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bioRxiv2017

Construction of soil defined media using quantitative exometabolomic analysis of soil metabolites

Exometabolomics enables analysis of metabolite utilization of low molecular weight organic substances by soil isolates. Environmentally-based defined media are needed to examine ecologically relevant patterns of substrate utilization. Here, we describe an approach for the construction of defined media using untargeted characterization of water soluble soil metabolites. To broadly characterize soil metabolites, both liquid chromatography mass spectrometry (LC/MS) and gas chromatography mass spectrometry (GC/MS) were used. With this approach, 96 metabolites were identified, including amino acids, amino acid derivatives, sugars, sugar alcohols, mono- and di-carboxylic acids, osmolytes, nucleobases, and nucleosides. From this pool of metabolites, 25 were quantified. Water soluble organic carbon was fractionated by molecular weight and measured to determine the fraction of carbon accounted for by the quantified metabolites. This revealed that, community structures, these soil metabolites have an uneven quantitative distribution, with a single metabolite, trehalose accounting for 9.9 percent of much like soil microbial the (< 1 kDa) water extractable organic carbon. This quantitative information was used to formulate two soil defined media (SDM), one containing 23 metabolites (SDM1) and one containing 46 (SDM2). To evaluate SDM for supporting the growth of bacteria found at this field site, we examined the growth of 30 phylogenetically diverse soil isolates obtained using standard R2A medium. The simpler SDM1 supported the growth of up to 13 isolates while the more complex SDM2 supported up to 25 isolates. One isolate, Pseudomonas corrugata strain FW300-N2E2 was selected for a time-series exometabolomics analysis to investigate SDM1 substrate preferences. Interestingly, it was found that this organism preferred lower-abundance substrates such as guanine, glycine, proline and arginine and glucose and did not utilize the more abundant substrates maltose, mannitol, trehalose and uridine. These results demonstrate the viability and utility of using exometabolomics to construct a tractable environmentally relevant media. We anticipate that this approach can be expanded to other environments to enhance isolation and characterization of diverse microbial communities.\n\nHighlights O_LILC/MS and GC/MS analyses of soil extracts revealed a diversity of 96 metabolites.\nC_LIO_LISoil defined media were constructed based on water extractable soil metabolomics data.\nC_LIO_LIThe defined media supported the growth of 25 out of 30 bacterial isolates.\nC_LIO_LIExometabolomics demonstrated preferential consumption of amino acids for one isolate.\nC_LIO_LIThese media can be used to understand environmentally relevant microbial substrate preferences.\nC_LI\n\nAbbreviationsDOM dissolved organic matter; SOM soil organic matter; WEOC water extractable organic carbon; LMWOS low molecular weight organic substances; SDM(1/2) soil defined media (1 and 2); R2A Reasoners 2A agar medium; ORFRC Oak Ridge Field Research Center; LC/MS liquid chromatography mass spectrometry; GC/MS gas chromatography/ mass spectrometry; TOC total organic carbon; HILIC hydrophilic interaction liquid chromatography

microbiology↗
bioRxiv2017

Metagenomics reveals niche partitioning within the phototrophic zone of a microbial mat

Hypersaline photosynthetic microbial mats are stratified microbial communities known for their taxonomic and metabolic diversity and strong light-driven day-night environmental gradients. In this study of the upper photosynthetic zone of hypersaline microbial mats of Elkhorn Slough, California (USA), we show how reference-based and reference-free methods can be used to meaningfully assess microbial ecology and genetic partitioning in these complex microbial systems. Mapping of metagenome reads to the dominant Cyanobacteria observed in the system, Coleofasciculus (Microcoleus) chthonoplastes, was used to examine strain variants within these metagenomes. Highly conserved gene subsystems indicate a core genome for the species, and a number of variant genes and subsystems suggest strain level differentiation, especially for carbohydrate utilization. Metagenome sequence coverage binning was used to assess ecosystem partitioning of remaining microbes. Functional gene annotation of these bins (primarily of Proteobacteria, Bacteroidetes, and Cyanobacteria) recapitulated the known biogeochemical functions in microbial mats using a genetic basis, and also revealed evidence of novel functional diversity within the Gemmatimonadetes and Gammaproteobacteria. Combined, these two approaches show how genetic partitioning can inform biogeochemical partitioning of the metabolic diversity within microbial ecosystems.

microbiology↗
bioRxiv2017

Widespread Negative Frequency-Dependent Selection Maintains Diversity in the Legume-Rhizobia Symbiosis: Balancing nodulation may explain the paradox of rhizobium diversity

The evolutionary origin and ecological maintenance of biodiversity is a central problem in biology. For diversity to be stable through time, each genotype or species must have an advantage when rare. This negative frequency-dependence prevents deterministic extinction and mitigates the stochastic loss of diversity (1-4). However, models of mutualism typically generate positive frequency-dependence that reduces diversity (5-8). Here, we report empirical evidence for negative frequency-dependence in the legume-rhizobium mutualism within a single host generation, a phenomenon that we term balancing nodulation. Balancing nodulation increases rare rhizobia across all 13 legume genera investigated to date, at high and low inoculum densities, and with minimal genetic differentiation between rhizobia strains. While the mechanism generating this phenomenon is currently unknown, balancing nodulation could actively maintain variation in the rhizobia-legume symbiosis.

plant biology↗
bioRxiv2017

150 million years of sustained increase in pterosaur flight efficiency

The long-term accumulation of biodiversity has been punctuated by remarkable evolutionary transitions that allowed organisms to exploit new ecological opportunities, and often resulted in large radiations of species. The Mesozoic flying reptiles - pterosaurs - which dominated the skies for over 150 million years (Myr), were the product of such a transition. The ancestors of pterosaurs were small and likely bipedal early archosaurs, which were certainly well adapted to terrestrial locomotion. More than 220 Myr ago, at some point in the Triassic, pterosaurs took flight and subsequently appear to have become capable and efficient flyers. However, the evolutionary processes that led to this efficiency remain enigmatic. Given the lack of proto-pterosaurs it is difficult to study how flight first evolved in this group, but we can test hypotheses about evolutionary changes to the energetics of locomotion following the transition to flight. Early pterosaurs were challenged by the c ...

evolutionary biology↗
bioRxiv2017

Genome-wide population diversity in Hymenoscyphus fraxineus points to an eastern Russian origin of European Ash dieback.

European forests are experiencing extensive invasion from the Ash pathogen Hymenoscyphus fraxineus, an ecological niche competitor to the non-pathogenic native congener H. albidus. We report the genome-wide diversity and population structure in Asia (native) and Europe (the introduced range). We show H. fraxineus underwent a dramatic bottleneck upon introduction to Europe around 30-40 generations ago, leaving a genomic signature, characterized by long segments of fixation, interspersed with \"diversity islands\" that are identical throughout Europe. This means no effective secondary contact with other populations has occurred. Genome-wide variation is consistently high within sampled locations in Japan and the Russian Far East, and lack of differentiation amongst Russian locations suggests extensive gene flow, similar to Europe. A local ancestry analysis supports Russia as a more likely source population than Japan. Negligible latency, rapid host-range expansion and viability of small founding populations specify strong biosecurity forewarnings against new introductions from outside Europe.

genomics↗
bioRxiv2017

The Molecular Genetic Basis of Herbivory between Butterflies and their Host-Plants

Interactions between herbivorous insects and their host-plants are a central component of terrestrial food webs and a critical topic in agriculture, where a substantial fraction of potential crop yield is lost annually to pests. Important insights into plant-insect interactions have come from research on specific plant defenses and insect detoxification mechanisms. Yet, much remains unknown about the molecular mechanisms that mediate plant-insect interactions. Here we use multiple genome-wide approaches to map the molecular basis of herbivory from both plant and insect perspectives, focusing on butterflies and their larval host-plants. Parallel genome-wide association studies in the Cabbage White butterfly, Pieris rapae, and its host-plant, Arabidopsis thaliana, pinpointed a small number of butterfly and plant genes that influenced herbivory. These genes, along with much of the genome, were regulated in a dynamic way over the time course of the feeding interaction. Comparative analyses, including diverse butterfly/plant systems, showed a variety of genome-wide responses to herbivory, yet a core set of highly conserved genes in butterflies as well as their host-plants. These results greatly expand our understanding of the genomic causes and evolutionary consequences of ecological interactions across two of Natures most diverse taxa, butterflies and flowering plants.

genomics↗
bioRxiv2017

The genetic basis and evolution of red blood cell sickling in deer

Crescent-shaped red blood cells, the hallmark of sickle cell disease, present a striking departure from the biconcave disc shape normally found in mammals. Characterized by increased mechanical fragility, sickled cells promote haemolytic anaemia and vaso-occlusions and contribute directly to disease in humans. Remarkably, a similar sickle-shaped morphology has been observed in erythrocytes from several deer species, without pathological consequences. The genetic basis of erythrocyte sickling in deer, however, remains unknown, limiting the utility of deer as comparative models for sickling. Here, we determine the sequences of human {beta}-globin orthologs in 15 deer species and identify a set of co-evolving, structurally related residues that distinguish sickling from non-sickling deer. Protein structural modelling indicates a sickling mechanism distinct from human sickle cell disease, coordinated by a derived valine (E22V) in the second alpha helix of the {beta}-globin protein. The evolutionary history of deer {beta}-globins is characterized by incomplete lineage sorting, episodes of gene conversion between adult and foetal {beta}-globin paralogs, and the presence of a trans-species polymorphism that is best explained by long-term balancing selection, suggesting that sickling in deer is adaptive. Our results reveal structural and evolutionary parallels and differences in erythrocyte sickling between human and deer, with implications for understanding the ecological regimes and molecular architectures that favour the evolution of this dramatic change in erythrocyte shape.

evolutionary biology↗
bioRxiv2017

Unravelling the genomic basis and evolution of the pea aphid male wing dimorphism

Wing dimorphisms have long served as models for examining the ecological and evolutionary tradeoffs associated with alternative morphologies [1], yet the mechanistic basis of morph determination remains largely unknown. Here we investigate the genetic basis of the pea aphid (Acyrthosiphon pisum) wing dimorphism, wherein males exhibit one of two alternative morphologies that differ dramatically in a set of correlated traits that inclused the presence or absence of wings [2-4]. Unlike the environmentally-induced asexual female aphid wing polyphenism [5], the male wing polymorphism is genetically determined by a single uncharacterized locus on the X chromosome called aphicarus (\"aphid\" plus \"Icarus\", api) [6, 7]. Using recombination and association mapping, we localized api to a 130kb region of the pea aphid genome. No nonsynonymous variation in coding sequences strongly associated with the winged and wingless phenotypes, indicating that api is likely a regulatory change. Gene expression level profiling revealed an aphid-specific gene from the region expressed at higher levels in winged male embryos, coinciding with the expected stage of api action. Comparison of the api region across biotypes (pea aphid populations specialized to different host plants that began diverging ~16,000 years ago [8, 9]) revealed that the two alleles were likely present prior to biotype diversification. Moreover, we find evidence for a recent selective sweep of a wingless allele since the biotypes diversified. In sum, this study provides insight into how adaptive, complex traits evolve within and across natural populations.

evolutionary biology↗
bioRxiv2017

Genetic variants affecting plant size and chemical defenses jointly shape herbivory in Arabidopsis

Herbivorous insects exhibit strong feeding preferences when choosing among plant genotypes, yet experiments to map loci mediating plant susceptibility to herbivory rarely incorporate host choice. To address this gap, we applied genome-wide association (GWA) mapping to uncover genetic polymorphisms mediating damage from foraging insects (two populations of Scaptomyza flava) across a mixture of Arabidopsis thaliana genotypes in experimental enclosures. The effect of chemical defenses (glucosinolates) on herbivory depended on herbivore genotype. Unlike many studies that minimize the effects of host choice behavior, we also found a large effect of plant size on herbivory--likely through its effect on plant apparency--that was independent of herbivore genotype. These herbivory-associated loci are polymorphic at fine spatial scales, and thus have potential to shape variation in herbivory within natural populations. We also show that the polymorphism with the largest effect on herbivory underlies adaptive latitudinal variation in Arabidopsis plant size across Europe. Overall, our results provide genetic support for ecological observations that variation in both chemical defenses and non-canonical defense traits (e.g., plant size and phenology) jointly shapes plant-herbivore interactions.

plant biology↗
bioRxiv2017

Reinforcement learning over time: spaced versus massed training establishes stronger value associations

Over the past few decades, neuroscience research has illuminated the neural mechanisms supporting learning from reward feedback, demonstrating a critical role for the striatum and midbrain dopamine system. Learning paradigms are increasingly being extended to understand learning dysfunctions in mood and psychiatric disorders as well as addiction in the area of computational psychiatry. However, one potentially critical characteristic that this research ignores is the effect of time on learning: human feedback learning paradigms are conducted in a single rapidly paced session, while learning experiences in ecologically relevant circumstances and in animal research are almost always separated by longer periods of time. Event spacing is known to have strong positive effects on item memory across species and in reward learning in animals. Remarkably, the effect of spaced training on human reinforcement learning has not been investigated. In our experiments, we examined reward learning distributed across weeks vs. learning completed in a traditionally-paced or \"massed\" single session. Participants learned to make the best response for landscape stimuli that were either associated with a positive or negative value. In our first study, as expected, we found that after equal amounts of extensive training, accuracy was high and equivalent between the spaced and massed conditions. However, in a final online test 3 weeks later, we found that participants exhibited significantly greater memory for the value of spaced-trained stimuli. In our second study, our methods allowed for a direct comparison of maintenance of conditioning. We found that spaced training again had a beneficial effect: more than 87% of conditioning was maintained for spaced-trained stimuli, while only 30% was maintained for massed-trained stimuli. In addition, supporting a role for working memory in massed learning, across both studies we found a significant positive correlation between initial learning and working memory capacity. Our results indicate that single-session learning tasks may not lead to the kind of robust and lasting value associations that are characteristic of \"habitual\" value associations. Overall, these studies begin to address a large gap in our knowledge of fundamental processes of human reinforcement learning, with potentially broad implications for our understanding of learning in mood disorders and addiction.

neuroscience↗
bioRxiv2017

Small subsets of highly connected taxa predict compositional change in microbial communities

For decades, ecological theory has predicted that the complexity of communities should be related to their stability. However, this prediction has rarely been tested empirically, because of both the difficulty of finding suitable systems where the question is tractable and the trouble of defining \"stability\" in real systems. Microbial communities provide the opportunity to investigate a related question: how does community connectivity relate to the rate of compositional turnover? We used a newly developed metric called community \"cohesion\" to test how microbial community connectivity relates to Bray-Curtis dissimilarity through time. In three long-term datasets, we found that stronger connectivity corresponded to lower rates of compositional turnover. Using two case studies of disturbed and reference communities, we found that the predictive power of community connectivity was diminished by external disturbance. Finally, we tested whether the highly connected taxa were disproportionately important in explaining compositional turnover. We found that subsets of highly connected \"keystone\" taxa, generally comprising 1-5% of community richness, explained community turnover better than using all taxa. Our results suggest that stronger biotic interactions within microbial community dynamics are stabilizing to community composition, and that highly connected taxa are good indicators of pending community shifts.

microbiology↗
bioRxiv2017

Fixed effect variance and the estimation of the heritability: Issues and solutions

Linear mixed effects models are frequently used for estimating quantitative genetic parameters, including the heritability, of traits of interest. Heritability is an important metric, because it acts as a filter that determines how efficiently phenotypic selection translates into evolutionary change. As a quantity of biological interest, it is important that the denominator, the phenotypic variance, actually reflects the amount of phenotypic variance in the relevant ecological stetting. The current practice of quantifying heritability from mixed effects models frequently deprives the heritability of variance explained by fixed effects (often leading to upward-bias) and it has been suggested to omit fixed effects when estimating heritabilities. We advocate an alternative option of fitting complex models incorporating all relevant effects, while including the variance explained by fixed effects into the estimation of heritabilities. The approach is easily implemented (an example is provided) and allows corrections for the estimation of heritability, such as the exclusion of variance arising from experimental design effects while still including all biologically relevant sources of variation. We explore the complications arising depending on the nature of the covariates included as fixed effects (e.g. biological or experimental origin, characteristics of biological covariates). Furthermore, we discuss fixed effects in non-linear and generalized linear models when fixed effects. In these cases, the variance parameters depend on the location of the intercept and hence on the scaling of the fixed effects. Integration over the biologically relevant range of fixed effects offers a preferred solution in those situations.

evolutionary biology↗
bioRxiv2017

Dynamics of venom composition across a complex life cycle

Little is known about venom in young developmental stages of animals. The appearance of stinging cells in very early life stages of the sea anemone Nematostella vectensis suggests that toxins and venom are synthesized already in eggs, embryos and larvae of this species. Here we harness transcriptomic and biochemical tools as well as transgenesis to study venom production dynamics in Nematostella. We find that the venom composition and arsenal of toxin-producing cells change dramatically between developmental stages of this species. These findings might be explained by the vastly different ecology of the larva and adult polyp as sea anemones develop from a miniature non-feeding mobile planula to a much larger sessile polyp that predates on other animals. Further, the results suggest a much wider and dynamic venom landscape than initially appreciated in animals with a complex life cycle.

evolutionary biology↗
bioRxiv2017

DddY is a bacterial dimethylsulfoniopropionate lyase representing a new cupin enzyme superfamily with unknown primary function

Dimethylsulfide (DMS) is released at rates of >107 tons annually and plays a key role in the oceanic sulfur cycle and ecology. Marine bacteria, algae, and possibly other organisms, release DMS via cleavage of dimethylsulfoniopropionate (DMSP). Different genes encoding proteins with DMSP lyase activity are known belonging to different superfamilies and exhibiting highly variable levels of DMSP lyase activity. DddY shows the highest activity among all reported bacterial lyases yet is poorly characterized. Here, we describe the characterization of recombinant DddY is from different marine bacteria. We found that DddY activity demands a transition metal ion cofactor. DddY also shares two sequence motifs with other bacterial lyases assigned as cupin-like enzymes, DddQ, DddL, DddK, and DddW. These cupin motif residues are essential for DddY activity, as for the other cupin DMSP lyases, and all these enzymes are characterized by a common metal-chelator inhibitor (TPEN). Analysis of all sequences carrying these cupin motifs defined a superfamily: Cupin-DLL (DMSP lyases and lyase-like). The DMSP lyase families are sporadically distributed suggesting that DMSP lyases evolved within this superfamily independently along multiple lineages. However, the specific activity levels, genomic context analysis, and systematic profiling of substrate selectivity as described in the accompanying paper, indicate that for only some of these families, most distinctly DddY and DddL, DMSP lyase is the primary, native activity. In other families, foremost DddQ, DMSP lyase seems to be merely a promiscuous activity. The native function of DddQ, and of nearly all members of this newly identified Cupin-DLL superfamily, remains unknown.\n\nAbbreviations\n\nFundingFinancial support by the Estate of Mark Scher, and the Sasson & Marjorie Peress Philanthropic Fund, are gratefully acknowledged. D.S.T. is the Nella and Leon Benoziyo Professor of Biochemistry.

biochemistry↗
bioRxiv2017

Parallel use of a shared genomic island of speciation in clinal and mosaic hybrid zones between cryptic seahorse lineages

Diverging semi-isolated lineages either meet in narrow clinal hybrid zones, or have a mosaic distribution associated with environmental variation. Intrinsic reproductive isolation is often emphasized in the former and local adaptation in the latter, although both can contribute to isolation. Rarely these two patterns of spatial distribution are reported in the same study system. Here we report that the long-snouted seahorse Hippocampus guttulatus is subdivided into discrete panmictic entities by both types of hybrid zones. Along the European Atlantic coasts, a northern and a southern lineage meet in the southwest of France where they coexist in sympatry with little hybridization. In the Mediterranean Sea, two lineages have a mosaic distribution, associated with lagoon-like and marine habitats. A fifth lineage was identified in the Black Sea. Genetic homogeneity over large spatial scales contrasts with isolation maintained in sympatry or close parapatry at a fine scale. A high variation in locus-specific introgression rates provides additional evidence that partial reproductive isolation must be maintaining the divergence. Surprisingly, fixed differences between lagoon and marine populations in the Mediterranean Sea belong to the most differentiated SNPs between the two Atlantic lineages, against the genome-wide pattern of structure. These parallel outlier SNPs cluster on a single chromosome-wide island of differentiation. Since Atlantic lineages do not match the lagoon-sea habitat variation, genetic parallelism at the genomic island suggests a shared genetic barrier contributes to reproductive isolation in contrasting contexts -i.e. spatial vs. ecological. We discuss how a genomic hotspot of parallel differentiation could have evolved and become associated either with space or with a patchy environment in a single study system.

evolutionary biology↗
bioRxiv2017

Practical unidentifiability of a simple vector-borne disease model: implications for parameter estimation and intervention assessment

BackgroundMathematical modeling has an extensive history in vector-borne disease epidemiology, and is increasingly used for prediction, intervention design, and understanding mechanisms. Many of these studies rely on parameter estimation to link models and data, and to tailor predictions and counterfactuals to specific settings. However, few studies have formally evaluated whether vector-borne disease models can properly estimate the parameters of interest given the constraints of a particular dataset.\n\nMethodology/Principle FindingsIdentifiability methods allow us to examine whether model parameters can be estimated uniquely--a lack of consideration of such issues can result in misleading or incorrect parameter estimates and model predictions. Here, we evaluate both structural (theoretical) and practical identifiability of a commonly used compartmental model of mosquitoborne disease, using 2010 dengue epidemic in Taiwan as a case study. We show that while the model is structurally identifiable, it is practically unidentifiable under a range of human and mosquito time series measurement scenarios. In particular, the transmission parameters form a practically identifiable combination and thus cannot be estimated separately, which can lead to incorrect predictions of the effects of interventions. However, in spite of unidentifiability of the individual parameters, the basic reproduction number was successfully estimated across the unidentifiable parameter ranges. These identifiability issues can be resolved by directly measuring several additional human and mosquito life-cycle parameters both experimentally and in the field.\n\nConclusionsWhile we only consider the simplest case for the model, without explicit environmental drivers, we show that a commonly used model of vector-borne disease is unidentifiable from human and mosquito incidence data, making it difficult or impossible to estimate parameters or assess intervention strategies. This work illustrates the importance of examining identifiability when linking models with data to make predictions, and particularly highlights the importance of combining experimental, field, and case data if we are to successfully estimate epidemiological and ecological parameters using models.\n\nAuthor SummaryMathematical models have seen increasing use in understanding transmission processes, developing interventions, and predicting disease incidence and prevalence. Vector-borne diseases in particular present both a challenge and an opportunity for modeling, due to the complex interactions between host and vector species. A key step in many of these studies is connecting transmission models with data to infer parameters and make useful predictions, which requires careful consideration of identifiability and uncertainty of the model parameters. Whether due to intrinsic limitations of the model structure, or practical limitations of the data collected, is common that many different parameter values may yield the same or very similar fits to the data, making it impossible to successfully estimate the parameters. This issue of parameter unidentifiability can have broad implications for our ability to draw conclusions from mechanistic models--in some cases making it difficult or impossible to generate specific predictions, forecasts, or parameter estimates from a given model and data. Here, we evaluate these questions for a commonly-used model of vectorborne disease, examining how parameter uncertainty and unidentifiability can affect intervention predictions, estimation of the basic reproduction number, and other public health conclusions drawn from the model.

epidemiology↗
bioRxiv2017

DNA barcoding British Euphrasia reveals deeply divergent polyploids but lack of species-level resolution

Background and aimsDNA barcoding is emerging as a useful tool not only for species identification but for studying evolutionary and ecological processes. Although plant DNA barcodes do not always provide species-level resolution, the generation of large DNA barcode datasets can provide insights into the mechanisms underlying the generation of species diversity. Here, we use DNA barcoding to study evolutionary processes in taxonomically complex British Euphrasia, a group with multiple ploidy levels, frequent self- fertilization, young species divergence and widespread hybridisation.\n\nMethodsWe sequenced the core plant barcoding loci, supplemented with additional nuclear and plastid loci, in representatives of all 19 British Euphrasia species. We analyse these data in a population genetic and phylogenetic framework. We then date the divergence of haplotypes in a global Euphrasia dataset using a time-calibrated Bayesian approach implemented in BEAST.\n\nKey resultsNo Euphrasia species has a consistent diagnostic haplotype. Instead, haplotypes are either widespread across species, or are population specific. Nuclear genetic variation is strongly partitioned by ploidy levels, with diploid and tetraploid British Euphrasia possessing deeply divergent ITS haplotypes (DXY = 5.1%), with haplotype divergence corresponding to the late Miocene. In contrast, plastid data show no clear division by ploidy, and instead reveal weakly supported geographic patterns.\n\nConclusionsUsing standard DNA barcoding loci for species identification in Euphrasia will be unsuccessful. However, these loci provide key insights into the maintenance of genetic variation, with divergence of diploids and tetraploids suggesting that ploidy differences act as a barrier to gene exchange in British Euphrasia, with rampant hybridisation within ploidy levels. The scarcity of shared diploid-tetraploid ITS haplotypes supports the polyploids being allotetraploid in origin. Overall, these results show that even when lacking species-level resolution, DNA barcoding can reveal insightful evolutionary patterns in taxonomically complex genera.

evolutionary biology↗
bioRxiv2017

Resilience mechanisms of small intestinal lactobacilli to the toxicity of soybean oil fatty acids

Over the past century, soybean oil (SBO) consumption in the United States increased dramatically. The main SBO fatty acid, linoleic acid (18:2), inhibits in vitro the growth of lactobacilli, beneficial members of the small intestinal microbiota. Human-associated lactobacilli have declined in prevalence in Western microbiomes, but how dietary changes may have impacted their ecology is unclear. Here, we compared the in vitro and in vivo effects of 18:2 on Lactobacillus reuteri and L. johnsonii. Directed evolution in vitro in both species led to strong 18:2 resistance with mutations in genes for lipid biosynthesis, acid stress, and the cell membrane or wall. Small-intestinal Lactobacillus populations in mice were unaffected by chronic and acute 18:2 exposure, yet harbored both 18:2- sensitive and resistant strains. This work shows that extant small intestinal lactobacilli are protected from toxic dietary components via the gut environment as well as their own capacity to evolve resistance.

microbiology↗