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bioRxiv2018

Daphnia stressor database: Taking advantage of a decade of Daphnia ‘-omics’ data for gene annotation

Gene expression patterns help to measure and characterize the effect of environmental perturbations at the cellular and organism-level. Complicating interpretation is the presence of uncharacterized or \"hypothetical\" gene functions for a large percentage of genomes. This is particularly evident in Daphnia genomes, which contains many regions coding for \"hypothetical proteins\" and are significantly divergent from many of the available arthropod model species, but might be ecologically important. In the present study, we developed a gene expression database, the Daphnia stressor database (http://www.daphnia-stressordb.uni-hamburg.de/dsdbstart.php), built from 90 published studies on Daphnia gene expression. Using a comparative genomics approach, we used the database to annotate D. galeata transcripts. The extensive body of literature available for Daphnia species allowed to associate stressors with gene expression patterns. We believe that our stressor based annotation strategy allows for better understanding and interpretation of the functional role of the understudied hypothetical or uncharacterized Daphnia genes, thereby increasing our understanding of Daphnias genetic and phenotypic variability.

genomics↗

bioRxiv2018

Standardization and validation of a panel of cross-species microsatellites to individually identify the Asiatic wild dog (Cuon alpinus): implications in population estimation and dynamics

BackgroundThe Asiatic wild dog or dhole (Cuon alpinus) is a highly elusive, monophyletic, forest dwelling, social canid distributed across south and Southeast Asia. Severe pressures from habitat loss, prey depletion, disease, human persecution and interspecific competition resulted in global population decline in dholes. Despite a declining population trend, detailed information on population size, ecology, demography and genetics is lacking. Generating reliable information and landscape level for dholes is challenging due to their secretive behaviour and monomorphic physical features. Recent advances in non-invasive DNA-based tools can be used to monitor populations and individuals across large landscapes. In this paper, we describe standardization and validation of faecal DNA-based methods for individual identification of dholes. We tested this method on field-collected dhole faeces in four tiger reserves of the central Indian landscape in the state of Maharashtra, India. Further, we conducted preliminary analyses of dhole population structure and demography in the study area.\n\nResultsWe tested a total of 18 cross-species markers and developed a panel of 12 markers for unambiguous individual identification of dholes. This marker panel identified 101 unique individuals from faecal samples collected across our pilot field study area. These loci showed varied level of amplification success (57-88%), polymorphism (3-9 alleles), heterozygosity (0.23-0.63) and produced a cumulative probability of identity (unbiased) and probability of identity (sibs) value of 4.7x10-10 and 1.5x10-4, respectively. Our preliminary analyses of population structure indicated four genetic subpopulations in dholes. Qualitative analyses of population demography show signal of population decline.\n\nConclusionOur results demonstrated that the selected panel of 12 microsatellite loci can conclusively identify dholes from poor quality, non-invasive biological samples and help in exploring various population parameters. Our methods can be used to estimate dhole populations and assess population trends for this elusive, social carnivore.

genetics↗

bioRxiv2018

Enhanced plasticity of programmed DNA elimination boosts adaptive potential in suboptimal environments

The impact of ecological changes on the development of new somatic genomes has thus far been neglected. This oversight yields an incomplete understanding of the mechanisms that underlie environmental adaptation and can be tackled leveraging the biological properties of ciliates. When Paramecium reproduces sexually, its polyploid somatic genome regenerates from the germline genome via a developmental process, Programmed DNA elimination (PDE), that involves the removal of thousands of ORF-interrupting germline sequences. Here, we demonstrate that exposure to sub-optimal temperatures impacts PDE efficiency, prompting the emergence of hundreds of alternative DNA splicing variants that dually embody cryptic (germline) variation and de novo induced (somatic) mutations. In contrast to trivial biological errors, many of these alternative DNA isoforms display a patterned genomic topography, are epigenetically controlled, inherited trans-somatically, and under purifying selection. Developmental thermoplasticity in Paramecium is a likely source of evolutionary innovation.

evolutionary biology↗

bioRxiv2018

Transduction of the Geomagnetic Field as Evidenced from Alpha-band Activity in the Human Brain

Magnetoreception, the perception of the geomagnetic field, is a sensory modality well-established across all major groups of vertebrates and some invertebrates, but its presence in humans has been tested rarely, yielding inconclusive results. We report here a strong, specific human brain response to ecologically-relevant rotations of Earth-strength magnetic fields. Following geomagnetic stimulation, a drop in amplitude of EEG alpha oscillations (8-13 Hz) occurred in a repeatable manner. Termed alpha event-related desynchronization (alpha-ERD), such a response is associated with sensory and cognitive processing of external stimuli. Biophysical tests showed that the neural response was sensitive to the dynamic components and axial alignment of the field but also to the static components and polarity of the field. This pattern of results implicates ferromagnetism as the biophysical basis for the sensory transduction and provides a basis to start the behavioral exploration of human magnetoreception.

biophysics↗

bioRxiv2018

ElectroPen: An ultralow-cost piezoelectric electroporator

Electroporation is a basic yet powerful method for delivering small molecules (RNA, DNA, drugs) across cell membranes by application of an electrical field. Due to its vital role, electroporation has wide applicability from genetically engineering cells, to drug- and DNA-based vaccine delivery. Despite its broad applications in biological research, the high cost of electroporators is an obstacle for many budget-conscious laboratories. To address this need, we describe a simple, inexpensive, and hand-held electroporator inspired by a common household piezoelectric gas lighter. The proposed \"ElectroPen\" device costs about 20 cents, is portable (13 g), is fabricated on-demand using 3D-printing, and delivers repeatable exponentially decaying pulses of about 2000 V in 5 ms. We provide a proof-of-concept demonstration by genetically transforming plasmids into E. coli strains and show comparable transformation efficiency and cell growth with commercial devices, but at a fraction of the cost. Our results are validated by an independent team across the globe, providing a real-world example of democratizing science through frugal tools. Thus, the simplicity, accessibility, and affordability of our device holds potential for making modern synthetic biology accessible in high-school, community, and field-ecology laboratories.

bioengineering↗

bioRxiv2018

Novel diversity within marine Mamiellophyceae (Chlorophyta) unveiled by metabarcoding

The Ocean Sampling Day (OSD) project provided metabarcoding data for the V4 hyper-variable regions of the 18S rRNA gene from 157 samples collected at 143 mostly coastal stations. In this paper we focus on the class Mamiellophyceae, which was found at nearly all OSD stations and represented 55 % of the green microalgae (Chlorophyta) reads in the 2014 OSD dataset. We performed phylogenetic analyses of unique OSD metabarcodes (ASV, amplicon single variants) and reference GenBank sequences from cultures and from the environment, focusing on the four most represented genera: Ostreococcus (45 % of the Mamiellophyceae reads), Micromonas (34 %), Bathycoccus (10 %) and Mantoniella (8.7 %). These analyses uncovered novel diversity within each genus except Bathycoccus. In Ostreococcus, a new clade (E) with 2 very clear base pair differences compared to the oceanic clade B in the V4 region was the second most represented clade after the coastal Ostreococcus \"lucimarinus\". Within Micromonas, ten clades were found exceeding the 4 species and 2 candidate species already described. Finally, we found 2 new environmental clades of Mantoniella. Each Mamiellophyceae clade had a specific distribution in the OSD dataset suggesting that they are adapted to different ecological niches.

microbiology↗

bioRxiv2018

A Versatile Rapture (RAD-Capture) Platform for Genotyping Marine Turtles

Advances in high-throughput sequencing (HTS) technologies coupled with increased interdisciplinary collaboration is rapidly expanding capacity in the scope and scale of wildlife genetic studies. While existing HTS methods can be directly applied to address some evolutionary and ecological questions, certain research goals necessitate tailoring methods to specific study organisms, such as high-throughput genotyping of the same loci that are comparable over large spatial and temporal scales. These needs are particularly common for studies of highly mobile species of conservation concern like marine turtles, where life history traits, limited financial resources and other constraints require affordable, adaptable methods for HTS genotyping to meet a variety of study goals. Here, we present a versatile marine turtle HTS targeted enrichment platform adapted from the recently developed Rapture (RAD-Capture) method specifically designed to meet these research needs. Our results demonstrate consistent enrichment of targeted regions throughout the genome and discovery of candidate variants in all species examined for use in various conservation genetics applications. Accurate species identification confirmed the ability of our platform to genotype over 1,000 multiplexed samples, and identified areas for future methodological improvement such as optimization for low initial concentration samples. Finally, analyses within green turtles supported the ability of this platform to identify informative SNPs for stock structure, population assignment and other applications over a broad geographic range of interest to management. This platform provides an additional tool for marine turtle genetic studies and broadens capacity for future large-scale initiatives such as collaborative global marine turtle genetic databases.

genomics↗

bioRxiv2018

Production of glycine-derived ammonia as a low-cost and long-distance antibiotic strategy by Streptomyces

Soil-inhabiting streptomycetes are Natures medicine makers, producing over half of all known antibiotics and many other bioactive natural products. However, these bacteria also produce many volatile compounds, and research into these molecules and their role in soil ecology is rapidly gaining momentum. Here we show that streptomycetes have the ability to kill bacteria over long distances via air-borne antibiosis. Our research shows that streptomycetes do so by producing surprisingly high amounts of the low-cost volatile antimicrobial ammonia, which travels over long distances and antagonises both Gram-positive and Gram-negative bacteria. Glycine is required as precursor to produce ammonia, and inactivation of the glycine cleavage system annihilated air-borne antibiosis. As a resistance strategy, E. coli cells acquired mutations resulting in reduced expression of the porin master regulator OmpR and its cognate kinase EnvZ, which was just enough to allow them to survive. We further show that ammonia enhances the activity of the more costly canonical antibiotics, suggesting that streptomycetes adopt a low-cost strategy to sensitize competitors for antibiosis over longer distances.

microbiology↗

bioRxiv2018

Pinnularia baetica sp. nov. (Bacillarophyceae): a new diatom species found in an alkaline mountain lagoon in the south of Europe (Granada, Spain)

A new benthic freshwater diatom species belonging to the genus Pinnularia was found in Laguna Seca of Sierra Seca in the north of the province of Granada, Spain. Pinnularia baetica sp.nov. is proposed as a new species based on observations under light (LM) and scanning electron microscopy (SEM) and its special ecology typical of a calcareous lagoon. The most similar taxa to P. baetica is P. atlasii and with more differences P. infirma and the last two were studied through material obtained in lagoons of northern Morocco. Although there are similarities in the morphological characters of the frustule, it was possible to verify through LM and SEM micrographs, evident differences between P. baetica and the other two taxa; on the one end, P. baetica has a panduriform shape more pronounced than P. infirma and bigger size. On the other hand, the absence of spines in P. baetica and the more convergent striation at the poles are the main differences with P. atlasi.\n\nPhylum Ochrophyta Caval.-Sm. (Cavalier-Smith 1995)\n\nClass Bacillariophyceae Haeckel emend. Medlin & Kaczmarska (Medlin & Kaczmarska 2004)\n\nSubclass Bacillariophycidae Round (Round et al. 1990)\n\nOrder Naviculales (Bessey 1907 sensu emend)\n\nFamily Pinnulariaceae D.G. Mann, 1990, Genus Pinnularia C.G. Ehrenberg, 1843\n\nPinnularia baetica Fernandez Moreno & Sanchez Castillo sp. nov

plant biology↗

bioRxiv2018

Genetic transformation of the dinoflagellate chloroplast

Coral reefs are some of the most important and ecologically diverse marine environments. At the base of the reef ecosystem are dinoflagellate algae, living in symbiosis with coral. Efforts to understand the relationship between alga and coral have been greatly hampered by the lack of an appropriate dinoflagellate genetic transformation technology. By making use of the plasmid-like fragmented chloroplast genome, we have introduced novel genetic material into the dinoflagellate chloroplast genome. We have shown that the introduced genes are expressed and confer the expected phenotypes. Genetically modified cultures have been grown for five months with subculturing, maintaining the introduced genes and phenotypes. This indicates that cells continue to divide after transformation and that the transformation is stable.

genetics↗

bioRxiv2018

Stimulus domain transfer in recurrent models for large scale cortical population prediction on video

To better understand the representations in visual cortex, we need to generate better predictions of neural activity in awake animals presented with their ecological input: natural video. Despite recent advances in models for static images, models for predicting responses to natural video are scarce and standard linear-nonlinear models perform poorly. We developed a new deep recurrent network architecture that predicts inferred spiking activity of thousands of mouse V1 neurons simulta-neously recorded with two-photon microscopy, while accounting for confounding factors such as the animals gaze position and brain state changes related to running state and pupil dilation. Powerful system identification models provide an opportunity to gain insight into cortical functions through in silico experiments that can subsequently be tested in the brain. However, in many cases this approach requires that the model is able to generalize to stimulus statistics that it was not trained on, such as band-limited noise and other parameterized stimuli. We investigated these domain transfer properties in our model and find that our model trained on natural images is able to correctly predict the orientation tuning of neurons in responses to artificial noise stimuli. Finally, we show that we can fully generalize from movies to noise and maintain high predictive performance on both stimulus domains by fine-tuning only the final layers weights on a network otherwise trained on natural movies. The converse, however, is not true.

neuroscience↗

bioRxiv2018

Genomic differentiation is initiated without physical linkage among targets of divergent selection in Fall armyworms

The process of speciation involves whole genome differentiation by overcoming gene flow between diverging populations. We have ample knowledge which evolutionary forces may cause genomic differentiation, and several speciation models have been proposed to explain the transition from genetic to genomic differentiation. However, it is still unclear what are critical conditions enabling genomic differentiation in nature. The Fall armyworm, Spodoptera frugiperda, is observed as two sympatric strains that have different host-plant ranges, suggesting the possibility of ecological divergent selection. In our previous study, we observed that these two strains show genetic differentiation across the whole genome with an unprecedentedly low extent, suggesting the possibility that whole genome sequences started to be differentiated between the strains. In this study, we analyzed whole genome sequences from these two strains from Mississippi to identify critical evolutionary factors for genomic differentiation. The genomic Fst is low (0.017) while 91.3% of 10kb windows have Fst greater than 0, suggesting genome-wide differentiation with a low extent. We identified nearly 400 outliers of genetic differentiation between strains, and found that physical linkage among these outliers is not a primary cause of genomic differentiation. Fst is not significantly correlated with gene density, a proxy for the strength of selection, suggesting that a genomic reduction in migration rate dominates the extent of local genetic differentiation. Our analyses reveal that divergent selection alone is sufficient to generate genomic differentiation, and any following diversifying factors may increase the level of genetic differentiation between diverging strains in the process of speciation.

evolutionary biology↗

bioRxiv2018

Bayesian learning ecosystem dynamics with delayed dependencies from incomplete multiple source data : an application to plant epidemiology

Ecosystem dynamics forecasting is central to major problems in ecology, society, and economy. The existing models serve as decision tools but their parameters valitity are usually not confronted to real data in a formalized approach. Dynamics bayesian network inference is promissing but limited when dealing with incomplete multiple source time series with delayed time dependencies. We propose here a temporal bayesian network with time delay and aproximate inference algorithm, to learn altogether cryptic ecosystem variables, missing data, and model parameters. The novelty in the approach is that it combines simulation-based and likelihood-based aproximate bayesian inference. The advantage of simulation based is that it allows to sample hidden processes. The advantage of likelihood based is that it provides a summary statistics that is really representing the model we are interested in. The ecosystem variables and the missing data are simulated from indicator variables using the probabilistic indicator-ecosystem model. The likelihood is estimated by averaging the probability of observed-simulated data over simulations, the parameter space is sampled with Metropolis Hasting algorithm. Another innovative proposition is to parametrize the network structure in order to learn model structure within a space provided by prior distribution. We apply to plant epidemiology.

epidemiology↗

bioRxiv2018

Computer vision and deep learning automates nocturnal rainforest ant tracking to provide insight into behavior and disease risk

Determining how ant colonies optimize foraging while mitigating disease risk provides insight into how the ants have achieved ecological success. Fungal infected cadavers surround the main foraging trails of the carpenter ant Camponotus rufipes, offering a system to study how foragers behave given the persistent occurrence of disease threats. Studies on social insect foraging behavior typically require many hours of human labor due to the high density of individuals. To overcome this, we developed deep learning based computer vision algorithms to track foraging ants, frame-by-frame, from video footage. We found foragers can be divided into behavioral categories based on how straight they walk across the trail. Eighty percent of ants walk directly across the trail, while 20% wander or circle when crossing the trail. Departure from the main trail encourages exploration of new areas and could enhance discovery of new food resources. Conversely, results from our agent-based model simulations suggest deviation from a straight path exposes foragers to more infectious fungal spores. Consistency in walking behavior may protect most ants from infection, while the foragers with increased exposure due to their mode of walking could be a sufficient number of new hosts to sustain disease in this environment.

animal behavior and cognition↗

bioRxiv2018

Increasing phylogenetic stochasticity at high elevations on summits across a remote North American wilderness

PREMISE OF THE STUDYAt the intersection of ecology and evolutionary biology, community phylogenetics can provide insights into overarching biodiversity patterns, particularly in remote and understudied ecosystems. To understand community assembly of the high-alpine flora of the Sawtooth National Forest, USA, we analyzed phylogenetic structure within and between nine summit communities.\n\nMETHODSWe used high-throughput sequencing to supplement existing data and infer a nearly completely sampled community phylogeny of the alpine vascular flora. We calculated mean nearest taxon distance (MNTD) and mean pairwise distance (MPD) to quantify phylogenetic divergence within summits, and assed how maximum elevation explains phylogenetic structure. To evaluate similarities between summits we quantified phylogenetic turnover, taking into consideration micro-habitats (talus vs. meadows).\n\nKEY RESULTSWe found different patterns of community phylogenetic structure within the six most species-rich orders, but across all vascular plants phylogenetic structure was largely no different from random. There was a significant negative correlation between elevation and tree-wide phylogenetic diversity (MPD) within summits: significant overdispersion degraded as elevation increased. Between summits we found high phylogenetic turnover, which was driven by greater niche heterogeneity on summits with alpine meadows.\n\nCONCLUSIONSThis study provides further evidence that stochastic processes shape the assembly of vascular plant communities in the high-alpine at regional scales. However, order-specific patterns suggest adaptations may be important for assembly of specific sectors of the plant tree of life. Further studies quantifying functional diversity will be important to disentangle the interplay of eco-evolutionary processes that likely shape broad community phylogenetic patterns in extreme environments.

evolutionary biology↗

bioRxiv2018

Bacteriophages dynamically modulate the gut microbiota and metabolome

The human gut microbiome is comprised of densely colonizing micro-organisms in dynamic interaction with each other and the host. While the bacterial component of the microbiome is under intense investigation, far less is known about how bacteriophages impact bacterial communities in the gut. We investigated the dynamic effects of phages on a model microbiome using gnotobiotic mice colonized by commensal bacteria that colonize the human infant gut, and found that phage predation not only directly impacts susceptible bacteria but also leads to cascading effects on other bacterial species via inter-bacterial interactions. Using metabolomic profiling, we also found that the shifts in the microbiome caused by phage predation have a direct consequence on the gut metabolome. Our work provides insight into the ecological importance of phages as modulators of bacterial colonization, and additionally suggests the potential impact of gut phages on the host with implications for the use of phages as therapeutic tools to rationally and precisely modulate the microbiome.

microbiology↗

bioRxiv2018

Venom Isosolenopsin A Delivers Rapid Knockdown of Fire Ant Competitors

Fire ant venoms are composed of insecticidal alkaloids named solenopsins. Whilst species-specific differences are reported, little attention was given to caste-specific venom adaptations. The venom of fire ants queens has remained poorly studied. Founding queens must succeed in isolation in the field, where venom is bound to play a role against competitor species. The venoms of fire ant queens are strikingly similar across different species, in being mainly composed of the alkaloid isosolenopsin A, regardless of the chemical diversity of the worker caste. From assuming this pattern as the evolutionary result of stabilising trait selection, we hypothesise a shared mechanism explaining the conserved venom composition among the fire ant queens of different species. Here we report that fire ant queen venom and its major compounds are much quicker to neutralise competitor ants than the more diverse venoms of workers. Three representative competitor ant species sympatric with invasive fire ants were selected, exposed on the head to venoms from invasive fire ant workers and queens of two main invasive species, Solenopsis invicta and S. geminata. The venom diversity in the worker caste of these species represent extremes in the chemical diversity of fire ants. Queen venoms delivers quicker knockdown of rival foragers than worker venoms. The effects are traced back to synthetic solenopsins demonstrating solenopsin A analogues are particularly efficient as contact neurotoxins. The observed effects are comparable to nicotine. Overall the venoms of S. invicta seem more lethal than of S. geminata, regardless of knockdown speed. We believe these are fundamental aspects in the chemical ecology of the invasive ants which have been long overlooked, and emphasise on the need for further studies into the venom biology of founding queens.

zoology↗

bioRxiv2018

Wood modification by furfuryl alcohol caused delayed decomposition response in Rhodonia (Postia) placenta

The aim of this study was to investigate differential expression profiles of the brown rot fungus Rhodonia placenta (previously Postia placenta) harvested at several time points when grown on Pinus radiata (radiata pine) and P. radiata with three different levels of modification by furfuryl alcohol, an environmentally benign commercial wood protection system. For the first time the entire gene expression pattern of a decay fungus is followed in untreated and modified wood from initial to advanced stages of decay. Results support the current model of a two-step decay mechanism, with an initial oxidative depolymerization followed by hydrolysis of cell-wall polysaccharides. The wood decay process is finished, and the fungus goes into starvation mode after five weeks when grown on unmodified P. radiata wood. The pattern of repression of oxidative processes and oxalate synthesis found in P. radiata at later stages of decay is not mirrored for the high furfurylation treatment. The high treatment level provided a more unpredictable expression pattern throughout the entire incubation period. Furfurylation does not seem to directly influence the expression of core plant cell wall hydrolyzing enzymes, as a delayed and prolonged, but similar pattern was observed in the P. radiata and the modified experiments. This indicates that the fungus starts a common decay process in the modified wood, but proceeds at a slower pace as access to the plant cell wall polysaccharides is restricted. This is further supported by the downregulation of hydrolytic enzymes for the high treatment level at the last harvest point (mass loss 14%). Moreover, the mass loss does not increase the last weeks. Collectively, this indicates a potential threshold for lower mass loss for highly modified wood.\n\nIMPORTANCEFungi are important decomposers of woody biomass in natural habitats. Investigation of the mechanisms employed by decay fungi in their attempt to degrade wood is important for both the basic scientific understanding of ecology and carbon cycling in nature, and for applied uses of woody materials. For wooden building materials long service life and carbon storage is essential, but decay fungi are responsible for massive losses of wood in service. Thus, optimizing durable wood products for the future are of major importance. In this study we have investigated the fungal genetic response to furfurylated wood, a commercial environmentally benign wood modification approach, that improves service life of wood in outdoor applications. Our results show that there is a delayed wood decay by the fungus as a response to furfurylated wood and new knowledge about the mechanisms behind the delay is provided.

genomics↗