111 Works

Data from: Intrinsic and realized generation intervals in infectious-disease transmission

David Champredon & Jonathan Dushoff
The generation interval is the interval between the time that an individual is infected by an infector and the time this infector was infected. Its distribution underpins estimates of the reproductive number and hence informs public health strategies. Empirical generation-interval distributions are often derived from contact-tracing data. But linking observed generation intervals to the underlying generation interval required for modeling purposes is surprisingly not straightforward, and misspecifications can lead to incorrect estimates of the reproductive...

Data from: Behavior, morphology, and microhabitat use: what drives individual niche variation?

Raul Costa-Pereira & Jonathan Pruitt
Generalist populations are often composed of individuals each specialized on only a subset of the resources exploited by the entire population. However, the traits underlying such niche variation remain underexplored. Classically, ecologists have focused on understanding why populations vary in their degree of intraspecific niche variation, with less attention paid to how individual-level traits lead to intraspecific differences in niches. We investigated how differences in behavior, morphology, and microhabitat affect niche variation between- and within-individuals...

Data from: What is a disease? Perspectives of the public, health professionals, and legislators

Kari A. O. Tikkinen, Janne S. Leinonen, Gordon H. Guyatt, Shanil Ebrahim & Teppo L. N. Järvinen
Objective: To assess the perception of diseases and the willingness to use public tax revenue for their treatment among relevant stakeholders. Design: A population-based, cross-sectional mailed survey. Setting: Finland Participants: 3 000 laypeople, 1 500 doctors, 1 500 nurses (randomly identified from the databases of the Finnish Population Register, the Finnish Medical Association and the Finnish Nurses Association), and all 200 parliament members. Main outcome measures: Respondents’ perspectives on a 5-point Likert scale on two...

Data from: How “simple” methodological decisions affect interpretation of population structure based on reduced representation library DNA sequencing: a case study using the lake whitefish

Carly F Graham, Douglas R Boreham, Richard G Manzon, Wendylee Stott, Joanna Y Wilson & Christopher M Somers
Reduced representation (RRL) sequencing approaches (e.g., RADSeq, genotyping by sequencing) require decisions about how much to invest in genome coverage and sequencing depth (library quality), as well as choices of values for adjustable bioinformatics parameters. To empirically explore the importance of these “simple” decisions, we generated two independent sequencing libraries for the same 142 individual lake whitefish (Coregonus clupeaformis) using a nextRAD RRL approach: (1) A small number of loci and low sequencing depth (library...

Mitonuclear interactions and introgression genomics of macaque monkeys (Macaca) highlight the influence of behaviour on genome evolution

Ben Evans
In most macaques, females are philopatric and males migrate from their natal ranges, which results in pronounced divergence of mitochondrial genomes within and among species. We therefore predicted that some nuclear genes would have to acquire compensatory mutations to preserve compatibility with diverged interaction partners from the mitochondria. We additionally expected that these sex-differences would have distinctive effects on gene flow in the X and autosomes. Using new genomic data from 29 individuals from eight...

Environmental drivers of Sphagnum growth in peatlands across the Holarctic region

Fia Bengtsson, Håkan Rydin, Jennifer Baltzer, Luca Bragazza, Zhao-Jun Bu, Simon Caporn, Ellen Dorrepaal, Kjell Ivar Flatberg, Olga Galanina, Mariusz Gałka, Anna Ganeva, Irina Goia, Nadezhda Goncharova, Michal Hajek, Akira Haraguchi, Lorna Harris, Elyn Humphreys, Martin Jiroušek, Katarzyna Kajukało, Edgar Karofeld, Natalia Koronatova, Natalia Kosykh, Anna Laine, Mariusz Lamentowicz, Elena Lapshina … & Richard J. Payne
The relative importance of global versus local environmental factors for growth and thus carbon uptake of the bryophyte genus Sphagnum – the main peat-former and ecosystem engineer in northern peatlands – remains unclear. 2) We measured length growth and net primary production (NPP) of two abundant Sphagnum species across 99 Holarctic peatlands. We tested the importance of previously proposed abiotic and biotic drivers for peatland carbon uptake (climate, N deposition, water table depth, and vascular...

Data from: Habitat disturbance alters color contrast and the detectability of cryptic and aposematic frogs

James Barnett, Brandon Varela, Ben Jennings, David Lesbarrères, Jonathan Pruitt & David Green
Animals use color both to conceal and signal their presence, with patterns that match the background, disrupt shape recognition, or highlight features important for communication. The forms that these color patterns take are responses to the visual systems that observe them and the environments within which they are viewed. Increasingly, however, these environments are being affected by human activity. We studied how pattern characteristics and habitat change may affect the detectability of three frog color...

Data from: Demographic expansion and genetic load of the halophyte model plant Eutrema salsugineum

Xiao-Juan Wang, Quan-Jun Hu, Xin-Yi Guo, Kun Wang, Da-Fu Ru, Dmitry A. German, Elizabeth A. Weretilnyk, Richard J. Abbott, Martin Lascoux & Jian-Quan Liu
Eutrema salsugineum is a widely distributed species, which provide a good model to study long-distance dispersal and accumulation of deleterious mutations. Based on population genomic data, we clarified demographic history of E. salsugineum and showed how deleterious alleles accumulated.

Data from: Ranking and characterization of established BMI and lipid associated loci as candidates for gene-environment interactions

Dmitry Shungin, Wei Q. Deng, Tibor V. Varga, Jian'an Luan, Evelin Mihailov, Andres Metspalu, Andrew P. Morris, Nita G. Forouhi, Cecilia Lindgren, Patrik K. E. Magnusson, Nancy L. Pedersen, Göran Hallmans, Audrey Y. Chu, Anne E. Justice, Mariaelisa Graff, Thomas W. Winkler, Lynda M. Rose, Claudia Langenberg, L. Adrienne Cupples, Paul M. Ridker, Nicholas J. Wareham, Ken K. Ong, Ruth J. F. Loos, Daniel I. Chasman, Erik Ingelsson … & Paul W. Franks
Phenotypic variance heterogeneity across genotypes at a single nucleotide polymorphism (SNP) may reflect underlying gene-environment (G·E) or gene-gene interactions. We modeled variance heterogeneity for blood lipids and BMI in up to 44,211 participants and investigated relationships between variance effects (Pv), G·E interaction effects (with smoking and physical activity), and marginal genetic effects (Pm). Correlations between Pv and Pm were stronger for SNPs with established marginal effects (Spearman's ρ=0.401 for triglycerides, and ρ=0.236 for BMI) compared...

Data from: Phylogeography and evolution of a fungal-insect association on the Tibetan Plateau

Yongjie Zhang, Shu Zhang, Yuling Li, Shaoli Ma, Chengshu Wang, Meichun Xiang, Xin Liu, Zhiqiang An, Jianping Xu & Xingzhong Liu
Parasitoidism refers to a major form of inter-species interactions where parasitoids sterilize and/or kill their hosts typically before hosts reach reproductive age. However, relatively little is known about the evolutionary dynamics of parasitoidism. Here we investigate the spatial patterns of genetic variation of Chinese cordyceps, including both the parasitoidal fungus Ophiocordyceps sinensis and its host insects. We sampled broadly from alpine regions on the Tibetan Plateau and obtained sequences on seven fungal and three insect...

Data from: Lichens: a limit to peat growth?

Lorna I. Harris, Tim R. Moore, Nigel T. Roulet & Andrew J. Pinsonneault
1. The fruticose lichens Cladina stellaris and Cladina rangiferina, form thick mats that can cover large areas of northern peatlands (above ~ 50° latitude), including the extensive peatlands of the Hudson Bay Lowland (HBL) in Canada, where lichens may cover up to 50 % of the landscape. Despite the abundance of lichens in northern peatlands, our understanding of their role within peatland ecosystems, and peat accumulation in particular, is limited. 2. We investigate the potential...

Data from: Aposematism: balancing salience and camouflage

James B. Barnett, Nicholas E. Scott-Samuel & Innes C. Cuthill
Aposematic signals are often characterized by high conspicuousness. Larger and brighter signals reinforce avoidance learning, distinguish defended from palatable prey and are more easily memorized by predators. Conspicuous signalling, however, has costs: encounter rates with naive, specialized or nutritionally stressed predators are likely to increase. It has been suggested that intermediate levels of aposematic conspicuousness can evolve to balance deterrence and detectability, especially for moderately defended species. The effectiveness of such signals, however, has not...

Data from: The legacy effects of keystone individuals on collective behavior scale to how long they remain within a group

Jonathan N. Pruitt & Noa Pinter-Wollman
The collective behaviour of social groups is often strongly influenced by one or few individuals, termed here ‘keystone individuals’. We examined whether the influence of keystone individuals on collective behaviour lingers after their departure and whether these lingering effects scale with their tenure in the group. In the social spider, Stegodyphus dumicola, colonies' boldest individuals wield a disproportionately large influence over colony behaviour. We experimentally manipulated keystones' tenure in laboratory-housed colonies and tracked their legacy...

Data from: Hybridization increases mitochondrial production of reactive oxygen species in sunfish

Sherry N. N. Du, Fariborz Khajali, Neal J. Dawson & Graham R. Scott
Mitochondrial dysfunction and oxidative stress have been suggested to be possible mechanisms underlying hybrid breakdown, as a result of mito-nuclear incompatibilities in respiratory complexes of the electron transport system. However, it remains unclear whether hybridization increases the production of reactive oxygen species (ROS) by mitochondria. We used high-resolution respirometry and fluorometry on isolated liver mitochondria to examine mitochondrial physiology and ROS emission in naturally occurring hybrids of pumpkinseed (Lepomis gibbosus) and bluegill (L. macrochirus). ROS...

Data from: Sensory-based niche partitioning in a multiple predator-multiple prey community

Jay J. Falk, Hannah M. Ter Hofstede, Patricia L. Jones, Marjorie M. Dixon, Paul A. Faure, Elisabeth K. V. Kalko & Rachel A. Page
Many predators and parasites eavesdrop on the communication signals of their prey. Eavesdropping is typically studied as dyadic predator–prey species interactions; yet in nature, most predators target multiple prey species and most prey must evade multiple predator species. The impact of predator communities on prey signal evolution is not well understood. Predators could converge in their preferences for conspicuous signal properties, generating competition among predators and natural selection on particular prey signal features. Alternatively, predator...

Data from: Fluc­tu­a­tion domains in adap­tive evo­lu­tion

Carl Boettiger, Jonathan Dushoff & Joshua S. Weitz
We derive an expression for the variation between parallel trajectories in phenotypic evolution, extending the well known result that predicts the mean evolutionary path in adaptive dynamics or quantitative genetics. We show how this expression gives rise to the notion of fluctuation domains–parts of the fitness landscape where the rate of evolution is very predictable (due to fluctuation dissipation) and parts where it is highly variable (due to fluctuation enhancement). These fluctuation domains are determined...

Data from: Phenotypic traits and resource quality as factors affecting male reproductive success in a toadfish

Aneesh P H Bose, Karen M Cogliati, Nick Luymes, Andrew H Bass, Margaret A Marchaterre, Joseph A Sisneros, Benjamin Bolker, Sigal Balshine & Benjamin M Bolker
A male’s reproductive success often depends on both his phenotypic quality and the quality of the resources he controls. An important and longstanding challenge for evolutionary biologists has been to disentangle these two often-correlated factors. Here, we present a large multi-year, multi-population field study along with complementary laboratory experiments aimed at disentangling the effects of male quality and nest quality in driving male reproductive success in the plainfin midshipman fish, Porichthys notatus. We investigate how...

Data from: Agreements between industry and academia on publication rights: a retrospective study of protocols and publications of randomized clinical trials

Benjamin Kasenda, Erik Von Elm, John J. You, Anette Blümle, Yuki Tomonaga, Ramon Saccilotto, Alain Amstutz, Theresa Bengough, Joerg J. Meerpohl, Mihaela Stegert, Kelechi K. Olu, Kari A. O. Tikkinen, Ignacio Neumann, Alonso Carrasco-Labra, Markus Faulhaber, Sohail M. Mulla, Dominik Mertz, Elie A. Akl, Dirk Bassler, Jason W. Busse, Ignacio Ferreira-González, Francois Lamontagne, Alain Nordmann, Viktoria Gloy, Heike Raatz … & Matthias Briel
Background: Little is known about publication agreements between industry and academic investigators in trial protocols and the consistency of these agreements with corresponding statements in publications. We aimed to investigate (i) the existence and types of publication agreements in trial protocols, (ii) the completeness and consistency of the reporting of these agreements in subsequent publications, and (iii) the frequency of co-authorship by industry employees. Methods and Findings: We used a retrospective cohort of randomized clinical...

Data from: Maladaptive phenotypic plasticity in cardiac muscle growth is suppressed in high-altitude deer mice

Jonathan Paul Velotta, Catherine M. Ivy, Cole J. Wolf, Graham R. Scott & Zachary A. Cheviron
How often phenotypic plasticity acts to promote or inhibit adaptive evolution is an ongoing debate among biologists. Recent work suggests that adaptive phenotypic plasticity promotes evolutionary divergence, though several studies have also suggested that maladaptive plasticity can potentiate adaptation. The role of phenotypic plasticity, adaptive or maladaptive, in evolutionary divergence remains controversial. We examined the role of plasticity in evolutionary divergence between two species of Peromyscus mice that differ in native elevations. We used cardiac...

Data from: DualPhos: a versatile, chemoselective reagent for two-carbon aldehyde to latent (E)-alkenal homologation and application in the total synthesis of phomolide G

David McLeod & James McNulty
Advances on the use of the 2-pinacolacetal-tripropylphosphonium salt DualPhos as a general reagent for the two-carbon aldehyde to alkenal homologation and a chemoselective iron (III) chloride mediated deprotection are described. The strategy allows isolation of the latent alkenal intermediates or direct hydrolysis to (E)-alkenals. The robust chemical stability of the latent alkenals is demonstrated in a total synthesis of the macrolactone phomolide G.

Data from: Experimental evidence of frequency-dependent selection on group behaviour

Jonathan N. Pruitt, Brendan L. McEwen, Steven T. Cassidy, Gabriella M. Najm & Noa Pinter-Wollman
Evolutionary ecologists often seek to identify the mechanisms maintaining intraspecific variation. In social animals, whole groups can exhibit between-group differences in their collective traits. We examined whether negative frequency-dependent selection (i.e., a rare-type advantage) could help to maintain between-group variation. We engineered neighborhoods of social spider colonies bearing bold or shy foraging phenotypes and monitored their fecundity in situ. We found that bold colonies enjoyed a rare-type advantage that is lost as the frequency of...

Data from: Road avoidance and its energetic consequences for reptiles

James Paterson, James Baxter-Gilbert, Frederic Beaudry, Sue Carstairs, Patricia Chow-Fraser, Christopher Edge, Andrew Lentini, Jacqueline Litzgus, Chantel Markle, Kassie McKeown, Jennifer Moore, Jeanine Refsnider, Julia Riley, Jeremy Rouse, David Seburn, J Zimmerling & Christina Davy
Roads are one of the most widespread human-caused habitat modifications that can increase wildlife mortality rates and alter behaviour. Roads can act as barriers with variable permeability to movement and can increase distances wildlife travel to access habitats. Movement is energetically costly, and avoidance of roads could therefore impact an animal's energy budget. We tested whether reptiles avoid roads or road crossings and explored whether the energetic consequences of road avoidance decreased individual fitness. Using...

Data from: Male and female bees show large differences in floral preference

Michael Roswell, Jonathan Dushoff & Rachael Winfree
Intraspecific variation in foraging niche can drive food web dynamics and ecosystem processes. In particular, male and female animals can exhibit different, often cascading, impacts on their interaction partners. Despite this, studies of plant-pollinator interaction networks have focused on the partitioning of the floral community between pollinator species, with little attention paid to intraspecific variation in plant preference between male and female bees. We designed a field study to evaluate the strength and prevalence of...

Data from: The genetic basis of variation in sexual aggression: evolution versus social plasticity

Andrew Scott, Janice Yan, Carling Baxter, Ian Dworkin & Reuven Dukas
Male sexual aggression towards females is a form of sexual conflict that can result in increased fitness for males through forced copulations or coercive matings at the cost of female lifetime fitness. We used male fruit flies (Drosophila melanogaster) as a model system to uncover the genomic contributions to variation in forced copulation, both due to standing variation in a wild population, and due to plastic changes associated with variation in social experience. We used...

Data from: Targeted genome-wide SNP genotyping in feral horses using non-invasive fecal swabs

Stefan Gavriliuc, Salman Reza, Chanwoori Jeong, Philip McLoughlin & Jocelyn Poissant
The development of high-throughput sequencing has prompted a transition in wildlife genetics from using microsatellites toward sets of Single Nucleotide Polymorphisms (SNPs). However, genotyping large numbers of targeted SNPs using non-invasive samples remains challenging due to relatively large DNA input requirements. Recently, target enrichment has emerged as a promising approach requiring little template DNA. We assessed the efficacy of Tecan Genomics’ Allegro Targeted Genotyping (ATG) for generating genome-wide SNP data in feral horses using DNA...

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