Topic 5

species evolutionary ecology diversity evolution population populations variation ecological environmental selection traits communities community genetic plant across among history microbial natural climate environments fitness phylogenetic genomes adaptation genomic between taxa than ecosystems change biodiversity habitat composition ecosystem more genome trait plants conservation patterns likely years most some rates habitats under environment size divergence lineages soil individuals phenotypic breeding were conditions differences genus diverse management distribution abundance reproductive their geographic temperature tree range may higher adaptive water found within hosts over organisms marine microbiome life relative bacterial loci strong influence north taxonomic three importance bacteria dispersal evolved genotypes host south collected

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Soil microbial diversity impacts plant microbiomes more than herbivory 17 5

Phylogenetic and metabolic diversity have contrasting effects on the ecological functioning of bacterial communities 17 5

Evolutionary ecology of natural comammox Nitrospira populations 5

Polygenic adaptation of rosette growth in Arabidopsis thaliana populations 21 5

Temporal environmental variation imposes differential selection on genomic and ecological traits of virtual plant communities 99 17 5

Taxonomic, temporal, and spatial variation in the dynamics of High-Arctic arthropod populations 17 5

Adaptation is influenced by the complexity of environmental change during evolution in a dynamic environment 21 5

Climate gradients explain population-level divergence in drought-induced plasticity of functional traits and gene expression in a South African Protea 86 21 5

Gene expression changes of seven stonefly species in responses to a latitudinal-environmental gradient. 86 5

Local adaptation can cause both peaks and troughs in nucleotide diversity within populations 21 5

Environmental and morphological constraints interact to drive the evolution of communication signals in frogs 132 21 5

Experimental evolution confirms signatures of sexual selection in genomic divergence. 21 5

The impact of microclimate and soil on the ecology and evolution of an arctic plant 86 17 5

Composition of the North American wood frog (Rana sylvatica) skin microbiome and seasonal variation in community structure 29 17 5

The evolution of realized niches within freshwater Synechococcus 5

Adaptive evolution shapes the present-day distribution of the thermal sensitivity of population growth rate 86 21 5

Genomics of experimental diversification of Pseudomonas aeruginosa in cystic fibrosis lung-like conditions 21 5

Assessing in vivo mutation frequencies and creating a high-resolution genome-wide map of fitness costs of Hepatitis C virus 21 5

Dispersal evolution diminishes the negative density dependence in dispersal 183 21 5

Rapid polygenic selection generates fine spatial structure among ecological niches in a well-mixed population 21 5

Heliconius butterflies host characteristic and phylogenetically structured adult-stage microbiomes 143 29 5

Different temporal trends in vascular plant and bryophytes communities along elevational gradients over four decades of warming 17 5

Temperature-dependent effects of house fly proto-Y chromosomes on gene expression act independently of the sex determination pathway 21 5

Recessive deleterious variation has a limited impact on signals of adaptive introgression in human populations 21 5 4

Seminal fluid protein divergence among populations exhibiting postmating prezygotic reproductive isolation 132 21 5

P-elements strengthen reproductive isolation within the Drosophila simulans species complex 81 21 5

Variable inbreeding depression may explain associations between the mating system and herbicide resistance 132 21 5

Phenotypic delay in the evolution of bacterial antibiotic resistance: mechanistic models and their implications 185 21 5

Natural bacterial assemblages in Arabidopsis thaliana tissues become more distinguishable and diverse during host development 29 17 5

Pathway-based and phylogenetically adjusted quantification of metabolic interaction between microbial species 143 29 4

Towards an evolutionarily appropriate null model: jointly inferring demography and purifying selection 83 21 5 4

Genetic diversity in global chicken breeds as a function of genetic distance to the wild populations 21 5

A time-lagged association between the gut microbiome, nestling growth and nestling survival in wild great tits 101 29 5

Molecular Evolution of the Sex Peptide Network in Drosophila 56 21 5

Priority effects and season length shape long-term competition dynamics 99 17 5

A global barley panel revealing genomic signatures of breeding in modern cultivars 53 5

Strain background, species frequency and environmental conditions are important in determining population dynamics and species co-existence between Pseudomonas aeruginosa and Staphylococcus aureus 99 5

An enhanced characterization of the human skin microbiome: a new biodiversity of microbial interactions 29 12 5

Pathway Analysis within Multiple Human Ancestries Reveals Novel Signals for Epistasis in Complex Traits 19 4

The genomic architecture of fitness drives population viability during rapid environmental change 21 19 5

An agent-based model of adaptation of holobionts with different microbial symbiont transmission modes 86 21 5

Predicting evolutionary change at the DNA level in a natural Mimulus population 21 5 4

Climate change and intensive land use reduce soil animal biomass through dissimilar pathways 17 5

Oceans apart: Heterogeneous patterns of parallel evolution in sticklebacks 21 5

Eco-evolutionary feedbacks and the maintenance of metacommunity diversity in a changing environment 99 21 17 5

Bacterial single-cell genomics enables phylogenetic analysis and reveals population structures from in vitro evolutionary studies 107 52 12 9 5 4

Fitness effects of competition within and between species change across species' ranges, and reveal limited local adaptation in rainforest Drosophila 99 21 17 5

The evolution of sex-biased gene expression in the Drosophila brain 56 21 9 5

Gene expression noise can promote the fixation of beneficial mutations in fluctuating environments 21 5

Studying models of balancing selection usingphase-type theory 21 5 4

Social environment drives sex and age-specific variation in Drosophila melanogaster microbiome composition and predicted function. 56 29 5

The complex genomic basis of rapid convergent adaptation to pesticides across continents in a fungal plant pathogen 21 19 5

Using high-throughput phenotypes to enable genomic selection by inferring genotypes 145 53 19 4

Systematic variation in the temperature dependence of bacterial carbon use efficiency 86 17 5

Large-scale metabarcoding analysis of epipelagic and mesopelagic copepods in the Pacific 17 5

Detecting selection with a genetic cross 21 19 5 4

Pervasive selection against microRNA target sites in human populations 21 5

Linking phenotype, genotype and ecology: antimicrobial resistance in the zoonotic pathogen Streptococcus suis 107 52 12 5

Reconstructing the history and biological consequences of a plant invasion on the Galapagos islands 21 5

Diversity of dominant soil bacteria increases with warming velocity at the global scale 17 5

The adaptive architecture is shaped by population ancestry and not by selection regime 7 5

Detection of complex genetic architecture using two-locus population differentiation: modeling epistasis 19 9 4

The evolutionary forces shaping cis and trans regulation of gene expression within a population of outcrossing plants. 21 19 5

Fitness-related traits are maximized in recently introduced, slow-growing populations of an invasive clam: is this a response to strong r-selection? 132 21 5

When the microbiome defines the host phenotype: selection on vertical transmission in varying environments 132 21 5

Multi-omics approach highlights differences between functional RLP classes in Arabidopsis thaliana 134 9 5

Genomic evolution of antibiotic resistance is contingent on genetic background following a long-term experiment with Escherichia coli 21 5

The role of higher-order biotic interactions on tropical tree growth 99 17 5

Ecological differentiation and incipient speciation in the fungal pathogen causing rice blast 5

Convergent evolution of niche structure in Northeast Pacific kelp forests 17 5

Genetic variance in fitness and its cross-sex covariance predict adaptation during experimental evolution 132 21 5

Plant diversity and community age shape soil microbial communities 29 17 5

Ecological success of sexual and asexual reproductive strategies invading an environmentally unstable habitat 5

Does diversity beget diversity in microbiomes? 143 29 5

A large accessory genome, high recombination rates, and selection of secondary metabolite genes help maintain global distribution and broad host range of the fungal plant pathogen Claviceps purpurea 21 5

Vast differences in strain-level diversity in the gut microbiota of two closely related honey bee species 29 5

Epigenetic mediation of the onset of reproduction in a songbird 86 5

Acquisition of Oral Microbiota is Driven by Environment, Not Host Genetics 29 12 5

Lagging strand encoding promotes adaptive evolution 21 5

A minimal yet flexible likelihood framework to assess correlated evolution 83 21 4

Candida albicans genetic background influences mean and heterogeneity of drug responses and genome stability during evolution to fluconazole 21 5

Adjacent terrestrial landscapes impact the biogeographical pattern of soil Escherichia coli in produce fields via modifying the importance of environmental selection and dispersal 17 5

Higher Variability in Fungi Compared to Bacteria in the Foraging Honey Bee 143 29 5

The search for sexually antagonistic genes: Practical insights from studies of local adaptation and statistical genomics 21 19 5 4

Dynamics of infection in a novel group of promiscuous phages and hosts of multiple bacterial genera retrieved from river communities 143 121 29 12 5

The Demographic History of Micro-endemics: Have Rare Species Always Been Rare? 84 5 4

Bridging parametric and nonparametric measures of species interactions unveils new insights of non-equilibrium dynamics 99 17 5

Drainage-structuring of ancestral variation and a common functional pathway shape limited genomic convergence in natural high- and low-predation guppies 21 5

Widespread conservation and lineage-specific diversification of genome-wide DNA methylation patterns across arthropods 81 40 31 21 9 5

The impact of biological invasion and genomic local adaptation on the geographical distribution of Aedes aegypti in Panama 21 5

Comparative genomics reveals different population structures associated with host and geographic origin in antimicrobial-resistant Salmonella enterica 107 52 12 5

A test of the Baldwin Effect: Differences in both constitutive expression and inducible responses to parasites underlie variation in host response to a parasite 21 5

Effects of extreme hot weather on the reproductive output of great tits (Parus major, L.) in urban and natural habitats 86 17 5

Elevated temperature increases genome-wide selection on de novo mutations 86 21 5

Parasites as niche modifiers for the microbiome: A field test with multiple parasites 29 17 5

The Evolution and Fate of Diversity Under Hard and Soft Selection 21 5

Ecology and molecular targets of hypermutation in the global microbiome. 29 5

Genomic prediction in the wild: A case study in Soay sheep 145 19 5 4

Identifying genomic markers associated with female re-mating rate in Drosophila pseudoobscura by replicated bulk segregant analysis. 19 5 4

Diversity in CRISPR-based immunity protects susceptible genotypes by restricting phage spread and evolution 21 5