We examined the hypothesis that ecological niche models (ENMs) more accurately predict species distributions when they incorporate information on population genetic structure, and concomitantly, local adaptation. Local adaptation is common in span a range of environmental gradients (e.g., soils climate). Moreover, garden studies have demonstrated covariance between neutral markers functional traits associated with species' ability to adapt change. therefore predicted genetically distinct...

This article presents a study on the quality and execution of research code from publicly-available replication datasets at Harvard Dataverse repository. Research is typically created by group scientists published together with academic papers to facilitate transparency reproducibility. For this study, we define ten questions address aspects impacting reproducibility reuse. First, retrieve analyze more than 2000 over 9000 unique R files 2010 2020. Second, execute in clean runtime environment...

Circumcision is associated with significant reductions in HIV, HSV-2 and HPV infections among men bacterial vaginosis their female partners.We assessed the penile (coronal sulci) microbiota 12 HIV-negative Ugandan before after circumcision. Microbiota were characterized using sequence-tagged 16S rRNA gene pyrosequencing targeting V3-V4 hypervariable regions. Taxonomic classification was performed RDP Naïve Bayesian Classifier. Among 42 unique families identified, Pseudomonadaceae...

Abstract Aim Intercomparison of mechanistic and empirical models is an important step towards improving projections potential species distribution abundance. We aim to compare suitability productivity estimates for a well‐understood crop evaluate the strengths weaknesses versus modelling. Location S outh A frica. Methods compared four habitat dryland maize based on climate soil predictors. Two were created using maximum entropy ( MAXENT ), first national points second only locations with...

Summary Network analysis is a useful approach for investigating complex and relational data in many fields including ecology, molecular evolutionary biology. Here, we introduce enaR , an r package Ecosystem Analysis (ENA). ENA analytical tool set rooted ecosystem ecology with over 30 years of development that examines the structure dynamics matter energy movement between discrete ecological compartments (e.g. food web). In addition to describing primary functionality package, highlight...

Abstract Network ecology provides a systems basis for approaching ecological questions, such as factors that influence biological diversity, the role of particular species or traits in structuring ecosystems, and long‐term dynamics (e.g., stability). Whereas introduction network theory has enabled ecologists to quantify not only degree, but also architecture complexity, these advances have come at cost introducing new challenges, including theoretical concepts metrics, increased data...

Summary Community genetics studies frequently focus on individual communities associated with plant genotypes, but little is known about the genetically based relationships among taxonomically and spatially disparate communities. We integrate of a wide range living same genotypes to understand how ecological evolutionary dynamics one community may be constrained or modulated by its underlying genetic connections another community. use pre‐existing data sets collected from Populus...

• Premise of the study: Fungal endophytes asymptomatically inhabit plant tissues where they have mutualistic, parasitic, or commensal relationships with their hosts. Although plant–fungal interactions at genotype scale broad ecological and evolutionary implications, sensitivity in woody to differences among genotypes is poorly understood. We hypothesize that (1) endophyte communities Populus angustifolia (Salicaceae) twigs vary tree genotypes, (2) variation linked quantitative traits, (3)...

Abstract In the last few decades, data-driven methods have come to dominate many fields of scientific inquiry. Open data and open-source software enabled rapid implementation novel manage analyze growing flood data. However, it has become apparent that exhibit distressingly low rates reproducibility. Although there are dimensions this issue, we believe is a lack formalism used when describing end-to-end published results, from source analysis final results. Even authors do their best make...

A major goal of community genetics is to understand the influence genetic variation within a species on ecological communities. Although well-documented for some organisms, additional research necessary relative and interactive effects genotype environment biodiversity, identify mechanisms through which tree influences communities, connect this emerging field with existing themes in ecology. We employ an underutilized but ecologically significant group epiphytic bark lichens, importance...

We examined the hypothesis that genetics-based interactions between strongly interacting foundation species, tree Populus angustifolia and aphid Pemphigus betae , affect arthropod community diversity, stability species interaction networks of which little is known. In a 2-year experimental manipulation its herbivore four major findings emerged: (i) these two determined composition an 139 species; (ii) both genotype presence significantly predicted diversity; (iii) aphids on genetically...

Summary Although the genetics of foundation plant species is known to be important drivers biodiversity and community structure, climate change have ecological evolutionary consequences for plants, no studies integrated these concepts. Here we examine how their combined effects are likely affect diversity future communities. We draw on several complimentary fields (community ecology, landscape biogeography) model will alter productivity associated focus three issues: (i) genetic variation...

Abstract Although genetics in a single species is known to impact whole communities, little about how genetic variation influences interaction networks complex ecosystems. Here, we examine the interactions community of arthropod on replicated genotypes (clones) foundation tree species, Populus angustifolia James (narrowleaf cottonwood), long‐term, common garden experiment using bipartite “genotype–species” network perspective. We combine this empirical work with simulation designed further...

Summary Natural systems of hybridizing plants are powerful tools with which to assess evolutionary processes between parental species and their associated arthropods. Here we report on these in a trispecific hybrid swarm Populus trees. Using field observations, common garden experiments genetic markers, tested the hypothesis that similarities among hosts underlie distributions 10 gall‐forming arthropods ability adapt new host genotypes. Key findings: degree relatedness determines whether...

Species of the genus Geopora are important ectomycorrhizal associates that can dominate communities some plant taxa, such as pinyon pine (Pinus edulis), a widespread tree western United States. Several members known only from root tips and thus have not been described formally. The sporocarps species occur infrequently because they depend on wet years for sporulation. In addition, be small may hypogeous at developmental stage, limiting opportunities describing their morphology. Using...

Open data and open source software might be part of the solution to sciences reproducibility crisis, but they are insufficient guarantee reproducibility. Requiring minimal end-user expertise, encapsulator system creates a time capsule with reproducible code in self-contained computational environment. provides end users fully featured desktop environment for research.