Within-species Variation Research Articles

Factors and effects of inter-individual variability in silver birch phenology using dense LiDAR time-series

Comprehending and quantifying local variability in plant phenology, alongside its impacts on tree growth, is challenging due to spatially and temporally heterogeneous environmental factors that interact to affect phenological events and periods. Although previous studies have focused on the climatic factors driving phenological events at the stand level, the influences of competition, neighborhood characteristics, species richness, and water availability on plant phenology remain unclear. In the present paper, we used hourly terrestrial LiDAR surveys performed between April 2020 and April 2021 to investigate the influence of local factors (neighborhood and topography) on the phenology of silver birch trees (Betula pendula Roth.). We also examined how phenological events affect growth in tree height and crown area. All response and explanatory variables were estimated using LiDAR time-series data and a field survey campaign. Our findings demonstrate a high within-species variability in plant phenology that is controlled by biotic and abiotic characteristics of the ecosystem. We found that between tree variation in leaf burst, completion of the leaf growth and length of canopy growth period were affected by tree size, neighborhood species richness, level of suppression and competition, which potentially indicate plant responses to light availability. The beginning of senescence, completion of leaf drop, and length of autumn phenology were mostly affected by topographic water index, which reflects water availability and can be linked to nutrient availability and exposure to wind. Furthermore, we demonstrated that an earlier leaf burst, and delayed beginning of senescence were associated with larger absolute growth in canopy area but found no clear relationship between height growth and phenology. Our study highlights the capability of dense, high-quality LiDAR time-series to detect significant phenological variation among individuals of the same species within the same locality, demonstrating the potential of LiDAR time-series as a tool for understanding phenology and its impacts.

Conflicting Views of Nature and Their Impact on Evolution Understanding

AbstractIn nature, competition within and between species is the norm, yet nature is also reputed to be a “peaceable kingdom” where animals cooperate rather than compete. This study explored how such contrasting views of nature influence students’ biological reasoning. College undergraduates (n = 165) assessed the prevalence of cooperative behaviors, such as food sharing and symbiotic cleaning, and competitive behaviors, such as cannibalism and parasitism, and these assessments were compared to their understanding of evolution as a process of differential survival and reproduction. Participants underestimated the prevalence of competitive behaviors relative to cooperative ones, particularly for behaviors directed toward other members of the same species, and the accuracy of their judgments predicted how well they understood evolution, even when controlling for other predictors of evolution understanding, including perceptions of within-species variation and perceptions of geologic time. These findings suggest that overly benevolent views of nature compete with more realistic views and may hamper our appreciation of the mechanisms of adaptation.

An integrated strain-level analytic pipeline utilizing longitudinal metagenomic data.

The advancement in DNA-sequencing technology has enabled the high-resolution identification of microorganisms in microbial communities. Since different microbial strains within species may contain extreme phenotypic variability (e.g., nutrition metabolism, antibiotic resistance, and pathogen virulence), investigating within-species variations holds great scientific promise in understanding the underlying mechanism of microbial biological processes. To fully utilize the shared genomic variants across longitudinal metagenomics samples collected in microbiome studies, we develop an integrated analytic pipeline (LongStrain) for longitudinal metagenomics data. It concurrently leverages the information on proportions of mapped reads for individual strains and genome-wide SNVs to enhance the efficiency and accuracy of strain identification. Our method helps to understand strains' dynamic changes and their association with genome-wide variants. Given the fast-growing longitudinal studies of microbial communities, LongStrain which streamlines analyses of large-scale raw sequencing data should be of great value in microbiome research communities.

SCREENING FLAX FOR IDENTIFYING CADMIUM TOLERANT CULTIVARS FOR GROWTH IN POLLUTED ENVIRONMENT

Toxic metal pollutants such as cadmium disrupt all stages of plant development. Flax (Linum usitatissimum L.) has demonstrated the ability to tolerate and accumulate high amounts of cadmium, making it suitable for phytoremediation. Within-species variability of cadmium tolerance and uptake needs to be examined in controled conditions to assess multiple beneficial, or even required traits for use in phytoremediation programs. In this study, 31 flax cultivars were screened for their ability to germinate and grow in the presence of a sublethal concentration of cadmium (20 mg.kg-1). Several parameters, including growth indicators and photosynthesis performance, were analyzed using principal component analysis. A subset of flax cultivars was then selected for measuring cadmium uptake using gamma spectrometry. The results showed that the cultivars Belinka, Diana, Laura, Marina, Flanders, and Jitka have comparable metal uptake and transfer to shoots. Among these, the cultivar Jitka proved to be the best candidate for phytoremediation, consistent with previous reports.

Physical, vibro-mechanical and optical properties of pernambuco in relation to bow-making qualitative evaluation and wood diversity

Abstract Pernambuco is the archetypal wood in modern bows of the violin-family. This species (Paubrasilia echinata) is endangered. Existing literature suggests remaining questions on how its properties’ variability relates to qualification in bow-making, and to diversity. Here 61 pernambuco specimens, with various qualitative evaluations by makers, are characterised for physical, elastic, dynamic, and optical properties. Results are compared with standard relations between-properties, and with 53 pre-selected tropical hardwoods. The tested pernambuco stands in the medium-upper range of these pre-selected species for density (ρ) and modulus of elasticity (E). It is exceptional for its very low damping coefficient (tanδ) and very intense colour (red a*, yellow b* and chroma C*). Within-species variability is high. Qualification is mostly associated to ρ, colour hue angle h° and gloss, then to elasticity – but E and E/ρ (specific modulus) overlap between groups. Qualification involves appearance (L*, h°, gloss) when freshly cut, and with anticipation of changes after ageing or finishing. The properties (damping, chroma) that make pernambuco exceptional among species, are not clearly related to the qualification within the studied sampling. Analyses help better understand the specificities of pernambuco, and highlight the multifactorial nature of wood selection at two levels: between-species preference, and within-species qualification.

De novo genome assembly of white clover (Trifolium repens L.) reveals the role of copy number variation in rapid environmental adaptation

BackgroundWhite clover (Trifolium repens) is a globally important perennial forage legume. This species also serves as an eco-evolutionary model system for studying within-species chemical defense variation; it features a well-studied polymorphism for cyanogenesis (HCN release following tissue damage), with higher frequencies of cyanogenic plants favored in warmer locations worldwide. Using a newly generated haplotype-resolved genome and two other long-read assemblies, we tested the hypothesis that copy number variants (CNVs) at cyanogenesis genes play a role in the ability of white clover to rapidly adapt to local environments. We also examined questions on subgenome evolution in this recently evolved allotetraploid species and on chromosomal rearrangements in the broader IRLC legume clade.ResultsIntegration of PacBio HiFi, Omni-C, Illumina, and linkage map data yielded a completely de novo genome assembly for white clover (created without a priori sequence assignment to subgenomes). We find that white clover has undergone extensive transposon diversification since its origin but otherwise shows highly conserved genome organization and composition with its diploid progenitors. Unlike some other clover species, its chromosomal structure is conserved with other IRLC legumes. We further find extensive evidence of CNVs at the major cyanogenesis loci; these contribute to quantitative variation in the cyanogenic phenotype and to local adaptation across wild North American populations.ConclusionsThis work provides a case study documenting the role of CNVs in local adaptation in a plant species, and it highlights the value of pan-genome data for identifying contributions of structural variants to adaptation in nature.

Species vary in within-species variability

Species vary in within-species variability

Detecting diversifying selection for a trait from within and between-species genotypes and phenotypes.

To quantify selection acting on a trait, methods have been developed using either within or between-species variation. However, methods using within-species variation do not integrate the changes at the macroevolutionary scale. Conversely, current methods using between-species variation usually discard within-species variation, thus not accounting for processes at the micro-evolutionary scale. The main goal of this study is to define a neutrality index for a quantitative trait, by combining withinand between-species variation. This neutrality index integrates nucleotide polymorphism and divergence for normalizing trait variation. As such, it does not require estimation of population size nor of time of speciation for normalization. Our index can be used to seek deviation from the null model of neutral evolution, and test for diversifying selection. Applied to brain mass and body mass at the mammalian scale, we show that brain mass is under diversifying selection. Finally, we show that our test is not sensitive to the assumption that population sizes, mutation rates and generation time are constant across the phylogeny, and automatically adjust for it.

Environmental versus phylogenetic controls on leaf nitrogen and phosphorous concentrations in vascular plants

Global patterns of leaf nitrogen (N) and phosphorus (P) stoichiometry have been interpreted as reflecting phenotypic plasticity in response to the environment, or as an overriding effect of the distribution of species growing in their biogeochemical niches. Here, we balance these contrasting views. We compile a global dataset of 36,413 paired observations of leaf N and P concentrations, taxonomy and 45 environmental covariates, covering 7,549 sites and 3,700 species, to investigate how species identity and environmental variables control variations in mass-based leaf N and P concentrations, and the N:P ratio. We find within-species variation contributes around half of the total variation, with 29%, 31%, and 22% of leaf N, P, and N:P variation, respectively, explained by environmental variables. Within-species plasticity along environmental gradients varies across species and is highest for leaf N:P and lowest for leaf N. We identified effects of environmental variables on within-species variation using random forest models, whereas effects were largely missed by widely used linear mixed-effect models. Our analysis demonstrates a substantial influence of the environment in driving plastic responses of leaf N, P, and N:P within species, which challenges reports of a fixed biogeochemical niche and the overriding importance of species distributions in shaping global patterns of leaf N and P.

Limited intraspecific variation in drought resistance along a pronounced tropical rainfall gradient

Assessing within-species variation in response to drought is crucial for predicting species' responses to climate change and informing restoration and conservation efforts, yet experimental data are lacking for the vast majority of tropical tree species. We assessed intraspecific variation in response to water availability across a strong rainfall gradient for 16 tropical tree species using reciprocal transplant and common garden field experiments, along with measurements of gene flow and key functional traits linked to drought resistance. Although drought resistance varies widely among species in these forests, we found little evidence for within-species variation in drought resistance. For the majority of functional traits measured, we detected no significant intraspecific variation. The few traits that did vary significantly between drier and wetter origins of the same species all showed relationships opposite to expectations based on drought stress. Furthermore, seedlings of the same species originating from drier and wetter sites performed equally well under drought conditions in the common garden experiment and at the driest transplant site. However, contrary to expectation, wetter-origin seedlings survived better than drier-origin seedlings under wetter conditions in both the reciprocal transplant and common garden experiment, potentially due to lower insect herbivory. Our study provides the most comprehensive picture to date of intraspecific variation in tropical tree species' responses to water availability. Our findings suggest that while drought plays an important role in shaping species composition across moist tropical forests, its influence on within-species variation is limited.

Intraspecific variation in fine-root traits is larger than in aboveground traits in European herbaceous species regardless of drought.

Differences within species (Intraspecific trait variation - ITV) contribute substantially to overall trait variability and environmental harshness can reduce among-species variation. While aboveground traits have received considerable attention, knowledge about ITV in fine-root traits and how it differs from ITV in aboveground traits remains limited. This study examined the partitioning of trait variation aboveground and fine-root traits in 52 European herbaceous species and how such proportions change in response to drought, offering valuable insights for accurate functional species characterization and inter-species comparisons. We studied seven morphological aboveground and fine-root traits under drought and well-watered conditions in a greenhouse experiment. Linear mixed effect models and permutational multivariate analysis of variance (PERMANOVA) were employed to decompose trait variation, ensuring the robustness of our results. We also calculated variance partitioning for the combination of aboveground traits and the combination of fine-root traits, as well as pairs of analogous leaf and fine-root traits (i.e., traits that fulfill similar functions) for each treatment (control and drought). Among-species trait differences explained a greater proportion of overall variance than within-species variation, except for root dry matter content (RDMC). Height and leaf area stood out, with species' identity accounting for 87-90% of total trait variation. Drought had no significant effect on the proportions of variation in any of the traits. However, the combination of fine-root traits exhibited higher intraspecific variability (44-44%) than aboveground traits (19-21%) under both drought and control. Analogous root traits also showed higher ITV (51-50%) than analogous leaf traits (27-31%). Our findings highlight substantial within-species variation and the nuanced responses of fine-root traits, particularly RDMC, suggesting root traits' flexibility to soil heterogeneity that fosters less differentiation among species. Among-species trait differences, especially aboveground, may underscore distinct strategies and competitive abilities for resource acquisition and utilization. This study contributes to elucidate the mechanisms underlying the multifunctionality of the above- and belowground plants compartments.

Recent genetic, phenetic and ecological divergence across the Mesoamerican highlands: a study case with Diglossa baritula (Aves: Thraupidae).

The topographical, geological, climatic and biodiversity complexity of Mesoamerica has made it a primary research focus. The Mesoamerican highlands is a region with particularly high species richness and within-species variation. The Cinnamon-bellied Flowerpiercer, Diglossa baritula (Wagler, 1832), is a species endemic to the Mesoamerican highlands, with three allopatric subspecies currently recognized. To characterize divergence within this species, we integrated genomics, morphology, coloration and ecological niche modeling approaches, obtained from sampling individuals across the entire geographic distribution of the species. Our results revealed a clear genomic divergence between the populations to the east versus the west of the Isthmus of Tehuantepec. In contrast to the genomic results, morphology and coloration analyses showed intermediate levels of differentiation, indicating that population groups within D. baritula have probably been under similar selective pressures. Our morphology results indicated that the only sexually dimorphic morphological variable is the wing chord, with males having a longer wing chord than females. Finally, ecological data indicated that there are differences in ecological niche within D. baritula. Our data suggest that D. baritula could contain two or more incipient species at the intermediate phase of the speciation continuum. These results highlight the importance of the geographical barrier of the Isthmus of Tehuantepec and Pleistocene climatic events in driving isolation and population divergence in D. baritula. The present investigation illustrates the speciation potential of the D. baritula complex and the capacity of Mesoamerican highlands to create cryptic biodiversity and endemism.

Within-species variability of antibiotic interactions in Gram-negative bacteria.

Treatments with antibiotic combinations are becoming increasingly important even though the supposed clinical benefits of combinations are, in many cases, unclear. Here, we systematically examined how several clinically used antibiotics interact and affect the antimicrobial efficacy against five especially problematic Gram-negative pathogens. A total of 232 bacterial isolates were tested against different pairwise antibiotic combinations spanning five classes, and the ability of all combinations in inhibiting growth was quantified. Descriptive statistics, principal component analysis (PCA), and Spearman's rank correlation matrix were used to determine the correlations between the different combinations on interaction outcome. Several important conclusions can be drawn from the 696 examined interactions. Firstly, within a species, the interactions are in general conserved but can be isolate-specific for a given antibiotic combination and can range from antagonistic to synergistic. Secondly, additive and antagonistic interactions are the most common observed across species and antibiotics, with 87.1% of isolate-antibiotic combinations being additive, 11.6% antagonistic, and only 0.3% showing synergy. These findings suggest that to achieve the highest precision and efficacy of combination therapy, not only isolate-specific interaction profiling ought to be routinely performed, in particular to avoid using drug combinations that show antagonistic interaction and an expected associated reduction in efficacy, but also discovering rare and potentially valuable synergistic interactions.IMPORTANCEAntibiotic combinations are often used to treat bacterial infections, which aim to increase treatment efficacy and reduce resistance evolution. Typically, it is assumed that one specific antibiotic combination has the same effect on different isolates of the same species, i.e., the interaction is conserved. Here, we tested this idea by examining how several clinically used antibiotics interact and affect the antimicrobial efficacy against several bacterial pathogens. Our results show that, even though within a species the interactions are often conserved, there are also isolate-specific differences for a given antibiotic combination that can range from antagonistic to synergistic. These findings suggest that isolate-specific interaction profiling ought to be performed in clinical microbiology routine to avoid using antagonistic drug combinations that might reduce treatment efficacy.

The evolution of the duckweed ionome mirrors losses in structural complexity.

The duckweeds (Lemnaceae) consist of 36 species exhibiting impressive phenotypic variation, including the progressive evolutionary loss of a fundamental plant organ, the root. Loss of roots and reduction of vascular tissues in recently derived taxa occur in concert with genome expansions of ≤14-fold. Given the paired loss of roots and reduction in structural complexity in derived taxa, we focus on the evolution of the ionome (whole-plant elemental contents) in the context of these fundamental changes in body plan. We expect that progressive vestigiality and eventual loss of roots might have both adaptive and maladaptive consequences that are hitherto unknown. We quantified the ionomes of 34 accessions in 21 species across all duckweed genera, spanning 70 Myr in this rapidly cycling plant (doubling times are as rapid as ~24 h). We related both micro- and macroevolutionary ionome contrasts to body plan remodelling and showed nimble microevolutionary shifts in elemental accumulation and exclusion in novel accessions. We observed a robust directional trend in calcium and magnesium levels, decreasing from the ancestral representative Spirodela genus towards the derived rootless Wolffia, with the latter also accumulating cadmium. We also identified abundant within-species variation and hyperaccumulators of specific elements, with this extensive variation at the fine (as opposed to broad) scale. These data underscore the impact of root loss and reveal the very fine scale of microevolutionary variation in hyperaccumulation and exclusion of a wide range of elements. Broadly, they might point to trade-offs not well recognized in ionomes.

Fatal Attraction: Argiope Spiders Lure Male Hemileuca Moth Prey with the Promise of Sex.

Predator-prey coevolution, particularly chemo-ecological arms races, is challenging to study as it requires the integration of behavioral, chemical ecology, and phylogenetic studies in an amenable system. Moths of the genus Hemileuca (Saturniidae) are colorful, diurnal, and fast and often fly well above the vegetation canopy layer. However, several Hemileuca species have been reported as being captured in spider webs, specifically Argiope species (Araneidae). Female Hemileuca are known to produce mating pheromones and spiders of the Araneidae family are known to use pheromone lures to attract lepidopteran prey. We presented primarily female Argiope aurantia, which are attractive to male Anisota pellucida (Saturniidae), to different populations of Hemileuca species across the southern and western United States to categorize the homing response strength of different species of male Hemileuca. When we mapped these Argiope lure attraction strength categories onto the most recently published Hemileuca phylogeny, the behavioral patterns suggested a potential co-evolutionary arms race between predators and prey. Males of Hemileuca maia, H. grotei, and H. nevadensis (all in the same clade) appeared to have no attraction to A. aurantia, while H. magnifica and H. hera (within a different, separate clade) appeared to be strongly attracted to A. aurantia, but H. nuttalli (also within the H. hera and H. magnifica clade) displayed no attraction. Furthermore, Hemileuca eglanterina (yet a different clade) displayed strong, weak, and no attraction to A. aurantia, depending on the population. These apparent clade partitioning patterns of Argiope lure effectiveness and within-species variation in Hemileuca lure responses suggest a predator-prey coevolutionary history of measures and countermeasures.

Assessing the genetic integrity of sugarcane germplasm in the USDA-ARS National Plant Germplasm System collection using single-dose SNP markers.

The World Collection of Sugarcane and Related Grasses, maintained at the USDA-ARS in Miami, FL, is one of the largest sugarcane germplasm repositories in the world. However, the genetic integrity of the Saccharum spp. germplasm in this collection has not been fully analyzed. In this study, we employed a single-dose SNP panel to genotype 901 sugarcane accessions, representing six Saccharum species and various hybrids. Our analysis uncovered a high rate of clone mislabeling in the collection. Specifically, we identified 86 groups of duplicates, characterized by identical SNP genotypes, which encompassed 211 accessions (23% of the total clones), while 135 groups, constituting 471 clones (52% of the total), exhibited near-identical genotypes. In addition, twenty-seven homonymous groups were detected, which shared the same clone name but differed in SNP genotypes. Hierarchical analysis of population structure partitioned the Saccharum germplasm into five clusters, corresponding to S. barberi, S. sinense, S. officinarum, S. spontaneum and S. robustum/S. edule. An assignment test, based on the five Saccharum species, enabled correcting 141 instances of mislabeled species memberships and inaccuracies. Moreover, we clarified the species membership and parentage of 298 clones that had ambiguous passport records (e.g., 'Saccharum spp', 'unknown', and 'hybrid'). Population structure and genetic diversity in these five species were further supported by Principal Coordinate Analysis and neighbor-joining clustering analysis. Analysis of Molecular Variance revealed that within-species genetic variations accounted for 85% of the total molecular variance, with the remaining 15% attributed to among-species genetic variations. The single-dose SNP markers developed in this study offer a robust tool for characterizing sugarcane germplasm worldwide. These findings have important implications for sugarcane genebank management, germplasm exchange, and crop genetic improvement.

The ability to inhibit impulses is related to social behavior in long-tailed macaques.

Performance in cognitive tasks has been linked to differences in species' social organization, yet to understand its function its relationship to within-species variation in behavior should also be explored. One important cognitive capacity, the ability to inhibit impulses, is typically better in egalitarian than despotic primate species and in primate species with strong fission-fusion dynamics. A different line of research indicates that a high ability to inhibit impulses is related to less aggressive behavior and more socio-positive behavior. However, within species the relationship between performance on cognitive inhibition tasks and variation in social behavior remains to be explored. Here we investigate how performance in a typical inhibition task in cognitive research is related to aggressive and socio-positive behavior in despotic long-tailed macaques. Twenty individuals living in two naturalistic mixed-sex groups were tested with the Plexiglass Hole Task. Aggressive behavior and three types of socio-positive behavior (neutral/friendly approaches, socio-positive signaling, and grooming others) among group members were measured. Individuals differed in their ability to inhibit impulses. Individuals that were not good at inhibiting impulses showed higher rates of aggressive behavior, but also more socio-positive signals, whereas inhibition was not related to neutral/friendly approaches and grooming. These results confirm the positive link between impulsiveness and aggression. In addition, the results indicate that some social-positive behavior may be enhanced when inhibition is limited. In this species, benefits potentially derived from aggression and socio-positive signals match a low ability to inhibit impulses, suggesting that a low ability to inhibit impulses may actually be advantageous. To understand differences between species in cognitive skills, understanding the benefits of variation in a cognitive capacity within a species is crucial.

Plumage microorganism communities of tidal marsh sparrows

Microorganism communities can shape host phenotype evolution but are often comprised of thousands of taxa with varied impact on hosts. Identification of taxa influencing host evolution relies on first describing microorganism communities and acquisition routes. Keratinolytic (keratin-degrading) microorganisms are hypothesized to be abundant in saltmarsh sediments and to contribute to plumage evolution in saltmarsh-adapted sparrows. Metabarcoding was used to describe plumage bacterial (16S rRNA) and fungal (ITS) communities in three sparrow species endemic to North America's Atlantic coast saltmarshes. Results describe limited within-species variability and moderate host species-level patterns in microorganism diversity and community composition. A small percentage of overall microorganism diversity was comprised of potentially keratinolytic microorganisms, warranting further functional studies. Distinctions between plumage and saltmarsh sediment bacteria, but not fungal, communities were detected, suggesting multiple bacterial acquisition routes and/or vertebrate host specialization. This research lays groundwork for future testing of causal links between microorganisms and avian host evolution.

Molecular evidence depicts genetic divergence among Agropyron elongatum and A. cristatum accessions from gene pool of Iran.

The genus Agropyron has an important role in soil protection and forage production in rangelands. The investigation utilized 37 ISSR primers, resulting in the detection of 956 loci within the A. elongatum genome and 705 loci within the A. cristatum genome. The findings revealed a high level of polymorphism, with 97% of loci in A. elongatum and 84% of loci in A. cristatum exhibiting variability. Notably, the primer (AC)8GCT emerged as a promising candidate for evaluating genetic diversity due to its ability to amplify numerous loci in both species. Using both the UPGMA algorithm and Bayesian analysis, the examined Agropyron accessions were categorized into two subgroups based on their respective species. The Q values associated with these subgroups suggested that certain accessions, namely "G16," "G19," "G20," "G21," "G22," "G23," "G24," and "G25," displayed potential admixture genomes. An analysis of molecular variance (AMOVA) underscored the significance of within-species variability, which accounted for 69% of the overall diversity, compared to between-species variability at 31%. Various genetic diversity parameters, including Na, Ne, I, He, and the number of private loci, were found to be higher in A. elongatum when compared to A. cristatum. Furthermore, Jaccard similarity coefficients ranged from 0.33 to 0.66 in A. cristatum and from 0.25 to 0.7 in A. elongatum, indicating the extent of genetic relatedness among these species. Intriguingly, the study identified two and three heterotic groups in A. cristatum and A. elongatum, respectively, which could be harnessed in the development of synthetic varieties to exploit heterosis. The results also indicated that a small proportion of ISSR loci pairs (5.2% in A. elongatum and 0.5% in A. cristatum) exhibited significant levels of linkage disequilibrium (LD) (P≤0.05), suggesting the potential utility of LD-based association mapping in Agropyron species. In conclusion, this research sheds light on the genetic diversity of Agropyron species and provides valuable insights into their potential applications in soil protection and forage production, as well as the prospects for enhancing genetic variability and heterosis in these species.

Mosaic environment-driven evolution of the deep-sea mussel Gigantidas platifrons bacterial endosymbiont

BackgroundThe within-species diversity of symbiotic bacteria represents an important genetic resource for their environmental adaptation, especially for horizontally transmitted endosymbionts. Although strain-level intraspecies variation has recently been detected in many deep-sea endosymbionts, their ecological role in environmental adaptation, their genome evolution pattern under heterogeneous geochemical environments, and the underlying molecular forces remain unclear.ResultsHere, we conducted a fine-scale metagenomic analysis of the deep-sea mussel Gigantidas platifrons bacterial endosymbiont collected from distinct habitats: hydrothermal vent and methane seep. Endosymbiont genomes were assembled using a pipeline that distinguishes within-species variation and revealed highly heterogeneous compositions in mussels from different habitats. Phylogenetic analysis separated the assemblies into three distinct environment-linked clades. Their functional differentiation follows a mosaic evolutionary pattern. Core genes, essential for central metabolic function and symbiosis, were conserved across all clades. Clade-specific genes associated with heavy metal resistance, pH homeostasis, and nitrate utilization exhibited signals of accelerated evolution. Notably, transposable elements and plasmids contributed to the genetic reshuffling of the symbiont genomes and likely accelerated adaptive evolution through pseudogenization and the introduction of new genes.ConclusionsThe current study uncovers the environment-driven evolution of deep-sea symbionts mediated by mobile genetic elements. Its findings highlight a potentially common and critical role of within-species diversity in animal-microbiome symbioses.CVLZncxgEcwzSBxr2fsxJvVideo