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bioRxiv2017

An analytical framework to understand regulatory novelty accompanying allopolyploidization

Allopolyploidy is a prevalent process in plants, having important physiological, ecological, and evolutionary consequences. Massive, genome-wide transcriptomic rewiring in response to genomic merger and doubling has been demonstrated in many allopolyploid systems, encompassing a diversity of phenomena, including homoeolog expression bias, genome dominance, expression-level dominance, and revamping of co-expression networks. Here we present an analytical framework to reconcile these patterns of regulatory novelty as governed by distinct sets of intra- and inter-subgenome cis-trans relationships. This approach is a novel extension of classic allele-specific expression analysis to incorporate and distinguish the separate effects of parental regulatory interactions as well as further complications at the allopolyploid level. We demonstrated that the cis-trans framework devised not only offers new perspective on disentangling genetic from epigenetic and higher-order effects that impact gene expression, but also provides the conceptual basis and tools to unify recently presented models for both genome-wide expression dominance and biased fractionation in allopolyploids.

evolutionary biology↗

bioRxiv2017

Equality between the sexes in plants for costs of reproduction; evidence from the dioecious Cape genus Leucadendron (Proteaceae)

It has been argued that sexual allocation is greater for female function than male function in plants in general and specifically for the large dioecious Cape genus Leucadendron. Here, we use new interpretations of published information to support the hypothesis of equality between sexes in this genus. The explanations are based on the fire ecology of the Cape that results in reproductive synchrony, reproductive doubling and competitive symmetry. Firstly, strict post-fire seedling establishment of the reseeder life-history in the Cape results in single-aged populations. Consequently, the reproductive and vegetative schedules of males must synchronously track that of females. This implies equal allocation to sex. Secondly, after fires, dioecious females have double the seedling to adult ratio of co-occurring hermaphrodites. This indicates that being liberated from male function allows females access to resources that double their fitness compared to hermaphrodites. Therefore, male and female costs of reproduction are equal in hermaphrodites. Thirdly, competitive symmetry must occur because males and female plants will frequently encounter each other as close near neighbours. Competitive asymmetry would both reduce mating opportunities and skew local sex ratios. The evidence to date is for 1:1 sex ratios in small plots and this indicates competitive symmetry and a lack of dimorphic niches. Finally, vegetatively dimorphic species must also allocate equally to sex, or else sexual asynchrony, lack of reproductive doubling or competitive asymmetry will occur.

evolutionary biology↗

bioRxiv2017

Testing the Efforts Model of Simultaneous Interpreting: An ERP Study

We utilized the event-related potential (ERP) technique to study neural activity associated with different levels of working memory (WM) load during simultaneous interpretation (SI) in an ecologically valid setting. The amplitude of N1 and P1 components elicited by task-irrelevant tone probes was significantly modulated as a function of WM load but not the direction of interpretation. Furthermore, the latency of the N1 increased insignificantly with WM load. The P1 latency, however, mostly did not depend on either WM load or direction of interpretation. Larger negativity under lower WM loads suggests deeper processing of the auditory stimuli, providing tentative electrophysiological evidence in support of the Efforts Model of SI. Relationships between the direction of interpretation and median WM load are also discussed.

neuroscience↗

bioRxiv2017

Evolutionary dynamics of mycorrhizal symbiosis in land plant diversification

Mycorrhizal symbiosis between soil fungi and land plants is one of the most widespread and ecologically important mutualisms on earth. It has long been hypothesized that the Glomeromycotina, the mycorrhizal symbionts of the majority of plants, facilitated colonization of land by plants in the Ordovician. This view was recently challenged by the discovery of mycorrhizal associations with Mucoromycotina in several early diverging lineages of land plants. Utilizing a large, species-level database of plants mycorrhizal associations and a Bayesian approach to state transition dynamics we here show that the recruitment of Mucoromycotina is the best supported transition from a non-mycorrhizal state. We further found that transitions between different combinations of either or both of Mucoromycotina and Glomeromycotina occur at high rates and found similar promiscuity among combinations that include either or both of Glomeromycotina and Ascomycota with a nearly fixed association with Basidiomycota. Our results demonstrate that under the most likely scenario symbiosis with Mucoromycotina enabled the establishment of early land plants.

evolutionary biology↗

bioRxiv2017

The Hallucination Machine: A Deep-Dream VR platform for Studying the Phenomenology of Visual Hallucinations

Altered states of consciousness, such as psychotic or pharmacologically-induced hallucinations, provide a unique opportunity to examine the mechanisms underlying conscious perception. However, the phenomenological properties of these states are difficult to isolate experimentally from other, more general physiological and cognitive effects of psychoactive substances or psychopathological conditions. Thus, simulating phenomenological aspects of altered states in the absence of these other more general effects provides an important experimental tool for consciousness science and psychiatry. Here we describe such a tool, the Hallucination Machine. It comprises a novel combination of two powerful technologies: deep convolutional neural networks (DCNNs) and panoramic videos of natural scenes, viewed immersively through a head-mounted display (panoramic VR). By doing this, we are able to simulate visual hallucinatory experiences in a biologically plausible and ecologically valid way. Two experiments illustrate potential applications of the Hallucination Machine. First, we show that the system induces visual phenomenology qualitatively similar to classical psychedelics. In a second experiment, we find that simulated hallucinations do not evoke the temporal distortion commonly associated with altered states. Overall, the Hallucination Machine offers a valuable new technique for simulating altered phenomenology without directly altering the underlying neurophysiology.

neuroscience↗

bioRxiv2017

Streptococcus pyogenes infection and the human proteome with a special focus on the IgG-cleaving enzyme IdeS

Infectious diseases are characterized by a complex interplay between host and pathogen, but how these interactions impact the host proteome is unclear. Here we applied a novel mass spectrometry based proteomics strategy to investigate how the human proteome is transiently modified by the pathogen Streptococcus pyogenes, with a particular focus on bacterial cleavage of IgG in vivo. In invasive diseases, S. pyogenes evokes a massive host response in blood, whereas superficial diseases are characterized by a local leakage of several blood plasma proteins at the site of infection including IgG. S. pyogenes produces IdeS, a protease cleaving IgG in the lower hinge region and we find highly effective IdeS-cleavage of IgG in samples from local IgG poor microenvironments. The results show that IdeS contributes to the adaptation of S. pyogenes to its normal ecological niches. Additionally, the work identifies novel clinical opportunities for in vivo pathogen detection.

microbiology↗

bioRxiv2017

Calcimycocavitological Studies on Seashells from Beaches of North Goa, India

Calcimycocavitology deals with the study of hollowing out of spaces in hard calcareous seashells by the fungi called calcimycocavites. Endolithic fungi in the shells were first reported and named as the trace fossils in 1889 by Bornet and Flahault. Endolithic fungi bore inside the shell by the process of bioturbation by using organic acids (oxalic acid, citrate) and enzymes (proteases, dehydrogenases and oxidoreductases). Previous reports show the presence of tunnels formed by fungal hyphae in the shells. The present work reports preliminary results of calcimycocavitological studies on the seashells from beaches of north Goa, India. The calcareous sand samples were collected from Arambol, Ashvem, Morjim, Vagator, Anjuna, Baga and Miramar beaches by pool sampling method and were separated into different fractions by using standard sieves. Each fraction of sand was subjected to stereomicroscopic studies which revealed that the sand fraction between 150-250 m included irregular shell fragments showing positive colonization by calcimycocavites. Hydrochloric acid treatment was used to dissolve the shells and release calcimycocavites biomass which was stained with Congo Red and tentatively identified as distinct microfungal forms. SEM studies of the calcareous shell fragments revealed the microtunneling behavior of the fungi. Digital analysis of SEM images using Mountain premium 7.2 software revealed the fine topography of calcimycocavites hyphae along with unidentified presumptive biomineral encrustations. The ecological, biological and biogeochemical implications of the findings are presented with respect to possible role of calcimycocavites in Calcium and Carbon cycling by breakdown of the calcareous shells and release of inorganic and organic components in the ecosystem.

microbiology↗

bioRxiv2017

MetQy: an R package to query metabolic functions of genes and genomes

SummaryWith the rapid accumulation of sequencing data from genomic and metagenomic studies, there is an acute need for better tools that facilitate their analyses against biological functions. To this end, we developed MetQy, an open-source R package designed for query-based analysis of functional units in [meta]genomes and/or sets of genes using the The Kyoto Encyclopedia of Genes and Genomes (KEGG) database. Furthermore, MetQy contains visualization and analysis tools and facilitates KEGGs flat file manipulation. Thus, MetQy enables better understanding of metabolic capabilities of known genomes or user-specified [meta]genomes by using the available information and can help guide studies in microbial ecology, metabolic engineering and synthetic biology.\n\nAvailability and ImplementationThe MetQy R package is freely available and can be downloaded from our groups website (http://osslab.lifesci.warwick.ac.uk) or GitHub (https://github.com/OSS-Lab/MetQy).\n\nContactO.Soyer@warwick.ac.uk

microbiology↗

bioRxiv2017

A primitive starfish ancestor from the Early Ordovician of Morocco reveals the origin of crown group Echinodermata

The somasteroids are Ordovician star-shaped animals widely regarded as ancestors of Asterozoa, the group of extant echinoderms that includes brittle stars and starfish. The phylogenetic position of somasteroids makes them critical for understanding the origin and early evolution of crown group Echinodermata. However, the early evolution of asterozoans, the origin of their distinctive body organization and their relationships with other Cambrian and Ordovician echinoderms, such as edrioasteroids, blastozoans, crinoids, and other asterozoans, remain problematic due to the difficulties of comparing the calcitic endoskeleton of these disparate groups. Here we describe the new somasteroid Cantabrigiaster fezouataensis from the Early Ordovician (Tremadocian) Fezouata Lagerstatte in Morocco. Cantabrigiaster shares with other somasteroids the presence of rod-like virgal ossicles that articulate with the ambulacrals, but differs from all other known asterozoans in the absence of adambulacral ossicles defining the arm margins. The unique arm construction evokes parallels with non-asterozoan echinoderms. Developmentally informed Bayesian and parsimony based phylogenetic analyses, which reflect the homology of the biserial ambulacral ossicles in Paleozoic echinoderms according to the Extraxial-Axial Theory, recover Cantabrigiaster as basal within stem group Asterozoa. Our results indicate that Cantabrigiaster is the earliest diverging stem group asterozoan, revealing the ancestral morphology of this major clade and clarifying the affinities of problematic Ordovician taxa. Somasteroids are resolved as a paraphyletic grade within stem and crown group Asterozoa (starfishes), whereas stenuroids are paraphyletic within stem group Ophiuroidea (brittle stars). Cantabrigiaster also illuminates the relationship between Ordovician crown group Echinodermata and its Cambrian stem lineage, which includes sessile forms with incipient radial symmetry such as edrioasteroids and blastozoans. The contentious Pelmatozoa hypothesis (i.e. monophyly of blastozoans and crinoids) is not supported; instead, blastozoans represent the most likely sister-taxon of crown group Echinodermata.\n\nAuthor summaryStarfish and brittle stars, collectively known as asterozoans, constitute a diverse and ecologically successful group of echinoderms that first appear in the fossil record some 480Ma. However, the early evolution of asterozoans, the origin of their distinctive body organization, and their phylogenetic relationships with Cambrian echinoderms remain largely unresolved. We describe Cantabrigiaster fezouataensis gen. et sp. nov., a primitive asterozoan from the Fezouata Lagerstatte, Morocco, with a unique endoskeletal arm organization that reveals the ancestral morphology of this major clade. Bayesian and parsimony based phylogenetic analyses indicate that Cantabrigiaster is the earliest diverging stem group asterozoan, and resolve the phylogenetic position of Ordovician asterozoans such as somasteroids. Our analyses clarify the origin of crown group echinoderms relative to their problematic Cambrian stem group representatives.

paleontology↗

bioRxiv2017

Comprehensive profiling of TCRβ repertoire in a non-model species (the bank vole) using high-throughput sequencing

In recent years, immune repertoire profiling with high-throughput sequencing (HTS) has advanced our understanding of adaptive immunity. However, fast progress in the field applied mostly to human and mouse research, with only few studies devoted to other model vertebrates. We present the first in-depth characterization of the TCR{beta} repertoire in a non-model mammal with limited genomic resources available - the bank vole (Myodes glareolus). We used 5'RACE and Illumina HTS to describe V and J segments and to qualitatively characterize preferential V-J segment usage and CDR3 length distribution. Finally, a molecular protocol integrating unique molecular identifiers was used for quantitative analysis of CDR3 repertoire with stringent error correction. We found 37 V and 11 J genes that were orthologous to mice genes. A conservative, lower bound estimation of the TCR{beta} repertoire was 1.7-2.3x105 clonotypes, and the degree of sharing of the observed repertoire between any two individuals was 3.6% of nucleotide sequences and 14.3% of amino acid sequences. Our work adds a crucial element to the immunogenetic resources available for the bank vole, an important species in ecological and evolutionary research. The workflow that we developed can be applied for immune repertoire sequencing of non-model species, including endangered vertebrates.

immunology↗

bioRxiv2017

Don’t throw out the sympatric species with the crater lake water: fine-scale investigation of introgression provides weak support for functional role of secondary gene flow in one of the clearest examples of sympatric speciation

Genomic data has revealed complex histories of colonization and repeated gene flow previously unrecognized in some of the most celebrated examples of sympatric speciation and radiation. However, much of the evidence for secondary gene flow into these radiations comes from genome-wide tests, which tells us little about how gene flow potentially influenced sympatric diversification. Here we investigated whole genomes of Barombi Mbo crater lake cichlids for fine-scale patterns of introgression between species with neighboring riverine cichlid populations. We did find evidence of secondary gene flow into the radiation scattered across < 0.24% of the genome; however, the functional and genetic diversity in these regions paint no clear picture of how that variation could have contributed to the ecological and morphological diversity found in the lake. Our results suggest that either variation in novel genetic pathways introduced during secondary gene flow contributed to the radiation, or that secondary gene flow was predominantly neutral with respect to the diversification processes. We also found evidence for differential assortment of ancestral polymorphism found in riverine populations between sympatric sister species, suggesting the presence of a hybrid swarm in the past. While the history of gene flow and colonization appears to be more complicated than once thought, the lack of compelling evidence for secondary gene flow influencing diversification suggests that we should not yet rule out one of the most celebrated examples of sympatric speciation in nature.

evolutionary biology↗

bioRxiv2017

The unrealized potential of herbaria in global change biology

Plant and fungal specimens in herbaria are becoming primary resources for investigating how plant phenology and geographic distributions shift with climate change, greatly expanding inferences across spatial, temporal, and phylogenetic dimensions. However, these specimens contain a wealth of additional data--including nutrients, defensive compounds, herbivore damage, disease lesions, and signatures of physiological processes--that capture ecological and evolutionary responses to the Anthropocene but which are less frequently utilized. Here, we outline the diversity of herbarium data, global change topics to which they have been applied, and new hypotheses they could inform. We find that herbarium data have been used extensively to study impacts of climate change and invasive species, but that such data are less commonly used to address other drivers of biodiversity loss, including habitat conversion, pollution, and overexploitation. In addition, we note that fungal specimens are under-explored relative to vascular plants. To facilitate broader application of plant and fungal specimens in global change research, we outline the limitations of these data and modern sampling and statistical tools that may be applied to surmount challenges they present. Using a case study of insect herbivory, we illustrate how novel herbarium data may be employed to test hypotheses for which few data exist, despite potentially large biases. With the goal of positioning herbaria as hubs for global change research, we suggest future research directions and curation priorities.

plant biology↗

bioRxiv2017

Balances: a new perspective for microbiome analysis

High-throughput sequencing technologies have revolutionized microbiome research by allowing the relative quantification of microbiome composition and function in different environments. One of the main goals in microbiome analysis is the identification of microbial species that are differentially abundant among groups of samples, or whose abundance is associated with a variable of interest. Most available methods for microbiome abundance testing perform univariate tests for each microbial species or taxa separately, ignoring the compositional nature of microbiome data.\n\nWe propose an alternative approach for microbiome abundance testing that consists on the identification of two groups of taxa whose relative abundance, or balance, is associated with the response variable of interest. This approach is appealing, since it has direct translation to the biological concept of ecological balance between species in an ecosystem. In this work, we present selbal, a greedy stepwise algorithm for balance selection. We illustrate the algorithm with 16s abundance data from an HIV-microbiome study and a Crohn-microbiome study.\n\nImportanceA more meaningful approach for microbiome abundance testing is presented. Instead of testing each taxon separately we propose to explore abundance balances among groups of taxa. This approach acknowledges the compositional nature of microbiome data.

bioinformatics↗

bioRxiv2017

Novel bacterial lineages associated with boreal moss species

Mosses are critical components of boreal ecosystems where they typically account for a large proportion of net primary productivity and harbor diverse bacterial communities that can be the major source of biologically-fixed nitrogen in these ecosystems. Despite their ecological importance, we have limited understanding of how microbial communities vary across boreal moss species and the extent to which local environmental conditions may influence the composition of these bacterial communities. We used marker gene sequencing to analyze bacterial communities associated with eight boreal moss species collected near Fairbanks, AK USA. We found that host identity was more important than site in determining bacterial community composition and that mosses harbor diverse lineages of potential N2- fixers as well as an abundance of novel taxa assigned to understudied bacterial phyla (including candidate phylum WPS-2). We performed shotgun metagenomic sequencing to assemble genomes from the WPS-2 candidate phylum and found that these moss-associated bacteria are likely anoxygenic phototrophs capable of carbon fixation via RuBisCo with an ability to utilize byproducts of photorespiration from hosts via a glyoxylate shunt. These results give new insights into the metabolic capabilities of understudied bacterial lineages that associate with mosses and the importance of plant hosts in shaping their microbiomes.

microbiology↗

bioRxiv2017

Metaproteomics of colonic microbiota unveils discrete protein functions among colitic mice and control groups

Metaproteomics can greatly assist established high-throughput sequencing methodologies to provide systems biological insights into the alterations of microbial protein functionalities correlated with disease-associated dysbiosis of the intestinal microbiota. Here, we utilized the well-characterized murine T cell transfer model of colitis to find specific changes within the intestinal luminal proteome associated with inflammation. MS proteomic analysis of colonic samples permitted the identification of {bsim}10,000-12,000 unique peptides that corresponded to 5,610 protein clusters identified across three groups, including the colitic Rag1-/- T cell recipients, isogenic Rag1-/- controls, and wild-type mice. We demonstrate that the colitic mice exhibited a significant increase in Proteobacteria and Verrucomicrobia and show that such alterations in the microbial communities contributed to the enrichment of specific proteins with transcription and translation gene ontology terms. In combination with 16S sequencing, our metaproteomics-based microbiome studies provide a foundation for assessing alterations in intestinal luminal protein functionalities in a robust and well-characterized mouse model of colitis, and set the stage for future studies to further explore the functional mechanisms of altered protein functionalities associated with dysbiosis and inflammation.\n\nStatement of significance of the studyThe commensal gut microbiota is essential to maintaining health and has a primary role in digestion/metabolism, homeostasis, and protection from pathogenic bacteria. High-throughput sequencing has established Bacteroidetes, Firmicutes, Proteobacteria, and Actinobacteria as the four major bacterial phyla that comprise the ecological makeup of the intestinal microbiota. However, the tremendous inter-/intra-variability in microbial composition across individuals, as well as along the length of the intestinal tract has made it difficult to definitively ascertain specific bacterial species associated with health or as drivers of disease states, including inflammatory bowel disease. In this study, we expanded upon the current metaproteomics techniques and use the robust and highly reproducible murine T cell transfer model of colitis as well as a comprehensive database of mouse, human, plant, and all microbial genomes sequenced to date to elucidate alterations in both host and gut microbial proteins associated with intestinal inflammation. Our results show that host genetics, gut microbiota, and inflammation have tremendous influences on the intestinal luminal proteomic landscape.

bioinformatics↗

bioRxiv2017

Fungal communities associated with the eastern larch beetle: diversity and variation within developmental stages

Bacterial and fungal communities associated with bark beetles, especially some Dendroctonus species, mediate challenging aspects of the subcortical habitat for their hosts. Filamentous fungi and yeasts are important in various metabolic processes of certain bark beetles, with involvement in nutrition, protection and detoxification of plant defense compounds. The eastern larch beetle, Dendroctonus simplex, is recognized as a serious forest pest in the upper part of North America. Although D. simplex is well studied, the fungal communities and their ecological role remain to be investigated. Here, using 18S rRNA gene pyrosequencing, we provide a comprehensive overview of the yeasts and filamentous fungi associated with the eastern larch beetle and compare fungal communities between different developmental stages and microenvironments. Fungal mycobiome associated with the galleries was also investigated. Our study has unveiled an unexpected fungal diversity associated with the developmental stages. Significant differences in species richness between the developmental stages were determined. Yeasts were found to be predominant in the adult and larval stages, whereas filamentous fungi were most prevalent in the pupae. Our results indicate a possible implication of yeasts in the eastern larch beetle nutrition.

microbiology↗

bioRxiv2017

The study of animal behaviour as a physical science

Behaviour is the ultimate output of an animals nervous system and choosing the right action at the right time can be critical for survival. The study of the organisation of behaviour in its natural context, ethology, has historically been a primarily qualitative science. A quantitative theory of behaviour would advance research in neuroscience as well as ecology and evolution. However, animal posture typically has many degrees of freedom and behavioural dynamics vary on timescales ranging from milliseconds to years, presenting both technical and conceptual challenges. Here we review 1) advances in imaging and computer vision that are making it possible to capture increasingly complete records of animal motion and 2) new approaches to understanding the resulting behavioural data sets. With the right analytical approaches, these data are allowing researchers to revisit longstanding questions about the structure and organisation of animal behaviour and to put unifying principles on a quantitative footing. Contributions from both experimentalists and theorists are leading to the emergence of a physics of behaviour and the prospect of discovering laws and developing theories with broad applicability. We believe that there now exists an opportunity to develop theories of behaviour which can be tested using these data sets leading to a deeper understanding of how and why animals behave.

animal behavior and cognition↗

bioRxiv2017

Improved genome assembly and annotation for the rock pigeon (Columba livia)

The domestic rock pigeon (Columba livia) is among the most widely distributed and phenotypically diverse avian species. This species is broadly studied in ecology, genetics, physiology, behavior, and evolutionary biology, and has recently emerged as a model for understanding the molecular basis of anatomical diversity, the magnetic sense, and other key aspects of avian biology. Here we report an update to the C. livia genome reference assembly and gene annotation dataset. Greatly increased scaffold lengths in the updated reference assembly, along with an updated annotation set, provide improved tools for evolutionary and functional genetic studies of the pigeon, and for comparative avian genomics in general.

genomics↗