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bioRxiv2017

Court and spark in the wild: communication at the limits of sensation

Sensory systems evolve in the ecological niches each species is occupying. Accordingly, the tuning of sensory neurons is expected to be adapted to the statistics of natural stimuli. For an unbiased quantification of sensory scenes we tracked natural communication behavior of the weakly electric fish Apteronotus rostratus in their Neotropical rainforest habitat with high spatio-temporal resolution over several days. In the context of courtship and aggression we observed large quantities of electrocommunication signals. Echo responses and acknowledgment signals clearly demonstrated the behavioral relevance of these signals. The known tuning properties of peripheral electrosensory neurons suggest, however, that they are barely activated by these obviously relevant signals. Frequencies of courtship signals are clearly mismatched with the frequency tuning of neuronal population activity. Our results emphasize the importance of quantifying sensory scenes derived from freely behaving animals in their natural habitats for understanding the evolution and function of neural systems.

neuroscience↗
bioRxiv2017

A DNA demethylase overexpression promotes early apical bud maturation in poplar through the biosynthesis and accumulation of flavonoids

ASBTRACTThe transition from active growth to dormancy is critical for the survival of perennial plants. We identified a DEMETER-like (CsDML) cDNA from a winter-enriched cDNA subtractive library in chestnut (Castanea sativa Mill.), an economically and ecologically important species. Next, we characterized this DNA demethylase and its putative orthologue in the more experimentally tractable hybrid poplar (Populus tremula x alba), under the signals that trigger bud dormancy in trees. We performed phylogenetic and protein sequence analysis, gene expression profiling and 5mC immunodetection studies to evaluate the role of CsDML and its homologue in poplar, PtaDML6. Transgenic hybrid poplars overexpressing CsDML were produced and analyzed. Short days (SD) and cold temperatures induced CsDML and PtaDML6. Overexpression of CsDML accelerated SD-induced bud formation, specifically from stage 1 to 0. Bud acquired a red-brown coloration earlier than wild type (WT) plants, alongside with the upregulation of flavonoid biosynthesis enzymes and accumulation of flavonoids in the SAM and bud scales. Our data shows that the CsDML gene induces bud formation needed for the survival of the apical meristem under the harsh conditions of winter. This study provides in planta evidence implicating chromatin remodeling by DNA demethylation during SD induction of bud maturation through the induction of flavonoids biosynthesis.

plant biology↗
bioRxiv2017

Daisy quorum drives for the genetic restoration of wild populations

An ideal gene drive system to alter wild populations would 1) exclusively affect organisms within the political boundaries of consenting communities, and 2) be capable of restoring any engineered population to its original genetic state. Here we describe daisy quorum drive systems that meet these criteria by combining daisy drive with underdominance. A daisy quorum drive system is predicted to spread through a population until all of its daisy elements have been lost, at which point its fitness becomes frequency-dependent: mostly altered populations become fixed for the desired change, while engineered genes at low frequency are swiftly eliminated by natural selection. The result is an engineered population surrounded by wild-type organisms with limited mixing at the boundary. Releasing large numbers of wild-type organisms or a few bearing a population suppression element can reduce the engineered population below the quorum, triggering elimination of all engineered sequences. In principle, the technology can restore any drive-amenable population carrying engineered genes to wild-type genetics. Daisy quorum systems may enable efficient, community-supported, and genetically reversible ecological engineering.\n\nSummaryLocal communities should be able to control their own environments without forcing those choices on others. Ideally, each community could reversibly alter local wild organisms in ways that cannot spread beyond their own boundaries, and any engineered population could be restored to its original genetic state. We've invented a 'daisy quorum' drive system that appears to meet these criteria.\n\n\"Daisy\" refers to a daisy drive, which typically uses a daisy-chain of linked genes to spread a change through a local population while losing links every generation until it stops spreading. \"Quorum\" reflects the system's ability to \"vote\" on whether a local population should be altered or not: once all daisy elements are lost, it favors replication by the altered version or the original depending on which is more abundant in the local area. Put together, they result in a change that first spreads through a local population, then either becomes locally prevalent is eliminating, inhibiting mixing at the boundary. All organisms in the target population are altered, but changes are unable to spread much beyond that area due to being greatly outnumbered by wild-type organisms and consequently less able to replicate.\n\nWe haven't yet performed any experiments involving daisy quorum systems. Rather, were describing what we intend to do, including the safeguards we will use and our assessment of risks, in the hope that others will evaluate our plans and tell us if there's anything wrong that we missed. We hope that all researchers working on gene drive systems - and other technologies that could impact the shared environment - will similarly pre-register their plans. Sharing plans can reduce needless duplication, accelerate progress, and make the proposed work safer for everyone.

synthetic biology↗
bioRxiv2017

A Theta Rhythm In Awake Macaque V1 And V4 And Its Attentional Modulation

Theta rhythms govern rodent sniffing and whisking, and human language processing. Human psychophysics suggests a role for theta also in visual attention. Yet, little is known about theta in visual areas and its attentional modulation. We used electrocorticography (ECoG) to record local field potentials (LFPs) simultaneously from areas V1, V2, V4 and TEO of two macaque monkeys performing a selective visual attention task. We found a {approx}4 Hz theta rhythm within both the V1-V2 and the V4-TEO region, and theta synchronization between them, with a predominantly feedforward directed influence. ECoG coverage of large parts of these regions revealed a surprising spatial correspondence between theta and visually induced gamma. Furthermore, gamma power was modulated with theta phase. Selective attention to the respective visual stimulus strongly reduced these theta-rhythmic processes, leading to an unusually strong attention effect for V1. Microsaccades (MSs) were partly locked to theta. Yet, neuronal theta rhythms tended to be even more pronounced for epochs devoid of MSs. Thus, we find an MS-independent theta rhythm specific to visually driven parts of V1-V2, which rhythmically modulates local gamma and entrains V4-TEO, and which is strongly reduced by attention. We propose that the less theta-rhythmic and thereby more continuous processing of the attended stimulus serves the exploitation of this behaviorally most relevant information. The theta-rhythmic and thereby intermittent processing of the unattended stimulus likely reflects the ecologically important exploration of less relevant sources of information.

neuroscience↗
bioRxiv2017

Pan-genome and phylogeny of Bacillus cereus sensu lato

BackgroundBacillus cereus sensu lato (s. l.) is an ecologically diverse bacterial group of medical and agricultural significance. In this study, I use publicly available genomes to characterize the B. cereus s. l. pan-genome and perform the largest phylogenetic and population genetic analyses of this group to date in terms of the number of genes and taxa included. With these fundamental data in hand, I identify genes associated with particular phenotypic traits (i.e., \"pan-GWAS\" analysis), and quantify the degree to which taxa sharing common attributes are phylogenetically clustered.\n\nMethodsA rapid k-mer based approach (Mash) was used to create reduced representations of selected Bacillus genomes, and a fast distance-based phylogenetic analysis of this data (FastME) was performed to determine which species should be included in B. cereus s. l. The complete genomes of eight B. cereus s. l. species were annotated de novo with Prokka, and these annotations were used by Roary to produce the B. cereus s. l. pan-genome. Scoary was used to associate gene presence and absence patterns with various phenotypes. The orthologous protein sequence clusters produced by Roary were filtered and used to build HaMStR databases of gene models that were used in turn to construct phylogenetic data matrices. Phylogenetic analyses used RAxML, DendroPy, ClonalFrameML, PAUP*, and SplitsTree. Bayesian model-based population genetic analysis assigned taxa to clusters using hierBAPS. The genealogical sorting index was used to quantify the phylogenetic clustering of taxa sharing common attributes.\n\nThe B. cereus s. l. pan-genome currently consists of {approx}60,000 genes, {approx}600 of which are \"core\" (common to at least 99% of taxa sampled). Pan-GWAS analysis revealed genes associated with phenotypes such as isolation source, oxygen requirement, and ability to cause diseases such as anthrax or food poisoning. Extensive phylogenetic analyses using an unprecedented amount of data produced phylogenies that were largely concordant with each other and with previous studies. Phylogenetic support as measured by bootstrap probabilities increased markedly when all suitable pan-genome data was included in phylogenetic analyses, as opposed to when only core genes were used. Bayesian population genetic analysis recommended subdividing the three major clades of B. cereus s. l. into nine clusters. Taxa sharing common traits and species designations exhibited varying degrees of phylogenetic clustering.

evolutionary biology↗
bioRxiv2017

Adaptation, Specialization, and Coevolution within Phytobiomes

Growth patterns of individual plants and evolutionary trajectories of plant communities are intimately linked with and are critically affected by host-associated microbiomes. Research across systems has begun to shed light on how these phytobiomes are established and under laboratory and natural conditions, and have cultivated hope that a better understanding of the governing principles for host-microbe interactions can guide attempts to engineer microbiomes to boost agricultural yields. One important, yet relatively understudied, parameter in regards to phytobiome membership is the degree to which specialization and coevolution between plant species and microbial strains structures these communities. In this article, I provide an broad overview about current knowledge concerning mechanisms enabling adaptation and specialization of phytobiome communties to host plants as well as the potential for plants themselves to recruit and cultivate interactions with beneficial microbes. I further explore the possibility of host-beneficial microbe coevolution and suggest interactions that could promote the evolution of such close-knit partnerships. It is my hope that this overview will encourage future experiments that can begin to fill in this black box of ecological and evolutionary interactions across phytobiomes.\n\n\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=155 SRC=\"FIGDIR/small/120493_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (26K):\norg.highwire.dtl.DTLVardef@16c5315org.highwire.dtl.DTLVardef@c298d7org.highwire.dtl.DTLVardef@1c073a6org.highwire.dtl.DTLVardef@1e8bd1d_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗
bioRxiv2017

A Dynamic Bioenergetic Model For Coral-Symbiodinium Symbioses And Coral Bleaching As An Alternate Stable State

Coral reef ecosystems owe their ecological success-and vulnerability to climate change-to the symbiotic metabolism of corals and Symbiodinium spp. The urgency to understand and predict the stability and breakdown of these symbioses (i.e., coral bleaching) demands the development and application of theoretical tools. Here, we develop a dynamic bioenergetic model of coral-Symbiodinium symbioses that demonstrates realistic steady-state patterns in coral growth and symbiont abundance across gradients of light, nutrients, and feeding. Furthermore, by including a mechanistic treatment of photo-oxidative stress, the model displays dynamics of bleaching and recovery that can be explained as transitions between alternate stable states. These dynamics reveal that healthy and bleached states correspond broadly to nitrogen- and carbon-limitation in the system, with transitions between them occurring as integrated responses to multiple environmental factors. Indeed, a suite of complex emergent behaviors reproduced by the model (e.g., bleaching is exacerbated by nutrients and attenuated by feeding) suggests it captures many important attributes of the system; meanwhile, its modular framework and open source R code are designed to facilitate further problem-specific development. We see significant potential for this modeling framework to generate testable hypotheses and predict integrated, mechanistic responses of corals to environmental change, with important implications for understanding the performance and maintenance of symbiotic systems.

systems biology↗
bioRxiv2017

The Genome Of The Contractile Demosponge Tethya wilhelma And The Evolution Of Metazoan Neural Signalling Pathways

Porifera are a diverse animal phylum with species performing important ecological roles in aquatic ecosystems, and have become models for multicellularity and early-animal evolution. Demosponges form the largest class in sponges, but previous studies have relied on the only draft demosponge genome of Amphimedon queenslandica. Here we present the 125-megabase draft genome of a contractile laboratory demosponge Tethya wilhelma, sequenced to almost 150x coverage. We explore the genetic repertoire of transporters, receptors, and neurotransmitter metabolism across early-branching metazoans in the context of the evolution of these gene families. Presence of many genes is highly variable across animal groups, with many gene family expansions and losses. Three sponge classes show lineage-specific expansions of GABA-B receptors, far exceeding the gene number in vertebrates, while ctenophores appear to have secondarily lost most genes in the GABA pathway. Both GABA and glutamate receptors show lineage-specific domain rearrangements, making it difficult to trace the evolution of these gene families. Gene sets in the examined taxa suggest that nervous systems evolved independently at least twice and either changed function or were lost in sponges. Changes in gene content are consistent with the view that ctenophores and sponges are the earliest-branching metazoan lineages and provide additional support for the proposed clade of Placozoa/Cnidaria/Bilateria.

genomics↗
bioRxiv2017

The Nuclear And Mitochondrial Genomes Of The Facultatively Eusocial Orchid Bee Euglossa dilemma

Bees provide indispensable pollination services to both agricultural crops and wild plant populations, and several species of bees have become important models for the study of learning and memory, plant-insect interactions and social behavior. Orchid bees (Apidae: Euglossini) are especially important to the fields of pollination ecology, evolution, and species conservation. Here we report the nuclear and mitochondrial genome sequences of the orchid bee Euglossa dilemma Bembe & Eltz. Euglossa dilemma was selected because it is widely distributed, highly abundant, and it was recently naturalized in the southeastern United States. We provide a high-quality assembly of the 3.3 giga-base genome, and an official gene set of 15,904 gene annotations. We find high conservation of gene synteny with the honey bee throughout 80 million years of divergence time. This genomic resource represents the first draft genome of the orchid bee genus Euglossa, and the first draft orchid bee mitochondrial genome, thus representing a valuable resource to the research community.

genomics↗
bioRxiv2017

Large scale and significant expression from pseudogenes in Sodalis glossinidius - a facultative bacterial endosymbiont

The majority of bacterial genomes have high coding efficiencies, but there are some genomes of intracellular bacteria that have low gene density. The genome of the endosymbiont Sodalis glossinidius contains almost 50% pseudogenes containing mutations that putatively silence them at the genomic level. We have applied multiple omic strategies, combining: Illumina and Pacific Biosciences Single-Molecule Real Time DNA-sequencing and annotation; stranded RNA-sequencing; and proteome analysis to better understand the transcriptional and translational landscape of Sodalis pseudogenes, and potential mechanisms for their control. Between 53% and 74% of the Sodalis transcriptome remains active in cell-free culture. Mean sense transcription from Coding Domain Sequences (CDS) is four-times greater than that from pseudogenes. Comparative genomic analysis of six Illumina-sequenced Sodalis isolates from different host Glossina species shows pseudogenes make up ~40% of the 2,729 genes in the core genome, suggesting that they are stable and/or Sodalis is a recent introduction across the Glossina genus as a facultative symbiont. These data further shed light on the importance of transcriptional and translational control in deciphering host-microbe interactions, and demonstrate that pseudogenes are more complex than a simple degrading DNA sequence. The combination of genomics, transcriptomics and proteomics give a multidimensional perspective for studying prokaryotic genomes with a view to elucidating evolutionary adaptation to novel environmental niches.\n\nImportanceBacterial genomes are generally 1Kb in length, organized efficiently (i.e. with few gaps between genes or operons), and few open reading frames (ORFs) lack any predicted function. Intracellular bacteria have been removed from extracellular selection pressures acting on pathways of declining importance to fitness and thus, these bacteria tend to delete redundant genes in favour of smaller functional repertoires - maintaining genome efficiency. In the genomes of endosymbionts with a recent evolutionary relationship with their host, however, this process of genome reduction is not complete; Genes and pathways may be at an intermediate stage, undergoing mutation linked to reduced selection and small population numbers being vertically transmitted from mother to offspring in their hosts, resulting in an increase in abundance of pseudogenes and reduced coding capacities. A greater knowledge of the genomic architecture of persistent pseudogenes, with respect to their DNA structure, mRNA transcription and even putative translation to protein products, will lead to a better understanding of the evolutionary trajectory of endosymbiont genomes, many of which have important roles in arthropod ecology.

genomics↗
bioRxiv2017

Evolutionary compromises to environmental toxins: ammonia and urea tolerance in Drosophila suzukii and Drosophila melanogaster.

The invasive species Drosophila suzukii has evolved morphological and behavioral adaptations to lay eggs under the skin of fresh fruits. This results in severe damage of a wide range of small and stone fruits, thus making this species a serious agricultural and economical threat.\n\nDrosophila suzukii females typically lay few eggs per fruit, preferring not infested fruits. Hence larvae are exposed to a reduced amount of nitrogenous waste products. On the contrary, the innocuous Drosophila melanogaster lays eggs on fermented fruits already infested by conspecifics, with larvae developing in a crowded environment characterized by accumulation of nitrogenous waste such as ammonia and urea. Given these differences in oviposition and larval ecological niche, we expected different behavioral and physiological mechanisms in the two species to cope with nitrogenous waste. We investigated the impact of different concentrations of ammonia and urea on fecundity and larval development in both species. Females and larvae of D. suzukii showed a greater sensitivity to high concentration of both compounds, with a dramatic decrease in fecundity and egg viability.\n\nTo better understand the pathways underlying these differences, we evaluated the effect on ornithine aminotransferase and glutathione-S-transferase, two enzymes involved in nitrogen metabolism and stress response that are expressed during larval development. Under ammonia and urea exposure, the expression of these enzymes was significantly reduced in D. suzukii.\n\nThe fact that D. suzukiis shift from rotten to fresh fruit as oviposition and larval substrate resulted in less efficient detoxifying and excretory mechanisms represents a potential approach for its control. Fecundity and larval development are in fact dramatically impaired by nitrogen waste products. These findings can help in planning effective strategies of sustainable pest management that targets both females and larvae.

evolutionary biology↗
bioRxiv2017

Polymorphisms In The Yeast Galactose Sensor Underlie A Natural Continuum Of Nutrient-Decision Phenotypes

In nature, microbes often need to \"decide\" which of several available nutrients to utilize, a choice that depends on a cells inherent preference and external nutrient levels. While natural environments can have mixtures of different nutrients, phenotypic variation in microbes decisions of which nutrient to utilize is poorly studied. Here, we quantified differences in the concentration of glucose and galactose required to induce galactose-responsive (GAL) genes across 36 wild S. cerevisiae strains. Using bulk segregant analysis, we found that a locus containing the galactose sensor GAL3 was associated with differences in GAL signaling in eight different crosses. Using allele replacements, we confirmed that GAL3 is the major driver of GAL induction variation, and that GAL3 allelic variation alone can explain as much as 90% of the variation in GAL induction in a cross. The GAL3 variants we found modulate the diauxic lag, a selectable trait. These results suggest that ecological constraints on the galactose pathway may have led to variation in a single protein, allowing cells to quantitatively tune their response to nutrient changes in the environment.\n\nAuthor summaryIn nature, microbes often need to decide which of many potential nutrients to consume. This decision making process is complex, involving both intracellular constraints and the organisms perception of the environment. To begin to mimic the complexity of natural environments, we grew cells in mixtures of two sugars, glucose and galactose. We find that in mixed environments, the sugar concentration at which cells decides to induce galactose-utilizing (GAL) genes is highly variable in natural isolates of yeast. By analyzing crosses of phenotypically different strains, we identified a locus containing the galactose sensor, a gene that in theory could allow cells to tune their perception of the environment. We confirmed that the galactose sensor can explain upwards of 90% of the variation in the decision to induce GAL genes. Finally, we show that the variation in the galactose sensor can modulate the time required for cells to switch from utilizing glucose to galactose. Our results suggest that signaling pathways can be highly variable across strains and thereby might allow for rapid adaption in fluctuating environments.

genetics↗
bioRxiv2017

Extensive phenotypic plasticity in a seasonal butterfly limits potential for evolutionary responses to environmental change

Understanding how populations adapt to changing environments is a major goal in evolutionary biology and ecology, and particularly urgent for predicting resilience to climate change. Phenotypic plasticity, the ability to express multiple phenotypes from the same genome, is a widespread adaptation to short-term environmental fluctuations, but whether it facilitates adaptation to environmental change on evolutionary timescales, such as those under climate change, remains contentious. Here, we investigate plasticity and adaptive potential in an African savannah butterfly displaying extensive plasticity as adaptation to predictable dry-wet seasonality. We assess the transcriptional architecture of seasonal plasticity and find pervasive gene expression differences between the seasonal phenotypes, reflecting a genome-wide plasticity programme. Strikingly, intra-population genetic variation for this response is highly depleted, possibly reflecting strong purifying selection in its savannah habitat where an environmental cue (temperature) reliably predicts seasonal transitions and the cost of a mismatched phenotype is high. Under climate change the accuracy of such cues may deteriorate, rendering dominant reactions norm maladaptive. Therefore, depleted variation for plasticity as reported here may crucially limit evolutionary potential when conditions change, and seasonally plastic species may in fact be especially vulnerable to climate change.

evolutionary biology↗
bioRxiv2017

Bacterial community composition and dynamics spanning five years in freshwater bog lakes

Bacteria play a key role in freshwater biogeochemical cycling, but long-term trends in freshwater bacterial community composition and dynamics are not yet well characterized. We used a multi-year time series of 16S rRNA gene amplicon sequencing data from eight bog lakes to census the freshwater bacterial community and observe annual and seasonal trends in abundance. Multiple sites and sampling events were necessary to begin to fully describe the bacterial communities. Each lake and layer contained a distinct bacterial community, with distinct levels of richness and indicator taxa that likely reflected the environmental conditions of each site. The community present in each year and site was also unique. Despite high interannual variability in community composition, we detected a core community of ubiquitous freshwater taxa. Although trends in abundance did not repeat annually, each freshwater lineage within the communities had a consistent lifestyle, defined by persistence, abundance, and variability. The results of our analysis emphasize the importance of long-term observations, as analyzing only a single year of data would not have allowed us to describe the dynamics and composition of these freshwater bacterial communities to the extent presented here.\n\nImportanceLakes are excellent systems for investigating bacterial community dynamics because they have clear boundaries and strong environmental gradients. The results of our research demonstrate that bacterial community dynamics operate on multi-year timescales, a finding which likely applies to other ecosystems, with implications for study design and interpretation. Understanding the drivers and controls of bacterial communities on long time scales would improve both our knowledge of fundamental properties of bacterial communities, and our ability to predict community states. In this specific ecosystem, bog lakes play a disproportionately large role in global carbon cycling, and the information presented here may ultimately help refine carbon budgets for these lakes. Finally, all data and code in this study are publicly available. We hope that this will serve as a resource to anyone seeking to answer their own microbial ecology questions using a multi-year time series.

microbiology↗
bioRxiv2017

Co-evolution of dispersal with behaviour favours social polymorphism

Dispersal determines gene flow among groups in a population and so plays a major role in many ecological and evolutionary processes, from biological invasions to species extinctions. Because patterns of gene flow shape kin structure, dispersal is also important to the evolution of social behaviours that influence reproduction and survival within groups. Conversely, dispersal patterns depend on kin structure and social behaviour. Dispersal and social behaviour therefore co-evolve but the nature and consequences of this interplay are not well understood. Here, we model this co-evolution and show that it readily leads to the emergence and maintenance of two broadly-defined social morphs: a sessile, benevolent morph expressed by individuals who tend to increase the fecundity of others within their group relative to their own; and a dispersive, selfserving morph expressed by individuals who tend to increase their own fecundity relative to others within their group. This social polymorphism arises as a consequence of a positive linkage between the loci responsible for dispersal and social behaviour, leading to benevolent individuals preferentially interacting with relatives and self-serving individuals with non-relatives. We find that this positive linkage is favoured under a large spectrum of conditions, which suggests that an association between dispersal proclivity and other social traits should be common in nature. In line with this prediction, dispersing individuals across a wide range of organisms have been reported to differ in their social tendencies from non-dispersing individuals.

evolutionary biology↗
bioRxiv2017

Predicting The Evolutionary Consequences Of Trophy Hunting On A Quantitative Trait

Some ecologists suggest that trophy hunting (e.g. harvesting males with a desirable trait above a certain size) can lead to rapid phenotypic change, which has led to an ongoing discussion about evolutionary consequences of trophy hunting. Claims of rapid evolution come from the statistical analyses of data, with no examination of whether these results are theoretically plausible. We constructed simple quantitative genetic models to explore how a range of hunting scenarios affects the evolution of a trophy such as horn length. We show that trophy hunting does lead to trophy evolution defined as change in the mean breeding value of the trait. However, the fastest rates of phenotypic change attributable to trophy hunting via evolution that are theoretically possible under standard assumptions of quantitative genetics are 1 to 2 orders of magnitude slower than the fastest rates reported from statistical analyses. Our work suggests a re-evaluation of the likely evolutionary consequences of trophy hunting would be appropriate when setting policy. Our work does not consider the ethical or ecological consequences of trophy hunting.

evolutionary biology↗
bioRxiv2017

Genomic regression of claw keratin, taste receptor and light-associated genes inform biology and evolutionary origins of snakes

Regressive evolution of anatomical traits corresponds with the regression of genomic loci underlying such characters. As such, studying patterns of gene loss can be instrumental in addressing questions of gene function, resolving conflicting results from anatomical studies, and understanding the evolutionary history of clades. The origin of snakes coincided with the regression of a number of anatomical traits, including limbs, taste buds and the visual system. By studying the genomes of snakes, I was able to test three hypotheses associated with the regression of these features. The first concerns two keratins that are putatively specific to claws. Both genes that encode these keratins were pseudogenized/deleted in snake genomes, providing additional evidence of claw- specificity. The second hypothesis is whether snakes lack taste buds, an issue complicated by unequivocal, conflicting results in the literature. I found evidence that different snakes have lost one or more taste receptors, but all snakes examined retained at least some capacity for taste. The final hypothesis I addressed is that the earliest snakes were adapted to a dim light niche. I found evidence of deleted and pseudogenized genes with light- associated functions in snakes, demonstrating a pattern of gene loss similar to other historically nocturnal clades. Together these data also provide some bearing on the ecological origins of snakes, including molecular dating estimates that suggest dim light adaptation preceded the loss of limbs.

evolutionary biology↗
bioRxiv2017

Quantification of inter-sample differences in T cell receptor sequences

Inter-sample comparisons of the T cell receptor (TCR) repertoire are crucial for gaining a better understanding into the immunological states determined by different collections of T cells from different donor sites, cell types, and genetic and pathological backgrounds. As a theoretical approach for the quantitative comparison, previous studies utilized the Poisson abundance models and the conventional methods in ecology, which focus on the abundance distribution of observed TCR sequences. However, these methods ignore the details of the measured sequences and are consequently unable to identify sub-repertoires that might have the contributions to the observed inter-sample differences. In this paper, we propose a new comparative approach based on TCR sequence information, which can estimate the low-dimensional structure by projecting the pairwise sequence dissimilarities in high-dimensional sequence space. The inter-sample differences are then quantified according to information-theoretic measures among the distributions of data estimated in the embedded space. Using an actual dataset of TCR sequences in transgenic mice that have strong restrictions on somatic recombination, we demonstrate that our proposed method can accurately identify the inter-sample hierarchical structure, which is consistent with that estimated by previous methods based on abundance or count information. Moreover, we identified the key sequences that contribute to the pairwise sample differences. Such identification of the sequences contributing to variation in immune cell repertoires may provide substantial insight for the development of new immunotherapies and vaccines.

immunology↗