Protocols

Plant species composition within 15cm of Castilleja individuals is compared to random background vegetation to statistically identify overrepresented taxa as potential hosts. This provides an indirect...

A microarray-based approach to profile DNA methylation at conserved CpG sites across diverse mammalian species without requiring species-specific reference genomes. Enables direct comparison of methyl...

Calculation and statistical analysis of plant biomass allocation between vegetative and reproductive tissues using arcsin transformations and three-way ANOVA.

Statistical analysis of stream chemistry data transformed to compositional units using PCA to evaluate spatial and temporal trends while removing effects of dilution.

Use of oat seedling growth parameters including root weight fraction to assess soil nutrient availability and quality following various treatments.

Sequential chemical extractions using water, sodium pyrophosphate, HCl, and sodium dithionite to selectively dissolve mineral phases of varying crystallinity and their associated organic carbon.

Calculation of Shannon diversity index (ln type) and Simpson dominance index (1-D) from species count data using online biodiversity calculator. Standard ecological diversity metrics for comparing com...

Path analysis using structural equation modeling to test competing hypotheses about causal relationships between nectar traits, robbing, pollination, and fitness.

Systematic search and evaluation of published literature examining relationships between phenological shifts and demographic consequences using specific search criteria in Web of Science.

A comprehensive systematic review using database searches, citation network expansion, and vote counting to assess evidence for macroecological rules in microorganisms across multiple taxonomic groups...

Systematic compilation and cleaning of plant trait records from multiple databases to create a comprehensive tundra plant trait dataset. Combined TRY database records with Tundra Trait Team contributi...

A comprehensive protocol for extracting, amplifying, sequencing and analyzing viral DNA from fecal samples to identify microviral genomes. Uses rolling circle amplification followed by high-throughput...

Sulfur K-edge X-ray Absorption Near Edge Structure spectroscopy was used to determine sulfur speciation in solid samples including bedrock, soils, and sediments. Linear combination fitting was used to...

Cellulose acetate electrophoresis to analyze genetic variation at enzyme loci in mayfly populations, involving initial enzyme screening, locus selection, and final allele frequency determination acros...

Statistical approach using the climwin package to determine optimal phenological windows of climate variables that best predict biological timing by testing multiple window lengths and start dates.

Construction of phylogenetic trees using concatenated ribosomal protein genes to determine evolutionary relationships. Uses IQ-TREE with maximum likelihood approach and bootstrap support.

Statistical modeling of capture-recapture data to estimate seasonal survival probabilities across age classes using program MARK with model selection via AICc.

Statistical analysis using zero-inflated negative binomial generalized linear mixed models to account for excess zeros in ecological count data, specifically pollen grain counts.

Integration of molecular phylogeny with life history and energetic data to identify evolutionary patterns of energy conservation traits across marmot species. Uses comparative analysis to distinguish ...

Statistical analysis comparing observed vs. expected species co-occurrence patterns using probabilistic models to identify positive, negative, or random associations between species pairs.

Standard analytical chemistry methods using ion chromatography for anions and inductively coupled plasma mass spectrometry for cations and trace elements in filtered water samples.

Real-time PCR using universal 16S primers to detect mite DNA in mammalian hair samples, with melting curve analysis for specificity assessment.

ABBA-BABA test implementation to detect historical introgression between species using genome-wide SNP data.

Negative binomial regression models compared using AICc with model averaging to assess relative importance of predictors via Akaike weights.

Standardized chlorination procedure to simulate drinking water treatment and quantify the potential for organic matter to form regulated disinfection byproducts under controlled conditions.

Species-level phylogenetic reconstruction using thousands of single-copy orthologous genes with coalescent-based species tree estimation.

Measurement of radiocarbon content in bulk sediments and density fractions using accelerator mass spectrometry after acid fumigation pretreatment to remove inorganic carbon.

Broadcasting and re-recording sounds at increasing distances in different habitats to quantify degradation patterns using spectrogram correlation analysis. Assesses how acoustic signals change with tr...

Analysis of high-resolution aerial photography to quantify conifer cover around host plants using color thresholding and spatial buffering techniques.

Transmission electron microscopy with energy dispersive X-ray spectroscopy performed under anoxic conditions using vacuum transfer holders to map elemental distributions in redox-sensitive particles.

Standard method for determining inorganic ash content of plant materials by high-temperature combustion at 500°C for 4 hours.

Standard protocol for measuring organic matter decomposition by separating detritus into size fractions, oven-drying, weighing, and ashing to determine ash-free dry mass (AFDM). Accounts for inorganic...

Calculation of reproductive synchrony using Augspurger's Index which quantifies the overlap of activity duration for each individual relative to the population, producing values from 0 to 1.

Measurement of specific surface area using Brunauer, Emmett and Teller modeled N₂ gas sorption isotherms for normalizing weathering rates.

Bayesian framework using Markov-chain Monte Carlo to infer groundwater residence time distributions from environmental tracer observations while quantifying parameter uncertainties.

Bayesian hierarchical Dirichlet regression models to analyze macronutrient composition patterns and niche overlap. Incorporates phylogenetic relationships and species traits to assess compositional di...

Multivariate capture-recapture models fitted in Bayesian framework to simultaneously estimate temporal variation and covariation in multiple demographic parameters. Uses multivariate normal distributi...

MCMC-based phylogenetic reconstruction using multiple gene fragments to establish evolutionary relationships among Prostigmata mites.

Bayesian inference method combining temperature index snow accumulation modeling with bucket hydrology to estimate basin mean precipitation from streamflow observations and snow remote sensing data. U...

A two-stage Bayesian hierarchical approach that identifies unique individuals across LiDAR scans by modeling observed locations as noisy transformations of latent true locations, then propagates linka...

Calculation of bedrock weathering rates using base cation export measurements combined with transmissivity feedback methods for subsurface flow estimation. Uses correlations between specific conductan...

Systematic exclusion of individual biogeochemical mechanisms to quantify their relative contributions to solute exports and carbon partitioning. Compares scenarios with and without specific processes ...

Community-level physiological profiling using 96-well plates with 31 different carbon sources to assess functional diversity of soil microbial communities.

Statistical testing for phylogenetic signal in species traits using Blomberg's K and Pagel's lambda to determine whether closely related species have more similar trait values than expected by chance.

Non-parametric statistical method using bootstrap resampling to generate confidence intervals for comparing treatment group means without distributional assumptions.

Computational simulation using multiple random dataset selections to assess the impact of pseudoreplication on statistical results.

Standard colorimetric method for protein quantification using bovine serum albumin as standard, measured at 596 nm spectrophotometer.

Standard Bray-1 extraction followed by automated molybdate colorimetry to quantify bioavailable phosphorus in soils.

Ordination analysis using Bray-Curtis distance to examine ecological relationships among bumble bee species based on host plant usage patterns from Pyke 1982 data.

Multi-component analysis of butterfly egg composition including protein content via Bradford dye-binding method, glycogen content via modified Giron protocol, and triglyceride content using commercial...