@misc{9857, author = {Schmidt, Tom and Barton, Nicholas H and Rasic, Gordana and Turley, Andrew and Montgomery, Brian and Iturbe Ormaetxe, Inaki and Cook, Peter and Ryan, Peter and Ritchie, Scott and Hoffmann, Ary and O’Neill, Scott and Turelli, Michael}, publisher = {Public Library of Science }, title = {{Supporting information concerning observed wMel frequencies and analyses of habitat variables}}, doi = {10.1371/journal.pbio.2001894.s015}, year = {2017}, } @misc{9858, author = {Schmidt, Tom and Barton, Nicholas H and Rasic, Gordana and Turley, Andrew and Montgomery, Brian and Iturbe Ormaetxe, Inaki and Cook, Peter and Ryan, Peter and Ritchie, Scott and Hoffmann, Ary and O’Neill, Scott and Turelli, Michael}, publisher = {Public Library of Science}, title = {{Excel file with data on mosquito densities, Wolbachia infection status and housing characteristics}}, doi = {10.1371/journal.pbio.2001894.s016}, year = {2017}, } @article{990, abstract = {Assortative mating is an important driver of speciation in populations with gene flow and is predicted to evolve under certain conditions in few-locus models. However, the evolution of assortment is less understood for mating based on quantitative traits, which are often characterized by high genetic variability and extensive linkage disequilibrium between trait loci. We explore this scenario for a two-deme model with migration, by considering a single polygenic trait subject to divergent viability selection across demes, as well as assortative mating and sexual selection within demes, and investigate how trait divergence is shaped by various evolutionary forces. Our analysis reveals the existence of sharp thresholds of assortment strength, at which divergence increases dramatically. We also study the evolution of assortment via invasion of modifiers of mate discrimination and show that the ES assortment strength has an intermediate value under a range of migration-selection parameters, even in diverged populations, due to subtle effects which depend sensitively on the extent of phenotypic variation within these populations. The evolutionary dynamics of the polygenic trait is studied using the hypergeometric and infinitesimal models. We further investigate the sensitivity of our results to the assumptions of the hypergeometric model, using individual-based simulations.}, author = {Sachdeva, Himani and Barton, Nicholas H}, issn = {00143820}, journal = {Evolution; International Journal of Organic Evolution}, number = {6}, pages = {1478 -- 1493 }, publisher = {Wiley-Blackwell}, title = {{Divergence and evolution of assortative mating in a polygenic trait model of speciation with gene flow}}, doi = {10.1111/evo.13252}, volume = {71}, year = {2017}, } @phdthesis{1125, abstract = {Natural environments are never constant but subject to spatial and temporal change on all scales, increasingly so due to human activity. Hence, it is crucial to understand the impact of environmental variation on evolutionary processes. In this thesis, I present three topics that share the common theme of environmental variation, yet illustrate its effect from different perspectives. First, I show how a temporally fluctuating environment gives rise to second-order selection on a modifier for stress-induced mutagenesis. Without fluctuations, when populations are adapted to their environment, mutation rates are minimized. I argue that a stress-induced mutator mechanism may only be maintained if the population is repeatedly subjected to diverse environmental challenges, and I outline implications of the presented results to antibiotic treatment strategies. Second, I discuss my work on the evolution of dispersal. Besides reproducing known results about the effect of heterogeneous habitats on dispersal, it identifies spatial changes in dispersal type frequencies as a source for selection for increased propensities to disperse. This concept contains effects of relatedness that are known to promote dispersal, and I explain how it identifies other forces selecting for dispersal and puts them on a common scale. Third, I analyse genetic variances of phenotypic traits under multivariate stabilizing selection. For the case of constant environments, I generalize known formulae of equilibrium variances to multiple traits and discuss how the genetic variance of a focal trait is influenced by selection on background traits. I conclude by presenting ideas and preliminary work aiming at including environmental fluctuations in the form of moving trait optima into the model.}, author = {Novak, Sebastian}, issn = {2663-337X}, pages = {124}, publisher = {Institute of Science and Technology Austria}, title = {{Evolutionary proccesses in variable emvironments}}, year = {2016}, } @phdthesis{1131, abstract = {Evolution of gene regulation is important for phenotypic evolution and diversity. Sequence-specific binding of regulatory proteins is one of the key regulatory mechanisms determining gene expression. Although there has been intense interest in evolution of regulatory binding sites in the last decades, a theoretical understanding is far from being complete. In this thesis, I aim at a better understanding of the evolution of transcriptional regulatory binding sequences by using biophysical and population genetic models. In the first part of the thesis, I discuss how to formulate the evolutionary dynamics of binding se- quences in a single isolated binding site and in promoter/enhancer regions. I develop a theoretical framework bridging between a thermodynamical model for transcription and a mutation-selection-drift model for monomorphic populations. I mainly address the typical evolutionary rates, and how they de- pend on biophysical parameters (e.g. binding length and specificity) and population genetic parameters (e.g. population size and selection strength). In the second part of the thesis, I analyse empirical data for a better evolutionary and biophysical understanding of sequence-specific binding of bacterial RNA polymerase. First, I infer selection on regulatory and non-regulatory binding sites of RNA polymerase in the E. coli K12 genome. Second, I infer the chemical potential of RNA polymerase, an important but unknown physical parameter defining the threshold energy for strong binding. Furthermore, I try to understand the relation between the lac promoter sequence diversity and the LacZ activity variation among 20 bacterial isolates by constructing a simple but biophysically motivated gene expression model. Lastly, I lay out a statistical framework to predict adaptive point mutations in de novo promoter evolution in a selection experiment.}, author = {Tugrul, Murat}, issn = {2663-337X}, pages = {89}, publisher = {Institute of Science and Technology Austria}, title = {{Evolution of transcriptional regulatory sequences}}, year = {2016}, } @article{1158, abstract = {Speciation results from the progressive accumulation of mutations that decrease the probability of mating between parental populations or reduce the fitness of hybrids—the so-called species barriers. The speciation genomic literature, however, is mainly a collection of case studies, each with its own approach and specificities, such that a global view of the gradual process of evolution from one to two species is currently lacking. Of primary importance is the prevalence of gene flow between diverging entities, which is central in most species concepts and has been widely discussed in recent years. Here, we explore the continuum of speciation thanks to a comparative analysis of genomic data from 61 pairs of populations/species of animals with variable levels of divergence. Gene flow between diverging gene pools is assessed under an approximate Bayesian computation (ABC) framework. We show that the intermediate "grey zone" of speciation, in which taxonomy is often controversial, spans from 0.5% to 2% of net synonymous divergence, irrespective of species life history traits or ecology. Thanks to appropriate modeling of among-locus variation in genetic drift and introgression rate, we clarify the status of the majority of ambiguous cases and uncover a number of cryptic species. Our analysis also reveals the high incidence in animals of semi-isolated species (when some but not all loci are affected by barriers to gene flow) and highlights the intrinsic difficulty, both statistical and conceptual, of delineating species in the grey zone of speciation.}, author = {Roux, Camille and Fraisse, Christelle and Romiguier, Jonathan and Anciaux, Youann and Galtier, Nicolas and Bierne, Nicolas}, journal = {PLoS Biology}, number = {12}, publisher = {Public Library of Science}, title = {{Shedding light on the grey zone of speciation along a continuum of genomic divergence}}, doi = {10.1371/journal.pbio.2000234}, volume = {14}, year = {2016}, } @article{1172, abstract = {A central issue in cell biology is the physico-chemical basis of organelle biogenesis in intracellular trafficking pathways, its most impressive manifestation being the biogenesis of Golgi cisternae. At a basic level, such morphologically and chemically distinct compartments should arise from an interplay between the molecular transport and chemical maturation. Here, we formulate analytically tractable, minimalist models, that incorporate this interplay between transport and chemical progression in physical space, and explore the conditions for de novo biogenesis of distinct cisternae. We propose new quantitative measures that can discriminate between the various models of transport in a qualitative manner-this includes measures of the dynamics in steady state and the dynamical response to perturbations of the kind amenable to live-cell imaging.}, author = {Sachdeva, Himani and Barma, Mustansir and Rao, Madan}, journal = {Scientific Reports}, publisher = {Nature Publishing Group}, title = {{Nonequilibrium description of de novo biogenesis and transport through Golgi-like cisternae}}, doi = {10.1038/srep38840}, volume = {6}, year = {2016}, } @article{1631, abstract = {Ancestral processes are fundamental to modern population genetics and spatial structure has been the subject of intense interest for many years. Despite this interest, almost nothing is known about the distribution of the locations of pedigree or genetic ancestors. Using both spatially continuous and stepping-stone models, we show that the distribution of pedigree ancestors approaches a travelling wave, for which we develop two alternative approximations. The speed and width of the wave are sensitive to the local details of the model. After a short time, genetic ancestors spread far more slowly than pedigree ancestors, ultimately diffusing out with radius ## rather than spreading at constant speed. In contrast to the wave of pedigree ancestors, the spread of genetic ancestry is insensitive to the local details of the models.}, author = {Kelleher, Jerome and Etheridge, Alison and Véber, Amandine and Barton, Nicholas H}, journal = {Theoretical Population Biology}, pages = {1 -- 12}, publisher = {Academic Press}, title = {{Spread of pedigree versus genetic ancestry in spatially distributed populations}}, doi = {10.1016/j.tpb.2015.10.008}, volume = {108}, year = {2016}, } @misc{5550, abstract = {We collected flower colour information on species in the tribe Antirrhineae from taxonomic literature. We also retreived molecular data from GenBank for as many of these species as possible to estimate phylogenetic relationships among these taxa. We then used the R package 'diversitree' to examine patterns of evolutionary transitions between anthocyanin and yellow pigmentation across the phylogeny. For full details of the methods see: Ellis TJ and Field DL "Repeated gains in yellow and anthocyanin pigmentation in flower colour transitions in the Antirrhineae”, Annals of Botany (in press)}, author = {Ellis, Thomas and Field, David}, publisher = {Institute of Science and Technology Austria}, title = {{Flower colour data and phylogeny (NEXUS) files}}, doi = {10.15479/AT:ISTA:34}, year = {2016}, } @misc{5551, abstract = {Data from array experiments investigating pollinator behaviour on snapdragons in controlled conditions, and their effect on plant mating. Data were collected as part of Tom Ellis' PhD thesis , submitted February 2016. We placed a total of 36 plants in a grid inside a closed organza tent, with a single hive of commercially bred bumblebees (Bombus hortorum). We used only the yellow-flowered Antirrhinum majus striatum and the magenta-flowered Antirrhinum majus pseudomajus, at ratios of 6:36, 12:24, 18:18, 24:12 and 30:6. After 24 hours to learn how to deal with snapdragons, I observed pollinators foraging on plants, and recorded the transitions between plants. Thereafter seeds on plants were allowed to develops. A sample of these were grown to maturity when their flower colour could be determined, and they were scored as yellow, magenta, or hybrid.}, author = {Ellis, Thomas}, publisher = {Institute of Science and Technology Austria}, title = {{Data on pollinator observations and offpsring phenotypes}}, doi = {10.15479/AT:ISTA:35}, year = {2016}, } @misc{5552, abstract = {Data on pollinator visitation to wild snapdragons in a natural hybrid zone, collected as part of Tom Ellis' PhD thesis (submitted February 2016). Snapdragon flowers have a mouth-like structure which pollinators must open to access nectar. We placed 5mm cellophane tags in these mouths, which are held in place by the pressure of the flower until a pollinator visits. When she opens the flower, the tag drops out, and one can infer a visit. We surveyed plants over multiple days in 2010, 2011 and 2012. Also included are data on phenotypic and demographic variables which may be explanatory variables for pollinator visitation.}, author = {Ellis, Thomas}, publisher = {Institute of Science and Technology Austria}, title = {{Pollinator visitation data for wild Antirrhinum majus plants, with phenotypic and frequency data.}}, doi = {10.15479/AT:ISTA:36}, year = {2016}, } @misc{5553, abstract = {Genotypic, phenotypic and demographic data for 2128 wild snapdragons and 1127 open-pollinated progeny from a natural hybrid zone, collected as part of Tom Ellis' PhD thesis (submitted) February 2016). Tissue samples were sent to LGC Genomics in Berlin for DNA extraction, and genotyping at 70 SNP markers by KASPR genotyping. 29 of these SNPs failed to amplify reliably, and have been removed from this dataset. Other data were retreived from an online database of this population at www.antspec.org.}, author = {Field, David and Ellis, Thomas}, keywords = {paternity assignment, pedigree, matting patterns, assortative mating, Antirrhinum majus, frequency-dependent selection, plant-pollinator interaction}, publisher = {Institute of Science and Technology Austria}, title = {{Inference of mating patterns among wild snapdragons in a natural hybrid zone in 2012}}, doi = {10.15479/AT:ISTA:37}, year = {2016}, } @misc{5554, abstract = {The data stored here is used in Murat Tugrul's PhD thesis (Chapter 3), which is related to the evolution of bacterial RNA polymerase binding. Magdalena Steinrueck (PhD Student in Calin Guet's group at IST Austria) performed the experiments and created the data on de novo promoter evolution. Fabienne Jesse (PhD Student in Jon Bollback's group at IST Austria) performed the experiments and created the data on lac promoter evolution.}, author = {Tugrul, Murat}, keywords = {RNAP binding, de novo promoter evolution, lac promoter}, publisher = {Institute of Science and Technology Austria}, title = {{Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase}}, doi = {10.15479/AT:ISTA:43}, year = {2016}, } @article{1518, abstract = {The inference of demographic history from genome data is hindered by a lack of efficient computational approaches. In particular, it has proved difficult to exploit the information contained in the distribution of genealogies across the genome. We have previously shown that the generating function (GF) of genealogies can be used to analytically compute likelihoods of demographic models from configurations of mutations in short sequence blocks (Lohse et al. 2011). Although the GF has a simple, recursive form, the size of such likelihood calculations explodes quickly with the number of individuals and applications of this framework have so far been mainly limited to small samples (pairs and triplets) for which the GF can be written by hand. Here we investigate several strategies for exploiting the inherent symmetries of the coalescent. In particular, we show that the GF of genealogies can be decomposed into a set of equivalence classes that allows likelihood calculations from nontrivial samples. Using this strategy, we automated blockwise likelihood calculations for a general set of demographic scenarios in Mathematica. These histories may involve population size changes, continuous migration, discrete divergence, and admixture between multiple populations. To give a concrete example, we calculate the likelihood for a model of isolation with migration (IM), assuming two diploid samples without phase and outgroup information. We demonstrate the new inference scheme with an analysis of two individual butterfly genomes from the sister species Heliconius melpomene rosina and H. cydno.}, author = {Lohse, Konrad and Chmelik, Martin and Martin, Simon and Barton, Nicholas H}, journal = {Genetics}, number = {2}, pages = {775 -- 786}, publisher = {Genetics Society of America}, title = {{Efficient strategies for calculating blockwise likelihoods under the coalescent}}, doi = {10.1534/genetics.115.183814}, volume = {202}, year = {2016}, } @inproceedings{1349, abstract = {Crossing fitness valleys is one of the major obstacles to function optimization. In this paper we investigate how the structure of the fitness valley, namely its depth d and length ℓ, influence the runtime of different strategies for crossing these valleys. We present a runtime comparison between the (1+1) EA and two non-elitist nature-inspired algorithms, Strong Selection Weak Mutation (SSWM) and the Metropolis algorithm. While the (1+1) EA has to jump across the valley to a point of higher fitness because it does not accept decreasing moves, the non-elitist algorithms may cross the valley by accepting worsening moves. We show that while the runtime of the (1+1) EA algorithm depends critically on the length of the valley, the runtimes of the non-elitist algorithms depend crucially only on the depth of the valley. In particular, the expected runtime of both SSWM and Metropolis is polynomial in ℓ and exponential in d while the (1+1) EA is efficient only for valleys of small length. Moreover, we show that both SSWM and Metropolis can also efficiently optimize a rugged function consisting of consecutive valleys.}, author = {Oliveto, Pietro and Paixao, Tiago and Heredia, Jorge and Sudholt, Dirk and Trubenova, Barbora}, booktitle = {Proceedings of the Genetic and Evolutionary Computation Conference 2016 }, location = {Denver, CO, USA}, pages = {1163 -- 1170}, publisher = {ACM}, title = {{When non-elitism outperforms elitism for crossing fitness valleys}}, doi = {10.1145/2908812.2908909}, year = {2016}, } @article{1356, author = {Barton, Nicholas H}, journal = {Genetics}, number = {1}, pages = {3 -- 4}, publisher = {Genetics Society of America}, title = {{Sewall Wright on evolution in Mendelian populations and the “Shifting Balance”}}, doi = {10.1534/genetics.115.184796}, volume = {202}, year = {2016}, } @article{1357, author = {Barton, Nicholas H}, journal = {Genetics}, number = {3}, pages = {865 -- 866}, publisher = {Genetics Society of America}, title = {{Richard Hudson and Norman Kaplan on the coalescent process}}, doi = {10.1534/genetics.116.187542}, volume = {202}, year = {2016}, } @article{1358, abstract = {Gene regulation relies on the specificity of transcription factor (TF)–DNA interactions. Limited specificity may lead to crosstalk: a regulatory state in which a gene is either incorrectly activated due to noncognate TF–DNA interactions or remains erroneously inactive. As each TF can have numerous interactions with noncognate cis-regulatory elements, crosstalk is inherently a global problem, yet has previously not been studied as such. We construct a theoretical framework to analyse the effects of global crosstalk on gene regulation. We find that crosstalk presents a significant challenge for organisms with low-specificity TFs, such as metazoans. Crosstalk is not easily mitigated by known regulatory schemes acting at equilibrium, including variants of cooperativity and combinatorial regulation. Our results suggest that crosstalk imposes a previously unexplored global constraint on the functioning and evolution of regulatory networks, which is qualitatively distinct from the known constraints that act at the level of individual gene regulatory elements.}, author = {Friedlander, Tamar and Prizak, Roshan and Guet, Calin C and Barton, Nicholas H and Tkacik, Gasper}, journal = {Nature Communications}, publisher = {Nature Publishing Group}, title = {{Intrinsic limits to gene regulation by global crosstalk}}, doi = {10.1038/ncomms12307}, volume = {7}, year = {2016}, } @article{1359, abstract = {The role of gene interactions in the evolutionary process has long been controversial. Although some argue that they are not of importance, because most variation is additive, others claim that their effect in the long term can be substantial. Here, we focus on the long-term effects of genetic interactions under directional selection assuming no mutation or dominance, and that epistasis is symmetrical overall. We ask by how much the mean of a complex trait can be increased by selection and analyze two extreme regimes, in which either drift or selection dominate the dynamics of allele frequencies. In both scenarios, epistatic interactions affect the long-term response to selection by modulating the additive genetic variance. When drift dominates, we extend Robertson ’ s [Robertson A (1960) Proc R Soc Lond B Biol Sci 153(951):234 − 249] argument to show that, for any form of epistasis, the total response of a haploid population is proportional to the initial total genotypic variance. In contrast, the total response of a diploid population is increased by epistasis, for a given initial genotypic variance. When selection dominates, we show that the total selection response can only be increased by epistasis when s ome initially deleterious alleles become favored as the genetic background changes. We find a sim- ple approximation for this effect and show that, in this regime, it is the structure of the genotype - phenotype map that matters and not the variance components of the population.}, author = {Paixao, Tiago and Barton, Nicholas H}, journal = {PNAS}, number = {16}, pages = {4422 -- 4427}, publisher = {National Academy of Sciences}, title = {{The effect of gene interactions on the long-term response to selection}}, doi = {10.1073/pnas.1518830113}, volume = {113}, year = {2016}, } @article{1382, abstract = {Background and aims Angiosperms display remarkable diversity in flower colour, implying that transitions between pigmentation phenotypes must have been common. Despite progress in understanding transitions between anthocyanin (blue, purple, pink or red) and unpigmented (white) flowers, little is known about the evolutionary patterns of flower-colour transitions in lineages with both yellow and anthocyanin-pigmented flowers. This study investigates the relative rates of evolutionary transitions between different combinations of yellow- and anthocyanin-pigmentation phenotypes in the tribe Antirrhineae. Methods We surveyed taxonomic literature for data on anthocyanin and yellow floral pigmentation for 369 species across the tribe. We then reconstructed the phylogeny of 169 taxa and used phylogenetic comparative methods to estimate transition rates among pigmentation phenotypes across the phylogeny. Key Results In contrast to previous studies we found a bias towards transitions involving a gain in pigmentation, although transitions to phenotypes with both anthocyanin and yellow taxa are nevertheless extremely rare. Despite the dominance of yellow and anthocyanin-pigmented taxa, transitions between these phenotypes are constrained to move through a white intermediate stage, whereas transitions to double-pigmentation are very rare. The most abundant transitions are between anthocyanin-pigmented and unpigmented flowers, and similarly the most abundant polymorphic taxa were those with anthocyanin-pigmented and unpigmented flowers. Conclusions Our findings show that pigment evolution is limited by the presence of other floral pigments. This interaction between anthocyanin and yellow pigments constrains the breadth of potential floral diversity observed in nature. In particular, they suggest that selection has repeatedly acted to promote the spread of single-pigmented phenotypes across the Antirrhineae phylogeny. Furthermore, the correlation between transition rates and polymorphism suggests that the forces causing and maintaining variance in the short term reflect evolutionary processes on longer time scales.}, author = {Ellis, Thomas and Field, David}, journal = {Annals of Botany}, number = {7}, pages = {1133 -- 1140}, publisher = {Oxford University Press}, title = {{Repeated gains in yellow and anthocyanin pigmentation in flower colour transitions in the Antirrhineae}}, doi = {10.1093/aob/mcw043}, volume = {117}, year = {2016}, }