bluuebunny/crossref_metadata_2025_split huggingface dataset:
Harvest-induced evolution: insights from aquatic and terrestrial systems
Authors: Kuparinen Anna , Festa-Bianchet Marco 
Published: December 2016

Commercial and recreational harvests create selection pressures for fitness-related phenotypic traits that are partly under genetic control. Consequently, harvesting can drive evolution in targeted traits. However, the quantification of harvest-induced evolutionary life history and phenotypic changes is challenging, because both density-dependent feedback and environmental changes may also affect these changes through phenotypic plasticity. Here, we synthesize current knowledge and uncertainties on six key points: (i) whether or not harvest-induced evolution is happening, (ii) whether or not it is beneficial, (iii) how it shapes biological systems, (iv) how it could be avoided, (v) its importance relative to other drivers of phenotypic changes, and (vi) whether or not it should be explicitly accounted for in management. We do this by reviewing findings from aquatic systems exposed to fishing and terrestrial systems targeted by hunting. Evidence from aquatic systems emphasizes evolutionary effects on age and size at maturity, while in terrestrial systems changes are seen in weapon size and date of parturition. We suggest that while harvest-induced evolution is likely to occur and negatively affect populations, the rate of evolutionary changes and their ecological implications can be managed efficiently by simply reducing harvest intensity.This article is part of the themed issue ‘Human influences on evolution, and the ecological and societal consequences'.
Effects of fragmentation on plant adaptation to urban environments
Authors: Dubois Jonathan , Cheptou Pierre-Olivier 
Published: December 2016

Urban ecosystems are relatively recent and heavily human-altered terrestrial ecosystems with a surprisingly high diversity of animals, plants and other organisms. Urban habitats are also strongly fragmented and subject to higher temperatures, providing a compelling model for studying adaptation to global change.Crepis sancta(Asteraceae), an annual Mediterranean wasteland weed, occupies fragmented urban environments as well as certain unfragmented landscapes in southern France. We tested for shifts in dispersal, reproductive traits and size across a rural–urban gradient to learn whether and how selection may be driving changes in life history in urban and fragmented habitats. We specifically compared the structure of quantitative genetic variation and of neutral markers (microsatellites) between urban and rural and between fragmented and unfragmented habitats. We showed that fragmentation provides a better descriptor of trait variation than urbanizationper sefor dispersal traits. Fragmentation also affected reproductive traits and plant size though one rural population did conform to this scheme. Our study shows the role of fragmentation for dispersal traits shift in urban environments and a more complex pattern for other traits. We discuss the role of pollinator scarcity and an inhospitable matrix as drivers of adaptation.This article is part of the themed issue ‘Human influences on evolution, and the ecological and societal consequences’.
Antibiotic resistance in the wild: an eco-evolutionary perspective
Authors: Hiltunen Teppo , Virta Marko , Laine Anna-Liisa 
Published: December 2016

The legacy of the use and misuse of antibiotics in recent decades has left us with a global public health crisis: antibiotic-resistant bacteria are on the rise, making it harder to treat infections. At the same time, evolution of antibiotic resistance is probably the best-documented case of contemporary evolution. To date, research on antibiotic resistance has largely ignored the complexity of interactions that bacteria engage in. However, in natural populations, bacteria interact with other species; for example, competition and grazing are import interactions influencing bacterial population dynamics. Furthermore, antibiotic leakage to natural environments can radically alter bacterial communities. Overall, we argue that eco-evolutionary feedback loops in microbial communities can be modified by residual antibiotics and evolution of antibiotic resistance. The aim of this review is to connect some of the well-established key concepts in evolutionary biology and recent advances in the study of eco-evolutionary dynamics to research on antibiotic resistance. We also identify some key knowledge gaps related to eco-evolutionary dynamics of antibiotic resistance, and review some of the recent technical advantages in molecular microbiology that offer new opportunities for tackling these questions. Finally, we argue that using the full potential of evolutionary theory and active communication across the different fields is needed for solving this global crisis more efficiently.
This article is part of the themed issue ‘Human influences on evolution, and the ecological and societal consequences'.
Sublethal streptomycin concentrations and lytic bacteriophage together promote resistance evolution
Authors: Cairns Johannes , Becks Lutz , Jalasvuori Matti , Hiltunen Teppo 
Published: December 2016

Sub-minimum inhibiting concentrations (sub-MICs) of antibiotics frequently occur in natural environments owing to wide-spread antibiotic leakage by human action. Even though the concentrations are very low, these sub-MICs have recently been shown to alter bacterial populations by selecting for antibiotic resistance and increasing the rate of adaptive evolution. However, studies are lacking on how these effects reverberate into key ecological interactions, such as bacteria–phage interactions. Previously, co-selection of bacteria by phages and antibiotic concentrations exceeding MICs has been hypothesized to decrease the rate of resistance evolution because of fitness costs associated with resistance mutations. By contrast, here we show that sub-MICs of the antibiotic streptomycin (Sm) increased the rate of phage resistance evolution, as well as causing extinction of the phage. Notably, Sm and the phage in combination also enhanced the evolution of Sm resistance compared with Sm alone. These observations demonstrate the potential of sub-MICs of antibiotics to impact key ecological interactions in microbial communities with evolutionary outcomes that can radically differ from those associated with high concentrations. Our findings also contribute to the understanding of ecological and evolutionary factors essential for the management of the antibiotic resistance problem.This article is part of the themed issue ‘Human influences on evolution, and the ecological and societal consequences’.
Does eutrophication-driven evolution change aquatic ecosystems?
Authors: Alexander Timothy J. , Vonlanthen Pascal , Seehausen Ole 
Published: December 2016

Eutrophication increases primary production and changes the relative abundance, taxonomic composition and spatial distribution of primary producers within an aquatic ecosystem. The changes in composition and location of resources alter the distribution and flow of energy and biomass throughout the food web. Changes in productivity also alter the physico-chemical environment, which has further effects on the biota. Such ecological changes influence the direction and strength of natural and sexual selection experienced by populations. Besides altering selection, they can also erode the habitat gradients and/or behavioural mechanisms that maintain ecological separation and reproductive isolation among species. Consequently, eutrophication of lakes commonly results in reduced ecological specialization as well as genetic and phenotypic homogenization among lakes and among niches within lakes. We argue that the associated loss in functional diversity and niche differentiation may lead to decreased carrying capacity and lower resource-use efficiency by consumers. We show that in central European whitefish species radiations, the functional diversity affected by eutrophication-induced speciation reversal correlates with community-wide trophic transfer efficiency (fisheries yield per unit phosphorus). We take this as an example of how evolutionary dynamics driven by anthropogenic environmental change can have lasting effects on biodiversity and ecosystem functioning.This article is part of the themed issue ‘Human influences on evolution, and the ecological and societal consequences'.
Human drivers of ecological and evolutionary dynamics in emerging and disappearing infectious disease systems
Authors: Rogalski Mary A. , Gowler Camden D. , Shaw Clara L. , Hufbauer Ruth A. , Duffy Meghan A. 
Published: December 2016

Humans have contributed to the increased frequency and severity of emerging infectious diseases, which pose a significant threat to wild and domestic species, as well as human health. This review examines major pathways by which humans influence parasitism by altering (co)evolutionary interactions between hosts and parasites on ecological timescales. There is still much to learn about these interactions, but a few well-studied cases show that humans influence disease emergence every step of the way. Human actions significantly increase dispersal of host, parasite and vector species, enabling greater frequency of infection in naive host populations and host switches. Very dense host populations resulting from urbanization and agriculture can drive the evolution of more virulent parasites and, in some cases, more resistant host populations. Human activities that reduce host genetic diversity or impose abiotic stress can impair the ability of hosts to adapt to disease threats. Further, evolutionary responses of hosts and parasites can thwart disease management and biocontrol efforts. Finally, in rare cases, humans influence evolution by eradicating an infectious disease. If we hope to fully understand the factors driving disease emergence and potentially control these epidemics we must consider the widespread influence of humans on host and parasite evolutionary trajectories.This article is part of the themed issue ‘Human influences on evolution, and the ecological and societal consequences’.
Life history trade-offs, the intensity of competition, and coexistence in novel and evolving communities under climate change
Authors: Lancaster Lesley T. , Morrison Gavin , Fitt Robert N. 
Published: December 2016

The consequences of climate change for local biodiversity are little understood in process or mechanism, but these changes are likely to reflect both changing regional species pools and changing competitive interactions. Previous empirical work largely supports the idea that competition will intensify under climate change, promoting competitive exclusions and local extinctions, while theory and conceptual work indicate that relaxed competition may in fact buffer communities from biodiversity losses that are typically witnessed at broader spatial scales. In this review, we apply life history theory to understand the conditions under which these alternative scenarios may play out in the context of a range-shifting biota undergoing rapid evolutionary and environmental change, and at both leading-edge and trailing-edge communities. We conclude that, in general, warming temperatures are likely to reduce life history variation among competitors, intensifying competition in both established and novel communities. However, longer growing seasons, severe environmental stress and increased climatic variability associated with climate change may buffer these communities against intensified competition. The role of life history plasticity and evolution has been previously underappreciated in community ecology, but may hold the key to understanding changing species interactions and local biodiversity under changing climates.This article is part of the themed issue ‘Human influences on evolution, and the ecological and societal consequences’.
MtrA is an essential regulator that coordinates antibiotic production and sporulation inStreptomycesspecies
Authors: Som Nicolle F. , Heine Daniel , Munnoch John T. , Holmes Neil A. , Knowles Felicity , Chandra Govind , Seipke Ryan F. , Hoskisson Paul A. , Wilkinson Barrie , Hutchings Matthew I. 
Published: December 2016

AbstractStreptomycesbacteria make numerous secondary metabolites, including half of all known antibiotics. Understanding the global regulation of secondary metabolism is important because mostStreptomycesnatural products are not made under laboratory conditions and unlocking ‘cryptic’ biosynthetic gene clusters (BGCs) is a major focus for natural product discovery. Production is coordinated with sporulation but the regulators that coordinate development with antibiotic biosynthesis are largely unknown. Here we characterise a highly conserved actinobacterial response regulator called MtrA in antibiotic-producingStreptomycesspecies. We show that MtrA is an essential global regulator of secondary metabolism that directly activates antibiotic production in inS. coelicolorandS. venezuelae. MtrA also controls key developmental genes required for DNA replication and cell division and we propose that MtrA is the missing link that coordinates secondary metabolism with development inStreptomycesspecies.
Cushing’s Syndrome mutant PKAL205Rexhibits altered substrate specificity
Authors: Lubner Joshua M. , Dodge-Kafka Kimberly L. , Carlson Cathrine R. , Church George M. , Chou Michael F. , Schwartz Daniel 
Published: December 2016

AbstractThe PKAL205Rhotspot mutation has been implicated in Cushing’s Syndrome through hyperactive gain-of-function PKA signaling, however its influence on substrate specificity has not been investigated. Here, we employ the Proteomic Peptide Library (ProPeL) approach to create high-resolution models for PKAWTand PKAL205Rsubstrate specificity. We reveal that the L205R mutation reduces canonical hydrophobic preference at the substrate P+1 position, and increases acidic preference in downstream positions. Using these models, we designed peptide substrates that exhibit altered selectivity for specific PKA variants, and demonstrate the feasibility of selective PKAL205Rloss-of-function signaling. Through these results, we suggest that substrate rewiring may contribute to Cushing’s Syndrome disease etiology, and introduce a powerful new paradigm for investigating mutation-induced kinase substrate rewiring in human disease.
Cross-tissue integration of genetic and epigenetic data offers insight into autism spectrum disorder
Authors: Andrews Shan V. , Ellis Shannon E. , Bakulski Kelly M. , Sheppard Brooke , Croen Lisa A. , Hertz-Picciotto Irva , Newschaffer Craig J. , Feinberg Andrew P. , Arking Dan E. , Ladd-Acosta Christine , Fallin M. Daniele 
Published: December 2016

ABSTRACTIntegration of emerging epigenetic information with Autism Spectrum Disorder (ASD) genetic results may elucidate functional insights not possible via either type of information in isolation. We use genotype and DNA methylation (DNAm) data from cord blood and peripheral blood to identify SNPs associated with DNA methylation (meQTL lists) and additionally use publicly available fetal brain and lung meQTL lists to assess enrichment of ASD GWAS results for tissue-specific meQTLs. ASD-associated SNPs are enriched for fetal brain (OR = 3.55; p < 0.001) and peripheral blood meQTLs (OR = 1.58; p < 0.001). The CpG targets of ASD meQTLs across cord, blood, and brain tissues are enriched for immune-related pathways, consistent with other expression and DNAm results in ASD, and reveal pathways not implicated by genetic findings. This joint analysis of genotype and DNAm demonstrates the potential of both brain and blood-based DNAm for insights into ASD and psychiatric phenotypes more broadly.
Splice Expression Variation Analysis (SEVA) for Inter-tumor Heterogeneity of Gene Isoform Usage in Cancer
Authors: Afsari Bahman , Guo Theresa , Considine Michael , Florea Liliana , Kagohara Luciane T. , Stein-O’Brien Genevieve L. , Kelley Dylan , Flam Emily , Zambo Kristina D. , Ha Patrick K. , Geman Donald , Ochs Michael F. , Califano Joseph A. , Gaykalova Daria A. , Favorov Alexander V. , Fertig Elana J. 
Published: December 2016

AbstractMotivationCurrent bioinformatics methods to detect changes in gene isoform usage in distinct phenotypes compare the relative expected isoform usage in phenotypes. These statistics model differences in isoform usage in normal tissues, which have stable regulation of gene splicing. Pathological conditions, such as cancer, can have broken regulation of splicing that increases the heterogeneity of the expression of splice variants. Inferring events with such differential heterogeneity in gene isoform usage requires new statistical approaches.ResultsWe introduce Splice Expression Variability Analysis (SEVA) to model increased heterogeneity of splice variant usage between conditions (e.g., tumor and normal samples). SEVA uses a rank-based multivariate statistic that compares the variability of junction expression profiles within one condition to the variability within another. Simulated data show that SEVA is unique in modeling heterogeneity of gene isoform usage, and benchmark SEVA’s performance against EBSeq, DiffSplice, and rMATS that model differential isoform usage instead of heterogeneity. We confirm the accuracy of SEVAin identifying known splice variants in head and neck cancer and perform cross-study validation of novel splice variants. A novel comparison of splice variant heterogeneity between subtypes of head and neck cancer demonstrated unanticipated similarity between the heterogeneity of gene isoform usage in HPV-positive and HPV-negative subtypes and anticipated increased heterogeneity among HPV-negative samples with mutations in genes that regulate the splice variant machinery.ConclusionThese results show that SEVA accurately models differential heterogeneity of gene isoform usage from RNA-seq data.AvailabilitySEVA is implemented in the R/Bioconductor package GSReg.Contactbahman@jhu.edu,favorov@sensi.org,ejfertig@jhmi.edu
Spatiotemporal characterization of the neural correlates of outcome valence and surprise during reward learning in humans
Authors: Fouragnan Elsa , Queirazza Filippo , Retzler Chris , Mullinger Karen J. , Philiastides Marios G. 
Published: December 2016

AbstractReward learning depends on accurate reward associations with potential choices. Two separate outcome dimensions, namely the valence (positive or negative) and surprise (the absolute degree of deviation from expectations) of an outcome are thought to subserve adaptive decision-making and learning, however their neural correlates and relative contribution to learning remain debated. Here, we coupled single-trial analyses of electroencephalography with simultaneously acquired fMRI, while participants performed a probabilistic reversal-learning task, to offer evidence of temporally overlapping but largely distinct spatial representations of outcome valence and surprise in the human brain. Electrophysiological variability in outcome valence correlated with activity in regions of the human reward network promoting approach or avoidance learning. Variability in outcome surprise correlated primarily with activity in regions of the human attentional network controlling the speed of learning. Crucially, despite the largely separate spatial extend of these representations we also found a linear superposition of the two outcome dimensions in a smaller network encompassing visuo-mnemonic and reward areas. This spatiotemporal overlap was uniquely exposed by our EEG-informed fMRI approach. Activity in this network was further predictive of stimulus value updating indicating a comparable contribution of both signals to reward learning.
Revealing compartmentalised membrane diffusion in living cells with interferometric scattering microscopy
Authors: de Wit G. , Albrecht D. , Ewers H. , Kukura P. 
Published: December 2016

AbstractSingle-particle tracking is a powerful tool for studying single molecule behaviour involving plasma membrane-associated events in cells. Here, we show that interferometric scattering microscopy (iSCAT) combined with gold nanoparticle labeling can be used to follow the motion of membrane proteins in the plasma membrane of live cultured mammalian cell lines and hippocampal neurons. The unique combination of microsecond temporal resolution and nanometer spatial precision reveals signatures of a compartmentalised plasma membrane in neurons.
The dynamic three-dimensional organization of the diploid yeast genome
Authors: Kim Seungsoo , Liachko Ivan , Brickner Donna G , Cook Kate , Noble William S , Brickner Jason H , Shendure Jay , Dunham Maitreya J 
Published: December 2016

AbstractThe budding yeast Saccharomyces cerevisiae is a long-standing model for the three-dimensional organization of eukaryotic genomes. Even in this well-studied model, it is unclear how homolog pairing in diploids and environment-induced gene relocalization influence overall genome organization. Here, we performed high-throughput chromosome conformation capture on diverged Saccharomyces hybrid diploids to obtain the first global view of chromosome conformation in diploid yeasts. After controlling for the Rabl-like orientation, we observe significant homolog proximity that increased in saturated culture conditions. Surprisingly, we observe a localized increase in homologous interactions between the HAS1 alleles specifically under galactose induction and saturated growth, mediated by association with nuclear pore complexes at the nuclear periphery. Together, these results reveal that the diploid yeast genome has a dynamic and complex 3D organization.
The innate immune systems of malacostracan crustaceans exhibit both conserved and evolutionarily distinct components
Authors: Lai Alvina G. , Aboobaker A. Aziz 
Published: December 2016

AbstractGrowing demands for aquatic sources of animal proteins have attracted significant investments in aquaculture research in recent years. The crustacean aquaculture industry has undergone substantial growth to accommodate a rising global demand, however such large-scale production is susceptible to pathogen-mediated destruction. It is clear that a thorough understanding of the crustacean innate immune system is imperative for future research into combating current and future pathogens of the main food crop species. Through a comparative genomics approach utilising extant data from 55 species, we describe the innate immune system of crustaceans from the Malacostraca class. We identify 7407 malacostracan genes from 39 gene families implicated in different aspects of host defence and demonstrate dynamic evolution of innate immunity components within this group. Malacostracans have achieved flexibility in recognising infectious agents through divergent evolution and expansion of pathogen recognition receptors genes. Antiviral RNAi, Toll and JAK-STAT signal transduction pathways have remained conserved within Malacostraca, although the Imd pathway appears to lack several key components. Immune effectors such as the antimicrobial peptides (AMPs) have unique evolutionary profiles, with many malacostracan AMPs not found in other arthropod groups. Lastly, we describe four putative novel immune gene families, characterised by distinct protein domains, potentially representing important evolutionary novelties of the malacostracan immune system.