DOI: 10.5061/dryad.v9s4mw734
title: Phenological scoring of citizen science observations of five native California milkweed species

description: Understanding phenological strategies can be complicated by organisms’ use
 of multiple cues, changing effects of cues over phenophases, and local
 adaptation. We investigated the importance of spring temperature and
 rain-year precipitation on phenology in five species of milkweeds
 (Asclepias spp.) in the western United States, a region with variable
 temperature and moisture conditions. We categorized participatory science
 milkweed observations into budding, flowering, and post-flowering
 phenophases, and matched observations to year- and site-specific climate
 conditions. We separated climate effects on phenology into variation
 across sites vs. variation across years to look for evidence of local
 adaptation in phenology. Warmer mean spring temperatures generally
 advanced phenology, while wetter rain-years generally delayed phenology.
 Across all milkweed species × phenophase combinations, spring mean
 temperature advanced phenology by 2.56 ± 1.71 days spring temp °C -1 (mean
 ± SD), and precipitation delayed phenology by 0.12 ± 0.079 days cm precip
 -1. We found evidence for local adaptation in phenology with respect to
 temperature in three of fifteen species × phenophase combinations, and for
 precipitation in four of fifteen species × phenophase combinations. All
 significant local adaptation with respect to temperature and precipitation
 reflected counter-gradient local adaptation (increasing phenological
 synchrony across the range). Combining analytical approaches for studying
 phenology using observation datasets with the wide availability of
 observational data from participatory science sources offers an exciting
 possibility to rapidly generate hypotheses about how organisms’ phenology
 may react to novel cue combinations under global change, and how these
 reactions may differ based on species traits.
description: # Phenological scoring of citizen science observations of five native
 California milkweed species
 [https://doi.org/10.5061/dryad.v9s4mw734](https://doi.org/10.5061/dryad.v9s4mw734) ## Description of the data and file structure Description of data file d.all_10082025.csv: These data reflect phenology, climate, and timing data created in connection with iNaturalist observations of milkweed species in the western United States. iNaturalist data download parameters: We downloaded milkweed (genus Asclepias, iNaturalist taxon ID 47906) observations on Nov. 9th, 2023, for the period spanning Jan. 1st, 2010 – Dec. 31st, 2021. We restricted our search to the western United States by including only observations from the iNaturalist region “Western United States and Canada” (place ID 65360) and then removing any observations from Canada (place ID 6712). We included only verifiable observations, but we included those that did not have enough identifications to reach research grade, because we looked through the photos associated with each observation ourselves and screened out incorrectly identified observations. Our exact query was: “quality_grade=any&identifications=any&place_id=65360&not_in_place=6712&taxon_id=47906&verifiable=true&d1=2010-01-01&d2=2021-12-31&spam=false” **Column Descriptions:** Column "id" contains a unique identifying number for each observation, which can be used to link our data back to complete observation information from iNaturalist ([www.inaturalist.org](http://www.inaturalist.org)) Column "phenology" contains our phenology annotations based on images associated with these iNaturalist observations as follows: * "1" = budding: plants that showed at least one flower bud, but no open flowers * "2" = flowering: plants that showed at least one open flower * "3" = post-flowering: plants that showed pods or senesced flowers, but no open flowers * "11" = small non-reproductive: plants that had &lt;3 It set of adult leaves did not show any evidence of reproductive structures * "12" = large non-reproductive: plants that had &gt;=3 sets of adult leaves and did not show any evidence of reproductive structures * "9" = incorrectly identified species observations * "8" = seemingly duplicate uploads * "7" = observations that for any other reason could not be assigned, including close-up images that did not display any reproductive structures or at least one stem tip - Columns "year", "month", "doy": include date information extracted from the iNaturalist observation date * Column "site_mean_temp": contains the spatial temperature residual. Positive values indicate that the observation site was, on average, warmer than other sites where this species was observed. - Column "year_mean_temp": contains the temporal temperature residual. Positive values indicate that the observation year was warmer than an average year at that site. * Column "abs_temp": contains the absolute mean temperature in degrees Celsius at the site of the milkweed observation, averaged over the first 90 days of the year of observation. This metric was calculated using the package daymetr to download daily min and max temperatures. - Columns "site_total_precip", "year_total_precip", "abs_precip": similar to the above three columns for precipitation instead of temperature. Precipitation was calculated as the total previous rain year precipitation at the site of interest using Daymet. * Column "species_abbrev": contains the abbreviated scientific name of the milkweed species corresponding to each entry.  - "a_cali" = Asclepias californica - "a_cord" = Asclepias cordifolia - "a_erio" = Asclepias eriocarpa - "a_fasc" = Asclepias fascicularis - "a_spec" = Asclepias speciosa ## Sharing/Access information * Observation data are available directly from iNaturalist at [https://www.inaturalist.org/observations.](https://www.inaturalist.org/observations) ## Code/Software Description of code file iNat_milkweed_analysis_10_08_2025_upload.Rmd: A R Markdown script used to analyze these data and generate figures is attached. Analyses were run in R version 4.1.1, using packages lubridate, ggplot2, plyr, dplyr, tidyverse, sf, elevatr, lme4, lmerTest, sjPlot, rgdal, daymetr, vegan, ggpubr, corrplot, and others.