876 Works

Data from: Daily blood feeding rhythms of laboratory-reared North American Culex pipiens

Megan L. Fritz, Edward D. Walker, Aaron J. Yunker & Ian Dworkin
Background: Blood feeding by free-living insect vectors of disease is rhythmic and can be used to predict when infectious bites will occur. These daily rhythms can also be targeted by control measures, as in insecticide-treated nets. Culex pipiens form pipiens and C.p. f. molestus are two members of the Culex pipiens assemblage and vectors of West Nile Virus throughout North America. Although Culex species vector human pathogens and parasites, the daily blood feeding rhythms of...

Data from: Plastic responses to parents and predators lead to divergent social behaviour in sticklebacks

Genevieve M. Kozak & Janette W. Boughman
Population divergence in antipredator defense and behaviour occurs rapidly and repeatedly. Genetic differences, phenotypic plasticity, or parental effects may all contribute to divergence, but the relative importance of each of these mechanisms remains unknown. We exposed juveniles to parents and predators to measure how induced changes contribute to shoaling behaviour differences between two threespine stickleback species (benthics and limnetics: Gasterosteus spp). We found that limnetics increased shoaling in response to predator attacks while benthics did...

Data from: Experimental test of phytoplankton competition for nutrients and light in poorly mixed water columns

Jarad P. Mellard, Kohei Yoshiyama, Christopher A. Klausmeier & Elena Litchman
A recent theory of the vertical distribution of phytoplankton considers how interacting niche construction processes such as resource depletion, behavior, and population dynamics contribute to spatial heterogeneity in the aquatic environment. In poorly mixed water columns with opposing resource gradients of nutrients and light, theory predicts that a species should aggregate at a single depth. This depth of aggregation, or biomass maximum, should change through time due to depletion of available resources. In addition, the...

Data from: The effect of historical legacy on adaptation: do closely related species respond to the environment in the same way?

Rachel Prunier, Kent E. Holsinger & Jane E. Carlson
The many documented examples of parallel and convergent evolution in similar environments are strong evidence for the role of natural selection in the evolution of trait variation. However, species may respond to selection in different ways; idiosyncrasies of their evolutionary history may affect how different species respond to the same selective pressure. To determine whether evolutionary history affects trait-environment associations in a recently diverged lineage, we investigated within-species trait-environment associations in the white proteas, a...

Data from: Trade-offs drive resource specialization and the gradual establishment of ecotypes

Bjørn Østman, Randall Lin & Christoph Adami
Background: Speciation is driven by many different factors. Among those are trade-offs between different ways an organism utilizes resources, and these trade-offs can constrain the manner in which selection can optimize traits. Limited migration among allopatric populations and species interactions can also drive speciation, but here we ask if trade-offs alone are sufficient to drive speciation in the absence of other factors. Results: We present a model to study the effects of trade-offs on specialization...

Data from: Effects of the landscape on boreal toad gene flow: does the pattern-process relationship hold true across distinct landscapes at the northern range margin?

Jennifer A. Moore, David A. Tallmon, Julie Nielsen & Sanjay Pyare
Understanding the impact of natural and anthropogenic landscape features on population connectivity is a major goal in evolutionary ecology and conservation. Discovery of dispersal barriers is important for predicting population responses to landscape and environmental changes, particularly for populations at geographic range margins. We used a landscape genetics approach to quantify the effects of landscape features on gene flow and connectivity of boreal toad (Bufo boreas) populations from two distinct landscapes in Southeast Alaska (Admiralty...

Data from: Female mate preferences for male body size and shape promote sexual isolation in threespine sticklebacks

Megan L. Head, Genevieve M. Kozak & Janette W. Boughman
Female mate preferences for ecologically relevant traits may enhance natural selection, leading to rapid divergence. They may also forge a link between mate choice within species and sexual isolation between species. Here, we examine female mate preference for two ecologically important traits: body size and body shape. We measured female preferences within and between species of benthic, limnetic, and anadromous threespine sticklebacks (Gasterosteus aculeatus species complex). We found that mate preferences differed between species and...

Data from: Divergent sexual selection via male competition: ecology is key

Alycia C. R. Lackey & Janette W. Boughman
Sexual selection and ecological differences are important drivers of speciation. Much research has focused on female choice, yet the role of male competition in ecological speciation has been understudied. Here, we test how mating habitats impact sexual selection and speciation through male competition. Using limnetic and benthic species of threespine stickleback fish, we find that different mating habitats select differently on male traits through male competition. In mixed habitat with both vegetated and open areas,...

Data from: Estimating abundance of the federally endangered Mitchell’s satyr butterfly using hierarchical distance sampling

Christopher A. Hamm
1. Estimates of animal abundance are essential to conservation biology and are sorely lacking for many endangered species in the United States of America. This lack of knowledge may disproportionately affect butterflies in the USA, which form the largest group of federally protected insects (20 of 62 species). 2. The Mitchell’s satyr butterfly, Neonympha mitchellii mitchellii, is a federally endangered species found at 18 highly isolated sites in the Eastern USA. Currently, surveys are conducted...

Data from: Can impacts of climate change and agricultural adaptation strategies be accurately quantified if crop models are annually re-initialized?

Bruno Basso, David W. Hyndman, Anthony D. Kendall, Peter R. Grace & G. Philip Robertson
Estimates of climate change impacts on global food production are generally based on statistical or process-based models. Process-based models can provide robust predictions of agricultural yield responses to changing climate and management. However, applications of these models often suffer from bias due to the common practice of re-initializing soil conditions to the same state for each year of the forecast period. If simulations neglect to include year-to-year changes in initial soil conditions and water content...

Data from: Contemporary evolution during invasion: evidence for differentiation, natural selection, and local adaptation

Robert I. Colautti & Jennifer A. Lau
Biological invasions are ‘natural’ experiments that can improve our understanding of contemporary evolution. We evaluate evidence for population differentiation, natural selection and adaptive evolution of invading plants and animals at two nested spatial scales: (i) among introduced populations (ii) between native and introduced genotypes. Evolution during invasion is frequently inferred, but rarely confirmed as adaptive. In common garden studies, quantitative trait differentiation is only marginally lower (~3.5%) among introduced relative to native populations, despite genetic...

Data from: Modeling and quantifying frequency-dependent fitness in microbial populations with cross-feeding interactions

Noah Ribeck & Richard E. Lenski
Coexistence of two or more populations by frequency-dependent selection is common in nature, and it often arises even in well-mixed experiments with microbes. If ecology is to be incorporated into models of population genetics, then it is important to represent accurately the functional form of frequency-dependent interactions. However, measuring this functional form is problematic for traditional fitness assays, which assume a constant fitness difference between competitors over the course of an assay. Here, we present...

Data from: A framework for developing ecosystem-specific nutrient criteria: integrating biological thresholds with predictive modeling

Patricia A. Soranno, Kendra Spence Cheruvelil, R. Jan Stevenson, Scott L. Rollins, Sarah W. Holden, Sylvia Heaton & Eric Torng
We present a novel ecosystem-specific framework for developing nutrient criteria from biological thresholds and predictive modeling (BTPM) and an application of this framework to lakes in Michigan, U.S. The four main components for the BTPM framework are: (1) to predict each ecosystem s expected nutrient concentration in the absence of human effects using a predictive model, (2) to identify important biological thresholds along a nutrient gradient (i.e., biological [BIO] benchmarks), (3) to determine each ecosystem...

Data from: Epistasis and allele specificity in the emergence of a stable polymorphism in Escherichia coli

Jessica Plucain, Thomas Hindré, Mickaël Le Gac, Olivier Tenaillon, Stéphane Cruveiller, Claudine Médigue, Nicholas Leiby, William R. Harcombe, Christopher J. Marx, Richard E. Lenski & Dominique Schneider
Ecological opportunities promote population divergence into coexisting lineages. However, the genetic mechanisms that enable new lineages to exploit these opportunities are poorly understood except in cases of single mutations. We examined how two Escherichia coli lineages diverged from their common ancestor at the outset of a long-term coexistence. By sequencing genomes and reconstructing the genetic history of one lineage, we showed that three mutations together were sufficient to produce the frequency-dependent fitness effects that allowed...

Data from: Long-term balanced fertilization improves the soil microbial functional diversity in a phosphorus-limited paddy soil

Jian-Qiang Su, Long-Jun Ding, Kai Xue, Huai-Ying Yao, John Quensen, Shi-Jie Bai, Wen-Xue Wei, Jin-Shui Wu, Jizhong Zhou, James M. Tiedje & Yong-Guan Zhu
The influence of long-term chemical fertilization on soil microbial communities has been one of the frontier topics of agricultural and environmental sciences and is critical for linking soil microbial flora with soil functions. In this study, 16S rRNA gene pyrosequencing and a functional gene array, GeoChip 4.0, were used to investigate the shifts in microbial composition and functional gene structure in paddy soils with different fertilization treatments over a 22-year period. These included a control...

Data from: Gene transfer from bacteria and archaea facilitated evolution of an extremophilic eukaryote

Gerald Schönknecht, Wei-Hua Chen, Chad M. Ternes, Guillaume G. Barbier, Roshan P. Shrestha, Mario Stanke, Andrea Bräutigam, Brett J. Baker, Jillian F. Banfield, R. Michael Garavito, Kevin Carr, Curtis Wilkerson, Stefan A. Rensing, David Gagneul, Nicholas E. Dickenson, Christine Oesterhelt, Martin J. Lercher & Andreas P. M. Weber
Some microbial eukaryotes, such as the extremophilic red alga Galdieria sulphuraria, can live in hot, toxic metal-rich, acidic environments. To elucidate the underlying molecular mechanisms of adaptation, we sequenced the 13.7 Mb genome of G. sulphuraria. This alga shows an enormous metabolic flexibility, growing either photoautotrophically or heterotrophically on more than 50 carbon sources. Environmental adaptation seems to have been facilitated by horizontal gene transfer from various bacteria and archaea, often followed by gene family...

Data from: Artificial bat roosts did not accelerate forest regeneration in abandoned pastures in southern Costa Rica

J. Leighton Reid, Ellen K. Holste & Rakan A. Zahawi
Artificial roosts have been proposed as a tool for augmenting bat populations and catalyzing tropical forest regeneration. In the best case scenario, roosts would attract seed-carrying bats (Family Phyllostomidae) into degraded pastures and form nucleating patches of native vegetation. We tested this scenario by monitoring 48 artificial roosts in pastures and adjacent forest fragments in southern Costa Rica over 2 years. Half of the pasture roosts were exposed to direct sunlight and half were affixed...

Data from: Biodiversity ensures plant-pollinator phenological synchrony against climate change

Ignasi Bartomeus, Mia G. Park, Jason Gibbs, Bryan N. Danforth, Alan N. Lakso & Rachael Winfree
Climate change has the potential to alter the phenological synchrony between interacting mutualists, such as plants and their pollinators. However, high levels of biodiversity might buffer the negative effects of species-specific phenological shifts and maintain synchrony at the community level, as predicted by the biodiversity insurance hypothesis. Here, we explore how biodiversity might enhance and stabilise phenological synchrony between a valuable crop, apple and its native pollinators. We combine 46 years of data on apple...

Data from: The conditional nature of genetic interactions: the consequences of wild-type backgrounds on mutational interactions in a genome-wide modifier screen

Sudarshan Chari & Ian Dworkin
The phenotypic outcome of a mutation cannot be simply mapped onto the underlying DNA variant. Instead, the phenotype is a function of the allele, the genetic background in which it occurs and the environment where the mutational effects are expressed. While the influence of genetic background on the expressivity of individual mutations is recognized, its consequences on the interactions between genes, or the genetic network they form, is largely unknown. The description of genetic networks...

Data from: Comparative genomics reveals insight into virulence strategies of plant pathogenic oomycetes

Bishwo N. Adhikari, John P. Hamilton, Marcelo M. Zerillo, Ned Tisserat, C. André Lévesque & C. Robin Buell
The kingdom Stramenopile includes diatoms, brown algae, and oomycetes. Plant pathogenic oomycetes, including Phytophthora, Pythium and downy mildew species, cause devastating diseases on a wide range of host species and have a significant impact on agriculture. Here, we report comparative analyses on the genomes of thirteen straminipilous species, including eleven plant pathogenic oomycetes, to explore common features linked to their pathogenic lifestyle. We report the sequencing, assembly, and annotation of six Pythium genomes and comparison...

Data from: Tempo and mode of genome evolution in a 50,000-generation experiment

Olivier Tenaillon, Jeffrey E. Barrick, Noah Ribeck, Daniel E. Deatherage, Jeffrey L. Blanchard, Aurko Dasgupta, Gabriel C. Wu, Sébastien Wielgoss, Stéphane Cruveiller, Claudine Médigue, Dominique Schneider & Richard E. Lenski
Adaptation by natural selection depends on the rates, effects and interactions of many mutations, making it difficult to determine what proportion of mutations in an evolving lineage are beneficial. Here we analysed 264 complete genomes from 12 Escherichia coli populations to characterize their dynamics over 50,000 generations. The populations that retained the ancestral mutation rate support a model in which most fixed mutations are beneficial, the fraction of beneficial mutations declines as fitness rises, and...

Data from: The importance of terrestrial subsidies in stream food webs varies along a stream size gradient

Sarah M. Collins, Tyler J. Kohler, Steven A. Thomas, William W. Fetzer & Alexander S. Flecker
Cross system subsidies of energy and materials can be a substantial fraction of food web fluxes in ecosystems, especially when autochthonous production is strongly limited by light or nutrients. We explored whether assimilation of terrestrial energy varied in specific consumer taxa collected from streams of different sizes and resource availabilities. Since headwater streams are often unproductive, we expected that inputs from surrounding terrestrial systems (i.e. leaf litter, terrestrial invertebrates) would be a more important food...

Data from: Diversity and population structure of northern switchgrass as revealed through exome capture sequencing

Joseph Evans, Emily Crisovan, Kerrie Barry, Chris Daum, Jerry Jenkins, Govindarajan Kunde-Ramamoorthy, Aruna Nandety, Chew Yee Ngan, Brieanne Vaillancourt, Chia-Lin Wei, Jeremy Schmutz, Shawn M. Kaeppler, Michael D. Casler, Carol Robin Buell & Chia-Lin Wei
Switchgrass (Panicum virgatum L.) is a polyploid, perennial grass species that is native to North America, and is being developed as a future biofuels feedstock crop. Switchgrass is present primarily in two ecotypes: a northern upland ecotype composed of tetraploid and octoploid accessions, and a southern lowland ecotype composed of primarily tetraploid accessions. We employed high-coverage exome capture sequencing (~2.4 Tb) to genotype 537 individuals from 45 upland and 21 lowland populations. From these data,...

Data from: Nitrous oxide emissions during establishment of eight alternative cellulosic bioenergy cropping systems in the North Central United States

Lawrence G. Oates, David S. Duncan, Ilya Gelfand, Neville Millar, G. Philip Robertson & Randall D. Jackson
Greenhouse gas (GHG) emissions from soils are a key sustainability metric of cropping systems. During crop establishment, disruptive land-use change is known to be a critical, but under reported period, for determining GHG emissions. We measured soil N2O emissions and potential environmental drivers of these fluxes from a three-year establishment-phase bioenergy cropping systems experiment replicated in southcentral Wisconsin (ARL) and southwestern Michigan (KBS). Cropping systems treatments were annual monocultures (continuous corn, corn–soybean–canola rotation), perennial monocultures...

Data from: Disintegrating the fly: a mutational perspective on phenotypic integration and covariation

Annat Haber & Ian Dworkin
The structure of environmentally induced phenotypic covariation can influence the effective strength and magnitude of natural selection. Yet our understanding of the factors that contribute to and influence the evolutionary lability of such covariation is poor. Most studies have either examined environmental variation without accounting for covariation, or examined phenotypic and genetic covariation without distinguishing the environmental component. In this study we examined the effect of mutational perturbations on different properties of environmental covariation, as...

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