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Spatial uncertainty in herbarium data: Simulated displacement but not error distance alters estimates of phenological sensitivity to climate in a widespread California wildflower

Citation

Gamble, Devin; Mazer, Susan (2022), Spatial uncertainty in herbarium data: Simulated displacement but not error distance alters estimates of phenological sensitivity to climate in a widespread California wildflower, Dryad, Dataset, https://doi.org/10.25349/D9X893

Abstract

This data package provides the herbarium, climate, and R markdown data and files used in creating the manuscript "Spatial uncertainty in herbarium data: Simulated displacement but not error distance alters estimates of phenological sensitivity to climate in a widespread California wildflower". 

Herbarium records provide a broad spatial and temporal range with which to investigate plant responses to environmental change. Research on plant phenology and its sensitivity to climate has advanced with the increasing availability of digitized herbarium specimens, but limitations of specimen-derived data can undermine the inferences derived from such research. One issue that has received little attention is collection site uncertainty (i.e., error distance), a measure of confidence in the location from which a specimen was collected. We conducted comparative analyses of phenoclimatic models to determine whether spatial deviations of 2, 5, 15, or 25 km between recorded and simulated collection sites, as well as the error distance reported in digitized records, affect estimates of the phenological sensitivity of flowering time to annual temperature and precipitation in a widespread annual California wildflower. In this approach, we considered both spatial and interannual variation in climatic conditions. Simulated site displacements led to increasingly weak estimates of phenological sensitivity to temperature and precipitation anomalies with increasing distances. However, we found no significant effect of reported error distance magnitude on estimates of phenological sensitivity to climate normals or anomalies. These findings suggest that the spatial uncertainty of collection sites among specimens of widely collected plant species may not adversely affect estimates of phenological sensitivity to climate, even though real discrepancies and georeferencing inaccuracy can negatively impact such estimates. Collection site uncertainty merits further attention as a potential source of noise in herbarium data, especially for research on how plant traits respond to spatial and interannual climatic variation.

Methods

Nemophila menziesii herbarium data were downloaded from the Consortium for California Herbaria (CCH) (https://ucjeps.berkeley.edu/consortium/) and cleaned to remove duplicate specimens (collected on the same date within ~1 km of one another). We then selected specimens collected between 1901 and 2019 (N=1677), the period for which climate data was available. Climate data for our analyses were extracted from ClimateNA v6.40 (see http://climatena.ca/Help for more information). The file 'nemo_full_1901_2019.csv' contains all herbarium records and their associated data, plus climate data associated with each individual herbarium record. New datasets were generated using this primary .csv file to investigate the effects of collection location discrepancies on phenological sensitivity to climate. Specifically, new collection coordinates were generated for each digitized herbarium record by displacing the original coordinates of each by one of four distances (2, 5, 15, or 25 km) in a random direction (replicated 200 times). These data were used to construct phenoclimatic models whose results were compared to those of the original data set. See the README file for more details.

Usage Notes

See README file. Contact Devin Gamble (dgamble@ucsb.edu) if you have questions about using these data or Rmd files.