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bioRxiv2017

Bistability In Fluorescence From A Purple Non-Sulfur Bacteria

Bistable optical emission has been observed for photosynthetic purple non-sulfur bacteria Rhodobacter capsulatus SB1003. The microbes respond to UV excitation (at 395nm) in a bifurcating way one branch corresponding to increase and the other corresponding to diminishing fluorescent emission in the range 590-685nm.The switching between such bifurcating branches can be observed when parameters like concentration, temperature are varied or static magnetic field is applied. Thus switching from amplification to reduction occurs if fluorophore concentration lowered. Again if temperature is lowered a steady quenching (instead of amplification) of fluorescence is observed. However presence of magnetic field of the order of 0.5 T reverts this and once again the systems resumes its fluoresence amplifying state. We propose that aggregation of bacterial porphyrin and regulation of such aggregation by photon excitation may explain this bistablity. Possible ecological implication of the photosynthetic bistability is suggested.

systems biology↗

bioRxiv2017

The Genomic Landscape Of Tree Rot In Phellinus noxius And Its Hymenochaetales Members

The order Hymenochaetales of white rot fungi contain some of the most aggressive wood decayers causing tree deaths around the world. Despite their ecological importance and the impact of diseases they cause, little is known about the evolution and transmission patterns of these pathogens. Here, we sequenced and undertook comparative genomics analyses of Hymenochaetales genomes using brown root rot fungus Phellinus noxius, wood-decomposing fungus Phellinus lamaensis, laminated root rot fungus Phellinus sulphurascens, and trunk pathogen Porodaedalea pini. Many gene families of lignin-degrading enzymes were identified from these fungi, reflecting their ability as white rot fungi. Comparing against distant fungi highlighted the expansion of 1,3-beta-glucan synthases in P. noxius, which may account for its fast-growing attribute. We identified 13 linkage groups conserved within Agaricomycetes, suggesting the evolution of stable karyotypes. We determined that P. noxius has a bipolar heterothallic mating system, with unusual highly expanded ~60 kb A locus as a result of accumulating gene transposition. We investigated the population genomics of 60 P. noxius isolates across multiple islands of the Asia Pacific region. Whole-genome sequencing showed this multinucleate species contains abundant poly-allelic single-nucleotide-polymorphisms (SNPs) with atypical allele frequencies. Different patterns of intra-isolate polymorphism reflect mono-/heterokaryotic states which are both prevalent in nature. We have shown two genetically separated lineages with one spanning across many islands despite the geographical barriers. Both populations possess extraordinary genetic diversity and show contrasting evolutionary scenarios. These results provide a framework to further investigate the genetic basis underlying the fitness and virulence of white rot fungi.

genomics↗

bioRxiv2017

Exon-Based Phylogenomics Strengthens The Phylogeny Of Neotropical Cichlids And Identifies Remaining Conflicting Clades (Cichlomorphae: Cichlidae: Cichlinae)

The phenotypic, geographic, and species diversity of cichlid fishes have made them a group of great interest for studying evolutionary processes. Here we present a targeted-exon next-generation sequencing approach for investigating the evolutionary relationships of cichlid fishes (Cichlidae), with focus on the Neotropical subfamily Cichlinae using a set of 923 primarily single-copy exons designed through mining of the Nile tilapia (Oreochromis niloticus) genome. Sequence capture and assembly were robust, leading to a complete dataset of 415 exons for 139 species (147 terminals) that consisted of 128 Neotropical species, six African taxa, and five Indo-Malagasy cichlids. Gene and species trees were calculated using alternative partitioning schemes and reconstruction methods. In general, all methods yielded similar topologies to previously hypothesized relationships within the Cichlinae and clarified several relationships that were previously poorly supported or in conflict. Additional work will be needed to fully resolve all aspects of Cichlinae phylogeny. Overall, this approach yielded a well-resolved phylogeny of Neotropical cichlids that will be of utility for future assessments of the evolutionary and ecological processes within this diverse group of fishes. Furthermore, the general methodology employed here of exon targeting and capture should be applicable to any group of organisms with the availability of a reference genome.

evolutionary biology↗

bioRxiv2017

Convergent evolution of the army ant syndrome and congruence in big-data phylogenetics

The evolution of the suite of morphological and behavioral adaptations underlying the ecological success of army ants has been the subject of considerable debate. This \"army ant syn-drome\" has been argued to have arisen once or multiple times within the ant subfamily Dorylinae. To address this question I generated data from 2,166 loci and a comprehensive taxon sampling for a phylogenetic investigation. Most analyses show strong support for convergent evolution of the army ant syndrome in the Old and New World but certain relationships are sensitive to analytics. I examine the signal present in this data set and find that conflict is diminished when only loci less likely to violate common phylogenetic model assumptions are considered. I also provide a temporal and spatial context for doryline evolution with timecalibrated, biogeographic, and diversification rate shift analyses. This study underscores the need for cautious analysis of phylogenomic data and calls for more efficient algorithms employing better-fitting models of molecular evolution.\n\nSignificanceRecent interpretation of army ant evolution holds that army ant behavior and morphology originated only once within the subfamily Dorylinae. An inspection of phylogenetic signal in a large new data set shows that support for this hypothesis may be driven by bias present in the data. Convergent evolution of the army ant syndrome is consistently supported when sequences violating assumptions of a commonly used model of sequence evolution are excluded from the analysis. This hypothesis also fits with a simple scenario of doryline biogeography. These results highlight the importance of careful evaluation of signal and conflict within phylogenomic data sets, even when taxon sampling is comprehensive.

evolutionary biology↗

bioRxiv2017

Fast Periodic Stimulation (FPS): A Highly Effective Approach In fMRI Brain Mapping

Functional magnetic resonance imaging (fMRI) is a major technique for human brain mapping. We present a Fast Periodic Stimulation (FPS) fMRI approach, demonstrating its high effectiveness in defining category-selective brain regions. Observers see a dynamic stream of widely variable natural object images alternating at a fast rate (6 images/sec). Every 9 seconds, a short burst of variable face images contrasting with objects in pairs induces an objective 0.111 Hz face-selective neural response in the ventral occipito-temporal cortex and beyond. A model-free Fourier analysis achieves a two-fold increase in signal-to-noise ratio compared to a conventional block-design approach with identical stimuli. Periodicity of category contrast and random variability among images minimize low-level visual confounds while preserving naturalness of the stimuli, leading to the highest values (80-90%) of test-retest reliability yet reported in this area of research. FPS-fMRI opens a new avenue for understanding brain function with low temporal resolution methods.\n\nHighlightsFPS-fMRI achieves a two-fold increase in peak SNR over conventional approach\n\nFPS-fMRI reveals comprehensive extended face-selective areas including ATL\n\nFPS-fMRI achieves high specificity by minimizing influence of low-level visual cues\n\nFPS-fMRI achieves very high test-retest reliability (80%-90%) in spatial activation map\n\neTOC BlurbIn Brief\n\nGao et al. present a novel FPS-fMRI approach, which achieves a two-fold increase in peak signal-to-noise ratio in defining the neural basis of visual categorization while preserving ecological validity, minimizing low-level visual confounds and reaching very high (80%-90%) test-retest reliability.

neuroscience↗

bioRxiv2017

Extensive Sexual Wing Shape Dimorphism In Drosophila melanogaster, Ceratitis capitata, And Musca domestica

The ability of powered flight in insects facilitated their great evolutionary success allowing them to occupy various ecological niches. Beyond this primary task, wings are often involved in various premating behaviors, such as the generation of courtship songs and the initiation of mating in flight. These specific functions imply special adaptations of wing morphology, as well as sex-specific wing morphologies. Although wing morphology has been extensively studied in Drosophila melanogaster, a comprehensive understa nding of sexual wing shape dimorphisms and developmental plasticity is missing for other Diptera. Therefore, we raised flies of the three Diptera species Drosophila melanogaster, Ceratitis capitata and Musca domestica at different environmental conditions and applied geometric morphometrics to analyze wing shape. Our data showed extensive interspecific differences in wing shape, as well as a clear sexual wing shape dimorphism in all three species. We revealed an impact of different rearing temperatures wing shape in all three species, which was mostly explained by plasticity in wing size in D. melanogaster. Rearing densities had significant effects on allometric wing shape in D. melanogaster, while no obvious effects were observed for the other two species. Additionally, we do not find evidence for sex-specific response to different rearing conditions in all three species. We determined species-specific and common trends in shape alterations, and we hypothesize developmental and functional implications of our data. Contribution to the Field StatementThe size and shape of organisms and organs must be tightly controlled during development to ensure proper functionality. However, morphological traits vary considerably in nature contributing to phenotypic diversity. Such variation can be the result of evolutionary adaptations as well as plasticity for example as reaction to changing environmental conditions during development. It is therefore a major aim in Biology to unravel the processes that control differences in adult morphology. Insect wings are excellent models to study how organ size and shape evolves because they facilitate basic tasks such as mating and feeding. Accordingly, a tremendous variety of wings sizes and shapes evolved in nature. Additionally, plasticity in wing morphology in response to different rearing conditions has been observed in many insects contributing to phenotypic diversity. In this work we applied Geometric Morphometrics to study wing shape in the three Diptera species: the Mediterranean fruit fly Ceratitis capitata, the Vinegar fly Drosophila melanogaster and the housefly Musca domestica. Flies were raised in different temperature and density regimes that allowed us to study the effects of these environmental factors on wing shape. Additionally, in accordance with different mating behaviors of these flies, we observed a clear sexual shape dimorphism in all three species. Since the three studied species represent serious pests and disease vectors, our findings may contribute to existing and future monitoring efforts.

zoology↗

bioRxiv2017

De Novo Assembly And Annotation Of The Eastern Fence Lizard (Sceloporus undulatus) Transcriptome

BackgroundThe eastern fence lizard (Sceloporus undulatus) has been a model species for ecological and evolutionary research. Genomic and transcriptomic resources for this species would promote investigation of genetic mechanisms that underpin plastic responses to environmental stress, such as climate warming. Moreover, such resources would aid comparative studies of complex traits at the molecular level, such as the transition from oviparous to viviparous reproduction, which happened at least four times within Sceloporus.\n\nFindingsA de novo transcriptome assembly for Sceloporus undulatus, Sund_v1.0, was generated using over 179 million Illumina reads obtained from three tissues (whole brain, skeletal muscle, and embryo) as well as previously reported liver sequences. The Sund_v1.0 assembly had an average contig length of 782 nucleotides and an E90N50 statistic of 2,550 nucleotides. Comparing S. undulatus transcripts with the benchmarking universal single-copy orthologs (BUSCO) for tetrapod species yielded 97.2% gene representation. A total of 13,422 protein-coding orthologs were identified in comparison to the genome of the green anole lizard, Anolis carolinensis, which is the closest related species with genomic data available.\n\nConclusionsThe multi-tissue transcriptome of S. undulatus is the first for a member of the family Phrynosomatidae, offering an important resource to advance studies of adaptation in this species and genomic research in reptiles.

genomics↗

bioRxiv2017

Coalescent Processes With Skewed Offspring Distributions And Non-Equilibrium Demography

Non-equilibrium demography impacts coalescent genealogies leaving detectable, well-studied signatures of variation. However, similar genomic footprints are also expected under models of large reproductive skew, posing a serious problem when trying to make inference. Furthermore, current approaches consider only one of the two processes at a time, neglecting any genomic signal that could arise from their simultaneous effects, preventing the possibility of jointly inferring parameters relating to both offspring distribution and population history. Here, we develop an extended Moran model with exponential population growth, and demonstrate that the underlying ancestral process converges to a time-inhomogeneous psi-coalescent. However, by applying a non-linear change of time scale - analogous to the Kingman coalescent - we find that the ancestral process can be rescaled to its time-homogeneous analogue, allowing the process to be simulated quickly and efficiently. Furthermore, we derive analytical expressions for the expected site-frequency spectrum under the time-inhomogeneous psi-coalescent and develop an approximate-likelihood framework for the joint estimation of the coalescent and growth parameters. By means of extensive simulation, we demonstrate that both can be estimated accurately given linkage equilibrium, while linkage disequilibrium systematically biases growth rate estimates. In addition, not accounting for demography can lead to serious biases in the inferred coalescent model, with broad implications for genomic studies ranging from ecology to conservation biology. Finally, we use our method to analyze sequence data from Japanese sardine populations and find evidence of high variation in individual reproductive success, but few signs of a recent demographic expansion.

evolutionary biology↗

bioRxiv2017

Comparative Genomics Sheds Light On Niche Differentiation And The Evolutionary History Of Comammox Nitrospira

The description of comammox Nitrospira spp., performing complete ammonium-to-nitrate oxidation, and their co-occurrence with canonical betaproteobacterial ammonium oxidizing bacteria ({beta}-AOB) in the environment, call into question the metabolic potential of comammox Nitrospira and the evolutionary history of their ammonium oxidation pathway. We report four new comammox Nitrospira genomes, constituting two novel species, and the first comparative genomic analysis on comammox Nitrospira.\n\nComammox Nitrospira has lost the potential to use external nitrite as energy and nitrogen source: compared to strictly nitrite oxidizing Nitrospira; they lack genes for assimilative nitrite reduction and reverse electron transport from nitrite. By contrast, compared to other Nitrospira, their ammonium oxidizer physiology is exemplified by genes for ammonium and urea transporters and copper homeostasis and the lack of cyanate hydratase genes. Two comammox clades are different in their ammonium uptake systems. Contrary to {beta}-AOB, comammox Nitrospira genomes have single copies of the two central ammonium oxidation pathway genes, lack genes involved in nitric oxide reduction, and encode genes that would allow efficient growth at low oxygen concentrations. Hence, comammox Nitrospira seems attuned to oligotrophy and hypoxia compared to {beta}-AOB.\n\n{beta}-AOBs are the clear origin of the ammonium oxidation pathway in comammox Nitrospira: reconciliation analysis indicates two separate early amoA gene transfer events from {beta}-AOB to an ancestor of comammox Nitrospira, followed by clade specific losses. For haoA, one early transfer from {beta}-AOB to comammox Nitrospira is predicted - followed by intra-clade transfers. We postulate that the absence of comammox genes in most Nitrospira genomes is the result of subsequent loss.\n\nSignificanceThe recent discovery of comammox bacteria - members of the Nitrospira genus able to fully oxidize ammonia to nitrate - upset the long-held conviction that nitrification is a two-step process. It also opened key questions on the ecological and evolutionary relations of these bacteria with other nitrifying prokaryotes. Here, we report the first comparative genomic analysis of comammox Nitrospira and related nitrifiers. Ammonium oxidation genes in comammox Nitrospira had a surprisingly complex evolution, originating from ancient transfer from the phylogenetically distantly related ammonia-oxidizing betaproteobacteria, followed by within-lineage transfers and losses. The resulting comammox genomes are uniquely adapted to ammonia oxidation in nutrient-limited and low-oxygen environments and appear to have lost the genetic potential to grow by nitrite oxidation alone.

microbiology↗

bioRxiv2017

Percentage-Based Author Contribution Index. A Universal Measure Of Author Contribution To Scientific Articles

Deciphering the amount of work provided by different co-authors of a scientific paper has been a recurrent problem in science. Despite the myriad of metrics available, the scientific community still largely relies on the position in the list of authors to evaluate contributions, a metric that attributes subjective and unfounded credit to co-authors. We propose an easy to apply, fair and universally comparable metric to measure and report co-authors contribution in the scientific literature. The proposed Author Contribution Index (ACI) is based on contribution percentages provided by the authors, preferably at the time of submission. Researchers can use ACI for a number of purposes, including comparing the contributions of different authors, describing the contribution profile of a researcher or analysing how contribution changes through time. We provide an example analysis based on data collected from 97 scientists from the field of ecology who voluntarily responded to an online anonymous survey.

scientific communication and education↗

bioRxiv2017

Dissecting HIV Virulence: Heritability Of Setpoint Viral Load, CD4+ T Cell Decline And Per-Parasite Pathogenicity

Pathogen strains may differ in virulence because they attain different loads in their hosts, or because they induce different disease-causing mechanisms independent of their load. In evolutionary ecology, the latter is referred to as \"per-parasite pathogenicity\". Using viral load and CD4+ T cell measures from 2014 HIV-1 subtype B infected individuals enrolled in the Swiss HIV Cohort Study, we investigated if virulence -- measured as the rate of decline of CD4+ T cells -- and per-parasite pathogenicity are heritable from donor to recipient. We estimated heritability by donor-recipient regressions applied to 196 previously identified transmission pairs, and by phylogenetic mixed models applied to a phylogenetic tree inferred from HIV pol sequences. Regressing the CD4+ T cell declines and per-parasite pathogenicities of the transmission pairs did not yield heritability estimates significantly different from zero. With the phylogenetic mixed model, however, our best estimate for the heritability of the CD4+ T cell decline is 17% (5%-30%), and that of the per-parasite pathogenicity is 17% (4%-29%). Further, we confirm that the set-point viral load is heritable, and estimate a heritability of 29% (12%-46%). Interestingly, the pattern of evolution of all these traits differs significantly from neutrality, and is most consistent with stabilizing selection for the set-point viral load, and with directional selection for the CD4+ T cell decline and the per-parasite pathogenicity. Our analysis shows that the viral genetype affects virulence mainly by modulating the per-parasite pathogenicity, while the indirect effect via the set-point viral load is minor.

evolutionary biology↗

bioRxiv2017

Functional Role Of Lanthanides In Enzymatic Activity And Transcriptional Regulation Of PQQ-Dependent Alcohol Dehydrogenases In Pseudomonas putida KT2440

The oxidation of alcohols and aldehydes is crucial for detoxification and efficient catabolism of various volatile organic compounds (VOCs). Thus, many Gram-negative bacteria have evolved periplasmic oxidation systems, based on pyrroloquinoline quinone-dependent alcohol dehydrogenases (PQQ-ADHs), which are often functionally redundant. Using purified enzymes from the soil-dwelling model organism Pseudomonas putida KT2440, the present study reports the first description and characterization of a lanthanide-dependent PQQ-ADH (PedH) in a non-methylotrophic bacterium. PedH exhibits enzyme activity on a similar substrate range as its Ca2+-dependent counterpart PedE, including linear and aromatic primary and secondary alcohols as well as aldehydes, however, only in the presence of lanthanide ions including La3+, Ce3+, Pr3+, Sm3+ or Nd3+. Reporter assays revealed that PedH not only has a catalytic function, but is also involved in the transcriptional regulation of pedE and pedH, most likely acting as a sensory module. Notably, the underlying regulatory network is responsive to as little as 1 - 10 nM of lanthanum, a concentration assumed to be of ecological relevance. The present study further demonstrates that the PQQ-dependent oxidation system is crucial for efficient growth with a variety of volatile alcohols. From these results we conclude that functional redundancy and inverse regulation of PedE and PedH represents an adaptive strategy of P. putida KT2440 to optimize growth with volatile alcohols in response to different lanthanide availability.\n\nIMPORTANCEDue to their low bioavailability, lanthanides have long been considered as biologically inert. In recent years however, the identification of lanthanides as a cofactor in methylotrophic bacteria has attracted tremendous interest among various biological fields. The present study reveals that one of the two PQQ-ADHs produced by the model organism P. putida KT2440 also utilizes lanthanides as a cofactor, thus expanding the scope of lanthanide employing bacteria beyond the methylotrophs. Similar to methyloptrophic bacteria, a complex regulatory network is involved in the lanthanide-responsive switch between the two PQQ-ADHs encoded by P. putida KT2440. We further show that functional production of at least one of the enzymes is crucial for efficient growth with several volatile alcohols. Overall, our study provides a novel understanding for the redundancy of PQQ-ADHs observed in many organisms and further highlights the importance of lanthanides for bacterial metabolism, particularly in soil environments.

microbiology↗

bioRxiv2017

An RNA Virome Associated To The Golden Orb-Weaver Spider Nephila clavipes

The golden orb-weaver spider Nephila clavipes, known for its sexual size dimorphism, is abundant and widespread in the New World. The first annotated genome of orb-weaver spiders, exploring N. clavipes, has recently been reported. The study, focused primarily on the diversity of silk specific genes, shed light into the complex evolutionary history of spiders. Furthermore, a robust transcriptome analysis provided a massive resource for N. clavipes RNA survey. Here, I present evidence of viral sequences corresponding to the first 10 extant virus species associated to N. clavipes and indeed, nephilids. The putatively new species are linked to ssRNA positive-strand viruses, such as Picornavirales, and to ssRNA negative-strand and dsRNA viruses. In addition, I detected sequence data of new strains of two recently reported arthropod viruses, which complemented and extended the corresponding sequence references. The identified viruses appear to be complete, potentially functional, and presenting the typical architecture and consistent viral domains. The intrinsic nature of the detected sequences and their absence in the recently generated genome assembly, suggest that they correspond to bona fide RNA virus sequences. The available RNA data allowed for the first time to address a tissue/organ specific analysis of virus loads/presence in spiders, suggesting a complex spatial and differential distribution of the tentative viruses, encompassing the spider brain and also silk and venom glands. Until recently, the virus landscape associated to spiders remained elusive. The discovered viruses described here provide only a fragmented glimpse of the potential magnitude of the Aranea virosphere. Future studies should focus not only on complementing and expanding these findings, but also on addressing the potential ecological role of these viruses, which might influence the biology of these outstanding arthropod species.\n\nFunding statementThe author received no specific funding for this study.\n\nEthics statements(Authors are required to state the ethical considerations of their study in the manuscript, including for cases where the study was exempt from ethical approval procedures)

microbiology↗

bioRxiv2017

A Novel Post Hoc Method For Detecting Index Switching Finds No Evidence For Increased Switching On The Illumina HiSeq X

High throughput sequencing using the Illumina HiSeq platform is a pervasive and critical molecular ecology resource, and has provided the data underlying many recent advances. A recent study has suggested that index switching, where reads are misattributed to the wrong sample, may be higher in new versions of the HiSeq platform. This has the potential to invalidate both published and in-progress work across the field. Here, we test for evidence of index switching in an exemplar whole genome shotgun dataset sequenced on both the Illumina HiSeq 2500, which should not have the problem, and the Illumina HiSeq X, which may. We leverage unbalanced heterozygotes, which may be produced by index switching, and ask whether the under-sequenced allele is more likely to be found in other samples in the same lane than expected based on the allele frequency. Although we validate the sensitivity of this method using simulations, we find that neither the HiSeq 2500 nor the HiSeq X have evidence of index switching. This suggests that, thankfully, index switching may not be a ubiquitous problem in HiSeq X sequence data. Lastly, we provide scripts for applying our method so that index switching can be tested for in other datasets.

bioinformatics↗

bioRxiv2017

Parasite-Driven Replacement Of A Sexual By A Closely Related Asexual Taxon In Nature

Asexual species are thought to suffer more from coevolving parasites than related sexuals. Yet, this prediction may be modulated by the fact that closely related sexuals and asexuals often differ in respects other than reproductive mode. Here, we follow the frequency dynamics of sexual and asexual Daphnia pulex in a natural pond that was initially dominated by sexuals. However, coinciding with an epidemic of a microsporidian parasite infecting both sexuals and asexuals, the pond was rapidly taken over by the initially rare asexuals. We experimentally confirm that asexuals are less susceptible and also suffer less from the parasite once infected. These results show the ecological replacement of a sexual taxon by a closely related asexual taxon, as driven by parasites. We suggest that this replacement is, however, not directly connected with the reproductive mode, but rather due to the recent introduction and invasive nature of the asexuals studied.

evolutionary biology↗

bioRxiv2017

The underestimated importance of acute infections by human papillomaviruses

Most infections by human papillomaviruses (HPVs) are acute, that is non-persistent. Yet, for HPVs, as for many other oncoviruses, there is a striking gap between our detailed understanding of chronic infections and our limited data on the early stages of infection. Here we argue that studying HPV acute infections is necessary and timely. Focusing on early interactions will help explain why certain infections are cleared while others become chronic or latent. From a molecular perspective, descriptions of immune effectors and pro-inflammatory pathways during the initial stages of infections have the potential to lead to novel treatments or to improved handling algorithms. From a dynamical perspective, adopting concepts from spatial ecology, such as meta-populations or meta-communities, can help explain why HPV acute infections sometimes last for years. Furthermore, cervical cancer screening and vaccines impose novel iatrogenic pressures on HPVs, implying that anticipating any viral evolutionary response remain essential. Finally, hints at the associations between HPV acute infections and fertility deserve further investigation given their high worldwide prevalence. Overall, understanding asymptomatic and benign infections may be instrumental in reducing HPV virulence.

epidemiology↗

bioRxiv2017

Biogeography & Environmental Conditions Shape Phage & Bacteria Interaction Networks Across The Human Microbiome

Viruses and bacteria are critical components of the human microbiome and play important roles in health and disease. Most previous work has relied on studying bacteria and viruses independently, thereby reducing them to two separate communities. Such approaches are unable to capture how these microbial communities interact, such as through processes that maintain community robustness or allow phage-host populations to co-evolve. We implemented a network-based analytical approach to describe phage-bacteria network diversity throughout the human body. We built these community networks using a machine learning algorithm to predict which phages could infect which bacteria in a given microbiome. Our algorithm was applied to paired viral and bacterial metagenomic sequence sets from three previously published human cohorts. We organized the predicted interactions into networks that allowed us to evaluate phage-bacteria connectedness across the human body. We observed evidence that gut and skin network structures were person-specific and not conserved among cohabitating family members. High-fat diets appeared to be associated with less connected networks. Network structure differed between skin sites, with those exposed to the external environment being less connected and likely more susceptible to network degradation by microbial extinction events. This study quantified and contrasted the diversity of virome-microbiome networks across the human body and illustrated how environmental factors may influence phage-bacteria interactive dynamics. This work provides a baseline for future studies to better understand system perturbations, such as disease states, through ecological networks.\n\nAuthor SummaryThe human microbiome, the collection of microbial communities that colonize the human body, is a crucial component to health and disease. Two major components of the human microbiome are the bacterial and viral communities. These communities have primarily been studied separately using metrics of community composition and diversity. These approaches have failed to capture the complex dynamics of interacting bacteria and phage communities, which frequently share genetic information and work together to maintain ecosystem homestatsis (e.g. kill-the-winner dynamics). Removal of bacteria or phage can disrupt or even collapse those ecosystems. Relationship-based network approaches allow us to capture this interaction information. Using this network-based approach with three independent human cohorts, we were able to present an initial understanding of how phage-bacteria networks differ throughout the human body, so as to provide a baseline for future studies of how and why microbiome networks differ in disease states.

microbiology↗

bioRxiv2017

The Gene Regulatory Landscape of Local Adaptation

Local adaptation is a key driver of ecological specialization and the formation of new species. Despite its importance, the evolution of gene regulatory divergence among locally-adapted populations is poorly understood, especially how that divergence manifests in nature. Here, we evaluate gene expression divergence and allele-specific gene expression responses for locally-adapted coastal perennial and inland annual accessions of the yellow monkeyflower, Mimulus guttatus, in a field reciprocal transplant experiment. Overall, 6765 (73%) of surveyed genes were differentially expressed between coastal and inland habitats, while 7213 (77%) were differentially expressed between the coastal perennial and inland annual accessions. Further, 18% of transcripts had significant genotype x site (GxE) effects. Habitat-specific differential expression was found for 62% of the GxE transcripts (differential expression in one habitat, but not the other), while only 94 ([~]5%) GxE transcripts had crossing reaction norms. Cis-regulatory variation was pervasive, affecting 79% (5532) of differentially expressed genes. We detected trans effects for 52% (3611) of differentially expressed genes. Consistent with the supergene hypothesis of chromosome inversion evolution, a locally adaptive inversion was enriched for cis-regulatory divergence. These results provide multiple new insights into the evolution of transcriptome-wide gene regulatory divergence and plasticity among locally adapted populations.

evolutionary biology↗