High Intraspecific Variability Research Articles

Integrative description of two new species of the Xenylla maritima species complex (Collembola: Hypogastruridae) from Crete (Greece), with notes on the high intraspecific genetic divergence found in X. maritima Tullberg, 1869

Integrative description of two new species of the Xenylla maritima species complex (Collembola: Hypogastruridae) from Crete (Greece), with notes on the high intraspecific genetic divergence found in X. maritima Tullberg, 1869

Diversity in Thrips palmi: exploration of genetic and ecological heterogeneity.

Thrips palmi Karny (Thysanoptera: Thripidae), an impactful pest in Southeast and East Asia, spread to Africa, Oceania, and the Americas in the past decades. Besides being a principal pest of vegetables, legumes, fibre, and ornamental crops, T. palmi serves as the vector for several plant viruses that cause substantial economic losses. The impact of intraspecies heterogeneity in the evolution of pesticide-resistant, host-specific, and geo-ecological strains is known for several thrips species. The present study aims to explore the genetic basis of the intraspecies heterogeneity of T. palmi populations if any. The genetic diversity within T. palmi has been recognized by 35 microsatellite markers, sequencing mitochondrial cytochrome oxidase subunit I (mtCOI), and internal transcribed spacer 2 (ITS2) markers. A total of 93 populations were collected from diverse ecological niches of India. Out of which 20 populations were identified as T. palmi. A total of 286 mtCOI and 66 ITS2 sequences of T. palmi originating from different parts of the world including the sequences generated in this study were considered to ascertain the genetic diversity. All the collected Indian populations are clustered into two distinct ancestries in Structure analysis, with a predominant inclination towards Ancestry II. A high intraspecific diversity of global populations of T. palmi up to 19% based on mtCOI sequences and 15% in ITS2 sequences is indicative of the presence of cryptic species. Phylogenetic analyses and haplotype networking clustered the global population of T. palmi into five lineages. Restricted gene flow was anticipated among the major lineages of T. palmi. The results suggest the existence of reproductively isolated populations due to potential geographical barriers. Excess of rare alleles suggested a recent selective sweep or population expansion after a recent bottleneck that seeks a further evolutionary understanding of T. palmi population globally, and its introduction and ecesis in new areas. The study proposes that T. palmi populations across the globe represent a species complex with broader genetic boundaries and reproductive isolation that suggest further taxonomical appraisal.

Helminths infection of Schizothorax niger in Kashmir, India: morphological and molecular characterization.

The identification of helminth parasites in Schizothorax spp. from Kashmir, including Schyzocotyle acheilognathi, Pomphorhynchus kashmirensis, and Adenoscolex oreini, is hindered by morphological limitations and high intraspecific variation. While previous studies have relied on morphological diagnosis, a comprehensive molecular characterization is lacking. To address these limitations and achieve more accurate species identification, this study employs molecular techniques such as DNA sequencing and phylogenetic analysis. Genomic DNA was extracted using standardized protocols. Partial amplification of 18S, ITS, and 28S rRNA was carried out using specific primer sets, followed by Sanger sequencing. Genetic characteristics were analyzed using bioinformatic approaches, focusing on Nucleotide divergence and Phylogenetic relationships. Phylogenetic analysis confirmed the monophyly of S. acheilognathi, revealing close relationships with S. nayarensis. Interspecific variation ranged from 2.0 - 4.1% for 18S and 0.8 - 2.2% for 28S rDNA, while P. kashmirensis showed high genetic similarity to P. tereticollis and P. laevis with variations ranging from 0.1 - 1.5% for 18S and 2.3-6.0% for ITS rDNA. A. oreini forms a monophyletic lineage separate from Caryophyllaeides and Caryophyllaeus species. Our study resolved persistent taxonomic ambiguities within the order Bothriocephalidea, resulting in the reassignment of Schyzocotyle acheilognathi (previously Bothriocephalus acheilognathi) to the reinstated genus Schyzocotyle. This study underscores the utility of ribosomal gene sequencing in characterizing fish parasites and highlights the need for taxonomic re-evaluation of A. oreini within the Capingentidae family.

Population structure of Clinostomum complanatum (Trematoda: Digenea) with new data on haplotype diversity of flukes from Slovakia and Italy.

The fluke Clinostomum complanatum, a parasite of piscivorous birds, but also reptiles and rarely mammals, has established several foci in the western Palaearctic regions. Previous studies pointed out the complicated taxonomy of the genus, but broader population genetic analysis of C. complanatum has not yet been carried out. The aim of this study was to determine the structure, intraspecific variability, and diversity of mitochondrial cox1 haplotypes of C. complanatum from different localities in Slovakia (Danube floodplain forests) and Italy (Emilia-Romagna and Tuscany), as well as to evaluate the interrelationships among populations from Europe, the Middle East, and North Africa. The genetic structure of C. complanatum from Slovakia and Italy was represented by a great number of haplotypes, showing stable populations with high intraspecific diversity. The haplotypes of samples from other localities (Romania, Turkey, Egypt, and Iran) showed possible gene flow among the populations from Central Europe down to the Mediterranean region, North Africa, and the Middle East. The genetic homogeneity of these samples can be linked to the distribution and migratory routes of the definitive hosts, aquatic piscivorous birds, mainly herons and cormorants, that spread parasite eggs among the continents.

Genome-wide analyses provide insights into genetic variation, phylo- and co-phylogenetic relationships, and biogeography of the entomopathogenic nematode genus Heterorhabditis.

Multigene, genus-wide phylogenetic studies have uncovered the limited taxonomic resolution power of commonly used gene markers, particularly of rRNA genes, to discriminate closely related species of the nematode genus Heterorhabditis. In addition, conflicting tree topologies are often obtained using the different gene markers, which limits our understanding of the phylo- and co-phylogenetic relationships and biogeography of the entomopathogenic nematode genus Heterorhabditis. Here we carried out phylogenomic reconstructions using whole nuclear and mitochondrial genomes, and whole ribosomal operon sequences, as well as multiple phylogenetic reconstructions using various single nuclear and mitochondrial genes. Using the inferred phylogenies, we then investigated co-phylogenetic relationships between Heterorhabditis and their Photorhabdus bacterial symbionts and biogeographical patterns. Robust, well-resolved, and highly congruent phylogenetic relationships were reconstructed using both whole nuclear and mitochondrial genomes. Similarly, whole ribosomal operon sequences proved valuable for phylogenomic reconstructions, though they have limited value to discriminate closely related species. In addition, two mitochondrial genes, the cytochrome c oxidase subunit I (cox-1) and the NADH dehydrogenase subunit 4 (nad-4), and two housekeeping genes, the fanconi-associated nuclease 1 (fan-1) and the serine/threonine-protein phosphatase 4 regulatory subunit 1 (ppfr-1), provided the most robust phylogenetic reconstructions compared to other individual genes. According to our findings, whole nuclear and/or mitochondrial genomes are strongly recommended for reconstructing phylogenetic relationships of the genus Heterorhabditis. If whole nuclear and/or mitochondrial genomes are unavailable, a combination of nuclear and mitochondrial genes can be used as an alternative. Under these circumstances, sequences of multiple conspecific isolates in a genus-wide phylogenetic context should be analyzed to avoid artefactual species over-splitting driven by the high intraspecific sequence divergence of mitochondrial genes and to avoid artefactual species lumping driven by the low interspecific sequence divergence of some nuclear genes. On the other hand, we observed that the genera Heterorhabditis and Photorhabdus exhibit diverse biogeographic patterns, ranging from cosmopolitan species to potentially endemic species, and show high phylogenetic congruence, although host switches have also occurred. Our study contributes to a better understanding of the biodiversity and phylo- and co-phylogenetic relationships of an important group of biological control agents and advances our efforts to develop more tools that are compatible with sustainable and eco-friendly agricultural practices.

Exploring the phylogenetic framework and trait evolution of Impatiens through chloroplast genome analysis

BackgroundThe genus Impatiens, which includes both annual and perennial herbs, holds considerable ornamental, economic, and medicinal value. However, it posed significant challenges for taxonomic and systematic reconstruction. This was largely attributed to its high intraspecific diversity and low interspecific variation in morphological characteristics. In this study, we sequenced samples from 12 Impatiens species native to China and assessed their phylogenetic resolution using the complete chloroplast genome, in conjunction with published samples of Impatiens. In addition, a comparative analysis of chloroplast genomes were conducted to explore the evolution of the chloroplast genome in Impatiens.ResultsThe chloroplast genomes of 12 Impatiens species exhibited high similarity to previously published samples in terms of genome size, gene content, and sequence. The chloroplast genome of Impatiens exhibited a typical four-part structure, with lengths ranging from 146,987 bp(I. morsei)- 152,872 bp(I. jinpingensis). Our results identified 10 mutant hotspot regions (rps16, rps16-trnG, trnS-trnR, and rpoB-trnC) that could serve as effective molecular markers for phylogenetic analyses and species identification within the Impatiens. Phylogenetic analyses supported the classification of Impatiens as a monophyletic taxon. The identified affinities supported the taxonomic classification of the subgenus Clavicarpa within the Impatiens, with subgenus Clavicarpa being the first taxon to diverge. In phylogenetic tree,the Impatiens was divided into eight distinct clades. The results of ancestral trait reconstruction suggested that the ancestral traits of Impatiens included a perennial life cycle, four sepals and three pollen grooves. However, the ancestral morphology regarding fruit shape, flower colour, and spacing length remained ambiguous.ConcludeOur study largely supported the family-level taxonomic treatment of Impatiens species in China and demonstrated the utility of whole chloroplast genome sequences for phylogenetic resolution. Comparative analysis of the chloroplast genomes of Impatiens facilitated the development of molecular markers.The results of ancestral trait reconstruction showed that the ancestor type of habit was perennial, the number of sepals was 4, and morphology and number of aperture was 3 colpus. The traits of capsule shape, flower colour, and spur length underwent a complex evolutionary process. Our results provided data support for further studies and some important new insights into the evolution of the Impatiens.

Redescription and validity of Formosania gilberti Oshima, 1919 (Cypriniformes: Balitoridae), an endemic hillstream loach from Taiwan

For over a century, only one species of Formosania has been recognised in Taiwanese waters. However, through the use of mitogenomic analyses and the identification of morphological differences, an endemic balitorid loach was revalidated and redescribed based on specimens herein of northern Taiwan. Formosania gilberti Oshima, 1919 was previously mistreated as a junior synonym of F. lacustris (Steindachner, 1908), but the two can be clearly differentiated by their vertebral counts (26+11 vs. 26+12) and body marking patterns (intensely mottled with vermicular markings vs. cloud-like blotches or brown and blotchless). Furthermore, mitogenomic analyses also showed high intra-specific diversity among Formosania loaches in Taiwan, which not only supports F. gilberti as a valid species but also hints the presence of a species complex distributed in western Taiwan.

Sexual Dimorphism in Wing Shape and Its Impact on Conspecific Identification of Neotropical Fannia Species (Diptera: Fanniidae)

Neotropical species of the genus Fannia remain poorly known despite their potential collection as biological evidence in criminal investigations. This is partly due to taxonomic difficulties and a lack of specialists. Identifying neotropical species of Fannia relies mainly on the classical morphological characters of adult males, as females show high similarity between species. Here, landmark-based geometric morphometrics of the wing could constitute an additional tool for associating adult females with conspecifics in this genus. In this study, we used a reference dataset of males belonging to ten putative species of Fannia from Colombia and molecular data to test this hypothesis. We found a strong wing shape sexual dimorphism, resulting in an almost perfect sex assignment based solely on this trait. However, the differences in wing shape between sexes were greater than those between species, making conspecific identification difficult. Our data show that wing shape could only feasibly be used for identifying adult males and females of F. lamosca, and males of F. dorsomaculata and F. pseudoconstricta. Low discrimination scores among remaining species may be partly explained by high intraspecific variation, slight wing shape differences among closely related species, or sampling bias. Although this study provides the first wing size and shape comparison among neotropical Fannia species, more samples and species are needed to validate these findings and identify the potential factors influencing this trait. Furthermore, the wing shape sexual dimorphism across Fannia species suggests different life-history strategies between sexes and possible genetic canalization mechanisms.

Phylogeography of Microphis retzii (Bleeker, 1856) and Microphis brachyurus (Bleeker, 1854) in the Pacific.

Syngnathidae are a charismatic family of teleost fishes, represented by seahorses, seadragons, and pipefishes. Syngnathidae are mainly composed of marine species, but about 30 species of pipefishes inhabit freshwater insular environments of the Indo-Pacific realm. Recent research has shown that some freshwater pipefish species are amphidromous and exhibit high intraspecific divergences across their distribution range, like Microphis brachyurus (Bleeker, 1854) distributed from Sri Lanka to French Polynesia and Microphis retzii (Bleeker, 1856) distributed from Taiwan to Indonesia. In this study, we used the mitochondrial cytochrome oxidase I (COI) partial gene of 91 specimens of M. brachyurus and 30 specimens of M. retzii from localities representative of their respective distribution area to improve knowledge on the population structure of these two widespread species. Genetic species delimitation and phylogeographic analyses were combined to explore spatial patterns of genetic diversity across the distribution ranges of the two species. We have highlighted deep genetic structuring within the two species and relate these results to various biotic and abiotic factors. For M. brachyurus, the population in Polynesia is distinct from those in the West Pacific, suggesting its distinctiveness and recognition as an evolutionary significant unit (ESU). For M. retzii, three lineages are delimited in its range distribution, suggesting the existence of two distinct species in Southeast Asia (Bali/Java/Lombok and China/Taiwan). Pipefish species are particularly vulnerable to anthropogenic pressures (inherent to Syngnathidae and insular environments). The present results, revising species delimitation and geographic distribution, will help implement effective conservation and management measures.

Intraspecific Variation in Parental Care May Reflect Variation in Parental Quality.

The existence of life-history trade-offs is a fundamental assumption of evolutionary biology and behavioural ecology, yet empirical studies have found mixed evidence for this. Such trade-offs are expected when individuals vary in how they allocate their limited resource budgets between different life-history functions (variation in resource allocation), but they may be masked when individuals vary in how many resources they have acquired that they can later allocate to life-history functions (variation in resource acquisition). We currently lack studies on the extent to which individual differences in behaviour reflect variation between individuals in resource acquisition and resource allocation. Here, we use parental care as a case study for exploring this question. We used the burying beetle Nicrophorus vespilloides, which exhibits facultative biparental care, comprising direct care (provisioning food or interacting with larvae) and indirect care (guarding or maintaining the carcass). We found some evidence for a positive relationship between these two components of care for both male and female parents. In addition, parents that spent more time providing care 24 h after hatching also tended to provide care for longer. Lastly, parents that provided more parental care did not experience a trade-off of reduced lifespan after the breeding attempt. On the contrary, we found a positive relationship between the duration of care provided and parents' post-breeding lifespan. Our finding of positive relationships between parental behaviours and between parental care and lifespan suggests that variation in care was mainly driven by differences in prior resource acquisition (i.e., parental quality) among individuals rather than differences in resource allocation. Our findings thus suggest that high intraspecific variation in parental quality can potentially mask reproductive investment trade-offs within populations.

Agronomic Evaluation and Chemical Characterization of Salvia lavandulifolia Vahl. over 3 Consecutive Years Cultivated Under Harsh Climatic Conditions in Southeast Spain.

The cultivation of Salvia lavandulifolia, Spanish sage, makes an important contribution to the economy of many rural areas in Southeastern Spain. This aromatic plant species is characterized by high intraspecific variability, which makes the selection process for the establishment of homogeneous crops difficult. Additionally, imminent climate change threatens to reduce its production, especially when cultivated in drylands. Therefore, to guarantee the continued production of this type of sage, it is essential to study its agronomic behavior and production quality. For this, clones from four ecotypes were cultivated for three years, assessing changes in their biomass production, essential oil yield and quality, and phenolic fraction, as well as the corresponding antioxidant activity. The results suggest that essential oil yield is genetically predetermined, greater biomass not being associated with higher quantities of essential oil. Weather conditions affected both essential oil and phenolic fraction secondary metabolism. Under very harsh conditions, Spanish sage produces higher concentrations of camphor and 1,-8-cineole along with luteolin-7-O-glucoside, and lithospermic, rosmarinic, and salvianolic A acids in its phenolic fraction. The synthesis of these components helps the species to withstand the hot and dry conditions typical of southeast Spain.

Expanding the Triangle of U: Comparative analysis of the Hirschfeldia incana genome provides insights into chromosomal evolution, phylogenomics and high photosynthesis-related traits.

The Brassiceae tribe encompasses many economically important crops and exhibits high intraspecific and interspecific phenotypic variation. After a shared whole-genome triplication (WGT) event (Br-α, ~15.9 million years ago), differential lineage diversification and genomic changes contributed to an array of divergence in morphology, biochemistry, and physiology underlying photosynthesis-related traits. Here, the C3 species Hirschfeldia incana is studied as it displays high photosynthetic rates under high-light conditions. Our aim was to elucidate the evolution that gave rise to the genome of H. incana and its high-photosynthesis traits. We reconstructed a chromosome-level genome assembly for H. incana (Nijmegen, v2.0) using nanopore and chromosome conformation capture (Hi-C) technologies, with 409Mb in size and an N50 of 52Mb (a 10× improvement over the previously published scaffold-level v1.0 assembly). The updated assembly and annotation was subsequently employed to investigate the WGT history of H. incana in a comparative phylogenomic framework from the Brassiceae ancestral genomic blocks and related diploidized crops. Hirschfeldia incana (x=7) shares extensive genome collinearity with Raphanus sativus (x=9). These two species share some commonalities with Brassica rapa and B. oleracea (A genome, x=10 and C genome, x=9, respectively) and other similarities with B. nigra (B genome, x=8). Phylogenetic analysis revealed that H. incana and R. sativus form a monophyletic clade in between the Brassica A/C and B genomes. We postulate that H. incana and R. sativus genomes are results of hybridization or introgression of the Brassica A/C and B genome types. Our results might explain the discrepancy observed in published studies regarding phylogenetic placement of H. incana and R. sativus in relation to the "Triangle of U" species. Expression analysis of WGT retained gene copies revealed sub-genome expression divergence, likely due to neo- or sub-functionalization. Finally, we highlighted genes associated with physio-biochemical-anatomical adaptive changes observed in H. incana which likely facilitate its high-photosynthesis traits under high light. The improved H. incana genome assembly, annotation and results presented in this work will be a valuable resource for future research to unravel the genetic basis of its ability to maintain a high photosynthetic efficiency in high-light conditions and thereby improve photosynthesis for enhanced agricultural production.

Temporal and inter-specific population genetics analyses of Sebastiscus marmoratus and S. tertius provide novel implications for fishery management

ABSTRACT Understanding population genetic diversity and evolutionary dynamics of marine fish species can provide theoretical bases for fishery management and germplasm conservation, especially facing a changing environment. The rockfish species in genus Sebastiscus are economically important species for farming and sport fisheries in China, Japan and Korea. In this study, inter-annual and inter-specific comparisons on genetic diversity, population differentiation and historical demography of S. marmoratus and S. tertius collected from coastal waters of Zhangzhou, China were conducted using mitochondrial control region sequences. High levels of genetic diversity were observed in both species, indicating high adaptive potential to environmental changes. Demographic analyses detected recent population expansion in population S. tertius (Ste-2020) and population S. marmoratus collected in 2020 (Sma-2020), yet failed in population collected in 2016 (Sma-2016). Moreover, in population Sma-2020, novel haplotypes were detected and grouped into a separate sub-branch, revealed by neighbour-joining topology. Detected recent population expansion and novel haplotypes might be considered as a response to environmental changes. Besides, results of genetic differentiation analysis suggested high intra-specific genetic variation in both species. These genetic data and information will provide novel implications for strengthening the management of S. marmoratus and S. tertius fisheries in climate change scenarios.

Cross-continental comparison of plant reproductive phenology shows high intraspecific variation in temperature sensitivity.

The success of plant species under climate change will be determined, in part, by their phenological responses to temperature. Despite the growing need to forecast such outcomes across entire species ranges, it remains unclear how phenological sensitivity to temperature might vary across individuals of the same species. In this study, we harnessed community science data to document intraspecific patterns in phenological temperature sensitivity across the multicontinental range of six herbaceous plant species. Using linear models, we correlated georeferenced temperature data with 23 220 plant phenological records from iNaturalist to generate spatially explicit estimates of phenological temperature sensitivity across the shared range of species. We additionally evaluated the geographic association between local historic climate conditions (i.e. mean annual temperature [MAT] and interannual variability in temperature) and the temperature sensitivity of plants. We found that plant temperature sensitivity varied substantially at both the interspecific and intraspecific levels, demonstrating that phenological responses to climate change have the potential to vary both within and among species. Additionally, we provide evidence for a strong geographic association between plant temperature sensitivity and local historic climate conditions. Plants were more sensitive to temperature in hotter climates (i.e. regions with high MAT), but only in regions with high interannual temperature variability. In regions with low interannual temperature variability, plants displayed universally weak sensitivity to temperature, regardless of baseline annual temperature. This evidence suggests that pheno-climatic forecasts may be improved by accounting for intraspecific variation in phenological temperature sensitivity. Broad climatic factors such as MAT and interannual temperature variability likely serve as useful predictors for estimating temperature sensitivity across species' ranges.

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.

The phenotypic and demographic response to the combination of copper and thermal stressors strongly varies within the ciliate species, Tetrahymena thermophila.

Copper pollution can alter biological and trophic functions. Organisms can utilise different tolerance strategies, including accumulation mechanisms (intracellular vacuoles, external chelation, etc.) to maintain themselves in copper-polluted environments. Accumulation mechanisms can influence the expression of other phenotypic traits, allowing organisms to deal with copper stress. Whether copper effects on accumulation strategies interact with other environmental stressors such as temperature and how this may differ within species are still unsolved questions. Here, we tested experimentally whether the combined effect of copper and temperature modulates traits linked to demography, morphology, movement and accumulation in six strains of the ciliate Tetrahymena thermophila. We also explored whether copper accumulation might modulate environmental copper concentration effects on phenotypic and demographic traits. Results showed high intraspecific variability in the phenotypic and demographic response to copper, with interactive effects between temperature and copper. In addition, they suggested an attenuation effect of copper accumulation on the sensitivity of traits to copper, but with great variation between strains, temperatures and copper concentrations. Diversity of responses among strains and their thermal dependencies pleads for the integration of intraspecific variability and multiple stressors approaches in ecotoxicological studies, thus improving the reliability of assessments of the effects of pollutants on biodiversity.

Phylogeography of the ambrosia beetle Euwallacea interjectus (Coleoptera: Curculionidae: Scolytinae): an emerging poplar pest and its Fusarium mutualists from poplar plantations in China.

Native to Asia, Euwallacea interjectus (Blandford) (Coleoptera: Curculionidae: Scolytinae) is a destructive and invasive pest of live trees, and now it has been found in the United States and Argentina. In recent years, this pest appeared in high densities in poplar monocultures from Eastern China (Jiangsu and Shanghai) and Argentina and caused significant poplar mortality. However, the origin of the pests related to tree damage and the Fusarium mutualists from some poplar zones in China remained unclear. Here, we provided a broader phylogeographic analysis of E. interjectus based on the mitochondrial gene (cytochrome c oxidase I) to determine the global genetic structure of this species. Five mitochondrial lineages were found in the native area. Populations introduced to the United States were originated from 4 localities. The Argentine population was derived from Japan. The species was observed with strikingly high level of cytochrome c oxidase I intraspecific divergence that exceeded interspecific divergence, but the high intraspecific variation was correlated with geographical locations among the native populations. Two nuclear genes (arginine kinase and carbamoyl-phosphate synthetase 2-aspartate transcarbamylase-dihydroorotase) were more conservative, and intraspecific differences were lower than interspecific differences. The mitochondrial genetic variation was probably caused by evolution of lineages among geographically isolated populations. But it is immature to infer the existence of cryptic species based on cytochrome c oxidase I differences. All samples collected from poplar populations were indigenous and formed close relationship with a specimen from eastern and southern China. Surprisingly, pests from poplar populations in Jiangsu and Shanghai showed different haplotypes and mutualists. This suggested that the control strategies should consider the genetic and mutualistic diversity of beetles at different poplar localities.

Rampant intraspecific variation of plastid genomes in Gentiana section Chondrophyllae.

Exploring the level of intraspecific diversity in taxa experienced radiation is helpful to understanding speciation and biodiversity assembly. Gentiana section Chondrophyllae sensu lato encompasses more than 180 species and occupies more a half of species in the genus. In this study, we collected samples across the range of three species (Gentiana aristata, G. crassuloides and G. haynaldii) in section Chondrophyllae s.l., and recovered the intra-species variation by comparing with closely related taxon. Using 25 newly sequenced plastid genomes together with previously published data, we compared structural differences, quantified the variations in plastome size, and measured nucleotide diversity in various regions. Our results showed that the plastome size variation in the three Chondrophyllae species ranged from 285 to 628 bp, and the size variation in LSC, IR and SSC ranged from 236 to 898 bp, 52 to 393 bp and 135 to 356 bp, respectively. Nucleotide diversity of plastome or any of the four regions was much higher than the control species. The average nucleotide diversity in plastomes of the three species ranged from 0.0010 to 0.0023 in protein coding genes, and from 0.0023 to 0.0061 in intergenic regions. More repeat sequence variations were detected within the three Chondrophyllae species than the control species. Various plastid sequence matrixes resulted in different backbone topology in two target species, showed uncertainty in phylogenetic relationship based inference. In conclusion, our results recovered that species of G. section Chondrophyllae s.l. has high intraspecific plastome variation, and provided insights into the radiation in this speciose lineage.

Closely related species differ in their traits, but competition induces high intra-specific variability.

Theories explaining community assembly assume that biotic and abiotic filters sort species into communities based on the values of their traits and are thus based on between-species trait variability (BTV). Nevertheless, these filters act on individuals rather than on species. Consequently, the selection is also influenced by intraspecific trait variability (ITV) and its drivers. These drivers may be abiotic (e.g., water availability) or biotic (e.g., competition). Although closely related species should have similar traits, many of them coexist. We investigated the relative magnitudes of BTV and ITV in coexisting closely related species and how their individual traits differ under different drivers of ITV. We manipulated conditions in a greenhouse pot experiment with four common Carex species, where individuals of each species originated from four source localities. Individuals were grown in factorial combinations of two moisture levels, with and without a competitor (grass species Holcus lanatus, a frequent competitor). We analyzed the variability of six morphological traits on individuals in the greenhouse and three morphological traits in the source localities. Species identity was the main determinant of differences in most traits. Competition exerted a greater effect than water availability. For leaf dry matter content (LDMC) and vegetative height, competition's effect even exceeded the variability among species. On the contrary, for specific leaf area (SLA) and clonal spread, the interspecific differences exceeded ITV induced by experimental treatments. SLA measured in the greenhouse closely correlated with values measured in field populations, while LDMC did not. The variability caused by source locality of ramets in the greenhouse was small, although sometimes significant. Closely related species differ in their traits, but for some traits, ITV can exceed BTV. We can expect that ITV can modify the processes of community assembly, particularly among coexisting closely related species.

Multiple-Locus Variable-Number Tandem Repeat Analysis of Helicobacter pylori Strains Isolated from Biopsy Samples

Background: Multiple-locus variable-number tandem-repeat analysis (MLVA) is a reliable, fast, and useful method for conducting phylogenetic and genotyping analyses. However, its application in Helicobacter pylori typing is limited. Objectives: This study aimed to determine the genetic diversity of H. pylori strains isolated from biopsy samples using six variable loci in MLVA typing. Methods: Over one year, we collected 70 non-duplicative biopsy samples from patients at Rohani Hospital, Babol, in northern Iran. After DNA extraction, H. pylori strains were confirmed through the amplification of the glmM gene in the PCR test. Multiple-locus variable-number tandem-repeat analysis typing utilized six VNTR markers: VNTR-180, VNTR-263, VNTR-614, VNTR-607, VNTR-2181, and VNTR-2457. The PHYLOViZE software was employed to construct the phylogenetic tree. Results: Out of the 70 specimens, 43 tested positive for H. pylori. The phylogenetic tree revealed some strains with completely similar MLVA patterns. Our findings indicated that type 2 is the dominant type in this region, with most patients infected with this type exhibiting gastritis. Conclusions: The high allelic variability observed at VNTR-614, -607, and -2457 indicates high intraspecific variability for these markers in all isolates from our region. Consequently, these VNTRs can be considered ideal sites for typing.