Protocols

Novel method using programmable LED devices to test color discrimination in free-flying hummingbirds through reward-based choice experiments. Birds choose between tubes displaying different colors in ...

Custom apparatus measuring salamander temperature selection behavior using water-cooled and heated runway with position and body temperature tracking over 3.5 hour trials.

Controlled behavioral experiments using salamanders in tanks with traps at either end to test preferences for different light stimuli and biofluorescent vs. non-biofluorescent mates. Salamanders place...

A comprehensive statistical framework for quality assurance and quality control of meteorological time series data involving preliminary data exploration, quality assessment with outlier detection, an...

Standardized substrate tiles deployed in stream channels for algae colonization, followed by systematic scraping, filtering, and microscopic enumeration of didymo cells.

Weekly counts of visitors at a facility to create a traffic volume index as a proxy for vehicle traffic on nearby roads during peak visitation periods.

Systematic vegetation sampling along parallel transects between sites to quantify matrix composition and calculate proportional cover of different vegetation types.

Systematic collection of seeds from plants along established transects for genetic analysis. Seeds collected within defined distances of sampling points and pooled by maternal plant.

Systematic field observation of trophic interactions between organisms, primarily plants and insects, with rotating temporal sampling across multiple sites to record feeding relationships and interact...

Deployment of camouflaged security cameras or GoPro cameras near nests to record predation events, with careful timing to minimize nest abandonment and standardized recording parameters.

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...

Deployment and operation of networked embedded sensor nodes for distributed acoustic monitoring using custom hardware and WaveScript programming language. Enables real-time processing and localization...

Standardized biochemical assays for quantifying protein, lipid, and carbohydrate content in pollen samples. Uses Bradford assay for proteins and sulfo-phospho-vanillin and anthrone-sulfuric acid assay...

High-resolution Weather Research and Forecasting model simulations using different microphysical parameterizations to assess precipitation sensitivity in complex mountain terrain. Three different micr...

Systematic walking surveys through grasshopper habitat to count and score individuals for wing color morphs (orange vs yellow) across multiple populations and years. Researchers targeted 100 individua...

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...

Method to quantify microbial load on different butterfly body parts by direct plating on agar media. Samples tarsi/proboscis by dragging across plate and thorax by washing technique.

Measurement of anogenital distance using dial or digital callipers to 1mm accuracy as a proxy for prenatal testosterone exposure and masculinization. Distance measured from centre of genital opening t...

Motion-activated camera deployment to detect and monitor presence of snow leopards and other wildlife in remote mountain environments.

Individual animals are uniquely marked and tracked through capture-recapture over multiple decades to estimate survival, reproduction, and productivity parameters. This generates individual life histo...

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.

Production of F2 hybrid generations with alternate cytoplasmic backgrounds through controlled hand-pollination crosses. Allows testing of cytoplasmic effects on physiological traits.

Standardized eddy covariance measurements of carbon dioxide, water vapor, and energy fluxes between ecosystems and atmosphere. Continuous automated measurements providing ground truth data for model t...

Direct observation of individual birds during foraging attempts, recording foraging success and behavior, followed by detailed vegetation structure surveys of the exact foraging microhabitat. Uses sta...

Multi-generation breeding program with controlled matings to estimate heritability of preference traits using pedigree-based models accounting for ZW sex determination system.

Controlled laboratory assay using prepared stigmas on growth medium to test pollen germination and tube growth across species boundaries. Stigmas are prepared from unopened buds, treated with pure pol...

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

Hummingbirds are captured using a gravity-based drop-net system that releases around a suspended feeder onto a platform when triggered.

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.

Standard protocol for locating Mountain White-crowned Sparrow nests using behavioral cues and rope-dragging, followed by regular monitoring every 2-5 days throughout the breeding cycle.

Conversion of reflectance spectra into bee and bird visual spaces using established photoreceptor sensitivity models. Uses color hexagon model for bees and receptor-noise limited model for birds to ca...

Long-term monitoring of tundra plant communities using standardized sampling within permanently marked study areas, employing various abundance quantification methods including point frame hits, visua...

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 ...

Classification of ponds into permanent, semi-permanent, and temporary categories based on historical drying patterns and hydroperiod duration from long-term data records.

Direct measurement of leaf stomatal conductance using porometer to assess plant water stress and physiological responses to watering treatments. Measured during flowering and early fruiting phases.

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

Experimental transplantation of completed mason bee nests from low to high elevation sites to test effects of season length and climate on offspring development. Uses trap-nest monitoring followed by ...

Non-destructive estimation of leaf chlorophyll concentration using reflectance spectroscopy and vegetation indices.

Measurement of six different soil extracellular enzyme activities using microplate spectrophotometry to understand microbial activity and nutrient cycling processes in response to plant removal treatm...

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

Stable isotope tracer experiment using 15N-labeled fertilizer to quantify nitrogen uptake rates and allocation in plants growing under different soil treatments.

PCR amplification of Acidobacteria 16S rRNA genes from soil DNA followed by cloning into vectors and Sanger sequencing to characterize bacterial community composition and phylogenetic diversity.

Standard protocol to isolate, culture, and identify bacteria using genomic DNA extraction, 16S rRNA gene sequencing, and NCBI database comparison.

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

Three-dimensional geological modeling using implicit modeling with radial basis functions to generate subsurface structure. Model incorporates strike, dip, and fault information from geological survey...

454 GS FLX Titanium sequencing of normalized cDNA libraries to generate reference transcriptome assembly for gene discovery and annotation.

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.