping intraspecific diversity and the migration patterns of this species within the Persian Gulf.

Dental morphology evolution in early peratheriines, including a new morphologically cryptic species and findings on the largest early Eocene European metatherian

ABSTRACT The initial stages of the evolutionary history of peratheriines, the European herpetotheriid metatherians, are largely unknown, primarily due to their limited morphological dental disparity throughout the Palaeogene, coupled with significant intraspecific variation. Based on eleven molars, we document a new early peratheriine species, Peratherium musivum sp. nov. which is larger than and morphologically similar to the earliest peratheriine, Peratherium constans (MP7). Subtle molar characters are shared with the largest early Eocene peratheriine, Peratherium maximum comb. nov. We illustrate the importance of studying possible changes in molar cusp – basin proportions and correlated characters that occured during peratheriine evolution. Peratherium musivum sp. nov. which spanned only part of the MP7-MP8 + 9 time interval, and the ~MP8 + 9 Peratherium maximum comb. nov. were probably widespread in Western Europe. The description of a well-preserved mandible of the latter, from La Borie (~MP8 + 9), reveals original features concerning relative size and shape of dental alveoli, partly corroborated using isolated molars. These traits are absent in the younger, most representative species of both peratheriine genera, Peratherium and Amphiperatherium. Based on the aforementioned data and a critical review, it is demonstrated that peratheriine genera lack consistent definitions, so that the Peratherium/Amphiperatherium dichotomy is plausibly inapplicable to early Eocene representatives. This article is registered in ZooBank under urn:lsid:zoobank.org:pub:A2B4DE58-855C-4CB8-BC1D-C9677E6DF97D

Evolutionary Modes of wtf Meiotic Driver Genes in Schizosaccharomyces pombe.

Killer meiotic drivers are a class of selfish genetic elements that bias inheritance in their favor by destroying meiotic progeny that do not carry them. How killer meiotic drivers evolve is not well understood. In the fission yeast, Schizosaccharomyces pombe, the largest gene family, known as the wtf genes, is a killer meiotic driver family that causes intraspecific hybrid sterility. Here, we investigate how wtf genes evolve using long-read-based genome assemblies of 31 distinct S. pombe natural isolates, which encompass the known genetic diversity of S. pombe. Our analysis, involving nearly 1,000 wtf genes in these isolates, yields a comprehensive portrayal of the intraspecific diversity of wtf genes. Leveraging single-nucleotide polymorphisms in adjacent unique sequences, we pinpoint wtf gene-containing loci that have recently undergone gene conversion events and infer their ancestral state. These events include the revival of wtf pseudogenes, lending support to the notion that gene conversion plays a role in preserving this gene family from extinction. Moreover, our investigation reveals that solo long terminal repeats of retrotransposons, frequently found near wtf genes, can act as recombination arms, influencing the upstream regulatory sequences of wtf genes. Additionally, our exploration of the outer boundaries of wtf genes uncovers a previously unrecognized type of directly oriented repeats flanking wtf genes. These repeats may have facilitated the early expansion of the wtf gene family in S. pombe. Our findings enhance the understanding of the mechanisms influencing the evolution of this killer meiotic driver gene family.

Variation in Thickness of Embryo Covering Structures and Their Role in the Regulation of Seed Physiological Dormancy of Chenopodium hircinum (Amaranthaceae)

Chenopodium hircinum, the putative wild ancestor of quinoa, is a source of traits that could improve the tolerance of crop quinoa to high temperatures. However, seeds of C. hircinum have physiological dormancy (PD), which is an obstacle for plant propagation and use in breeding programs. We studied the intraspecific variability in morpho-anatomical traits of embryo covering structures and their association with PD. We also evaluated the effects of different dormancy-breaking treatments on PD alleviation and germination. Seeds were dispersed with a remnant perianth and a persistent pericarp that could be removed by scraping. The seed coat was formed by palisade cells impregnated with tannins, and the seed contained a thin layer of peripheral endosperm surrounding the embryo. In our investigation, the thickness of the pericarp (P) and/or seed coat (SC) varied among populations. Populations with higher P and/or SC thickness showed lower percentages of germination and water absorption. The combined dormancy-breaking treatment (bleach + perforated coverings + gibberellic acid) promoted dormancy release and increased germination. C. hircinum seeds showed non-deep physiological dormancy. Based on previous knowledge about quinoa, and our results, we conclude that embryo coverings, especially the seed coat, have an important role in dormancy control, imposing a mechanical restraint on radicle emergence.

Revision of the endemic South African genus Moegistorhynchus Macquart (Diptera: Nemestrinidae), with a species key, description of three new species and comments on pollination biology and biogeography

The genus Moegistorhynchus Macquart is revised and its relationships are discussed. The genus is distributed across lowland and montane areas of the Western and Northern Cape provinces, extending from Cape Town (Western Cape province) in the south to Port Nolloth (Northern Cape province) in the north. Three new species are described from Western Cape specimens: Moegistorhynchus manningi sp. nov. (Stettynsberg and Hottentots Holland mountains); M. strillii sp. nov. (Groot Winterhoek mountains); and M. turneri sp. nov. (Groot Winterhoek mountains and Waboomsberg). The four known species of the genus are redescribed: M. braunsi Bequaert, 1935; M. brevirostris (Wiedemann, 1821); M. longirostris (Wiedemann, 1819); and M. perplexus Bequaert, 1935. Moegistorhynchus longirostris and M. brevirostris are the only two species which extend their distribution northwards into the Northern Cape. There is marked intraspecific variation in M. perplexus and it may represent a species complex. Moegistorhynchus braunsi and M. strillii sp. nov. are possibly extinct. All species are fully illustrated, inclusive of the male postabdomen, where possible. A comprehensive identification key to the species is presented as is a distribution map, with some commentary on pollination biology and biogeography.

Proteolytic degradation of seed proteins of vetch species (Vicia L. subgenus Vicia) of section Peregrinae Kupicha during SDS-electrophoresis and its prevention

Background. Due to its simplicity and good reproducibility, SDS-electrophoresis of seed proteins is widely used for investigating the gene pool of legumes and other plants, for species and varietal identification, analyzing the intraspecific variability, and registering collection material. The data obtained by this method agree well with the DNA analysis results complement them. Typically, legume seed proteins, including representatives of the genus Vicia L., show clear informative SDS electrophoretic profiles. When analyzing seed accessions of vetch species of the section Peregrinae Kupicha using standard approaches previously developed at VIR and approved by ISTA (the International Seed Testing Association), clear electrophoretic protein profiles could not be obtained for many accessions. This called into question the applicability of standard approaches to identifying vetch species in the section Peregrinae. The objective of the work was to clarify the nature of seed proteins degradation in representatives of the Peregrinae section and to find ways to prevent it to ensure the possibility of carrying out species identification and registration of all accessions in the vetch collection using a unified approach. Material and methods. Seed proteins of a number of vetch species Vicia L. from sections Bithynicae (B. Fedtsch.) Maxted, Hypechusa (Alef.) Aschers. et Graebner, Microcarinae Maxted and Peregrinae, members of the subgenus Vicia, were analyzed by SDS-electrophoresis using the standard method of protein extraction from flour with 0.025 M Tris-glycine buffer pH 8.3 at room temperature and its modifications, including heating the extract at 80°C or 100°C with or without the addition of 2-mercaptoethanol, as well as the addition of cysteine and serine protease inhibitors. Results and discussion. An analysis of seed proteins of representatives of most sections of the subgenus Vicia yielded informative species-specific protein profiles, whereas species of the section Peregrinae were characterized by the protein profiles, which indicated protein degradation, and species of this section differed in the frequency of such profile occurrence. While such profiles were obtained for all seeds of seven accessions of V. aintabensis Boiss & Hausskn. ex Boiss differing in geographical origin, year and place of regeneration, and 12 out of 13 of V. peregrine L. accessions demonstrated profiles of partially or completely degraded proteins, complete seed protein profiles were obtained for six out of nine V. michauxii Sprengel accessions. A change in conditions for protein isolation, namely replacement of their extraction from flour with Tris-glycine buffer pH 8.3 at room temperature with extraction in the same buffer by a short-term heating at 100°C in the presence of 2-mercaptoethanol, made it possible to obtain complete protein profiles for all accessions representing the section Peregrinae. The protein profiles of representatives of other vetch sections, as well as the profile of soybean proteins used as a standard for legume species identification, did not differ from the original ones under the modified conditions. Conclusions. The obtained results suggest that protein degradation in species of the Peregrinae section is associated with the abnormal activity of endogenous seed proteases under standard protein extraction conditions, and this trait is determined genotypically. A new modification of the method for isolating proteins from seeds makes it possible to apply the generally accepted approaches based on SDS-electrophoresis in the analysis of the gene pool of the Peregrinae section of the subgenus Vicia, as well as other vetch species.

How does anthropogenic food influence the trophic ecology of Rocky Mountain Red Fox?

Abstract Providing novel food subsidies to wildlife can influence behavior, resource use, disease dynamics, and food web interactions. Studies examining impacts of anthropogenic food have primarily occurred in urban landscapes where anthropogenic resources are consistently accessible. National parks, however, experience similar issues regarding wildlife exploiting anthropogenic food, but access to anthropogenic food is contingent on human visitation, which can fluctuate dramatically between seasons. We evaluated how fluctuating availability of anthropogenic food and demographic factors influenced the isotopic niche of Rocky Mountain Red Fox (Vulpes vulpes macroura) at the population and individual level in Grand Teton National Park, Wyoming. From 2016 to 2021, we assessed diet-related questions by collecting 55 whisker samples and 52 hair samples from 40 unique individuals and analyzed them using stable isotope analysis (δ13C and δ15N). We discovered that Rocky Mountain red foxes have a broad isotopic niche, with seasonal differences in their consumption of anthropogenic food. Contrary to our expectations, foxes demonstrated increased reliance on anthropogenic food (higher δ13C values) during winter months, whereas natural food consumption or dietary mixing was more prominent in summer months. Natural food scarcity could be driving foxes to seek out more anthropogenic food in the winter, whereas the increased abundance of natural food items in the summer could result in a lower need for foxes to supplement their diet with anthropogenic food. Adults had consistently higher δ13C values relative to juveniles, indicating either intraspecific variation in boldness or dominance leading to increased exploitation of anthropogenic food, which could be a learned behavior coinciding with habituation. Finally, we observed that increasing densities of human features within the home range of a fox was a strong predictor of anthropogenic food reliance at the individual level. Our work provided a deeper understanding of the trophic ecology of Rocky Mountain Red Fox in relation to human activity in a nature preserve, and equipped managers with insight into potential patterns associated with food-conditioned foxes.

Intraspecific diversity of Erwinia amylovora strains from northern Algeria

BackgroundFire blight, caused by Erwinia amylovora, is the most destructive bacterial disease affecting plants in the Rosaceae family, leading to significant economic losses. In Algeria, this disease has been reported since 2010. This study aimed to investigate the origin of fire blight in Algeria, in order to increase knowledge of the epidemiology of this serious disease and contribute to its management. A comprehensive characterization of 18 E. amylovora isolates recovered from northern Algeria between 2016 and 2021 to evaluate their phenotypical and genotypical diversity was conducted.ResultsPhenotypic differences, particularly in growth kinetics, virulence, and fatty acid profiles, allowed differentiation of strains into five groups, possibly indicating distinct introduction events. Genetic characterization revealed that only one strain lacked the ubiquitous plasmid pEA29, which is correlated with reduced virulence, while none harbored the pEI70 plasmid. Phylogenetic analysis using concatenated sequences of the recA, groEL, rpoS, ams, and hrpN genes grouped Algerian strains with those from a broadly prevalent clade. CRISPR genotyping identified a novel CR1 pattern and three genotypes, two of them previously unreported.ConclusionsThis study represents the first phenotypic, genetic, and phylogenetic investigation of E. amylovora strains in the region, and provides valuable information on the possible pathways of the introduction of this fire blight pathogen in northern Africa. The findings suggest one or more introduction events from a common ancestor, likely originating in northern Italy, followed by dispersal in various regions of Algeria.

Sequence-based analysis of the rice CAMTA family: haplotype and network analyses

The calmodulin-binding transcription activator (CAMTA) family contributes to stress responses in many plant species. The Oryza sativa ssp. japonica genome harbors seven CAMTA genes; however, intraspecific variation and functional roles of this gene family have not been determined. Here, we comprehensively evaluated the structure and characteristics of the CAMTA genes in japonica rice using bioinformatics approaches and RT-qPCR. Within the CAMTA gene and promoter sequences, 527 single nucleotide polymorphisms were retrieved from 3,024 rice accessions. The CAMTA genes could be subdivided into 5–14 haplotypes. Association analyses between haplotypes and phenotypic traits, such as grain weight and salt stress parameters, identified phenotypic differences between rice subpopulations harboring different CAMTA haplotypes. Co-expression analyses and the identification of CAMTA-specific binding motifs revealed candidate genes regulated by CAMTA. A Gene Ontology functional enrichment analysis of 690 co-expressed genes revealed that CAMTA genes have key roles in defense responses. An interaction analysis identified 30 putative CAMTA interactors. Three genes were identified in co-expression and interaction network analyses, suggesting that they are potentially regulated by CAMTAs. Based on all information obtained together with the phenotypes of the CRISPR-Cas9 knockout mutant lines of three OskCAMTA genes generated, CAMTA1 likely plays important roles in the response to salt stress in rice. Overall, our findings suggest that the CAMTA gene family is involved in development and the salt stress response and reveal candidate target genes, providing a basis for further functional characterization.

Classification, identification, and DNA barcoding study for common cockroach species (Dictyoptera: Blattaria) from China

Cockroaches are well-known pests and quarantined organisms worldwide. Due to morphological diversity and a lack of molecular data, their classification and identification are facing challenges. This study performed classification, identification, and DNA barcoding for cockroaches collected from China. Seventy-six samples were morphologically identified as seven species of two superfamilies that included Blattella germanica, Eublaberus posticus and Blaptica dubia belonging to the superfamily Blaberoidea, and Periplaneta americana, Periplaneta lateralis, Periplaneta fuliginosa and Periplaneta australasiae belonging to the superfamily Blattoidea. Based on sequence alignments of nine ribosomal and mitochondrial genes across the order Blattaria retrieved from GenBank, rDNA ITS2-517 bp and mtDNA 16S-327 bp were screened as candidates for molecular identification. Universal primers were designed for PCR amplification, cloning, and sequencing of the 37 representative samples. Sequence alignments and phylogeny analysis showed that both ITS2 and 16S confirmed samples 1–9, 20–24, and 25–29 as B. germanica, P. americana, and P. lateralis, respectively; only 16S (not ITS2) confirmed samples 10–14, 15–19, 30–34, and 35–37 as E. posticus, Blap. dubia, P. fuliginosa, and P. australasiae, respectively, indicating that 16S was a better target than ITS2 for molecular identification of cockroaches. Conservative motif and divergence analysis further revealed that ITS2 sequences vary significantly among different taxa, whereas 16S sequences are relatively conserved. There is an obvious barcoding gap between maximum intraspecific divergence and minimum interspecific divergence (2.57 % vs. 5.62 %) for ITS2, but not for 16S (6.15 % vs. 2.63 %). Therefore, it was confirmed that ITS2 is an ideal DNA barcode for molecular identification of cockroaches at lower category.

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.

Individual variation in Macrovipera lebetinus obtusa (blunt-nosed viper) venom from a limited area in Southeastern Anatolia (Türkiye)

Intraspecific variation in snake venom composition has been the subject of many studies, revealing the differences in venom proteomes according to age, diet, sex, and geographic region. Previous research on M. lebetinus venom mainly focused on protein purification, proteomic characterization, and biological activities. Although venom proteomes of its subspecies from different geographical areas were compared, it is a widespread species and there is limited knowledge regarding the individual venom variation of M. lebetinus in the same area. In this study, individual variation in M. lebetinus obtusa venom was investigated in terms of protein profiles, protease, phospholipase A2, ʟ-amino acid oxidase, hyaluronidase and phosphodiesterase, and hemolytic activities based on nine individuals collected in the province of Şanlıurfa (southeastern Türkiye). HPLC analysis indicated more striking differences compared to SDS-PAGE. Phosphodiesterase activity varied most between the individuals, followed by hyaluronidase and phospholipase A2. Hemolytic activity did not show significant alteration based on the blood agar method. The results of this initial study revealed that M. lebetinus venom shows variation between the individuals inhabiting the same habitat, which should be taken into account in the development of antivenoms and the clinical assessment of the bite cases.

Genus-targeted markers for the taxonomic identification and monitoring of coagulase-positive and coagulase-negative Staphylococcus species

The Staphylococcus genus comprises multiple pathogenic and opportunistic species that represent a risk to public health. Epidemiological studies require accurate taxonomic classification of isolates with enough resolution to distinguish clonal complexes. Unfortunately, 16 S rRNA molecular analysis and phenotypic characterization cannot distinguish all species and do not offer enough resolution to assess intraspecific diversity. Other approaches, such as Multilocus Sequence Tagging, provide higher resolution; however, they have been developed for Staphylococcus aureus and a few other species. Here, we developed a set of genus-targeted primers using five orthologous genes (pta, tuf, tpi, groEs, and sarA) to identify all Staphylococcus species within the genus. The primers were initially evaluated using 20 strains from the Collection of Microorganisms of Interest in Animal Health from AGROSAVIA (CMISA), and their amplified sequences were compared to a set of 33 Staphylococcus species. This allowed the taxonomic identification of the strains even on close species and the establishment of intraspecies diversity. To enhance the scope and cost-effectiveness of the proposed strategy, we customized the primer sets for an Illumina paired-end amplicon protocol, enabling gene multiplexing. We assessed five genes across 177 strains, generating 880 paired-end libraries from the CMISA. This approach significantly reduced sequencing costs, as all libraries can be efficiently sequenced in a single MiSeq run at a fraction (one-fourth or less) of the cost associated with Sanger sequencing. In summary, this method can be used for precise identification and diversity analysis of Staphylococcus species, offering an advancement over traditional techniques in both resolution and cost-effectiveness.Graphical