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Search indexed bioRxiv preprints in genomics, neuroscience, cell biology and bioinformatics. Read source abstracts and check manuscript versions; preprints are not peer reviewed.

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At least 991 records · Page 55Linked to original sources

bioRxiv2015

Disruption of endosperm development is a major cause of hybrid seed inviability between Mimulus guttatus and M. nudatus

O_LIDivergence of developmental mechanisms within populations may lead to hybrid developmental failure, and may be a factor driving speciation in angiosperms.\nC_LIO_LIWe investigate patterns of endosperm and embryo development in Mimulus guttatus and the closely related, serpentine endemic M. nudatus, and compare them to those of reciprocal hybrid seed. We address whether disruption in hybrid seed development is the primary source of reproductive isolation between these sympatric taxa.\nC_LIO_LIM. guttatus and M. nudatus differ in the pattern and timing of endosperm and embryo development. Some hybrid seed exhibit early disruption of endosperm development and are completely inviable, while others develop relatively normally at first, but later exhibit impaired endosperm proliferation and low germination success. These developmental patterns are reflected in mature hybrid seed, which are either small and flat (indicating little to no endosperm), or shriveled (indicating reduced endosperm volume). Hybrid seed inviability forms a potent reproductive barrier between M. guttatus and M. nudatus.\nC_LIO_LIWe shed light on the extent of developmental variation between closely related species within the M. guttatus species complex, an important ecological model system, and provide a partial mechanism for the hybrid barrier between M. guttatus and M. nudatus.\nC_LI

Evolutionary Biology↗

bioRxiv2015

Variation in linked selection and recombination drive genomic divergence during allopatric speciation of European and American aspens

Despite the global economic and ecological importance of forest trees, the genomic basis of differential adaptation and speciation in tree species is still poorly understood. Populus tremula and P. tremuloides are two of the most widespread tree species in the Northern Hemisphere. Using whole-genome re-sequencing data of 24 P. tremula and 22 P. tremuloides individuals, we find that the two species diverged [~]2.2-3.1 million years ago, coinciding with the severing of the Bering land bridge and the onset of dramatic climatic oscillations during the Pleistocene. Both species have experienced substantial population expansions following long-term declines after species divergence. We detect widespread and heterogeneous genomic differentiation between species, and in accordance with the expectation of allopatric speciation, coalescent simulations suggest that neutral evolutionary processes can account for most of the observed patterns of genomic differentiation. However, there is an excess of regions exhibiting extreme differentiation relative to those expected under demographic simulations, which is indicative of the action of natural selection. Overall genetic differentiation is negatively associated with recombination rate in both species, providing strong support for a role of linked selection in generating the heterogeneous genomic landscape of differentiation between species. Finally, we identify a number of candidate regions and genes that may have been subject to positive and/or balancing selection during the speciation process.

Evolutionary Biology↗

bioRxiv2015

A highly diverse, desert-like microbial biocenosis on solar panels in a Mediterranean city

Microorganisms colonize a wide range of natural and artificial environments although there are hardly any data on the microbial ecology of one the most widespread man-made extreme structures: solar panels. Here we show that solar panels in a Mediterranean city (Valencia, Spain) harbor a highly diverse microbial community with more than 500 different species per panel, most of which belong to drought-, heat- and radiation-adapted bacterial genera, and sun-irradiation adapted epiphytic fungi. The taxonomic and functional profiles of this microbial community and the characterization of selected culturable bacteria reveal the existence of a diverse mesophilic microbial community on the panels surface. This biocenosis proved to be more similar to the ones inhabiting deserts than to any human or urban microbial ecosystem. This unique microbial community shows different day/night proteomic profiles; it is dominated by reddish pigment- and sphingolipid-producers, and is adapted to withstand circadian cycles of high temperatures, desiccation and solar radiation.

Microbiology↗

bioRxiv2015

Adaptation to an invasive host is collapsing a native ecotype

Locally adapted populations are often used as model systems for the early stages of ecological speciation, but most of these young divergent lineages will never become complete species. While the collapse of incipient species is theoretically common, very few examples have been documented in nature. Here I show that soapberry bugs (Jadera haematoloma) have lost adaptations to their native host plant (Cardiospermum corindum) and are regionally specializing on an invasive host plant (Koelreuteria elegans), collapsing a classic and well-documented example of local adaptation. All populations that were adapted to the native host - including those still found on that host today - are now better adapted to the invasive in multiple phenotypes. Weak differentiation remains in two traits, suggesting that homogenization across the region is incomplete. This study highlights the potential for adaptation to invasive species to disrupt native communities by swamping adaptation to native conditions through maladaptive gene flow.

Evolutionary Biology↗

bioRxiv2015

Dead or gone? Bayesian inference on mortality for the dispersing sex

O_LIEstimates of age-specific mortality are regularly used in ecology, evolution, and conservation research. However, existing methods to estimate mortality from re-sighting records of marked individuals fail at estimating mortality of males for species with male natal dispersal due to the uncertainty surrounding disappearances of adult males from study populations.\nC_LIO_LIHere, we develop a mortality model that imputes dispersal state (i.e., died or left) for uncertain male records as a latent state jointly with the coefficients of a parametric mortality model in a Bayesian hierarchical framework. To check the performance of our model, we first conduct a simulation study. We then apply our model to a long-term data set for African lions. Using these data, we further scrutinise the mortality estimates derived from our model by incrementally reducing the level of uncertainty in the male records. We achieve this by taking advantage of an experts intuition on the likely fate of each uncertain male record.\nC_LIO_LIWe find that our new model produces accurate mortality parameters for simulated data of varying sample sizes and proportions of uncertain male records. From the empirical study we learned that our model provides similar mortality estimates for different levels of uncertainty in male records. However, a sensitivity of the mortality estimates to varying uncertainty is, as can be expected, detectable.\nC_LIO_LIWe conclude that our model provides a solution to the challenge of estimating male mortality in species with data-deficiency for males due to natal dispersal. Given the utility of sex-specific mortality estimates in biological and conservation research and the virtual ubiquity of sex-biased dispersal, our model will be useful to a wide variety of applications.\nC_LI

Preprint↗

bioRxiv2015

pong: fast analysis and visualization of latent clusters in population genetic data

1 MotivationA series of methods in population genetics use multilocus genotype data to assign individuals membership in latent clusters. These methods belong to a broad class of mixed-membership models, such as latent Dirichlet allocation used to analyze text corpora. Inference from mixed-membership models can produce different output matrices when repeatedly applied to the same inputs, and the number of latent clusters is a parameter that is often varied in the analysis pipeline. For these reasons, quantifying, visualizing, and annotating the output from mixed-membership models are bottlenecks for investigators across multiple disciplines from ecology to text data mining.\n\n2 ResultsWe introduce pong, a network-graphical approach for analyzing and visualizing membership in latent clusters with a native D3.js interactive visualization. pong leverages efficient algorithms for solving the Assignment Problem to dramatically reduce runtime while increasing accuracy compared to other methods that process output from mixed-membership models. We apply pong to 225,705 unlinked genome-wide single-nucleotide variants from 2,426 unrelated individuals in the 1000 Genomes Project, and identify previously overlooked aspects of global human population structure. We show that pong outpaces current solutions by more than an order of magnitude in runtime while providing a customizable and interactive visualization of population structure that is more accurate than those produced by current tools.\n\n3 Availabilitypong is freely available and can be installed using the Python package management system pip. pongs source code is available at https://github.com/abehr/pong.\n\n4 Contactaaron_behr@alumni.brown.edu,\n\nsramachandran@brown.edu

Genomics↗

bioRxiv2015

Adaptive Protein Evolution in Animals and the Effective Population Size Hypothesis.

The rate at which genomes adapt to environmental changes and the prevalence of adaptive processes in molecular evolution are two controversial issues in current evolutionary genetics. Previous attempts to quantify the genome-wide rate of adaptation through amino-acid substitution have revealed a surprising diversity of patterns, with some species (e.g. Drosophila) experiencing a very high adaptive rate, while other (e.g. humans) are dominated by nearly-neutral processes. It has been suggested that this discrepancy reflects between-species differences in effective population size. Published studies, however, were mainly focused on model organisms, and relied on disparate data sets and methodologies, so that an overview of the prevalence of adaptive protein evolution in nature is currently lacking. Here we extend existing estimators of the amino-acid adaptive rate by explicitly modelling the effect of favourable mutations on non-synonymous polymorphism patterns, and we apply these methods to a newly-built, homogeneous data set of 44 non-model animal species pairs. Data analysis uncovers a major contribution of adaptive evolution to the amino-acid substitution process across all major metazoan phyla - with the notable exception of humans and primates. The proportion of adaptive amino-acid substitution is found to be positively correlated to species effective population size. This relationship, however, appears to be primarily driven by a decreased rate of nearly-neutral amino-acid substitution due to more efficient purifying selection in large populations. Our results reveal that adaptive processes dominate the evolution of proteins in most animal species, but do not corroborate the hypothesis that adaptive substitutions accumulate at a faster rate in large populations. Implications regarding the factors influencing the rate of adaptive evolution and positive selection detection in humans vs. other organisms are discussed.\n\nAuthor summaryThe rate at which species adapt to environmental changes is a controversial topic. The theory predicts that adaptation is easier in large than in small populations, and the genomic studies of model organisms have revealed a much higher adaptive rate in large population-sized flies than in small population-sized humans and apes. Here we build and analyse a large data set of protein-coding sequences made of thousands of genes in 44 pairs of species from various groups of animals including insects, molluscs, annelids, echinoderms, reptiles, birds, and mammals. Extending and improving existing data analysis methods, we show that adaptation is a major process in protein evolution across all phyla of animals: the proportion of amino-acid substitutions that occurred adaptively is above 50% in a majority of species, and reaches up to 90%. Our analysis does not confirm that population size, here approached through species genetic diversity and ecological traits, does influence the rate of adaptive molecular evolution, but points to human and apes as a special case, compared to other animals, in terms of adaptive genomic processes.

Evolutionary Biology↗

bioRxiv2015

Male sex pheromone components in the butterfly Heliconius melpomene

Sex specific pheromones are known to play an important role in butterfly courtship, and may influence both individual reproductive success and reproductive isolation between species. Extensive ecological, behavioural and genetic studies of Heliconius butterflies have made a substantial contribution to our understanding of speciation. Male pheromones, although long suspected to play an important role, have received relatively little attention in this genus. Here, we combine morphological, chemical, and behavioural analyses of male pheromones in the Neotropical butterfly Heliconius melpomene. First, we identify putative androconia that are specialized brush-like scales that lie within the shiny grey region of the male hindwing. We then describe putative male sex pheromone compounds, which are largely confined to the androconial region of the hindwing of mature males, but are absent in immature males and females. Finally, behavioural choice experiments reveal that females of H. melpomene, H. erato and H. timareta strongly discriminate against conspecific males which have their androconial region experimentally blocked. As well as demonstrating the importance of chemical signalling for female mate choice in Heliconius butterflies, the results describe structures involved in release of the pheromone and a list of potential male sex pheromone compounds.

Evolutionary Biology↗

bioRxiv2015

Evolutionary dynamics of a quantitative trait in a finite asexual population.

In finite populations, mutation limitation and genetic drift can hinder evolutionary diversification. We consider the evolution of a quantitative trait in an asexual population whose size can vary and depends explicitly on the trait. Previous work showed that evolutionary branching is certain (\"deterministic branching\") above a threshold population size, but uncertain (\"stochastic branching\") below it. Using the stationary distribution of the populations trait variance, we identify three qualitatively different sub-domains of \"stochastic branching\" and illustrate our results using a model of social evolution. We find that in very small populations, branching will almost never be observed; in intermediate populations, branching is intermittent, arising and disappearing over time; in larger populations, finally, branching is expected to occur and persist for substantial periods of time. Our study provides a clearer picture of the ecological conditions that facilitate the appearance and persistence of novel evolutionary lineages in the face of genetic drift.

Evolutionary Biology↗

bioRxiv2015

Dynamics of microbial community composition and soil organic carbon mineralization in soil following addition of pyrogenic and fresh organic matter

Pyrogenic organic matter (PyOM) additions to soils can have large impacts on soil organic C (SOC) cycling. Because the soil microbial community drives SOC fluxes, understanding how PyOM additions affect soil microbes is essential to understanding how PyOM affects SOC. We studied SOC dynamics and surveyed soil microbial communities after OM additions in a field experiment. We produced and applied either 350{degrees}C corn stover PyOM or an equivalent amount of dried corn stover to a Typic Fragiudept soil. Stover increased SOC-derived and total CO2 fluxes (up to 6x), and caused rapid and persistent changes in bacterial community composition over 82 days. In contrast, PyOM only temporarily increased total soil CO2 fluxes (up to 2x) and caused fewer changes in bacterial community composition. 70% of the OTUs that increased in response to PyOM additions also responded to stover additions. These OTUs likely thrive on easily-mineralizable C that is found both in stover and, to a lesser extent, in PyOM. In contrast, we also identified unique PyOM-responders, which may respond to substrates such as polyaromatic C. In particular, members of Gemmatimonadetes tended to increase in relative abundance in response to PyOM but not to fresh organic matter. We identify taxa to target for future investigations of the mechanistic underpinnings of ecological phenomena associated with PyOM additions to soil.

Microbiology↗

bioRxiv2015

Low virulence evolves as a bet-hedging strategy in fluctuating environment

The effect of fluctuating environmental conditions (i.e. environmental stochasticity) on the evolution of virulence has been broadly overlooked, presumably due to a lack of connection between the fields of evolutionary epidemiology and insect ecology. Practitioners of the latter have known for a long time that stochastic environmental variations can impact the population dynamics of many insects, some of which are vectors of infectious diseases. Here we investigate whether environmental stochasticity affecting a vectors life history can have an indirect impact on the evolutionarily expected virulence of the parasite, using Chagas disease as an example. We model the evolution of virulence using the adaptive dynamics framework, showing that parasite virulence should decrease when the vector's dynamics randomly change in time. The decrease is even more pronounced when environmental variations are frequent and ample. This decrease in virulence can be viewed as a bet-hedging strategy: when a parasite is at a risk of not being transmitted (e.g. because vectors are scarce), its best option is to stay in the host longer - that is, to be less virulent. Lowering virulence is thus very similar to increasing iteroparity, a well-known risk-spreading strategy, and should be expected to evolve whenever parasite transmission varies randomly in time.

Evolutionary Biology↗

bioRxiv2015

Structural specialities, curiosities and record-breaking features of crustacean reproduction

Crustaceans are a morphologically, physiologically and ecologically highly diverse animal group and correspondingly diverse are their reproductive characteristics. They have evolved structural specialities with respect to penis construction, sperm form, sperm storage, fertilization and brood care. Unique in the animal kingdom are safety lines that safeguard hatching and first molting. Further curiosities are dwarf males in parasitic and sessile taxa and bacteria-induced gigantism and infectious feminization in crustacean hosts. Record-breaking features in animals are relative penis length, clutch size, sperm size, chromosome number, viability of resting eggs, and fossil ages of penis, sperm and brooded embryos. These reproductive peculiarities are reviewed and their implication for basic and applied biology is discussed, including the early evolution and diversification of brood care in arthropods, sperm competition and assurance of paternity, posthumous paternity and sustainable male-based fishery, and ecotype changes by man-made pollution.

Zoology↗

bioRxiv2015

Meta3C analysis of a mouse gut microbiome

Microbial populations as well as they biochemical activities are important components of environmental ecosystems, including the human microbiome. Deciphering the genomic content of these complex mixes of species is an important challenge but is essential to fully understand the regulation of their ecological balance. Here we apply meta3C, an experimental and computational approach that exploits the physical contacts between chromosomes to characterize large genomic regions of bacterial species mixed together, on a truly complex ecosystem: the mouse gut microbiota. Meta3C, which was initially described and applied onto controlled mixes of microorganisms, allowed the de novo assembly and scaffolding of numerous bacteria present into this natural mix. Importantly, the scaffolds analyzed exhibit the structural properties expected from typical bacterial chromosomes. Meta3C therefore paves the way to the in-depth analysis of genomic structuration of complex populations.

Genomics↗

bioRxiv2016

On the optimal use of isotherm models for the characterization of biosorption of lead onto algae

For the first time we apply a new method based on the mathematical derivation of some known isotherm from the Burr function which describes many birth-death (sorption-desorption) phenomena in ecology and economy. Therefore, in this study the experimental isotherm data of biosorption of Pb(II) onto algae was modeled to Langmuir, Hill-Sips, Brouers-Sotolongo, Brouers-Gaspard, and Redlich-Peterson isotherm models. The parameters of each model were determined by non linear fitting algorithms using Mathematica program. The maximum Pb(II) removal rate increased with the increase of temperature and reached the maximum value (98%) at the temperature of 40 {degrees}C. The results showed that the Hill-Sips and the Brouers-Sotolongo isotherms were definitely the most suitable models to satisfactorily describe biosorption of Pb(II) on the algal biomass. In addition, as these two models gave very close results, the use of an intermediate one the Brouers-Gaspard isotherm model could also describe the sorption in most cases. High coefficient of determination values were obtained by using non linear methods and these findings are contrary to most works in this field that use linearization methods. Further, this study showed that a complete set of data is necessary to have a good representation of the isotherm and using only coefficient of determination is not always an adequate tool to compare the goodness of the non linear fit of an isotherm models.

Bioengineering↗

bioRxiv2016

The genealogical sorting index and species delimitation

The Genealogical Sorting Index (gsi) has been widely used in species-delimitation studies, where it is usually interpreted as a measure of the degree to which each of several predefined groups of specimens display a pattern of divergent evolution in a phylogenetic tree. Here we show that the gsi value obtained for a given group is highly dependent on the structure of the tree outside of the group of interest. By calculating the gsi from simulated datasets we demonstrate this dependence undermines some of desirable properties of the statistic. We also review the use of the gsi delimitation studies, and show that the gsi has typically been used under scenarios in which it is expected to produce large and statistically significant results for samples that are not divergent from all other populations and thus should not be considered species. Our proposed solution to this problem performs better than the gsi in under these conditions. Nevertheless, we show that our modified approach can produce positive results for populations that are connected by substantial levels of gene flow, and are thus unlikely to represent distinct species. We stress that the properties of gsi made clear in this manuscript must be taken into account if the statistic is used in species-delimitation studies. More generally, we argue that the results of genetic species-delimitation methods need to be interpreted in the light the biological and ecological setting of a study, and not treated as the final test applied to hypotheses generated by other data.

Evolutionary Biology↗

bioRxiv2016

Skew in ovarian activation depends on domicile size in a facultatively social thrips

Costs and benefits of group living are a fundamental topic in behavioural ecology. Resource availability affects individuals breeding prospects alone and in groups, as well as how reproduction is distributed within groups (\"reproductive skew\"). Here, we provide correlational evidence in facultatively social thrips that breeding resources are associated with (1) whether solitary or social living is favoured, and (2) the degree of ovarian skew.\n\nDunatothrips aneurae (Thysanoptera, Phlaeothripidae) cooperatively build silk \"domiciles\" on Australian Acacias, feeding exclusively from internal phyllode surfaces. Per capita productivity scaled differently with group size depending on domicile volume - females in small domiciles did better alone than in groups, whereas in large domiciles single and group-nesting females did equally well. Ovarian dissections revealed that in small domiciles some females were nonreproductive, indicating ovarian (i.e. reproductive) skew. Skew increased as domicile size decreased and group size increased. Breeders had smaller oocyte volume in smaller domiciles, especially those containing nonreproductives.\n\nThese findings suggest group formation and reproductive skew in D. aneurae may be influenced by reproductive competition for breeding resources. Nonreproductive females in small domiciles may be reproductively suppressed, subfertile, or waiting to reproduce. We speculate they may avoid eviction by contributing as \"helpers\" to domicile maintenance.

Evolutionary Biology↗

bioRxiv2016

Getting the hologenome concept right: An eco-evolutionary framework for hosts and their microbiomes

Given the complexity of host-microbiota symbioses, scientists and philosophers are asking questions at new biological levels of hierarchical organization - What is a holobiont and hologenome? When should this vocabulary be applied? Are these concepts a null hypothesis for host-microbe systems or limited to a certain spectrum of symbiotic interactions such as host-microbial coevolution? Critical discourse is necessary in this nascent area, but productive discourse requires that skeptics and proponents use the same lexicon. For instance, critiquing the hologenome concept is not synonymous with critiquing coevolution, and arguing that an entity is not a primary unit of selection dismisses that the hologenome concept has always embraced multi-level selection. Holobionts and hologenomes are incontrovertible, multipartite entities that result from ecological, evolutionary and genetic processes at varying levels. They are not restricted to one special process but constitute a wider vocabulary and framework for host biology in light of the microbiome.

Evolutionary Biology↗

bioRxiv2016

Disentangling incomplete lineage sorting and introgression to refine species-tree estimates for Lake Tanganyika cichlid fishes

Adaptive radiation is thought to be responsible for the evolution of a great portion of the past and present diversity of life. Instances of adaptive radiation, characterized by the rapid emergence of an array of species as a consequence to their adaptation to distinct ecological niches, are important study systems in evolutionary biology. However, because of the rapid lineage formation in these groups, and the occurrence of hybridization between the participating species, it is often difficult to reconstruct the phylogenetic history of species that underwent an adaptive radiation. In this study, we present a novel approach for species-tree estimation in rapidly diversifying lineages, where introgression is known to occur, and apply it to a multimarker dataset containing up to 16 specimens per species for a set of 45 species of East African cichlid fishes (522 individuals in total), with a main focus on the cichlid species flock of Lake Tanganyika. We first identified, using age distributions of most recent common ancestors in individual gene trees, those lineages in our dataset that show strong signatures of past introgression. This led us to formulate three hypotheses of introgression between different lineages of Tanganyika cichlids: the ancestor of Boulengerochromini (or of Boulengerochromini and Bathybatini) received genomic material from the derived H-lineage; the common ancestor of Cyprichromini and Perissodini experienced, in turn, introgression from Boulengerochromini and/or Bathybatini; and the Lake Tanganyika Haplochromini and closely related riverine lineages received genetic material from Cyphotilapiini. We then applied the multispecies coalescent model to estimate the species tree of Lake Tanganyika cichlids, but excluded the lineages involved in these introgression events, as the multispecies coalescent model does not incorporate introgression. This resulted in a robust species tree, in which the Lamprologini were placed as sister lineage to the H-lineage (including the Eretmodini), and we identify a series of rapid splitting events at the base of the H-lineage. Divergence ages estimated with the multispecies coalescent model were substantially younger than age estimates based on concatenation, and agree with the geological history of the Great Lakes of East Africa. Finally, we formally tested the three hypotheses of introgression using a likelihood framework, and find strong support for introgression between some of the cichlid tribes of Lake Tanganyika.

Evolutionary Biology↗