29 Works

Data from: Opposing effects of allogrooming on disease transmission in ant societies

Fabian J. Theis, Line V. Ugelvig, Carsten Marr & Sylvia Cremer
To prevent epidemics, insect societies have evolved collective disease defences that are highly effective at curing exposed individuals and limiting disease transmission to healthy group members. Grooming is an important sanitary behaviour—either performed towards oneself (self-grooming) or towards others (allogrooming)—to remove infectious agents from the body surface of exposed individuals, but at the risk of disease contraction by the groomer. We use garden ants (Lasius neglectus) and the fungal pathogen Metarhizium as a model system...

Data from: The consequences of an introgression event

Nicholas H. Barton
The spread of adaptive alleles is fundamental to evolution, and in theory, this process is well‐understood. However, only rarely can we follow this process—whether it originates from the spread of a new mutation, or by introgression from another population. In this issue of Molecular Ecology, Hanemaaijer et al. (2018) report on a 25‐year long study of the mosquitoes Anopheles gambiae (Figure 1) and Anopheles coluzzi in Mali, based on genotypes at 15 single‐nucleotide polymorphism (SNP)....

Early queen infection shapes developmental dynamics and induces long-term disease protection in incipient ant colonies

Barbara Casillas-Pérez, Christopher Pull, Filip Naiser, Elisabeth Naderlinger, Jiri Matas & Sylvia Cremer
Infections early in life can have enduring effects on an organism’s development and immunity. In this study, we show that this equally applies to developing “superorganisms” – incipient social insect colonies. When we exposed newly mated Lasius niger ant queens to a low pathogen dose, their colonies grew more slowly than controls before winter, but reached similar sizes afterwards. Independent of exposure, queen hibernation survival improved when the ratio of pupae to workers was small....

Supplementary code for: Polygenic local adaptation in metapopulations: a stochastic eco-evolutionary model

Eniko Szep, Himani Sachdeva & Nick Barton
This paper analyzes the conditions for local adaptation in a metapopulation with infinitely many islands under a model of hard selection, where population size depends on local fitness. Each island belongs to one of two distinct ecological niches or habitats. Fitness is influenced by an additive trait which is under habitat-dependent directional selection. Our analysis is based on the diffusion approximation and accounts for both genetic drift and demographic stochasticity. By neglecting linkage disequilibria, it...

Data from: Pupal cocoons affect sanitary brood care and limit fungal infections in ant colonies

Simon Tragust, Line V. Ugelvig, Michel Chapuisat, Jürgen Heinze & Sylvia Cremer
Background: The brood of ants and other social insects is highly susceptible to pathogens, particularly those that penetrate the soft larval and pupal cuticle. We here test whether the presence of a pupal cocoon, which occurs in some ant species but not in others, affects the sanitary brood care and fungal infection patterns after exposure to the entomopathogenic fungus Metarhizium brunneum. We use a) a comparative approach analysing four species with either naked or cocooned...

Data from: An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice

João P. L. Castro, Michelle N. Yancoskie, Marta Marchini, Stefanie Belohlavy, Layla Hiramatsu, Marek Kučka, William H. Beluch, Ronald Naumann, Isabella Skuplik, John Cobb, Nick H. Barton, Campbell Rolian & Yingguang Frank Chan
Evolutionary studies are often limited by missing data that are critical to understanding the history of selection. Selection experiments, which reproduce rapid evolution under controlled conditions, are excellent tools to study how genomes evolve under selection. Here we present a genomic dissection of the Longshanks selection experiment, in which mice were selectively bred over 20 generations for longer tibiae relative to body mass, resulting in 13% longer tibiae in two replicates. We synthesized evolutionary theory,...

Clines on the seashore: The genomic architecture underlying rapid divergence in the face of gene flow

Anja Marie Westram, Anja M. Westram, Marina Rafajlović, Pragya Chaube, Rui Faria, Tomas Larsson, Marina Panova, Mark Ravinet, Anders Blomberg, Bernhard Mehlig, Kerstin Johannesson & Roger Butlin
Adaptive divergence and speciation may happen despite opposition by gene flow. Identifying the genomic basis underlying divergence with gene flow is a major task in evolutionary genomics. Most approaches (e.g., outlier scans) focus on genomic regions of high differentiation. However, not all genomic architectures potentially underlying divergence are expected to show extreme differentiation. Here, we develop an approach that combines hybrid zone analysis (i.e., focuses on spatial patterns of allele frequency change) with system-specific simulations...

Data from: Ret and Etv4 promote directed movements of progenitor cells during renal branching morphogenesis

Paul Riccio, Cristina Cebrian, Hui Zong, Simon Hippenmeyer & Frank Costantini
Branching morphogenesis of the epithelial ureteric bud forms the renal collecting duct system and is critical for normal nephron number, while low nephron number is implicated in hypertension and renal disease. Ureteric bud growth and branching requires GDNF signaling from the surrounding mesenchyme to cells at the ureteric bud tips, via the Ret receptor tyrosine kinase and coreceptor Gfrα1; Ret signaling up-regulates transcription factors Etv4 and Etv5, which are also critical for branching. Despite extensive...

Data from: Social transfer of pathogenic fungus promotes active immunisation in ant colonies

Matthias Konrad, Meghan L. Vyleta, Fabian J. Theis, Miriam Stock, Simon Tragust, Martina Klatt, Verena Drescher, Carsten Marr, Line V. Ugelvig & Sylvia Cremer
Due to the omnipresent risk of epidemics, insect societies have evolved sophisticated disease defences at the individual and colony level. An intriguing yet little understood phenomenon is that social contact to pathogen-exposed individuals reduces susceptibility of previously naive nestmates to this pathogen. We tested whether such social immunisation in Lasius ants against the entomopathogenic fungus Metarhizium anisopliae is based on active upregulation of the immune system of nestmates following contact to an infectious individual or...

Data from: Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis

Eva Koch, Hernán Morales, Jenny Larsson, Anja Westram, Rui Faria, Alan Lemmon, Emily Lemmon, Kerstin Johannesson & Roger Butlin
Chromosomal inversion polymorphisms, segments of chromosomes that are flipped in orientation and occur in reversed order in some individuals, have long been recognized to play an important role in local adaptation. They can reduce recombination in heterozygous individuals and thus help to maintain sets of locally adapted alleles. In a wide range of organisms, populations adapted to different habitats differ in frequency of inversion arrangements. However, getting a full understanding of the importance of inversions...

VCF files of synonymous SNPs related to: Genomic inference of complex domestication histories in three Solanaceae species

Stéphanie Arnoux, Christelle Fraïsse & Christopher Sauvage
Domestication is a human-induced selection process that imprints the genomes of domesticated populations over a short evolutionary time scale, and that occurs in a given demographic context. Reconstructing historical gene flow, effective population size changes and their timing is therefore of fundamental interest to understand how plant demography and human selection jointly shape genomic divergence during domestication. Yet, the comparison under a single statistical framework of independent domestication histories across different crop species has been...

Data from: Increased grooming after repeated brood care provides sanitary benefits in a clonal ant

Claudia Westhus, Line V. Ugelvig, Edouard Tourdot, Jürgen Heinze, Claudie Doums & Sylvia Cremer
Repeated pathogen exposure is a common threat in colonies of social insects, posing selection pressures on colony members to respond with improved disease-defense performance. We here tested whether experience gained by repeated tending of low-level fungus-exposed (Metarhizium robertsii) larvae may alter the performance of sanitary brood care in the clonal ant, Platythyrea punctata. We trained ants individually over nine consecutive trials to either sham-treated or fungus-exposed larvae. We then compared the larval grooming behavior of...

Data from: Hemimetabolous genomes reveal molecular basis of termite eusociality

Mark C Harrison, Evelien Jongepier, Hugh M. Robertson, Nicolas Arning, Tristan Bitard-Feildel, Hsu Chao, Christopher P. Childers, Huyen Dinh, Harshavardhan Doddapaneni, Shannon Dugan, Johannes Gowin, Carolin Greiner, Yi Han, Haofu Hu, Daniel S.T. Hughes, Ann-Kathrin Huylmans, Carsten Kemena, Lukas P.M. Kremer, Sandra L. Lee, Alberto Lopez-Ezquerra, Ludovic Mallet, Jose M. Monroy-Kuhn, Annabell Moser, Shwetha C. Murali, Donna M. Muzny … & Erich Bornberg-Bauer
Around 150 million years ago, eusocial termites evolved from within the cockroaches, 50 million years before eusocial Hymenoptera, such as bees and ants, appeared. Here, we report the 2-Gb genome of the German cockroach, Blattella germanica, and the 1.3-Gb genome of the drywood termite Cryptotermes secundus. We show evolutionary signatures of termite eusociality by comparing the genomes and transcriptomes of three termites and the cockroach against the background of 16 other eusocial and non-eusocial insects....

Data from: Down syndrome cell adhesion molecule 1: testing for a role in insect immunity, behaviour and reproduction

Robert Peuß, Kristina U. Wensing, Luisa Woestmann, Hendrik Eggert, Barbara Milutinović, Marlene G. U. Sroka, Jörn P. Scharsack, Joachim Kurtz & Sophie A. O. Armitage
Down syndrome cell adhesion molecule 1 (Dscam1) has wide-reaching and vital neuronal functions although the role it plays in insect and crustacean immunity is less well understood. In this study, we combine different approaches to understand the roles that Dscam1 plays in fitness-related contexts in two model insect species. Contrary to our expectations, we found no short-term modulation of Dscam1 gene expression after haemocoelic or oral bacterial exposure in Tribolium castaneum, or after haemocoelic bacterial...

Data from: Is embryo abortion a postzygotic barrier to gene flow between Littorina ecotypes?

Kerstin Johannesson, Zuzanna Zagrodzka, Rui Faria, Anja Westram & Roger Butlin
Genetic incompatibilities contribute to reproductive isolation between many diverging populations, but it is still unclear to what extent they play a role if divergence happens with gene flow. In contact zones between the "Crab" and "Wave" ecotypes of the snail Littorina saxatilis divergent selection forms strong barriers to gene flow, while the role of postzygotic barriers due to selection against hybrids remains unclear. High embryo abortion rates in this species could indicate the presence of...

BayesW time-to-event analysis posterior outputs and summary statistics

Sven Erik Ojavee & Matthew Robinson
Here, we develop a Bayesian approach (BayesW) that provides probabilistic inference of the genetic architecture of age-at-onset phenotypes in a hybrid-parallel sampling scheme that facilitates Bayesian time-to-event large-scale biobank analyses. We show in extensive simulation work that BayesW achieves a greater number of discoveries, better model performance and improved genomic prediction as compared to other approaches. In the UK Biobank, we find many thousands of common genomic regions underlying the age-at-onset of high blood pressure...

Wolbachia frequency data from: Why did the Wolbachia transinfection cross the road? Drift, deterministic dynamics and disease control

Michael Turelli & Nicholas Barton
Maternally inherited Wolbachia transinfections are being introduced into natural mosquito populations to reduce the transmission of dengue, Zika and other arboviruses. Wolbachia-induced cytoplasmic incompatibility provides a frequency-dependent reproductive advantage to infected females that can spread transinfections within and among populations. However, because transinfections generally reduce host fitness, they tend to spread within populations only after their frequency exceeds a critical threshold. This produces bistability with stable equilibrium frequencies at both 0 and 1, analogous to...

Data from: Genetic architecture of repeated phenotypic divergence in Littorina saxatilis ecotype evolution

Eva L Koch, Mark Ravinet, Anja M Westram, Kerstin Johannesson & Roger K. Butlin
Chromosomal inversions have been shown to play a major role in local adaptation by suppressing recombination between alternative arrangements and maintaining beneficial allele combinations. However, so far, their importance relative to the remaining genome remains largely unknown. Understanding the genetic architecture of adaptation requires better estimates of how loci of different effect sizes contribute to phenotypic variation. Here, we used three Swedish islands where the marine snail Littorina saxatilis has repeatedly evolved into two distinct...

Data from: CRISPR-based herd immunity limits phage epidemics in bacterial populations

Pavel Payne, Lukas Geyrhofer, Nick H Barton, Jonathan P Bollback & Nicholas H Barton
Herd immunity, a process in which resistant individuals limit the spread of a pathogen among susceptible hosts has been extensively studied in eukaryotes. Even though bacteria have evolved multiple immune systems against their phage pathogens, herd immunity in bacteria remains unexplored. Here we experimentally demonstrate that herd immunity arises during phage epidemics in structured and unstructured Escherichia coli populations consisting of differing frequencies of susceptible and resistant cells harboring CRISPR immunity. In addition, we develop...

Data from: A sting in the spit: widespread cross-infection of multiple RNA viruses across wild and managed bees

Dino P. McMahon, Matthias A. Fürst, Jesicca Caspar, Panagiotis Theodorou, Mark J. F. Brown & Robert J. Paxton
1.Declining populations of bee pollinators are a cause of concern, with major repercussions for biodiversity loss and food security. RNA viruses associated with honeybees represent a potential threat to other insect pollinators, but the extent of this threat is poorly understood. 2.This study aims to attain a detailed understanding of the current and on going risk of emerging infectious disease (EID) transmission between managed and wild pollinator species across a wide range of RNA viruses....

Data from: Selection history and epistatic interactions impact dynamics of adaptation to novel environmental stresses

Mato Lagator, Nick Colegrave & Paul Neve
In rapidly changing environments, selection history may impact the dynamics of adaptation. Mutations selected in one environment may result in pleiotropic fitness trade-offs in subsequent novel environments, slowing the rates of adaptation. Epistatic interactions between mutations selected in sequential stressful environments may slow or accelerate subsequent rates of adaptation, depending on the nature of that interaction. We explored the dynamics of adaptation during sequential exposure to herbicides with different modes of action in Chlamydomonas reinhardtii....

Data from: Transformation of stimulus correlations by the retina

Kristina D. Simmons, Jason S. Prentice, Gašper Tkačik, Jan Homann, Heather K. Yee, Stephanie E. Palmer, Philip C. Nelson & Vijay Balasubramanian
Redundancies and correlations in the responses of sensory neurons may seem to waste neural resources, but they can also carry cues about structured stimuli and may help the brain to correct for response errors. To investigate the effect of stimulus structure on redundancy in retina, we measured simultaneous responses from populations of retinal ganglion cells presented with natural and artificial stimuli that varied greatly in correlation structure; these stimuli and recordings are publicly available online....

Probabilistic inference of the genetic architecture of functional enrichment of complex traits

Matthew Robinson
We develop a Bayesian model (BayesRR-RC) that provides robust SNP-heritability estimation, an alternative to marker discovery, and accurate genomic prediction, taking 22 seconds per iteration to estimate 8.4 million SNP-effects and 78 SNP-heritability parameters in the UK Biobank. We find that only $\leq$ 10\% of the genetic variation captured for height, body mass index, cardiovascular disease, and type 2 diabetes is attributable to proximal regulatory regions within 10kb upstream of genes, while 12-25% is attributed...

Improving genome-wide association discovery and genomic prediction accuracy in biobank data

Matthew Robinson, Etienne J. Orliac, Daniel Trejo Banos, Sven E. Ojavee, Kristi Läll, Reedik Mägi, Peter M. Visscher & Matthew R. Robinson
Genetically informed, deep-phenotyped biobanks are an important research resource and it is imperative that the most powerful, versatile, and efficient analysis approaches are used. Here, we apply our recently developed Bayesian grouped mixture of regressions model (GMRM) in the UK and Estonian Biobanks and obtain the highest genomic prediction accuracy reported to date across 21 heritable traits. When compared to other approaches, GMRM accuracy was greater than annotation prediction models run in the LDAK or...

Using replicate hybrid zones to understand the genomic basis of adaptive divergence

Anja Marie Westram, Rui Faria, Kerstin Johannesson & Roger Butlin
Combining hybrid zone analysis with genomic data is a promising approach to understanding the genomic basis of adaptive divergence. It allows for the identification of genomic regions underlying barriers to gene flow. It also provides insights into spatial patterns of allele frequency change, informing about the interplay between environmental factors, dispersal and selection. However, when only a single hybrid zone is analysed, it is difficult to separate patterns generated by selection from those resulting from...

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