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Search indexed bioRxiv preprints in genomics, neuroscience, cell biology and bioinformatics. Read source abstracts and check manuscript versions; preprints are not peer reviewed.

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bioRxiv2018

Microbial diversity and toxin risk in tropical freshwater reservoirs of Cape Verde

The Cape Verde islands are part of the African Sahelian arid belt that possesses an irregular rainy season between August and October. This erratic rain pattern has prompted the need for water reservoirs, now critical for the countrys sustainability. Worldwide, freshwater cyanobacterial blooms are increasing in frequency due to global climate change and eutrophication of water bodies, particularly in reservoirs. To date there have been no risk assessments of cyanobacterial toxin production in these man-made structures. We evaluated this potential risk using 16S rRNA gene amplicon sequencing and full metagenome sequencing in freshwater reservoirs of Cape Verde.\n\nOur analysis revealed the presence of several potentially toxic cyanobacterial genera in all sampled reservoirs (Poilao, Saquinho and Faveta). In Faveta Microcystis sp., a genus well known for toxin production and bloom-formation, dominated our samples, while a green algae of the genus Cryptomonas and Gammaproteobacteria dominated Saquinho and Poilao.\n\nTaking advantage of the dominance of Microcystis in the Faveta reservoir, we were able to reconstruct and assemble its genome, extracted from a metagenome of bulk DNA from Faveta water. We named it Microcystis cf. aeruginosa CV01, for which a phylogenetic analysis revealed to have a close relationship with other genomes from those taxa, as well as other continental African strains, suggesting geographical coherency. In addition, it revealed several clusters of known toxin-producing genes. This assessment of Cape Verdean freshwater microbial diversity and potential for toxin production reinforces the need to better understand the microbial ecology as a whole of water reservoirs on the rise.

microbiology↗
bioRxiv2018

Gene expression is stronger associated with behaviour than with age and fertility in ant workers

The ecological success of social insects is based on division of labour, not only between queens and workers, but also among workers. Whether a worker tends the brood or forages is strongly influenced by age, fertility and nutritional status, with brood carers being younger, more fecund and corpulent. Here, we experimentally disentangle behaviour from age and fertility in Temnothorax longispinosus ant workers and analyse how these parameters are linked to whole-body gene expression. Our transcriptome analysis reveals four times more genes associated with behaviour than with age and only few fertility-associated genes. Brood carers exhibited an upregulation of genes involved in lipid biosynthesis, whereas foragers invested in metabolism. Additional simulations revealed that the experimental disassociation of co-varying factors reduces transcriptomic noise, potentially explaining discrepancies between transcriptomic studies on worker behaviour in other social insects. Our study highlights the influence of nutritional status on task choice in ant workers.

evolutionary biology↗
bioRxiv2018

Quantifying genetic, environmental and individual stochastic variability in Plantago lanceolata

Predicting ecological and evolutionary population dynamics requires understanding how genetic and environmental parameters influence variation in survival and reproduction among individuals. However such a focus often neglects the stochastic events that individuals experience throughout their lives that also influence survival and reproduction. With an illustrative example, we quantify and illustrate the influence of such non-selective demographic variability on population dynamics using size-structured matrix models of an experimental population of Plantago lanceolata. Our analysis shows that variation in survival and reproduction among individuals explained by environment, genes, and their interaction was modest compared to the stochastic variation in lifespan and reproduction. We illustrate how expectations on population growth, based on expected lifetime reproduction and generation time, can be misleading when variance in reproduction among individuals of the same genotype (full sibs) was large. Such large within genotype variance can lower population growth, fitness. Our results accompany recent investigations that call for more focus on stochastic variation in survival and reproduction, rather than dismissal of this variation as uninformative noise.

evolutionary biology↗
bioRxiv2018

The contraction in inverted repeat regions in the complete plastome sequence of Cressa cretica L

Plastome studies have been the focus of research in plant molecular evolution and systematics. C. cretica L. (Convolvulaceae) is a halophyte, habitat in the ecologically challenged area with high salinity and drought. The complete physical map of plastome revealed that it is 141,419bp long, circular molecule. It contains typical quadripartite structure of large single copy region (LSC 94,808bp), small single copy region (SSC 32,527bp) separated by a pair of inverted repeat regions (IRs 7042bp). This plastome is compared with the complete plastomes of other members of Convolvulaceae showed notable distinctions. An exceptional shift in IRs to SC regions is experienced in C. cretica led to many genes shift in both SC regions and contraction in IRs. The size of IRs reduced to 2 to 4 times as compared to those of the Convolvulaceae members studied. The shifted IRs regions showed remarkable variation in nucleotides patterns. Further, the shift was from the IR boundaries and in between the IR regions led to segment IRs. It is concluded that the shift in IRs may be the strategic move for adaptation in the harsh environment.

genomics↗
bioRxiv2018

A bHLH-PAS protein regulates light-dependent rhythmic processes in the marine diatom Phaeodactylum tricornutum

Periodic light-dark cycles govern the timing of basic biological processes in organisms inhabiting land as well as the sea, where life evolved. Although prominent marine phytoplanktonic organisms such as diatoms show robust diurnal rhythms in growth, cell cycle and gene expression, the molecular foundations controlling these processes are still obscure. By exploring the regulatory landscape of diatom diurnal rhythms, we unveil the function of a Phaeodactylum tricornutum bHLH-PAS protein, PtbHLH1a, in the regulation of light-dependent diurnal rhythms. Peak expression of PtbHLH1a mRNA occurs toward the end of the light period and it adjusts to photoperiod changes. Ectopic over-expression of PtbHLH1a results in lines showing a phase shift in diurnal cell fluorescence, compared to the wild-type cells, and with altered cell cycle progression and gene expression. Reduced oscillations in gene expression are also observed in overexpression lines compared to wild-type in continuous darkness, showing that the regulation of rhythmicity by PtbHLH1a is not directly dependent on light inputs and cell division. PtbHLH1a homologs are widespread in diatom genomes which may indicate a common function in many species. This study adds new elements to understand diatom biology and ecology and offers new perspectives to elucidate timekeeping mechanisms in marine organisms belonging to a major, but underinvestigated branch of the tree of life.\n\nSIGNIFICANCE STATEMENTMost organisms experience diurnal light-dark changes and show rhythms of basic biological processes such that they occur at optimal times of the day. The ocean harbours a huge diversity of organisms showing light-dependent rhythms, but their molecular foundations are still largely unknown. In this study, we discover a novel protein, PtbHLH1a that regulates cell division, gene expression and the diurnal timing of these events in the marine diatom Phaedoactylum tricornutum. The identification of PtbHLH1a-like genes in many diatom species suggests a conserved function in diurnal rhythm regulation in the most species-rich group of algae in the ocean. This study unveils critical features of diatom biology and advances the field of marine rhythms and their environmental regulation.

molecular biology↗
bioRxiv2018

Pathogen susceptibility and fitness costs explain variation in immune priming across natural populations of flour beetles

In many insects, individuals primed with low doses of pathogens live longer after being exposed to the same pathogen later in life. Yet, our understanding of the evolutionary and ecological history of priming of immune response in natural insect populations is limited. Previous work demonstrated population-, sex- and- stage specific variation in the survival benefit of priming response in flour beetles (Tribolium castaneum) infected with their natural pathogen Bacillus thuringiensis. However, the evolutionary forces responsible for this natural variation remained unclear. Here, we tested whether the strength of the priming response (measured as the survival benefit after priming and subsequent infection relative to unprimed controls) was associated with multiple fitness parameters across 10 flour beetle populations. Our results suggest two major selective pressures that may explain the observed inter-population variation in priming: (A) Basal pathogen susceptibility - populations that were more susceptible to infection produced a stronger priming response, and (B) Reproductive success - populations where primed females produced more offspring had lower survival benefit, suggesting a trade-off between priming response and reproduction. Our work is the first empirical demonstration of multiple selective pressures that may govern the adaptive evolution of immune priming in the wild. We hope that this motivates further experiments to establish the role of pathogen-imposed selection and fitness costs in the evolution of priming in natural insect populations.

evolutionary biology↗
bioRxiv2018

Comparative demography elucidates the longevity of parasitic and symbiotic relationships.

Parasitic and symbiotic relationships govern vast nutrient and energy flows1,2, but controversy surrounds their longevity. Enduring relationships may engender parallel phylogenies among hosts and parasites3,4, but so may more ephemeral relationships when parasites disproportionately colonize related hosts5. When considering these relationships temporal durability, it would be useful to understand whether parasite and host populations have grown and contracted in concert. Here, we devised methods to compare demographic histories, derived from genomic data6. We used these methods to compare the historical growth of the agent of severe human malaria, Plasmodium falciparum, to human and primate histories7,8 and to that of their mosquito vector Anopheles gambiae9, thereby discerning long-term parallels and anthropogenic population explosions10,11. The growth history of Trichinella spiralis, a zoonotic parasite disseminated by swine domestication12,13, proved regionally-specific, paralleling distinctive growth histories for wild boar in Asia and Europe14. Parallel histories were inferred for an anemone and its algal symbiont (Aiptasia pallida15 and Symbiodinium minutum16). Concerted growth in potatoes and the agent of potato blight (Solanum tuberosum17 and Phytophthora infestans18) did not commence until the age of potato domestication, helping date the acquisition of this historically consequential fungal plant pathogen. Therefore, comparative historical demography provides a powerful new means by which to interrogate the history of myriad ecological relationships, enriching our understanding of their origins and durability.

evolutionary biology↗
bioRxiv2018

Prediction of Optimal Growth Temperature using only Genome Derived Features

Optimal growth temperature is a fundamental characteristic of all living organisms. Knowledge of this temperature is central to the study the organism, the thermal stability and temperature dependent activity of its genes, and the bioprospecting of its genome for thermally adapted proteins. While high throughput sequencing methods have dramatically increased the availability of genomic information, the growth temperatures of the source organisms are often unknown. This limits the study and technological application of these species and their genomes. Here, we present a novel method for the prediction of growth temperatures of prokaryotes using only genomic sequences. By applying the reverse ecology principle that an organisms genome includes identifiable adaptations to its native environment, we can predict a species optimal growth temperature with an accuracy of 4.69 {degrees}C root-mean-square error and a correlation coefficient of 0.908. The accuracy can be further improved for specific taxonomic clades or by excluding psychrophiles. This method provides a valuable tool for the rapid calculation of organism growth temperature when only the genome sequence is known.

bioinformatics↗
bioRxiv2018

Quantifying the unquantifiable: why Hymenoptera -- not Coleoptera -- is the most speciose animal order

BackgroundWe challenge the oft-repeated claim that the beetles (Coleoptera) are the most species-rich order of animals. Instead, we assert that another order of insects, the Hymenoptera, are more speciose, due in large part to the massively diverse but relatively poorly known parasitoid wasps. The idea that the beetles have more species than other orders is primarily based on their respective collection histories and the relative availability of taxonomic resources, which both disfavor parasitoid wasps. Though it is unreasonable to directly compare numbers of described species in each order, the ecology of parasitic wasps - specifically, their intimate interactions with their hosts - allows for estimation of relative richness. We present a simple logical model that shows how the specialization of many parasitic wasps on their hosts suggests few scenarios in which there would be more beetle species than parasitic wasp species. We couple this model with an accounting of what we call the \"genus-specific parasitoid-host ratio\" from four well-studied genera of insect hosts, a metric by which to generate extremely conservative estimates of the average number of parasitic wasp species attacking a given beetle or other insect host species. Synthesis of our model with data from real host systems suggests that the Hymenoptera may have 2.5 - 3.2x more species than the Coleoptera. While there are more described species of beetles than all other animals, the Hymenoptera are almost certainly the larger order.

zoology↗
bioRxiv2018

Fractionated follow-up chemotherapy delays the onset of resistance in bone metastatic prostate cancer

Prostate cancer to bone metastases are almost always lethal. This results from the ability of metastatic prostate cancer cells to co-opt bone remodeling leading to what is known as the vicious cycle. Understanding how tumor cells can disrupt bone homeostasis through their interactionswith the stroma and how metastatic tumors respond to treatment is key to the development of new treatments for what remains an incurable disease. Here we describe an evolutionary game theoretical model of both the homeostatic bone remodeling and its co-option by prostate cancer metastases. This model extends past the evolutionary aspects typically considered in game theoretical models by also including ecological factors such as the physical microenvironment of the bone. Our model recapitulates the current paradigm of the \"vicious cycle\" driving tumor growth and sheds light on the interactions of heterogeneous tumor cells with the bone microenvironment and treatment response. Our results show that resistant populations naturally become dominant in the metastases under conventional cytotoxic treatment and that novel schedules could be used to better control the tumor and the associated bone disease compared to the current standard of care. Specifically, we introduce fractionated follow up therapy - chemotherapy where dosage is administered initially in one solid block followed by alternating smaller doeses and holidays - and argue that it is better than either a continuous application or a periodic one. Furthermore, we also show that different regimens of chemotherapy can lead to different amounts of pathological bone that are known to correlate with poor quality of life for bone metastatic prostate cancer patients.

cancer biology↗
bioRxiv2018

Investigating established EEG parameter during real-world driving

In real life, behavior is influenced by dynamically changing contextual factors and is rarely limited to simple tasks and binary choices. For a meaningful interpretation of brain dynamics underlying more natural cognitive processing in active humans, ecologically valid test scenarios are essential. To understand whether brain dynamics in restricted artificial lab settings reflect the neural activity in complex natural environments, we systematically tested the eventrelated P300 in both settings. We developed an integrative approach comprising an initial P300-study in a highly controlled laboratory set-up and a subsequent validation within a realistic driving scenario. Using a simulated dialog with a speech-based input system, increased P300 amplitudes reflected processing of infrequent and incorrect auditory feedback events in both the laboratory setting and the real world setup. Environmental noise and movement-related activity in the car driving scenario led to higher data rejection rates but revealed no effect on signal-to-noise ratio in theta and alpha frequency band or the amplitudes of the event-related P300. Our results demonstrate the possibility to investigate cognitive functions like context updating in highly adverse driving scenarios and encourage the consideration of more realistic task settings in prospective brain imaging approaches.

neuroscience↗
bioRxiv2018

Foraging theory and the propensity to be obese: an alternative to thrift

The evolutionary origin of obesity is classically believed to be genetic or developmentally induced thrift, as an adaptation to ancestral feast and famine conditions. However, recently the thrift family of hypotheses have attracted serious criticism necessitating alternative thinking. Optimization of foraging behaviour is an important aspect of behavioural evolution. For a species evolved for optimizing nutritional benefits against predation or other foraging risks, reduction in foraging risk below a threshold dramatically increases the steady-state body weight. In modern life where feeding is detached from foraging, the behavioural regulation mechanisms are likely to fail resulting into escalation of adiposity. At a proximate level the signalling pathways for foraging optimization involve fear induced signal molecules in the brain including Cocaine and Amphetamine Regulated Transcript (CART) interacting with adiposity signals such as leptin. While leptin promotes the expression of the fear peptides, the fear peptides promote anorectic action of leptin. This interaction promotes foraging drive and risk tolerance when the stored energy is low and suppresses hunger and foraging drive when the perceived risk is high. The ecological model of foraging optimization and the molecular model of interaction of these peptides converge in the outcome that the steady state adiposity is an inverse square root function of foraging risk. The foraging optimization model is independent of thrift or insurance hypotheses, but not mutually exclusive. We review existing evidence and suggest testable predictions of the model. Understanding obesity simultaneously at proximate and ultimate levels is likely to suggest effective means to curb the obesity epidemic.

evolutionary biology↗
bioRxiv2018

EukRef: phylogenetic curation of ribosomal RNA to enhance understanding of eukaryotic diversity and distribution

Environmental sequencing has greatly expanded our knowledge of micro-eukaryotic diversity and ecology by revealing previously unknown lineages and their distribution. However, the value of these data is critically dependent on the quality of the reference databases used to assign an identity to environmental sequences. Existing databases contain errors, and struggle to keep pace with rapidly changing eukaryotic taxonomy, the influx of novel diversity, and computational challenges related to assembling the high-quality alignments and trees needed for accurate characterization of lineage diversity. EukRef (eukref.org) is a community driven initiative that addresses these challenges by bringing together taxonomists with expertise spanning the complete eukaryotic tree of life and microbial ecologists that actively use environmental sequencing data for the purpose of developing reliable reference databases across the diversity of microbial eukaryotes. EukRef organizes and facilitates rigorous sequence data mining and annotation by providing protocols, guidelines and tools to do so.

microbiology↗
bioRxiv2018

Binaural fusion involves weak interaural suppression

The brain combines sounds from the two ears, but what is the algorithm used to achieve this summation of signals? Here we combine psychophysical amplitude modulation discrimination and steady-state electroencephalography (EEG) data to investigate the architecture of binaural combination for amplitude-modulated tones. Discrimination thresholds followed a dipper shaped function of pedestal modulation depth, and were consistently lower for binaural than monaural presentation of modulated tones. The EEG responses were greater for binaural than monaural presentation of modulated tones, and when a masker was presented to one ear, it produced only weak suppression of the response to a signal presented to the other ear. Both data sets were well-fit by a computational model originally derived for visual signal combination, but with suppression between the two channels (ears) being much weaker than in binocular vision. We suggest that the distinct ecological constraints on vision and hearing can explain this difference, if it is assumed that the brain avoids over-representing sensory signals originating from a single object. These findings position our understanding of binaural summation in a broader context of work on sensory signal combination in the brain, and delineate the similarities and differences between vision and hearing.

neuroscience↗
bioRxiv2018

Karyotype-environment associations support a role for a chromosomal inversion in local adaptation among North American populations of the seaweed fly Coelopa frigida

Large chromosomal rearrangements are thought to facilitate adaptation to heterogeneous environments by limiting genomic recombination. Indeed, inversions have been implicated in adaptation along environmental clines and in ecotype specialisation. Here, we combine classical ecological studies and population genetics to investigate an inversion polymorphism previously documented in Europe among natural populations of the seaweed fly Coelopa frigida along a latitudinal cline in North America. We test if the inversion is present in North America and polymorphic, assess which environmental conditions modulate the inversion karyotype frequencies, and document the relationship between inversion karyotype and adult size. We sampled nearly 2,000 flies from 20 populations along several environmental gradients to quantify associations of inversion frequencies to heterogeneous environmental variables. Genotyping and phenotyping showed a widespread and conserved inversion polymorphism between Europe and America. Variation in inversion frequency was significantly associated with environmental factors, with parallel patterns between continents, indicating that the inversion may play a role in local adaptation. The three karyotypes of the inversion are differently favoured across micro-habitats and represent life-history strategies likely maintained by the collective action of several mechanisms of balancing selection. Our study adds to the mounting evidence that inversions are facilitators of adaptation and enhance within-species diversity.

evolutionary biology↗
bioRxiv2018

Testing the behavioral origins of novelty: did increased aggression lead to scale-eating in pupfishes?

How novelty evolves is still largely unknown. Environmental changes are often assumed to precede novelty; however, behavioral shifts may also play a role. Here, we examine whether a shift in aggression explains the origin of a novel scale-eating pupfish species (Cyprinodon desquamator) within an adaptive radiation on San Salvador Island, Bahamas. We compared aggression using behavioral and gene expression data across three sympatric species in the San Salvador radiation (generalist, snail-eating specialist, and scale-eating specialist), and additionally measured behavioral aggression in an outgroup generalist from North Carolina. Surprisingly, we found increased behavioral aggression and differential expression of aggression-related genes in both the scale-eating and snail-eating species. Furthermore, male scale-eaters and female snail-eaters showed the highest levels of aggression compared to other groups. Differential gene expression in each specialist during larval development also suggested sex-mediated differences in male-male aggression and maternal care. Ultimately, our data indicate that aggression is not unique to scale-eating specialists. Instead, selection may increase aggression in other contexts such as niche specialization, mate competition, or selection on other ecologically relevant traits, including jaw size. Indeed, some adaptive variants associated with oral jaw size in the San Salvador radiation occur in genetic pathways with pleiotropic effects on aggression.

evolutionary biology↗
bioRxiv2018

Strain-level diversity drives alternative community types in millimeter scale granular biofilms

Microbial communities are often highly diverse in their composition, both at the level of coarse-grained taxa such as genera as well as at the level of strains within species. This variability can be driven by both extrinsic factors like temperature, pH, etc., as well as by intrinsic ones, such as demographic fluctuations or ecological interactions. The relative contributions of these factors and the taxonomic level at which they influence community structure remain poorly understood, in part because of the difficulty of identifying true community replicates assembled under the same environmental parameters. Here, we address this problem using an activated granular sludge reactor in which millimeter scale biofilm granules represent true community replicates whose differences in composition are expected to be driven primarily by biotic factors. Using 142 shotgun metagenomes of single biofilm granules we found that, at the commonly used genuslevel resolution, community replicates varied much more in their composition than would be expected from neutral assembly processes. This variation, however, did not translate into any clear partitioning into discrete community types, i.e. the equivalent of enterotypes in the human gut. However, a strong partition into community types did emerge at the strain level for the most abundant organism: strains of Candidatus Accumulibacter that coexisted in the metacommunity--i.e. the reactor--excluded each other within community replicates. Single-granule communities maintained a significant lineage structure, whereby the strain phylogeny of Accumulibacter correlated with the overall species composition of the community, indicating high potential for co-diversification among species and communities. Our results suggest that due to the high functional redundancy and competition between close relatives, alternative community types are most likely observed at the level of recently differentiated genotypes but not higher orders of genetic resolution.

microbiology↗
bioRxiv2018

The contribution of mitochondrial metagenomics to largescale data mining and phylogenetic analysis of Coleoptera

A phylogenetic tree at the species level is still far off for highly diverse insect orders, including the Coleoptera, but the taxonomic breadth of public sequence databases is growing. In addition, new types of data may contribute to increasing taxon coverage, such as metagenomic shotgun sequencing for assembly of mitogenomes from bulk specimen samples. The current study explores the application of these techniques for large-scale efforts to build the tree of Coleoptera. We used shotgun data from 17 different ecological and taxonomic datasets (5 unpublished) to assemble a total of 1942 mitogenome contigs of >3000 bp. These sequences were combined into a single dataset together with all mitochondrial data available at GenBank, in addition to nuclear markers widely used in molecular phylogenetics. The resulting matrix of nearly 16000 species with two or more loci produced trees (RAxML) showing overall congruence with the Linnaean taxonomy at hierarchical levels from suborders to genera. We tested the role of full-length mitogenomes in stabilizing the tree from GenBank data, as mitogenomes might link terminals with non-overlapping gene representation. However, the mitogenome data were only partly useful in this respect, presumably because of the purely automated approach to assembly and gene delimitation, but improvements in future may be possible by using multiple assemblers and manual curation. In conclusion, the combination of data mining and metagenomic sequencing of bulk samples provided the largest phylogenetic tree of Coleoptera to date, which represents a summary of existing phylogenetic knowledge and a defensible tree of great utility, in particular for studies at the intra-familial level, despite some shortcomings for resolving basal nodes.

evolutionary biology↗