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Results for “evolutionary biology”

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bioRxiv2016

A new improved and extended version of the multicell bacterial simulator gro

gro is a cell programming language developed in Klavins Lab for simulating colony growth and cell-cell communication. It is used as a synthetic biology prototyping tool for simulating multicellular biocircuits. In this work, we present several extensions made to gro that improve the performance of the simulator, make it easier to use and provide new functionalities. The new version of gro is between one and two orders of magnitude faster than the original version. It is able to grow microbial colonies with up to 105 cells in less than 20 minutes. A new library, CellEngine, accelerates the resolution of spatial physical interactions between growing and dividing cells by implementing a new shoving algorithm. A genetic library, CellPro, based on Probabilistic Timed Automata, simulates gene expression dynamics using simplified and easy to compute digital proteins. We also propose a more convenient language specification layer, ProSpec, based on the idea that proteins drive cell behavior. CellNutrient, another library, implements Monod-based growth and nutrient uptake functionalities. The intercellular signaling management was improved and extended in a library called CellSignals. Finally, bacterial conjugation, another local cell-cell communication process, was added to the simulator. To show the versatility and potential outreach of this version of gro, we provide studies and novel examples ranging from synthetic biology to evolutionary microbiology. We believe that the upgrades implemented for gro have made it into a powerful and fast prototyping tool capable of simulating a large variety of systems and synthetic biology designs.

synthetic biology↗

bioRxiv2017

Cell type-specific expression profiling sheds light on the development of a peculiar neuron, housing a complex organelle

Specialized neurons called cnidocytes define the phylum Cnidaria. They possess an explosive organelle called cnidocyst that is important for prey capture and antipredator defense. An extraordinary morphological and functional complexity of the cnidocysts has inspired numerous studies to investigate their structure and development. However, the transcriptomes of the cells bearing these unique organelles are yet to be characterized, impeding our understanding of the genetic basis of their biogenesis. By generating transgenic lines of the sea anemone Nematostella vectensis using the CRISPR/Cas9 system, we have characterized cell-type specific transcriptomic profiles of various stages of cnidocyte maturation and show that nematogenesis (the formation of functional cnidocysts) is underpinned by dramatic shifts in the spatiotemporal gene expression. We also highlight the stark fall in transcriptional-levels of toxin and structural protein coding genes within cnidocytes with the maturation of capsule. We further reveal that the majority of upregulated genes and enriched biochemical pathways specific to cnidocytes are yet to be characterized. Finally, we unravel the recruitment of a metazoan stress-related transcription factor complex into nematogenesis and highlight its role in the formation of a structural protein of the cnidocyst wall. Thus, we provide novel insights into the biology, development, and evolution of cnidocytes.

evolutionary biology↗

bioRxiv2018

Laboratory evolution from social to solitary behavior in the N2 reference strain is unnecessary for its fitness advantages

The standard reference Caenorhabditis elegans strain, N2, has evolved marked behavioral changes since its isolation from the wild 67 years ago. Laboratory-derived variation in two genes, npr-1 and glb-5, suppress aerotaxis behaviors on food, resulting in N2 animals evolving from social to solitary feeding strategies. We show here that the derived alleles of npr-1 and glb-5 can confer large fitness advantages in standard laboratory conditions, suggesting that the changes in feeding strategies were beneficial to the N2 strain. However, by using environmental manipulations that suppress social behaviors, we showed the fitness advantages of the derived alleles remained unchanged, suggesting selection on these alleles acted through biological traits unrelated to solitary behavior. Transcriptomics analysis, developmental timing assays, and feeding assays showed that N2 animals mature faster, produce more sperm, and eat more food than a strain containing ancestral alleles of these genes (CX12311) regardless of the behavioral strategies. The O2-sensing neurons URX, AQR, and PQR and the pheromone biosynthesis and lipid regulating enzyme encoded by daf-22 are necessary for the full fitness advantages. We suggest that changes to social/solitary behavior in N2 were a pleiotropic consequence of npr-1 and glb-5s ability to modify integrated O2 and pheromone neural circuits that regulate feeding rate and reproductive development. Together, our results demonstrate how laboratory evolution can lead to profound changes in a strain used as a model by for understanding a variety of fundamental biological processes.

evolutionary biology↗

bioRxiv2018

Comparative genomics of ten new Caenorhabditis species

The nematode Caenorhabditis elegans has been central to the understanding of metazoan biology. However, C. elegans is but one species among millions and the significance of this important model organism will only be fully revealed if it is placed in a rich evolutionary context. Global sampling efforts have led to the discovery of over 50 putative species from the genus Caenorhabditis, many of which await formal species description. Here, we present species descriptions for ten new Caenorhabditis species. We also present draft genome sequences for nine of these new species, along with a transcriptome assembly for one. We exploit these whole-genome data to reconstruct the Caenorhabditis phylogeny and use this phylogenetic tree to dissect the evolution of morphology in the genus. We show unexpected complexity in the evolutionary history of key developmental pathway genes. The genomic data also permit large scale analysis of gene structure, which we find to be highly variable within the genus. These new species and the associated genomic resources will be essential in our attempts to understand the evolutionary origins of the C. elegans model.

evolutionary biology↗

bioRxiv2018

Domestication and temperature modulate gene expression signatures and growth in the Australasian snapper Chrysophrys auratus

ABSTRACT\n\nIdentifying genes and pathways involved in domestication is critical to understand how species change in response to human-induced selection pressures. We experimentally manipulated temperature conditions for F1-hatchery and wild Australasian snapper (Chrysophrys auratus) for 18 days and measured differences in growth, white muscle RNA transcription and haematological blood parameters. Over 2.2 Gb paired-end reads were assembled de novo for a total set of 33,017 transcripts (N50 = 2,804). We found pronounced growth and gene expression differences between wild and domesticated individuals related to global developmental and immune pathways. Temperature modulated growth responses were linked to major pathways affecting metabolism, cell regulation and signalling. This study is the first step towards gaining an understanding of the changes occurring in the early stages of domestication, and the mechanisms underlying thermal adaptation and associated growth in poikilothermic vertebrates. Our study further provides the first transcriptome resources for studying biological questions in this non-model fish species.

evolutionary biology↗

bioRxiv2014

Panpulmonate habitat transitions: tracing the evolution of Acochlidia (Heterobranchia,Gastropoda)

The evolution and diversification of euthyneuran slugs and snails was likely strongly influenced by habitat transitions from marine to terrestrial and limnic systems. Well-supported euthyneuran phylogenies with detailed morphological data can provide information on the historical, biological and ecological background in which these habitat shifts took place allowing for comparison across taxa. Acochlidian slugs are basal pulmonates with uncertain relationships to other major panpulmonate clades. They present a unique evolutionary history with representatives in the marine mesopsammon, but also benthic lineages in brackish water, limnic habitats and (semi-)terrestrial environments. We present the first comprehensive molecular phylogeny on Acochlidia, based on a global sampling that covers nearly 85 % of the described species diversity, and additionally, nearly doubles known diversity by undescribed taxa. Our phylogenetic hypotheses are highly congruent with previous morphological analyses and confirm all included recognized families and genera. We further establish an ancestral area chronogram for Acochlidia, document changes in diversification rates in their evolution via the birth-death-shift-model and reconstruct the ancestral states for major ecological traits. Based on our data, Acochlidia originated from a marine, mesopsammic ancestor adapted to tropical waters, in the mid Mesozoic Jurassic. We found that the two major subclades present a remarkably different evolutionary history. The Microhedylacea are morphologically highly-adapted to the marine mesopsammon. They show a circum-tropical distribution with several independent shifts to temperate and temperate cold-habitats, but remained in stunning morphological and ecological stasis since the late Mesozoic. Their evolutionary specialization, which includes a remarkable and potentially irreversible meiofaunal syndrome, guaranteed long-term survival and locally high species densities but also resembles a dead-end road to morphological and ecological diversity. In contrast, the Hedylopsacea are characterized by morphological flexibility and ecologically by independent habitat shifts out of the marine mesopsammon, conquering (semi-)terrestrial and limnic habitats. Originating from interstitial ancestors with moderate adaptations to the mesopsammic world, they reestablished a benthic lifestyle and secondary gigantism in body size. The major radiations and habitat shifts in hedylopsacean families occured in the central Indo-West Pacific in the Paleogene. In the Western Atlantic only one enigmatic representative is known probably presenting a relict of a former pan-Tethys distribution of the clade. This study on acochlidian phylogeny and biogeography adds another facet of the yet complex panpulmonate evolution and shows the various parallel pathways in which these snails and slugs invaded non-marine habitats. Given the complex evolutionary history of Acochlidia, which represent only a small group of Panpulmonata, this study highlights the need to generate comprehensively-sampled species-level phylogenies to understand euthyneuran evolution.

Evolutionary Biology↗

bioRxiv2016

Resurrected protein interaction networks reveal the strong rewiring that leads to network organisation after whole genome duplication

The evolution of plants is characterized by several rounds of ancient whole genome duplication, sometimes closely associated with the origin of large groups of species. A good example is the {gamma} triplication at the origin of core eudicots. Core eudicots comprise about 75% of flowering plants and are characterized by the canalization of reproductive development. To better understand the impact of this genomic event, we studied the protein interaction network of MADS-domain transcription factors, which are key regulators of reproductive development. We accurately inferred, resurrected and tested the interactions of ancestral proteins before and after the triplication and directly compared these ancestral networks to the networks of Arabidopsis and tomato. We find that the {gamma} triplication generated a dramatically innovated network that strongly rewired through the addition of many new interactions. Many of these interactions were established between paralogous proteins and a new interaction partner, establishing new redundancy. Simulations show that both node and edge addition through the triplication were important to maintain modularity in the network. In addition to generating insights into the impact of whole genome duplication and elementary processes involved in network evolution, our data provide a resource for comparative developmental biology in flowering plants.

Evolutionary Biology↗

bioRxiv2017

Horizontal gene cluster transfer increased hallucinogenic mushroom diversity

Secondary metabolites are heterogeneous natural products that often mediate interactions between species. The tryptophan-derived secondary metabolite, psilocin, is a serotonin receptor agonist that induces altered states of consciousness. A phylogenetically disjunct group of mushroom-forming fungi in the Agaricales produce the psilocin prodrug, psilocybin. Spotty phylogenetic distributions of fungal compounds are sometimes explained by horizontal transfer of metabolic gene clusters among unrelated fungi with overlapping niches. We report the discovery of a psilocybin gene cluster in three hallucinogenic mushroom genomes, and evidence for its horizontal transfer between fungal lineages. Patterns of gene distribution and transmission suggest that psilocybin provides a fitness advantage in the dung and late wood-decay niches, which may be reservoirs of fungal indole-based metabolites that alter behavior of mycophagous and wood-eating invertebrates. These hallucinogenic mushroom genomes will serve as models in neurochemical ecology, advancing the prospecting and synthetic biology of novel neuropharmaceuticals.

evolutionary biology↗

bioRxiv2018

Diversification rates and phylogenies: what are we estimating, and how good are the estimates?

O_LISpecies-specific diversification rates, or \"tip rates\", can be computed quickly from phylogenies and are widely used to study diversification rate variation in relation to geography, ecology, and phenotypes. These tip rates provide a number of theoretical and practical advantages, such as the relaxation of assumptions of rate homogeneity in trait-dependent diversification studies. However, there is substantial confusion in the literature regarding whether these metrics estimate speciation or net diversification rates. Additionally, no study has yet compared the relative performance and accuracy of tip rate metrics across simulated diversification scenarios.\nC_LIO_LIWe compared the statistical performance of three model-free rate metrics (inverse terminal branch lengths; node density metric; DR statistic) and a model-based approach (BAMM). We applied each method to a large set of simulated phylogenies that had been generated under different diversification processes; scenarios included multi-regime time-constant and diversity-dependent trees, as well as trees where the rate of speciation evolves under a diffusion process. We summarized performance in relation to the type of rate variation, the magnitude of rate heterogeneity and rate regime size. We also compared the ability of the metrics to estimate both speciation and net diversification rates.\nC_LIO_LIWe show decisively that model-free tip rate metrics provide a better estimate of the rate of speciation than of net diversification. Error in net diversification rate estimates increases as a function of the relative extinction rate. In contrast, error in speciation rate estimates is low and relatively insensitive to extinction. Overall, and in particular when relative extinction was high, BAMM inferred the most accurate tip rates and exhibited lower error than non-model-based approaches. DR was highly correlated with true speciation rates but exhibited high error variance, and was the best metric for very small rate regimes.\nC_LIO_LIWe found that, of the metrics tested, DR and BAMM are the most useful metrics for studying speciation rate dynamics and trait-dependent diversification. Although BAMM was more accurate than DR overall, the two approaches have complementary strengths. Because tip rate metrics are more reliable estimators of speciation rate, we recommend that empirical studies using these metrics exercise caution when drawing biological interpretations in any situation where the distinction between speciation and net diversification is important.\nC_LI

evolutionary biology↗

bioRxiv2018

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

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

evolutionary biology↗

bioRxiv2016

An In Silico Model to Simulate the Evolution of Biological Aging

Biological aging is characterized by an age-dependent increase in the probability of death and by a decrease in the reproductive capacity. Individual age-dependent rates of survival and reproduction have a strong impact on population dynamics, and the genetic elements determining survival and reproduction are under different selective forces throughout an organism lifespan. Here we develop a highly versatile numerical model of genome evolution -- both asexual and sexual -- for a population of virtual individuals with overlapping generations, where the genetic elements affecting survival and reproduction rate at different life stages are free to evolve due to mutation and selection. Our model recapitulates several emerging properties of natural populations, developing longer reproductive lifespan under stable conditions and shorter survival and reproduction in unstable environments. Faster aging results as the consequence of the reduced strength of purifying selection in more unstable populations, which have large portions of the genome that accumulate detrimental mutations. Unlike sexually reproducing populations under constant resources, asexually reproducing populations fail to develop an age-dependent increase in death rates and decrease in reproduction rates, therefore escaping senescence. Our model provides a powerful in silico framework to simulate how populations and genomes change in the context of biological aging and opens a novel analytical opportunity to characterize how real populations evolve their specific aging dynamics.

Evolutionary Biology↗

bioRxiv2016

A Multidisciplinary Approach to Explain Biological Aging and Longevity

Scientists have been unable to reach a consensus on why organisms age and why they live as long as they do. Here, a multidisciplinary approach was taken in an attempt to understand the root causes of aging. Nonequilibrium thermodynamics may play a previously unappreciated role in determining longevity by governing the dynamics of degradation and renewal within biomolecular ensembles and dictating the inevitability of fidelity loss. The proposed model offers explanations for species longevity trends that have been previously unexplained and for aging-related observations that are considered paradoxical within current paradigms--for example, the elevated damage levels found even in youth within many long-lived species, such as the naked mole-rat. This framework questions whether declining selective pressure is the primary driver of aging, and challenges major tenets of the disposable soma theory. Unifying pertinent principles from diverse disciplines leads to a theoretical framework of biological aging with fewer anomalies, and may be useful in predicting outcomes of experimental attempts to modulate the aging phenotype.

Evolutionary Biology↗

bioRxiv2017

With Our Powers Combined: Integrating Behavioral And Genetic Data To Estimate Mating Success And Sexual Selection

The analysis of sexual selection classically relies on the regression of individual phenotypes against the marginal sums of a males x females matrix of pairwise reproductive success, assessed by genetic parentage analysis. When the matrix is binarized, the marginal sums give the individual mating success. Because such analysis treats male and female mating/reproductive success independently, it ignores that the success of a male x female sexual interaction can be attributable to the phenotype of both individuals. Also, because it is based on genetic data only, it is oblivious to costly yet unproductive matings, which may be documented by behavioral observations. To solve these problems, we propose a statistical model which combines matrices of offspring numbers and behavioral observations. It models reproduction on each mating occasion of a mating season as three stochastic and interdependent pairwise processes, each potentially affected by the phenotype of both individuals and by random individual effect: encounter (Bernoulli), concomitant gamete emission (Bernoulli), and offspring production (Poisson). Applied to data from a mating experiment on brown trout, the model yielded different results from the classical regression analysis, with only a limited effect of male body size on the probability of gamete release and a negative effect of female body size on the probability of encounter and gamete release. Because the general structure of the model can be adapted to other partitioning of the reproductive process, it can be used for a variety of biological systems where behavioral and genetic data are available.

evolutionary biology↗

bioRxiv2018

A generalization of the informational view of non-random mating: Models with variable population frequencies

Mate choice may generate non-random mating patterns. It has been recently shown that the mating distribution caused by mate choice can be expressed as a gain in information with respect to random mating. In that model, the population phenotypic frequencies were assumed as constant during the breeding season. In the present work such restriction was relaxed to consider different encounter-mating processes in which the population frequencies of available individuals change over mating rounds. As with the constant case, here we describe the change in the mating phenotypes by the flow of information with respect to random mating. This information can be partitioned into sexual selection, sexual isolation and a mixed effect. Likewise, the pairwise statistics for total change, sexual selection and sexual isolation are generalized for variable population frequencies.\n\nThe new tests had more power for the detection of the effects of non-random mating when the population frequencies vary during the breeding season. The differences in power were high for sexual selection but slight for sexual isolation scenarios. However, the application of the new formulas require the estimation of frequencies at each mating round. Therefore, choosing one or another type of statistics would depend on the biological scenario as well as in the availability and easiness to split the sampling in more than one mating round.

evolutionary biology↗

bioRxiv2015

Geographic range size is predicted by plant mating system

Species geographic ranges vary enormously, and even closest relatives may differ in range size by several orders of magnitude. With data from hundreds of species spanning 20 genera in 15 families, we show that plant species that autonomously reproduce via self-pollination consistently have larger geographic ranges than their close relatives that generally require two parents for reproduction. Further analyses strongly implicate autonomous self-fertilization in causing this relationship, as it is not driven by traits such as polyploidy or annual life history whose evolution is sometimes correlated with autonomous self-fertilization. Furthermore, we find that selfers occur at higher maximum latitudes and that disparity in range size between selfers and outcrossers increases with time since their separation. Together, these results show that autonomous reproduction -- a critical biological trait that eliminates mate limitation and thus potentially increases the probability of establishment -- increases range size.

Evolutionary Biology↗

bioRxiv2016

Co-estimating Reticulate Phylogenies and Gene Trees from Multi-locus Sequence Data

The multispecies network coalescent (MSNC) is a stochastic process that captures how gene trees grow within the branches of a phylogenetic network. Coupling the MSNC with a stochastic mutational process that operates along the branches of the gene trees gives rise to a generative model of how multiple loci from within and across species evolve in the presence of both incomplete lineage sorting (ILS) and reticulation (e.g., hybridization). We report on a Bayesian method for sampling the parameters of this generative model, including the species phylogeny, gene trees, divergence times, and population sizes, from DNA sequences of multiple independent loci. We demonstrate the utility of our method by analyzing simulated data and reanalyzing three biological data sets. Our results demonstrate the significance of not only co-estimating species phylogenies and gene trees, but also accounting for reticulation and ILS simultaneously. In particular, we show that when gene flow occurs, our method accurately estimates the evolutionary histories, coalescence times, and divergence times. Tree inference methods, on the other hand, underestimate divergence times and overestimate coalescence times when the evolutionary history is reticulate. While the MSNC corresponds to an abstract model of \"intermixture,\" we study the performance of the model and method on simulated data generated under a gene flow model. We show that the method accurately infers the most recent time at which gene flow occurs. Finally, we demonstrate the application of the new method to a 106-locus yeast data set. [Multispecies network coalescent; reticulation; incomplete lineage sorting; phylogenetic network; Bayesian inference; RJMCMC.]

evolutionary biology↗

bioRxiv2018

De novo genome and transcriptome analyses provide insights into the biology of the trematode human parasite Fasciolopsis buski

Many trematode parasites cause infection in humans and are thought to be a major public health problem. Their ecological diversity in different regions provides challenging questions on evolution of these organisms. In this report, we perform transcriptome analysis of the giant intestinal fluke, Fasciolopsis buski, using next generation sequencing technology. Short read sequences derived from polyA containing RNA of this organism were assembled into 30677 unigenes that led to the annotation of 12380 genes. Annotation of the assembled transcripts enabled insight into processes and pathways in the intestinal fluke, such as RNAi pathway and energy metabolism. The expressed kinome of the organism was characterized by identifying all protein kinases. We have also carried out whole genome sequencing and used the sequences to confirm absence of some of the genes, not observed in transcriptome data, such as genes involved in fatty acid biosynthetic pathway. Transcriptome data also helped us to identify some of the expressed transposable elements. Though many Long Interspersed elements (LINEs) were identified, only two Short Interspersed Elements (SINEs) were visible. Overall transcriptome and draft genome analysis of F. buski helped us to characterize some its important biological characteristics and provided enormous resources for development of a suitable diagnostic system and anti-parasitic therapeutic molecules.

evolutionary biology↗

bioRxiv2015

The evolution, diversity and host associations of rhabdoviruses

Metagenomic studies are leading to the discovery of a hidden diversity of RNA viruses. These new viruses are poorly characterised and new approaches are needed predict the host species these viruses pose a risk to. The rhabdoviruses are a diverse family of RNA viruses that includes important pathogens of humans, animals and plants. We have discovered 32 new rhabdoviruses through a combination of our own RNA sequencing of insects and searching public sequence databases. Combining these with previously known sequences we reconstructed the phylogeny of 195 rhabdovirus sequences, and produced the most in depth analysis of the family to date. In most cases we know nothing about the biology of the viruses beyond the host they were identified from, but our dataset provides a powerful phylogenetic approach to predict which are vector-borne viruses and which are specific to vertebrates or arthropods. By reconstructing ancestral and present host states we found that switches between major groups of hosts have occurred rarely during rhabdovirus evolution. This allowed us to propose 76 new likely vector-borne vertebrate viruses among viruses identified from vertebrates or biting insects. Based on currently available data, our analysis suggests it is likely there was a single origin of the known plant viruses and arthropod-borne vertebrate viruses, while vertebrate-specific and arthropod-specific viruses arose at least twice. There are also few transitions between aquatic and terrestrial ecosystems. Viruses also cluster together at a finer scale, with closely related viruses tending to be found in closely related hosts. Our data therefore suggest that throughout their evolution, rhabdoviruses have occasionally jumped between distantly related host species before spreading through related hosts in the same environment. This approach offers a way to predict the most probable biology and key traits of newly discovered viruses.

Evolutionary Biology↗