Intraspecific Variation Research Articles

Adaptive divergence in response to shared environmental pressures: examining gastropod shell exploitation by intertidal hermit crabs.

Adaptive divergence in response to shared environmental pressures: examining gastropod shell exploitation by intertidal hermit crabs.

The mytilin gene cluster: Shedding light on the enigmatic origin of mussel dispensable genes.

Mussels exhibit a sophisticated innate immune response characterized by many highly variable molecules responsible for recognizing and killing potential pathogenic microorganisms. The complexity of this molecular arsenal is marked by the occurrence of gene presence-absence (PAV), a phenomenon that targets numerous expanded lineage-specific gene families. This phenomenon enhances inter-individual sequence variability, further enriching the diversity of the repertoire of molecules involved in the immune response. Until now, the origin of mussel dispensable genes, which, unlike core genes, are not shared by all individuals, has remained elusive. In this study, by analyzing the resequenced genomes of more than 160 individuals in four distinct species of the Mytilus complex, we characterize the repertoire of mytilin genes encoding hemocyte-specific antimicrobial peptides (AMPs). We define a canonical gene architecture comprising four protein-coding genes and two pseudogenes in most haplotypes. However, the organization of the locus displays a marked intra-specific diversity due to the presence of variable alleles, the frequent pseudogenization of mytilin G1 and structural variants associated with additional dispensable mytilin genes, which often retain features that support functional preservation. Molecular phylogeny supports an ancient origin for dispensable mytilin genes, predating the radiation of modern Mytilus species. This suggests that most widespread extant haplotypes derive from a larger and more complex ancestral mytilin gene cluster and that dispensable mytilin genes are vestigial AMPs that have been retained only in a few populations where their presence may have contributed to fitness advantages and local adaptation.

Aphid Colony Size in Tansy is Affected by Plant Chemical Composition but not by Belowground Herbivory

Plants are hosts for above- and belowground insect communities that can influence each other via above-belowground plant-physiological dynamics. To mediate interactions, plants produce secondary metabolites, including terpenoids, and mixtures can differ intraspecifically. While intraspecific variation in plant chemistry gained increased interest, the extent to which intraspecific differences in plant chemistry mediate above-belowground interactions of herbivores remains unclear. We used a full factorial design with six distinct terpenoid chemotypes, differing in their chemical diversity of tansy (Tanacetum vulgare). We exposed these to the aboveground herbivore Macrosiphoniella tanacetaria (Hemiptera: Aphididae), the belowground herbivore Agriotes sp. (Coleoptera: Elateridae), no herbivore or both herbivores, to determine if chemotypes or the chemical diversity of plant compounds affected aphid performance and if the interactions between herbivores were mediated by the chemical profile. We found that aphid colony size differed between chemotypes, with the strongest colony increase over time in a mixed chemotype, and the weakest in a β-thujone chemotype. Root herbivory had no effect on aphid colony size, regardless of the chemotype. Aphid colony size was positively correlated with terpenoid evenness, but not with terpenoid Shannon diversity, terpenoid richness, or relative terpenoid concentration. Tansy chemotypes differed in their morphological responses (final plant height and final plant dry weight) and average leaf chlorophyll content to aboveground herbivory, whereas belowground herbivory exerted minimal impacts. Overall, our results show that intraspecific variation in terpenoid profiles directly modify ecological interactions on a plant, with plant chemistry mediating aphid performance and chemotypes differing in their morphological responses to herbivory.

Tridacna maxima ‘Rediscovered’ in the Eastern Indian Ocean

Giant clams are ecologically important coral reef animals, with many species facing imminent local extinction. While many regions have undertaken recent assessments of their biodiversity assets, persistent gaps remain even in otherwise well-surveyed areas. This study sought to understand the geographic distribution of smaller-bodied and morphologically similar giant clams, specifically Tridacna maxima and T. noae, in the eastern Indian Ocean. Due to the difficulties in reliably identifying these species using morphological characters, we confirmed species identity and investigated intraspecific variation using sequence data from the mitochondrial cytochrome C oxidase subunit I gene (COI). Seventy whole animal vouchers were newly sampled from a 1500 km span of remote northwestern Australian coastline over a decade, as part of an ongoing coral reef survey expedition of the Western Australian Museum and partners. Tridacna maxima had a limited distribution and was only genotyped from offshore oceanic reefs in the Rowley Shoals and Cocos Keeling Islands. In contrast, T. noae was well established beyond Ningaloo Reef, and was abundant at inshore sites throughout the Pilbara and Kimberley, and even offshore to Ashmore Reef. Phylogeographically, T. maxima did not group with conspecifics from the Western Pacific Ocean, including the east coast of Australia, but instead clustered with individuals from Malaysia, China, Taiwan, and Indonesia; T. noae exhibited a similar pattern. The affinity of Western Australian individuals with representatives from the Indo-Malay region and not eastern Australia will be an important consideration for these commercially important species. Novel haplotypes in both tested species occur in Western Australia. Continued sampling of eastern and central Indian Ocean giant clams, especially to continue to document the range of T. noae, is encouraged to understand connectivity in this basin. Together, these findings contribute to an improved baseline for conservation initiatives of these iconic coral reef animals in Western Australia.

Intraspecific variation in the sexual pattern of red-belted anthias, Pseudanthias rubrizonatus.

Recent studies indicate that the sexual patterns of some species can vary with local population size and density, suggesting that protogynous species may shift to gonochorism in larger populations. Red-belted anthias Pseudanthias rubrizonatus, a protogynous hermaphrodite, forms diverse-sized groups in Kagoshima Bay, Japan (31.58°N, 130.66°E), from typical polygynous medium-sized groups with a few males and several females, to an unusually large group exceeding 10,000 individuals. This study aimed to determine the sexual pattern of P. rubrizonatus in different-sized groups. The research was conducted from July 2019 to June 2022. This study revealed the process from sexual differentiation to maturation, and discovered primary males through gonadal histology and otolith growth analysis. All juvenile gonads developed an ovarian lumen before sexual differentiation. Most differentiated to mature females (38.0-77.0 mm standard length [SL], 0-3 years, n = 197), then changed sex (52.0-79.3 mm SL, 2-3 years, n = 14) to secondary males. Sex change occurred year-round. All mature males (50.2-95.1 mm SL, 1-5 years, n = 83) exhibited distinct dimorphic and dichromatic features. Some juveniles underwent bisexuality around 100 days post-hatching; spermatocytes were found with primary-growth stage oocytes (25.5-46.9 mm SL, ≤1 year, n = 24). Primary males (50.2-65.5 mm SL, 1 year, n = 9) were collected only in the large group. These findings indicate intraspecific variation in sexual pattern depending on the group sizes, with diandric protogyny in the large group and monandric protogyny in medium groups. Diandric protogyny is unprecedented in Anthiinae. Although primary males emerge as group size increases, protogyny remains consistently maintained in P. rubrizonatus in Kagoshima Bay, with no evidence of gonochorism observed.

Leaf shape of quinoa’s wild ancestor Chenopodium hircinum (Amaranthaceae) in a geographic context

Leaf shape of quinoa’s wild ancestor <i>Chenopodium hircinum</i> (Amaranthaceae) in a geographic context

Group size affects spontaneous quantity discrimination performance in wild Western Australian magpies (Gymnorhina tibicen dorsalis)

Animals may benefit from the ability to discriminate between quantities in their environment; for example, when choosing between foraging patches differing in food availability or assessing the size of rival groups. Numerous studies utilising spontaneous quantity discrimination tasks have found that a wide range of species possess the ability to discriminate between quantities, with large interspecific differences being found in these capabilities. However, the causes of variation in quantity discrimination have received less attention, particularly when considering intraspecific variation. Here, we use a spontaneous quantity discrimination task to (i) investigate if Western Australian magpies possess quantity discrimination abilities, and (ii) determine the factors that underlie individual variation in this ability. We found that magpies were able to discriminate between two discrete quantities of a food reward and chose the larger quantity of food more often than expected by chance, with their accuracy increasing as the difference between the two quantities of food items increased (i.e. as the ratio decreased). Individual performance on the assay was significantly affected by group size, with individuals from smaller groups choosing the larger quantity of food more often than individuals from larger groups when presented with the 2 vs. 5 combination. This group size difference may arise because individuals from smaller groups benefit more from enhanced quantity discrimination abilities compared to individuals from larger groups due to the greater risk of competition and loss of resources from intergroup conflict with larger groups. Our study is the first to investigate and identify group size as a source of intraspecific variation in spontaneous quantity discrimination abilities and highlights the importance of considering the causes of individual variation in cognitive performance.

Consistent inter-individual variability in movement traits shapes the wild boar movement syndrome

Abstract Consistent intraspecific variation in behavior directly impacts reactions to environmental challenges, including life in human-altered landscapes. Yet, it is rarely considered in free-ranging species thriving in anthropogenic landscapes and causing human-wildlife conflict. Here, we examine the consistent inter-individual variability in wild boar movement traits and highlight its potential for ecology and practical management. We used satellite telemetry data from 95 GPS-tracked wild boars monitored in Czechia and computed weekly movement rate (activity), intensity of space use (exploration), and diurnality (boldness). Using a variance partitioning approach, we tested whether these traits were repeatable over time and therefore considered personality traits, and using Bayesian multivariate mixed-effect models, we examined the correlations among these traits to describe a behavioral syndrome while controlling for external and internal sources of variation. Wild boar showed significant consistent inter-individual variation in all three traits, with repeatability ranging from 0.16 to 0.35. We found significant correlations between traits, indicating the existence of a remarkable movement syndrome. Individuals staying within familiar areas were less nocturnal and moved slower, as opposed to individuals roaming more outside familiar areas, faster and with striking nocturnality. The movement syndrome and, most importantly, its variability, with individuals ranging in between extremes of activity and exploration, likely contributes to the success of this species and helps them thrive in human-dominated landscapes while maximizing resource acquisition. Integrating intraspecific behavioral variation into ecology and practical population management could improve models predicting wild boar movement and alleviate the biodiversity and economic loss caused by expanding wild boar populations.

Inter- and intraspecific variation in the degree of marine-derived resources of amphidromous fishes.

Migratory animals often transport allochthonous materials, energy or organisms from donor to recipient ecosystems, thereby affecting the dynamics of consumers, communities and ecosystems in the recipient systems. The biomass of migrants is commonly assumed to be equal to that of the allochthonous materials they transport, with the inherent assumption that migrant bodies are produced purely from allochthonous resources. However, the extent to which the body composition of many migratory animals consists of allochthonous materials [e.g., the proportion of total body mass consisting of allochthonous resources, hereafter degree of allochthony (DOA)] may gradually decrease if the animals consume autochthonous resources during their migration. Ignoring this process leads to an overestimation of the magnitude and temporal features of material subsidies. In this study, we quantified the DOA of nine amphidromous fish species that migrate from marine to rivers, using the sulphur stable isotope (δ34S) analysis. The DOA varied substantially among species (11%-82%) and even within species (Sicyopterus japonicus had the highest DOA: 22%-97%). Species with larger body sizes tended to exhibit a lower DOA. This trend was also observed at the species level for six of the nine species, with five species showing an additional pattern of later migrating individuals with lower DOA. These results imply that quantifying DOA is important for accurately estimating material subsidies across ecosystems, owing to the upstream migration of amphidromous fish. Life-history studies of amphidromous fishes are crucial for elucidating the mechanisms behind inter- and intraspecific variation in DOA, which ultimately contributes to a better understanding of marine-river ecosystem linkages mediated by these fishes.

The genetic variability and phylogenetic relationships of African yam bean using the rbcL marker

The African yam bean, AYB (Sphenostylis stenocarpa), a beneficial legume, is valuable in terms of food, nutrition, and income security. While the plant plays a crucial role in small-scale farming systems in sub-Saharan Africa, insufficient genomic data hamper the breeding potential of its germplasm. Our recent dataset based on the ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit (rbcl) gene marker underscores the utility of nucleotide substitution for deciphering genetic relationships among a subset of AYB accessions. Twenty-four accessions of AYB, originating from Nigeria, Ghana, and Bangladesh, were used for this study. The rbcl gene marker reveals significant intraspecific genetic variability among AYB accessions, facilitating the delineation of distinct phylogenetic clusters that correspond to their geographic origins. The rbcl genes of the accessions were sequenced using Sanger’s technique. The obtained sequence data were analyzed using DnaSP v6.12.03, MEGA11, and descriptive statistics. Transitional base changes of C/T, T/C, A/G, and G/A varied significantly (p &lt; 0.05) from transversion substitutions. A high gene diversity of 0.60, in addition to 13 polymorphic sites and 5 haplotypes, was recorded for the accessions. Nine accessions, including TSs 13, TSs 24, TSs 303, TSs 331, TSs 334, TSs 38, TSs 49, TSs 67, and TSs 98, had variant sequences at 531 nucleotide base positions with a variant frequency of 37.50%. The estimates of evolutionary divergence between the sequences ranged from 0.00 (TSs 4 and TSs 24) to 1.38 (TSs 1, TSs 311, and TSs 331). An analysis of the phylogenetic relationship showed a significant degree of genetic diversity with &lt;50% bootstrap values, indicating the genetic distinctiveness of the accessions. Accessions TSs 333 and TSs 357 were the most genetically distinct accessions with a low bootstrap value of 45%. TSs 303 surprisingly had a very close relationship with the outgroup Vigna unguiculata (100%). The information presented herein could be leveraged to extend the limited genetic base of AYB through modern mutational breeding methods.

Whole-Genome Sequencing and Comparative Genomic Analysis of Three Clinical Bloodstream Infection Isolates of Trichosporon austroamericanum.

Trichosporon austroamericanum is a recently described yeast species related to Trichosporon inkin and exclusively isolated from clinical specimens. However, its genomic features and pathogenic potential remain poorly understood. In this study, we performed whole-genome sequencing on three blood-derived isolates from patients with invasive fungal infections and comparative analyses with 13 related Trichosporon species. The three isolates yielded high-quality assemblies of 9-10 scaffolds (~21 Mb), facilitating reliable comparisons. While most species had comparable genome sizes, Trichosporon ovoides, Trichosporon coremiiforme, and Cutaneotrichosporon mucoides displayed large, fragmented genomes, suggestive of polyploidy. ANI analysis and phylogenetic trees based on ANI and single-copy orthologs supported the classification of T. austroamericanum as a distinct clade with moderate intraspecific divergence. Using the Galleria mellonella, a model for fungal pathogenicity, all T. austroamericanum strains reduced larval survival, and NIIDF 0077300 exhibited virulence comparable to T. asahii and greater than T. inkin. To explore the gene-level differences associated with pathogenicity, we performed ortholog analysis based on single-copy genes. This revealed a unique Zn(II)2Cys6-type transcription factor gene (OG0010545) present only in NIIDF 0077300 and T. asahii. These findings highlight the genomic diversity and infection-associated traits of T. austroamericanum, providing a framework for future functional studies.

Phenotypic and Molecular Characterization of Multidrug-Resistant Clinical Isolates of the Candidozyma haemuli Species Complex (Formerly Candida haemulonii Species Complex) from the Brazilian Amazon Reveals the First Case of Candidozyma pseudohaemuli in Brazil.

This study included 24 isolates of the Candidozyma haemuli species complex from patients in the Brazilian Amazon between 2021 and 2024. These isolates were identified by sequencing as C. duobushaemuli (54.2%), C. haemuli sensu stricto (29.2%), C. haemuli var. vulneris (12.5%), and C. pseudohaemuli (4.2%). The finding of C. pseudohaemuli represents the first case reported in Brazil. Haplotype and phylogenetic analysis of these species, along with other isolates from Brazil, revealed low intraspecific genetic diversity. Resistance to at least one antifungal was observed in 83.3% of isolates, with multidrug resistance in 58.3%, including one isolate resistant to all tested antifungals. The isolates demonstrated active biofilm production, lytic enzyme activity, and thermotolerance. Notably, one C. duobushaemuli isolate exhibited tolerance to 42 °C, a phenotype not previously described. It is crucial for Brazil and other countries to recognize the emergence of these species as a public health threat and to take proactive measures to prevent outbreaks.

Population and species neighbor identity impact trait–trait relationships and plant performance

AbstractEvaluating restoration practices such as admixture provenancing or mixing of multiple source populations for greater intraspecific variation in plant restorations helps to understand the utility of the practice in different scenarios. We do not know whether any population mixtures in admixture provenancing will deliver positive outcomes when interacting. To understand how population and species' identity influence plant performance and trait outcomes in mixtures, we assessed trait variation among populations of two forb species native to the Western United States (Dieteria canescens and Heterotheca villosa) following pairwise competition in pots with single‐population monocultures, two‐population mixtures, and two‐species mixtures with D. canescens as a focal plant in a greenhouse common environment. Plants were harvested after 7 weeks and height, leaf count, root length, and root mass fraction (RMF) traits were measured, as well as whole plant biomass. We found two‐population mixtures and single‐population monocultures to have similar biomass while some two‐species mixtures differed from respective single‐population monocultures. Neighbor trait differences in shoot height and root length best predicted plant growth following interactions, while increasing neighbor trait differences resulted in positive growth outcomes for all but one trait by treatment interaction (R2 = 0.17, p &lt; 0.001). In this single case, plant growth decreased with increasing differences in RMF for the two‐species mixture treatment, surprisingly. These findings show nuance in the outcomes of interactions within and between populations and species: they are highly dependent on population identity and traits measured, which are aspects that must be considered when evaluating restoration materials and strategies.

The complete chloroplast genomes and phylogenetic analysis of Lilium leichtlinii var. maximowiczii from Northeast Asia

Lilium leichtlinii var. maximowiczii, native to Northeast Asia, shows morphological differences between Korean and Japanese varieties. This study analyzed chloroplast (cp) genomes of three diploid L. leichtlinii groups: Korean (KR), Japanese broad-leaved (JB), and Japanese narrow-leaved (JN). Genome sizes ranged from 152,053 bp to 152,588 bp with GC contents of 37.02–37.06%. All had typical quadripartite structures and contained 129 genes. Phylogenetic analysis of 48 Lilium cp genomes revealed at least three distinct L. leichtlinii varieties. Most genomic variation was found in non-coding regions, providing insights into intraspecific genomic diversity in L. leichtlinii.

Diversity and the Origin of Perlodinella Klapálek 1912 (Plecoptera: Perlodidae) in Qinghai Province, China.

The article presents integrative research of the perlodid genus Perlodinella in Qinghai Province, northwestern China. P. tatunga Wu, 1973 is considered a junior synonym of P. kozlovi Klapálek, 1912, with a further description of intraspecific morphological variability, while P. unimacula Klapálek, 1912 is considered to be nomen dubium. The COI barcodes of the three valid species in Qinghai, P. epiproctalis (Zwick, 1997), P. kozlovi Klapálek, 1912, and P. microlobata Wu, 1938 are firstly sequenced, enabling adult-larva matching and the analysis of genetic diversity. The larval morphology of P. kozlovi and P. microlobata is described for the first time. Additionally, the biology, ecological adaptability, and fungal infections of Perlodinella are firstly recorded with an environment-related comparison. The discussion of the origin and immigration of the genus is also provided.

Anatomical distribution and flight control function of wing sensory hairs in Seba's short-tailed bat.

Bats use sensory systems such as echolocation and vision to track prey, avoid obstacles, and inform their trajectories. In addition, though less studied, bats also have extensive networks of sensory hairs across their wings. Preliminary evidence has shown that these hairs are involved in flow sensing and relay sensory information during flight. However, little is known about the functional role of sensory hairs in flight control or potential intraspecific variation in hair distribution. Through a morphological study of specimens of Seba's short-tailed bat (Carollia perspicillata), we find relatively low intraspecific variability in sensory hair distribution and consistent regional density patterns. We compare flight kinematics from the same species in wind tunnel experiments before and after removal of sensory hairs from the ventral wings. Depilation of sensory hairs resulted in changes to kinematic variables at the whole- and within-wingbeat levels, such as wingbeat frequency, chordwise wing folding, and wing extension. Taken together, these findings indicate that sensory hairs relay sensory information and function to alter fine-scale wing shape and positioning, thereby impacting flight kinematics and dynamics.

Leaf Size Indices and Outline-Based Geomorphometric Analysis of Five Philippine Endemic Saurauia Willd. (Actinidiaceae)

Species discrimination among species of Saurauia is challenging due to large morphological variation. This study examines the intraspecific variations of the 5 Philippine endemic Saurauia species using leaf size indices (LSI) and outline-based geometric morphometrics to facilitate species discrimination. Leaf samples were measured using the traditional method, scanned, converted to binary images, subjected to elliptic Fourier Analyses, and quantitatively analyzed using principal component analysis (PCA). The leaf morphology significantly differed among species based on the results of LSI and leaf shape outline analyses. The results showed 7 effective principal components (PCs), which accounted for 94.16% of the total variation. Significant differences were observed in all PCs. Discriminant analysis of the leaf shape outline confirmed the delimitation of species with scores relatively higher than the cut-off value. The tree topology from leaf shape outline, and leaf size indices all exhibited similarity in the clustering at the species level. A key to the species based on leaf morphology is also provided. Keywords: elliptic fourier analysis, kiwi, leaf size index, leaf variation, principal component analysis

Inter- and Intra-Specific Differences in Seed Germination Responding to Varying Osmotic Potentials in 261 Echinochloa Populations Collected from Rice Fields in Eastern China

Echinochloa crus-galli (L.) P. Beauv. (EC), E. crus-galli var. mitis (Pursh) Petermann (ECM), and E. glabrescens Munro ex Hook.f. (EG) are all troublesome weeds and frequently managed as one species on rice (Oryza sativa) fields. To examine inter- and intra-specific differences in seed germination responses to drought stresses, we conducted seed germination experiments with 57 EC, 112 ECM, and 92 EG populations. In all drought stress treatments, EC exhibited higher and faster germination than ECM and EG. Under 0 MPa, seed germinations of all populations initiated on 3 DAT (day after treatment). Accumulative seed germination percentages of EC, ECM, and EG under −0.1 MPa did not show significant differences with the same species treated with 0 MPa, while significantly decreased with the osmotic potential treated decreasing to −0.4 MPa or lower. OR50 values (the osmotic potential at which 50% germination occurs) for EC, ECM, and EG were −0.55 MPa, −0.49 MPa, and −0.45 MPa, respectively. Intra-specific variation within all three species increased as osmotic potential decreased from −0.1 MPa to −0.8 MPa. Moreover, seed germination was significantly correlated with 1000-seed weight and latitudes of population-collected locations. In four treatments, seeds produced by Echinochloa weeds growing in transplanted rice fields exhibited significantly higher germination percentages than those from direct-seeded rice fields.

Intraspecific variation in spruce seed palatability perceived by bank voles

AbstractMast seeding in Norway spruce (Picea abies) provides an abundant food source for rodents, such as bank voles (Clethrionomys glareolus). While seed quantity effects are well known, intraspecific variation in seed palatability is not. In this study, I tested whether voles show preferences for spruce seeds from different batches of seeds (sampled from different mast years). In controlled trials, voles did not show significant preferences for seeds from different years, suggesting limited variation in seed characteristics detectable by voles. The results support that variations in the small spruce seeds may be primarily a quantitative burst of food (i.e., during mast seeding) rather than a qualitative variation that influences foraging behavior. Understanding these dynamics contributes to our knowledge of resource‐driven rodent ecology and the role of mast seeding on granivore behavior.

Global intraspecific diversity of marine forests of brown macroalgae predicted by past climate conditions

Global patterns of intraspecific genetic diversity are key to understanding evolutionary and ecological processes. However, insights into the distribution and drivers of genetic diversity remain limited, particularly for marine species. Here, we explain and predict the genetic diversity of cold and temperate brown macroalgae using genetic data from 29 species and a machine-learning algorithm that incorporates contemporary and past climate conditions during the Last Glacial Maximum (~20,000 years ago) based on the niche centroid hypothesis. We apply this model to the distribution of 280 species and predict their global genetic diversity. Our results show reduced genetic diversity away from the niche centroid, identifying past climate conditions as key drivers of contemporary genetic diversity. Regions with high genetic diversity for multiple species emerge, matching biogeographic patterns of species richness. The mapped diversity hotspots establish timely baselines for brown macroalgae biogeography, evolutionary potential and conservation, contributing to the Post-2020 Global Biodiversity Framework.