Search Results (41)

The wolf fish Hoplias malabaricus is a Neotropical species characterized by remarkable karyotypic diversity, including seven karyomorphs (KarA-G) with distinct sex chromosome systems. This study investigated the homologous XY (KarF) and XY₁Y₂ (KarG) sex chromosome systems present in this species by integrating cytogenetics and genomics to examine sex chromosomes’ composition through characterization of repeatome (satellite DNA and transposable elements) and sex-linked markers. Our analysis indicated that both karyomorphs are little differentiated in their sex chromosomes content revealed by satDNA mapping and putative sex-linked markers. Both repeatomes were mostly composed of transposable elements, but neither intra- (male versus female) nor interspecific (KarF x KarG) variations were found. In both systems, we demonstrated the occurrence of sex-specific sequences probably located on the non-recombining region of the Y chromosome supported by the accumulation of sex-specific haplotypes of HmfSat10-28/HmgSat31-28. This investigation offered valuable insights by highlighting the composition of homologous XY and XY₁Y₂ multiple sex chromosomes. Although homologous, the large Y chromosome in KarF corresponds to two separate linkage groups (Y₁ and Y₂) in KarG implying a specific meiotic arrangement involving the X chromosome in a meiotic trivalent chain. This scenario likely influenced recombination rates and, as a result, the genomic composition of these chromosomes. Full article

A total of 18 Humidophila strains isolated from soil samples from Cát Tiên National Park have been studied. Based on morphometric analysis and molecular data for the V4 18S rDNA and rbcL regions, we proposed the presence of four new species: H. vietnamica, H. paravietnamica, H. cattiensis, and H. concava. This is the first study that provides molecular data for such a large number of Humidophila strains. Furthermore, we encountered some Humidophila strains with clear morphological differences (which we assigned to several morphotypes) that cannot be separated using the selected genetic markers and cannot be attributed to phenotypic variations in one species; these require further study of their genetic structure. We also observed the opposite case, where in the absence of morphological differences, clear genetic differentiation is shown, which demonstrates the presence of cryptic taxa in our sample. The maximum differences for these strains were observed in the V4 18S rDNA region. Our results show that the effectiveness of commonly used genetic markers V4 18S rDNA and rbcL for separating species can vary greatly. Our study highlights the need to research different genetic markers and their use for proper species separation, as well as the genetic diversity of diatoms, and the need for further studies of intra- and interspecific genetic distances. Full article

Background: One of the greatest challenges to biologists is to understand the adaptive mechanisms of how plants will respond to climate at all levels from individual physiology to whole populations. For example, variation (plasticity) in the composition and concentration of metabolites will determine productivity, reproduction, and ultimately survival and distribution of plants, especially those subjected to rapid climate change. Objectives: Our aim was to study how interspecific and intraspecific metabolic variation in plant species within a single community can be elucidated. Methods: We used a metabolomics approach to study metabolic acclimation (by measuring the metabolome between plants under “common garden” controlled environment conditions) and metabolic plasticity (using field based reciprocal transplant studies) in a set of Atlantic sand dune annual communities along a latitudinal gradient from Portugal to England. Results: In the common garden study, metabolically phenotyping (using a fingerprinting direct injection mass spectrometry approach) five species of annual plants showed that species living together in a community have distinct metabolic phenotypes (high inter-specific metabolic variation). There was low intra-specific metabolic variation between populations growing under standard environmental conditions. The metabolic variation in one species Veronica arvensis was measured in the reciprocal transplant study. Metabolic phenotypes obtained from all samples were similar across all sites regardless of where the plants originated from. Conclusions: This implies that the metabolome is highly plastic and the measurable metabolome in this study was influenced more by local environmental factors than inherent genetic factors. This work highlights that species are fulfilling different niches within this community. Furthermore, the measurable metabolome was highly plastic to environmental variation. Full article

The genus Ephedra Tourn. ex L. (Ephedraceae) still exhibits taxonomic complexity that has not yet been resolved. This study aimed to determine the taxonomic identity of the Ephedra species in Egypt and identify the fatty acid profile and its diversity at the gender level as a taxonomic tool for specimens lacking reproductive cones. The current study provides a pioneering approach that distinguishes Ephedra species at the gender level. A total of 120 fresh individuals were collected from 20 locations representing different habitats where Ephedra plants grow in Egypt. In addition, herbarium specimens were deposited in Egyptian herbaria. The studied morphological traits included 30 vegetative characteristics and 72 traits of the reproductive organs of both genders. The fatty acid content was measured using gas–mass chromatography (GC-Mass). The taxonomic revision revealed that the Genus Ephedra was represented in the Egyptian flora by five species, Ephedra alata in section Alatae and E. aphylla, E. ciliata, E. foemina, and E. pachyclada in section Ephedra. South Sinai hosts these five species and represents the center of diversity for this genus in Egypt. The vegetative characteristics were subjected to principal component analysis (PCA), which revealed a distinct separation of the five studied species. Similarly, the cone traits treated by hierarchical clustering revealed intra-gender variations. The taxonomic key was developed based on the morphological traits to distinguish the studied species at the gender level. In total, 51 fatty acids were identified from the studied species and grouped as 18 saturated, 16 monounsaturated, and 17 polyunsaturated fatty acids. In the absence of reproductive cones, the lipid content and fatty acid composition of the vegetative parts displayed significant interspecific and intra-gender variations. Therefore, fatty acids can be used to efficiently identify the studied species when they lack reproductive cones. This study proved the efficacy of a multidisciplinary approach to identify Ephedra species at the gender level and recommends this trend for future studies of this genus. Full article

Plant functional traits are an important indicator for the comprehensive evaluation of community stability and resilience. Therefore, exploring the variations and relationships among leaf functional traits at different maturity levels during forest restoration can deepen the understanding of plant adaptation strategies and community assembly. In this study, we measured the leaf area (LA), specific leaf area (SLA), photosynthetic pigments, non-structural carbohydrates (NSCs), leaf nitrogen content (LNC), and leaf phosphorus content (LPC) of dominant tree species in three communities with different maturity levels (defined by species composition, biodiversity and spatial structure) in a monsoon forest located in the northern margin of the tropics in China, and explored the variation and relationships among different leaf traits at individual, species, and community scales. The results showed that maturity levels significantly affected leaf functional traits. With the increase in maturity levels, SLA increased, and leaf SS and NSCs decreased, while other leaf functional traits did not show a consistent pattern. In different communities, NSCs, Chl (a:b), SS:St or Car had a trade-off or synergistic relationship with leaf economic spectrum. Additionally, the LPC, LNC, and starch were the key traits in response to selection pressure at maturity levels, inter-specific and intra-specific scales, respectively, and the trait–trait relationships were stronger or more extreme as the scale was narrowed. Therefore, when evaluating the development and succession of tropical monsoon forest communities, the selection of leaf functional characteristics and the determination of the research scale should be comprehensively and systematically considered. Full article

Although Chalcidoidea is one of the megadiverse superfamilies in Hymenoptera, numerous species are still being discovered and described. However, the difficulties in delimiting intra- and interspecific variation hinder this process. In this study, DNA barcoding methods using the COI gene were employed to investigate the morphological variation within Dzhanokmenia Kostjukov, 1977. The nuclear locus, 28S D2, was used to infer a phylogeny to gain an understanding of the relationship of Dzhanokmenia with other potentially close genera. Through a preliminary DNA barcode library established here, including eight species, we calibrated the intraspecific variation in certain diagnostic characters for the new species described here, D. brevifunis Ganbaatar & Cao sp. nov. Maximum likelihood results show that Dzhanokmenia is clustered with the genera associated with Tetrastichus, such as Chaenotetrastichus Graham, 1987, Baryscapus Förster, 1856, Tetrastichus Haliday, 1844, and Oomyzus Rondani, 1870 involved in this study. Our results indicate that the species diversity of Dzhanokmenia is understudied and tentatively confirm that Dzhanokmenia has a potential close relationship with Baryscapus. Along with the DNA barcode library, the referenced phylogeny datasets improve the understanding of the systematic position of Dzhanokmenia within the subfamily Tetrastichinae and the definition of this genus in terms of morphology, thereby facilitating species delimitation, discovery, and description within Dzhanokmenia. Full article

Sedum is the largest succulent genus in Crassulaceae. Because of predominant maternal inheritance, little recombination, and slow evolution, plastomes can serve as powerful super barcodes for inter- or intra-species phylogenetic analyses. While previous research has focused on plastomes between Sedum species, intra-species studies are scarce. Here, we sequenced plastomes from three Sedum species (Sedum alfredii, Sedum plumbizincicola, and Sedum japonicum) to understand their evolutionary relationships and plastome structural evolution. Our analyses revealed minimal size and GC content variation across species. However, gene distribution at IR boundaries, repeat structures, and codon usage patterns showed diversity at both inter-specific and intra-specific levels. Notably, an rps19 gene expansion and a bias toward A/T-ending codons were observed. Codon aversion motifs also varied, potentially serving as markers for future studies. Phylogenetic analyses confirmed the non-monophyly of Sedum and divided the Acre clade into two groups. Individuals from the same species clustered together, with strong support for the relationships between S. alfredii, S. tricarpum, and S. plumbizincicola. Additionally, S. japonicum clearly affiliates with the Acre clade. This study provides valuable insights into both intra-specific and intra-generic plastome variation in Sedum, as well as overall plastome evolution within the genus. Full article

Parental care behavior has evolved as a life history strategy to improve reproductive success, particularly in organisms facing challenging environments. However, the variation in maternal care, such as egg-guarding behavior in response to the social environment and the associated ecological consequence of competition, remains largely unknown. This study addresses a gap in current knowledge by examining the plasticity of maternal care behavior in the predatory mite C. eruditus and its impact on offspring survival and intra- and interspecific competition. Our results demonstrated that the reproductive females frequently exhibit egg-guarding behaviors, with enhanced maternal care efforts when the interspecific competitor is present. Egg masses are significantly more vulnerable to predation in the absence of maternal care. Guarding females increased egg survival rates and adversely influenced the survival of both con- and heterospecific competitors, with higher mortality rates being detected. Our findings highlight the ecological significance of maternal care behaviors and suggest that releasing C. eruditus and Neoseiulus cucumeris (Oudemans) together is not recommended for pest management in storage products. Full article

Corals are habitat-forming organisms on tropical and sub-tropical reefs, often displaying diverse phenotypic behaviors that challenge field-based monitoring and assessment efforts. Symbiont chlorophyll (Chl) is a long-recognized indicator of intra- and inter-specific variation in coral’s response to environmental variability and stress, but the quantitative Chl assessment of corals at the reef scale continues to prove challenging. We integrated field, airborne, and laboratory techniques to test and apply the use of reflectance spectroscopy for in situ and reef-scale estimation of Chl a and Chl c2 concentrations in a shallow reef environment of Kāne‘ohe Bay, O‘ahu. High-fidelity spectral signatures (420–660 nm) derived from field and airborne spectroscopy quantified Chl a and Chl c2 concentrations with demonstrable precision and accuracy. Airborne imaging spectroscopy revealed a 10-fold range of Chl concentrations across the reef ecosystem. We discovered a differential pattern of Chl a and Chl c2 use in symbiont algae in coexisting corals indicative of a physiological response to decreasing light levels with increasing water depth. The depth-dependent ratio of Chl c2:a indicated the presence of two distinct light-driven habitats spanning just 5 m of water depth range. Our findings provide a pathway for further study of coral pigment responses to environmental conditions using field and high-resolution airborne imaging spectroscopy. Full article

The availability of multiple sequenced genomes from a single species made it possible to explore intra- and inter-specific genomic comparisons at higher resolution and build clade-specific pan-genomes of several crops. The pan-genomes of crops constructed from various cultivars, accessions, landraces, and wild ancestral species represent a compendium of genes and structural variations and allow researchers to search for the novel genes and alleles that were inadvertently lost in domesticated crops during the historical process of crop domestication or in the process of extensive plant breeding. Fortunately, many valuable genes and alleles associated with desirable traits like disease resistance, abiotic stress tolerance, plant architecture, and nutrition qualities exist in landraces, ancestral species, and crop wild relatives. The novel genes from the wild ancestors and landraces can be introduced back to high-yielding varieties of modern crops by implementing classical plant breeding, genomic selection, and transgenic/gene editing approaches. Thus, pan-genomic represents a great leap in plant research and offers new avenues for targeted breeding to mitigate the impact of global climate change. Here, we summarize the tools used for pan-genome assembly and annotations, web-portals hosting plant pan-genomes, etc. Furthermore, we highlight a few discoveries made in crops using the pan-genomic approach and future potential of this emerging field of study. Full article

Measuring the inequality of leaf area distribution per plant (ILAD) can provide a useful tool for quantifying the influences of intra- and interspecific competition, foraging behavior of herbivores, and environmental stress on plants’ above-ground architectural structures and survival strategies. Despite its importance, there has been limited research on this issue. This paper aims to fill this gap by comparing four inequality indices to measure ILAD, using indices for quantifying household income that are commonly used in economics, including the Gini index (which is based on the Lorenz curve), the coefficient of variation, the Theil index, and the mean log deviation index. We measured the area of all leaves for 240 individual plants of the species Shibataea chinensis Nakai, a drought-tolerant landscape plant found in southern China. A three-parameter performance equation was fitted to observations of the cumulative proportion of leaf area vs. the cumulative proportion of leaves per plant to calculate the Gini index for each individual specimen of S. chinensis. The performance equation was demonstrated to be valid in describing the rotated and right shifted Lorenz curve, given that >96% of root-mean-square error values were smaller than 0.004 for 240 individual plants. By examining the correlation between any of the six possible pairs of indices among the Gini index, the coefficient of variation, the Theil index, and the mean log deviation index, the data show that these indices are closely related and can be used interchangeably to quantify ILAD. Full article

The Afrotropical hoverflies remain an understudied group of hoverflies. One of the reasons for the lack of studies on this group resides in the difficulties to delimit the species using the available identification keys. DNA barcoding has been found useful in such cases of taxonomical uncertainty. Here, we present a molecular study of hoverfly species from the eastern Free State of South Africa using the mitochondrial cytochrome-c oxidase subunit I gene (COI). The identification of 78 specimens was achieved through three analytical approaches: genetic distances analysis, species delimitation models and phylogenetic reconstructions. In this study, 15 nominal species from nine genera were recorded. Of these species, five had not been previously reported to occur in South Africa, namely, Betasyrphus inflaticornis Bezzi, 1915, Mesembrius strigilatus Bezzi, 1912, Eristalinus tabanoides Jaennicke, 1876, Eristalinus vicarians Bezzi, 1915 and Eristalinus fuscicornis Karsch, 1887. Intra- and interspecific variations were found and were congruent between neighbour-joining and maximum likelihood analyses, except for the genus Allograpta Osten Sacken, 1875, where identification seemed problematic, with a relatively high (1.56%) intraspecific LogDet distance observed in Allograpta nasuta Macquart, 1842. Within the 78 specimens analysed, the assembled species by automatic partitioning (ASAP) estimated the presence of 14–17 species, while the Poisson tree processes based on the MPTP and SPTP models estimated 15 and 16 species. The three models showed similar results (10 species) for the Eristalinae subfamily, while for the Syrphinae subfamily, 5 and 6 species were suggested through MPTP and SPTP, respectively. Our results highlight the necessity of using different species delimitation models in DNA barcoding for species diagnoses. Full article

Eumerus Meigen, 1822 is one of the largest Syrphidae genera in the Palaearctic Region, with the highest levels of taxonomic diversity found in the Eumerus tricolor species group. Despite its high diversity, the interspecific levels of morphological variability can be low. Additionally, some species may show certain levels of intraspecific variability. Hence, species delimitation may become challenging. In this work, we assessed the diversity of the E. tricolor group in the Iberian Peninsula through an integrative analysis of nomenclature, morphology and the 5′ (COI-5′) and 3′ (COI-3′) end regions of the Cytochrome c oxidase subunit I gene. Two new species, Eumerus ancylostylus Aguado-Aranda & Ricarte sp. n. and Eumerus petrarum Aguado-Aranda, Nedeljković & Ricarte sp. n., were described, and their intra- and interspecific variations discussed. In addition, the first barcodes of Iberian members of the E. tricolor group were obtained, and the distribution ranges of all species were mapped within the study area. The systematic position of the new species is discussed based on the resulting COI-based trees. The male genitalia of Eumerus hispanicus van der Goot, 1966 and Eumerus bayardi Séguy, 1961 were studied and illustrated. A lectotype was designated for Eumerus lateralis (Zetterstedt, 1819). An updated dichotomous key for all known European species of the E. tricolor group is provided. The egg of E. petrarum sp. n. is also described. Full article

Assessing interspecific adaptive genetic variation across environmental gradients offers insight into the scale of habitat-dependent heritable heterotic effects, which may ultimately enable pre-breeding for abiotic stress tolerance and novel climates. However, environmentally dependent allelic effects are often bypassed by intra-specific single-locality genome-wide associations studies (GWAS). Therefore, in order to bridge this gap, this study aimed at coupling an advanced panel of drought/heat susceptible common bean (Phaseolus vulgaris L.) × tolerant tepary bean (P. acutifolius A. Gray) interspecific lines with last-generation multi-environment GWAS algorithms to identify novel sources of heat and drought tolerance to the humid and dry subregions of the Caribbean coast of Colombia, where the common bean typically exhibits maladaptation to extreme weather. A total of 87 advanced lines with interspecific ancestries were genotyped by sequencing (GBS), leading to the discovery of 15,645 single-nucleotide polymorphism (SNP) markers. Five yield traits were recorded for each genotype and inputted in modern GWAS algorithms (i.e., FarmCPU and BLINK) to identify the putative associated loci across four localities in coastal Colombia. Best-fit models revealed 47 significant quantitative trait nucleotides (QTNs) distributed in all 11 common bean chromosomes. A total of 90 flanking candidate genes were identified using 1-kb genomic windows centered in each associated SNP marker. Pathway-enriched analyses were done using the mapped output of the GWAS for each yield trait. Some genes were directly linked to the drought tolerance response; morphological, physiological, and metabolic regulation; signal transduction; and fatty acid and phospholipid metabolism. We conclude that habitat-dependent interspecific polygenic effects are likely sufficient to boost common bean adaptation to the severe climate in coastal Colombia via introgression breeding. Environmental-dependent polygenic adaptation may be due to contrasting levels of selection and the deleterious load across localities. This work offers putative associated loci for marker-assisted and genomic selection targeting the common bean’s neo-tropical lowland adaptation to drought and heat. Full article

The persistence of subtropical seasonally dry forests urgently requires the implementation of ex situ conservation and restoration programs. We studied variation in seed traits and dormancy of six native species growing in seasonally dry Chaco forests of Argentina. We documented high intra- and interspecific variability in seed traits and dormancy. Fresh seeds of Geoffroea decorticans and Parasenegalia visco (Fabaceae) were water-permeable and nondormant (ND), while those of Parkinsonia praecox and Vachellia aroma (Fabaceae) were water-impermeable and had physical dormancy (PY). Seeds of Schnopsis lorentzii (Anacardiaceae) and Sarcomphalus mistol (Rhamnaceae) were water-permeable and had physiological dormancy (PD). Mechanical and chemical scarification were the most effective methods to break PY, and dry storage for 3 months was effective in breaking PD. Seeds of large-seeded species were ND or had PD, and those of small-seeded species had PY. Species inhabiting moist habitats had ND seeds, whereas those from seasonally dry habitats had seeds with PY or PD. These results suggest that seed traits and dormancy are species-specific and that intraspecific variation in seed traits is likely associated with high phenotypic plasticity of species in response to local environmental heterogeneity. These findings should be considered at the time of implementation of conservation techniques and for seed sourcing decisions for restoration. Full article