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bioRxiv2018

The dimensions of species diversity

Diversification processes underpin the patterns of species diversity that fascinate biologists. Two competing hypotheses disagree about the effect of competition on these processes. The bounded hypothesis suggests that species diversity is limited (bounded) by competition between species for finite niche space, while the unbounded hypothesis proposes that evolution and ecological opportunity associated with speciation, render competition unimportant. We use phylogenetically structured niche modelling, to show that processes consistent with both these diversification models have driven species accumulation in conifers. In agreement with the bounded hypothesis, niche competition constrained diversification, and in line with the unbounded hypothesis, niche evolution and partitioning promoted diversification. We then analyse niche traits to show that these diversification enhancing and inhibiting processes can occur simultaneously on different niche dimensions. Together these results suggests a new hypothesis for lineage diversification based on the multi-dimensional nature of ecological niches that accommodates both bounded and unbounded diversification processes.

evolutionary biology↗

bioRxiv2018

Convergent evolution of bird-mammal shared characteristics for adapting to nocturnality

The diapsid lineage (birds) and synapsid lineage (mammals), share a suite of functionally similar characteristics (e.g., endothermy) that are considered to be a result of their convergent evolution, but the candidate selections leading to this convergent evolution are still under debates. Here, we used a newly developed molecular phyloecological approach to reconstruct the diel activity pattern of the common ancestors of living birds. Our results strongly suggest that they had adaptations to nocturnality during their early evolution, which is remarkably similar to that of ancestral mammals. Given their similar adaptation to nocturnality, we propose that the shared traits in birds and mammals may have evolved as a result of the convergent evolution of their early ancestors adapting to ecological factors (e.g., low ambient temperature) associated with nocturnality. Finally, a conceptually unifying ecological model on the evolution of endothermy in diverse organisms with an emphasis on low ambient temperature is proposed. We reason that endothermy may evolve as an adaptive strategy to enable organisms to effectively implement various life cycle activities under relatively low-temperature environments. In particular, a habitat shift from high-temperature to relatively low-temperature environments is identified as a common factor underlying the evolution of endothermy.

evolutionary biology↗

bioRxiv2018

Profiling grapevine trunk pathogens in planta: A case for community-targeted DNA metabarcoding

DNA metabarcoding, commonly used in exploratory microbial ecology studies, is a promising method for the simultaneous in planta-detection of multiple pathogens associated with disease complexes, such as the grapevine trunk diseases. Their detection is particularly challenging, due to the presence within an individual wood lesion of multiple co-infecting trunk pathogens and other wood-colonizing fungi, which span a broad range of taxa in the Fungal Kingdom. As such, we designed metabarcoding primers, using as template the ribosomal internal transcribed spacer of grapevine trunk-associated Ascomycete fungi (GTAA) and compared them to two universal primer widely used in microbial ecology. We first performed in silico simulations and then tested the primers by high-throughput amplicon sequencing of (i) multiple combinations of mock communities, (ii) time-course experiments with controlled inoculations, and (iii) diseased field samples from vineyards under natural levels of infection. All analyses showed that GTAA had greater affinity and sensitivity, compared to those of the universal primers. Importantly, with GTAA, profiling of mock communities and comparisons with shotgun-sequencing metagenomics of field samples gave an accurate representation of genera of important trunk pathogens, namely Phaeomoniella, Phaeoacremonium, and Eutypa, the abundances of which were greatly over- or under-estimated with universal primers. Overall, our findings not only demonstrate that DNA metabarcoding gives qualitatively and quantitatively accurate results when applied to grapevine trunk diseases, but also that primer customization and testing are crucial to ensure the validity of DNA metabarcoding results.

microbiology↗

bioRxiv2018

When one phenotype is not enough - divergent evolutionary trajectories govern venom variation in a widespread rattlesnake species

Understanding the relationship between genome, phenotypic variation, and the ecological pressures that act to maintain that variation, represents a fundamental challenge in evolutionary biology. Functional polymorphisms typically segregate in spatially isolated populations [1, 2] and/or discrete ecological conditions [3-5], whereas dissecting the evolutionary processes involved in adaptive geographic variation across a continuous spatial distribution is much more challenging [6]. Additionally, pleiotropic interactions between genes and phenotype often complicate the identification of specific genotype-phenotype links [7-8], and thus of the selective pressures acting on them. Animal venoms are ideal systems to overcome these constraints: they are complex and variable, yet easily quantifiable molecular phenotypes with a clear function and a direct link to both genome and fitness [9]. Here, we use dense and widespread population-level sampling of the Mohave rattlesnake, Crotalus scutulatus, and show that genomic structural variation at multiple loci underlies extreme geographic variation in venom composition, which is maintained despite extensive gene flow. Unexpectedly, selection for diet does not explain venom variation, contrary to the dominant paradigm of venom evolution, and neither does neutral population structure caused by past vicariance. Instead, different toxin genes correlate with distinct environmental factors, suggesting that divergent selective pressures can act on individual loci independently of their genomic proximity or co-expression patterns. Local-scale spatial heterogeneity thus appears to maintain a remarkably ancient complex of molecular phenotypes, which have been retained in populations that diverged more than 1.5-2 MYA, representing an exceptional case of long-term structural polymorphism. These results emphasize how the interplay between genomic architecture and spatial heterogeneity in selective pressures may facilitate the retention of functional polymorphisms of an adaptive phenotype.

evolutionary biology↗

bioRxiv2018

Biofilm thickness matters: Deterministic assembly of different functions and communities in nitrifying biofilms

Microbial biofilms are important in natural ecosystems and in biotechnological applications. Biofilm architecture influences organisms spatial positions, who their neighbors are, and redox gradients, which in turn determine functions. We ask if and how biofilm thickness influences community composition, architecture and functions. But biofilm thickness cannot easily be isolated from external environmental factors. We designed a metacommunity system in a wastewater treatment plant, where either 50 or 400 {micro}m thick nitrifying biofilms were grown simultaneously on biofilm carriers in the same reactor. Model simulations showed that the 50 {micro}m biofilms could be fully oxygenated whereas the 400 {micro}m biofilms contained anaerobic zones. The 50 and 400 {micro}m biofilms developed significantly different communities. due to deterministic factors were stronger than homogenizing dispersal forces in the reactor, despite the fact that biofilms experienced the same history and external conditions. Relative abundance of aerobic nitrifiers was higher in the 50 {micro}m biofilms, while anaerobic ammonium oxidizers were more abundant in the 400 {micro}m biofilms. However, turnover was larger than the nestedness component of between-group beta-diversity, i.e. the 50 {micro}m biofilm was not just a subset of the thicker 400 {micro}m biofilm with reduced taxa richness. Furthermore, the communities had different nitrogen transformation rates. The study shows that biofilm thickness has a strong impact on community composition and ecosystem function, which has implications for biotechnological applications, and for our general understanding of biofilms.\n\nIMPORTANCEMicroorganisms colonize all surfaces in water and form biofilms. Diffusion limitations form steep gradients of energy and nutrient sources from the water phase into the deeper biofilm parts, influencing community composition through the biofilm. Thickness of the biofilm will affect diffusion gradients, and is therefore presumably important for biofilm composition. Since environmental factors determine thickness, studies of how thickness influences biofilm functions and community assembly, have been difficult to perform. We studied biofilms for wastewater treatment with fixed thicknesses of 50 and 400 {micro}m during otherwise similar conditions and history. Despite growing in the same wastewater reactor, 16S rRNA gene sequencing and confocal microscopy showed the formation of two different communities, performing different ecosystem functions. Using statistical methods, we show for the first time, how biofilm thickness influences community assembly. The results help our understanding of the ecology of microbial biofilms, and in designing engineered systems based on ecological principles.

microbiology↗

bioRxiv2018

Estimating the current burden of Chagas disease in Mexico: a systematic review of epidemiological surveys from 2006 to 2017

BackgroundIn Mexico, estimates of Chagas disease prevalence and burden vary widely. Updating surveillance data is therefore an important priority to ensure that Chagas disease does not remain a barrier to the development of Mexicos most vulnerable populations.\n\nMethodology/Principal FindingsThe aim of this systematic review was to analyze the literature on epidemiological surveys to estimate Chagas disease prevalence and burden in Mexico, during the period 2006 to 2017. A total of 2,764 articles were screened and 38 were retained for the final analysis. Epidemiological surveys have been performed in most of Mexico, but with variable geographic coverage. Based on studies reporting confirmed cases, i.e. using at least 2 serological tests, the national seroprevalence of Trypanosoma cruzi infection was 2.26% [95% Confidence Interval (CI) 2.12-2.41], suggesting that there are 2.71 million cases in Mexico. Studies focused on pregnant women, which may transmit the parasite to their newborn during pregnancy, reported a seroprevalence of 1.00% [95% CI 0.87-1.14], suggesting that there are 22,930 births from T. cruzi infected pregnant women per year, and 1,445 cases of congenitally infected newborns per year. Children under 18 years had a seropositivity rate of 1.49% [95% CI 1.20-1.85], which indicate ongoing transmission. Finally, cases of T. cruzi infection in blood donors have also been reported in most states, with a national seroprevalence of 0.51% [95% CI 0.49-0.53].\n\nConclusions/SignificanceOur analysis suggests a disease burden for T. cruzi infection higher than previously recognized, highlighting the urgency of establishing Chagas disease surveillance and control as a key national public health priority in Mexico, to ensure that it does not remain a major barrier to the economic and social development of the countrys most vulnerable populations.\n\nAuthor summaryIn Mexico, estimates of Chagas disease prevalence and burden vary widely due to the ecology and epidemiology of this disease resulting of many geographical, ecological, biological, and social interactions. Better data are thus urgently needed to help develop appropriate public health programs for disease control and patient care. In this study we analyzed published data on T. cruzi seroprevalence infection in Mexico between 2006 and 2017. This systematic review shows a national seroprevalence of T. cruzi infection of 2.26% [95%CI 2.12-2.41], with over 2.71 million cases in Mexico, which is higher than previously recognized. The presence of T. cruzi infection in specific subpopulations such as pregnant women, children and blood donors also informs on specific risks of infection and call for the implementation of well-established control interventions. This work confirms the place of Mexico as the country with the largest number of cases, highlighting the urgency of establishing Chagas disease control as a key national public health priority.

epidemiology↗

bioRxiv2018

A large close relative of C. elegans is slow-developing but not long-lived

BackgroundVariation in body size is thought to be a major driver of a wide variety of ecological and evolutionary patterns, including changes in development, reproduction, and longevity. Caenorhabditis inopinata is a recently-discovered fig-associated nematode that is unusually large relative to other members of the genus, including the closely related model system C. elegans. Here we test whether the dramatic increase in body size has led to correlated changes in key life history and developmental parameters within this species.\n\nResultsUsing four developmental milestones, C. inopinata was found to have a slower rate of development than C. elegans across a range of temperatures. Despite this, C. inopinata did not reveal any differences in adult lifespan from C. elegans after accounting for differences in developmental timing and reproductive mode. C. inopinata fecundity was generally lower than that of C. elegans, but fitness improved under continuous-mating, consistent with sperm-limitation under gonochoristic (male/female) reproduction. C. inopinata also revealed greater fecundity and viability at higher temperatures.\n\nConclusionConsistent with observations in other ectotherms, slower growth in C. inopinata indicates a potential trade-off between body size and developmental timing, whereas its unchanged lifespan suggests that longevity is largely uncoupled from its increase in body size. Additionally, temperature-dependent patterns of fitness in C. inopinata are consistent with its geographic origins in subtropical Okinawa. Overall, these results underscore the extent to which changes in ecological context and body size can shape life history traits.

evolutionary biology↗

bioRxiv2018

pavo 2.0: new tools for the spectral and spatial analysis of colour in R

O_LIBiological colouration presents a canvas for the study of ecological and evolutionary processes. Enduring interest in colour-based phenotypes has driven, and been driven by, improved techniques for quantifying colour patterns in ever-more relevant ways, yet the need for flexible, open frameworks for data processing and analysis persists.\nC_LIO_LIHere we introduce pavo 2, the latest iteration of the R package pavo. This release represents the extensive refinement and expansion of existing methods, as well as a suite of new tools for the cohesive analysis of the spectral and (now) spatial structure of colour patterns and perception. At its core, the package retains a broad focus on (a) the organisation and processing of spectral and spatial data, and tools for the alternating (b) visualisation, and (c) analysis of data. Significantly, pavo 2 introduces image-analysis capabilities, providing a cohesive workflow for the comprehensive analysis of colour patterns.\nC_LIO_LIWe demonstrate the utility of pavo with a brief example centred on mimicry in Heliconius butterflies. Drawing on visual modelling, adjacency, and boundary strength analyses, we show that the combined spectral (colour and luminance) and spatial (pattern element distribution and boundary salience) features of putative models and mimics are closely aligned.\nC_LIO_LIpavo 2 offers a flexible and reproducible environment for the analysis of colour, with renewed potential to assist researchers in answering fundamental questions in sensory ecology and evolution.\nC_LI

animal behavior and cognition↗

bioRxiv2018

Coexistence and cooperation in structured habitats

Many natural habitats are structured, which imposes certain environmental conditions on extant populations. Which conditions are important for coexistence of diverse communities, and how social traits in such populations stabilize, have been important ecological and evolutionary questions. We investigate a minimal ecological model of microbial population dynamics, that exhibits crucial features to show coexistence: Populations are repeatedly separated into compartmentalized habitats on a timescale typically longer than growth. In this framework, we consider several scenarios for possible interactions between different strains and their environments, which includes sharing a common nutrient source or expression of public goods that potentially increase population size. Examples for these public good dynamics are collective resistance against antibiotics, and enhanced iron-availability due to pyoverdine. We show that the two features of a long mixing timescale and spatial compartmentalization are already enough to enable coexisting strains. In the case of public goods, stable coexistence immediately entails cooperation.

evolutionary biology↗

bioRxiv2018

Experimental evolution of reproductive isolation from a single natural population

Ecological speciation occurs when local adaptation generates reproductive isolation as a by-product of natural selection1-3. Although ecological speciation is a fundamental source of diversification, the mechanistic link between natural selection and reproductive isolation remains poorly understood, especially in natural populations2-6. Here we show that experimental evolution of parasite body size over four years (ca. 60 generations) leads to reproductive isolation in natural populations of feather lice on birds. When lice are transferred to pigeons of different sizes they rapidly evolve differences in body size that are correlated with host size. These size differences trigger mechanical mating isolation between lice that are locally adapted to the different sized hosts. Size differences among lice also influence the outcome of competition between males for access to females. Thus, body size directly mediates reproductive isolation through its influence on both inter-sexual compatibility and intra-sexual competition. Our results confirm that divergent natural selection acting on a single phenotypic trait can cause reproductive isolation to emerge from a single natural population in real time.

evolutionary biology↗

bioRxiv2018

Trait evolution and historical biogeography shape assemblages of annual killifish

Reconstructions of evolutionary and historical biogeographic processes can improve our understanding of how species ssemblages developed and permit inference of ecological drivers affecting coexistence. We explore this approach in Austrolebias, a genus of annual fishes possessing a wide range of body sizes. Regional assemblages composed of different species with similar size distributions are found in four areas of eastern South America. Using phylogenetic trees, species distribution models and size data we show how trait evolution and historical biogeography have affected the composition of species assemblages. We extend age-range correlations to improve estimates of local historical biogeography. We find that size variation principally arose in a single area and infer that ecological interactions drove size divergence. This large-size lineage spread to two other areas. One of these assemblages was likely shaped by adaptation to a new environment, but this was not associated with additional size divergence. We found only weak evidence that environmental filtering has been important in the construction of the remaining assemblage with the smallest range of sizes. The repeated assemblage structures were the result of different evolutionary and historical processes. Our approach sheds light on how species assemblages were built when typical clustering approaches may fall short.

evolutionary biology↗

bioRxiv2018

Absence of general rules governing molluscan body-size response to climatic fluctuation during Cenozoic

Body size is a key factor in dictating the fate of interaction between an organism and its surrounding environment. A negative temperature-size relationship (TSR) has been suggested as one of the universal responses to climatic warming. It is also predicted that groups with narrow latitudinal range, tropical affinity and higher body size, would show higher sensitivity to climatic fluctuation. Moreover, because of the difference in thermal sensitivity, it is also expected that the response to climatic fluctuation would be different between epifaunal and infaunal groups. To confirm the generality of these relationship among marine families, we compiled the relationship between body-size and global temperature trends over Cenozoic using a database of marine benthic molluscs of class gastropoda and bivalvia resolved to temporal stages. We evaluated the dependence of climate induced body-size response to the existing size and latitudinal spread via correlating the first-difference correlation coefficient of temperature-size ({rho}1st (size-temp)) with maximum size and latitudinal spread of family respectively. Cenozoic record of this highly diverse group does not show any signature of TSR for molluscan class or for any other regional, ecological groups during the past 66My long climatic fluctuation. We did not find any evidence supporting heightened response to climatic fluctuation in groups with limited latitudinal spread or with large body-size. The tropical species did not show significant difference in their body-size response in comparison to temperate species. It also shows lack of any difference in response between ecological groups of molluscs with varying substrate relationship and hence, refutes the predicted variation due to difference in thermal specialization. Although a negative correlation between maximum latitudinal spread and {rho}1st (size-temp) is observed for infaunal families, it is not statistically significant. Our results highlight the limited validity of \"universal rules\" in explaining the climate induced morphological response of marine communities in deep time and underscores the complexity in generalizing the biotic outcome of future climatic fluctuation.

paleontology↗

bioRxiv2018

Microbial and Metabolic Succession on Common Building Materials Under High Humidity Conditions

Despite considerable efforts to characterize the ecology of bacteria and fungi in the built environment (BE), the metabolic mechanisms underpinning their colonization and successional dynamics remain unclear. Here, we applied bacterial/viral particle counting, qPCR, 16S and ITS rRNA amplicon sequencing, and metabolomics to longitudinally characterize the ecological dynamics of four commonly used building materials maintained at high humidity conditions (~94% RH). We varied the natural inoculum provided to each material by placing them in different occupied spaces, and we wet the surface of half of the samples of each material to simulate a flooding event. As expected, different materials showed different bacterial and viral particle abundance, with wet materials having higher growth rates and lower alpha diversity compared to non-wetted materials. Wetting described the majority of the variance in bacterial, fungal and metabolite structure, and material type only influenced bacterial and metabolic diversity, while location of inoculation was only weakly associated with bacterial and fungal beta diversity. Metabolites indicative of microbial activity were identified, as were those that were native to the surface material. Glucose-phosphate was abundant on all materials (except mold-free gypsum) and was correlated with Enterobacteriaceae, which could indicate a potential bacterial nutrient source. A compound consistent with scopoletin, a plant metabolite with antimicrobial activity, was significantly negatively correlated with Bacillus and positively correlated with Pseudomonas and enriched in medium density fiberboard (MDF) materials. In wet samples, the alkaloids nigragillin and fumigaclavine C, both with antimicrobial properties, were significantly positively correlated with the fungal phylum Ascomycota. Nigragillin, was also negatively correlated with Bacillus and Pseudomonas abundance. Thiabendazole and azoxystrobin (anti-fungal compounds) were highly abundant on mold-resistant gypsum wallboard and likely directly influenced the decreased fungal growth observed on this material. The mold-resistant gypsum material also showed a significant increase in bacterial alpha diversity, and bacterial and viral particle abundance, as well as a decrease in metabolite diversity, likely a result of reduced fungal growth. Penicillium taxa were positively correlated with thiabendazole, which suggested the persistence of resistant strains. Also, specific to the wet samples, Bacillus abundance was positively correlated with the azoxystrobin, suggesting bi-directional competitive adaptation, and positively correlated with metabolites known to interfere with Pseudomonas biofilm formation, which could explain the anti-correlation between these taxa. As expected, high moisture conditions enabled faster growth of inoculating microorganisms, whose composition, chemistry, and competition was shaped by surface material, suggesting that both fungal and bacterial growth need to be considered when determining the impact of dampness in built environments.

microbiology↗

bioRxiv2018

Hydrogenotrophic methanogens of the mammalian gut: functionally similar, thermodynamically different. A modelling approach

Methanogenic archaea occupy a functionally important niche in the gut microbial ecosystem of mammals. Our purpose was to quantitatively characterize the dynamics of methanogenesis by integrating microbiology, thermodynamics and mathematical modelling. For that, in vitro growth experiments were performed with pure cultures of key methanogens from the human and ruminant gut, namely Methanobrevibacter smithii, Methanobrevibacter ruminantium and Methanobacterium formicium. Microcalorimetric experiments were performed to quantify the methanogenesis heat flux. We constructed an energetic-based mathematical model of methanogenesis. Our model captured efficiently the dynamics of methanogenesis with concordance correlation coefficients of 0.94 for CO2, 0.99 for H2 and 0.97 for CH4. Together, experimental data and model enabled us to quantify metabolism kinetics and energetic patterns that were specific and distinct for each species despite their use of analogous methane-producing pathways. Then, we tested in silico the interactions between these methanogens under an in vivo simulation scenario using a theoretical modelling exercise. In silico simulations suggest that the classical competitive exclusion principle is inapplicable to gut ecosystems and that kinetic information alone cannot explain gut ecological aspects such as microbial coexistence. We suggest that ecological models of gut ecosystems require the integration of microbial kinetics with nonlinear behaviours related to spatial and temporal variations taking place in mammalian guts. Our work provides novel information on the thermodynamics and dynamics of methanogens. This understanding will be useful to construct new gut models with enhanced prediction capabilities and could have practical applications for promoting gut health in mammals and mitigating ruminant methane emissions.

microbiology↗

bioRxiv2018

Independent mechanisms for acquired salt tolerance versus growth resumption induced by mild ethanol pretreatment in Saccharomyces cerevisiae

All living organisms must recognize and respond to various environmental stresses throughout their lifetime. In natural environments, cells frequently encounter fluctuating concentrations of different stressors that can occur in combination or sequentially. Thus, the ability to anticipate an impending stress is likely ecologically relevant. One possible mechanism for anticipating future stress is acquired stress resistance, where cells pre-exposed to a mild sub-lethal dose of stress gain the ability to survive an otherwise lethal dose of stress. We have been leveraging wild strains of Saccharomyces cerevisiae to investigate natural variation in the yeast ethanol stress response and its role in acquired stress resistance. Here, we report that a wild vineyard isolate possesses ethanol-induced cross-protection against severe concentrations of salt. Because this phenotype correlates with ethanol-dependent induction of the ENA genes, which encode sodium efflux pumps already associated with salt resistance, we hypothesized that variation in ENA expression was responsible for differences in acquired salt tolerance across strains. Surprisingly, we found that the ENA genes were completely dispensable for ethanol-induced survival of high salt concentrations in the wild vineyard strain. Instead, the ENA genes were necessary for the ability to resume growth on high concentrations of salt following a mild ethanol pretreatment. Surprisingly, this growth acclimation phenotype was also shared by the lab yeast strain despite lack of ENA induction under this condition. This study underscores that cross protection can affect both viability and growth through distinct mechanisms, both of which likely confer fitness effects that are ecologically relevant.\n\nIMPORTANCEMicrobes in nature frequently experience \"boom or bust\" cycles of environmental stress. Thus, microbes that can anticipate the onset of stress would have an advantage. One way microbes anticipate future stress is through acquired stress resistance, where cells exposed to a mild dose of one stress gain the ability survive an otherwise lethal dose of a subsequent stress. In the budding yeast Saccharomyces cerevisiae, certain stressors can cross protect against high salt concentrations, though the mechanisms governing this acquisition of higher stress resistance are not well understood. In this study, we took advantage of wild yeast strains to understand the mechanism underlying ethanol-induced cross protection against high salt concentrations. We found that mild ethanol stress allows cells to resume growth on high salt, which involves a novel role for a well-studied salt transporter. Overall, this discovery highlights how leveraging natural variation can provide new insights into well-studied stress defense mechanisms.

microbiology↗

bioRxiv2026

BioIMA: a one-click desktop tool for standardized extraction of phenotypic traits from biological images

Standardized extraction of quantitative phenotypes from images is increasingly important across plant biology, from ecological and evolutionary studies to genetics, breeding, and functional genomics. However, as large image datasets are increasingly used for trait analysis, many biologically relevant traits, including size, shape, color, and spatial patterning, are still measured manually or using fragmented semi-automated workflows. These limitations reduce throughput, reproducibility, and accessibility, especially for researchers without computational expertise. Here, we present BioIMA, an open-source desktop tool for rapid and standardized phenotyping from biological images. BioIMA integrates foundation model-based segmentation with automated trait computation, allowing users to extract quantitative measurements from images through an intuitive graphical interface and without model training. To validate its performance, we quantified a set of knot morphological traits in two Populus species, as these measurements are typically time-consuming to perform manually. Automatic measurements showed strong agreement with manual ImageJ-based measurements (R2 > 0.95), while reducing per-image processing time by approximately 75% (from ~15 s to ~4 s). BioIMA was further applied to diverse plant datasets, including Helianthus and Rhododendron images with varying morphologies and background conditions. Although developed for plant phenotyping, BioIMA may also be extended to other biological samples where region-based size, shape, or color traits are of interest. By combining accessibility and standardization in a lightweight local application, BioIMA provides a practical community resource for image-based phenotyping in ecological and evolutionary studies.

bioinformatics↗

bioRxiv2026

Plaque microbial community restructuring in rampant dental caries after exclusion of a confirmed Streptococcus mutans ASV: an analysis of public 16S rRNA sequencing data

Background: Dental caries is increasingly understood as an ecological biofilm disorder rather than the consequence of a single organism. Although Streptococcus mutans is strongly implicated in cariogenesis, it remains unclear whether caries-associated plaque-community differences persist beyond this organism. Methods: We reanalysed publicly available supragingival-plaque 16S rRNA sequencing data from 88 preschool children with rampant caries (n=44) or who were caries-free (n=44; BioProject PRJNA1141721). Single-end DADA2 processing yielded 25,669 amplicon sequence variants (ASVs), including one ASV confirmed as S. mutans by an eHOMD reference-window procedure. The pre-specified primary analysis compared Bray-Curtis community composition after exclusion of this ASV. Results: Non-S. mutans community composition differed between groups (PERMANOVA pseudo-R2=0.0462, pseudo-F=4.16, P<0.001), without evidence of unequal multivariate dispersion (P=0.796); rarefaction produced a nearly identical result. Shannon diversity did not differ (P=0.486). The confirmed S. mutans ASV was detected in 8/44 rampant-caries and 42/44 caries-free samples and was lower in abundance in rampant caries. Among 758 prevalence-filtered non-S. mutans ASVs, 239 showed conventional FDR-significant differential abundance, with more showing lower than higher bias-corrected abundance in rampant caries (176 versus 63); 239 additional ASVs were classified as structural zeros. Individual ASV findings were sensitive to prevalence filtering. Adjustment for S. mutans abundance attenuated the global caries-group association (marginal pseudo-R2=0.0149, P=0.085) in the presence of strong collinearity. Conclusions: Rampant caries was associated with modest but reproducible plaque-community restructuring after exclusion of a confirmed S. mutans ASV, without a corresponding Shannon-diversity difference. These findings support a community-level ecological interpretation but do not establish statistical independence from S. mutans or a causal role for individual taxa.

microbiology↗

bioRxiv2013

Sampling principles for biodiversity study

Sampling is a fundamental tool in ecology and critical for biodiversity measurement. However, basic principles of biodiversity sampling have been overlooked for many years. In this paper, I proposed and explored five principles of sampling for a specific area and biodiversity study. The first principle of sampling, species increasing with area, is that the number of species increases with the area. The second principle of sampling, individuals increasing with area, is that the number of individuals increases with the area. The third principle of sampling, sum of species number, is that the sum of species number in one area and species number in another area is no less than the total species number in the two areas. The fourth principle of sampling, individual complement, is that the sum of the mathematical expectation of individual number of one or several species in the area a and that of the same one or several species in the area A-a is the total individual number N of the same one or several species in the total area A. The fifth principle of sampling, species-area theory, is that the sum of the mathematical expectation of number of species in the area a and that of number of species lost if area A-a is cleared is the total species number M in the total area A.

Ecology↗