Collection site uncertainty in herbarium data: geographic deviations but not specimen error distance affect estimates of phenological sensitivity to climate
Creators: name: Gamble, Devin
name: Mazer, Susan
Publisher: name: Zenodo
Year: 2021
Subjects: herbarium
spatial uncertainty
Nemophila menziesii
plant phenology
Linear Regression

description: This data package provides the herbarium, climate, and R markdown data and files used in creating the manuscript "<em>Collection site uncertainty in herbarium data: geographic deviations but not specimen error distance affect estimates of phenological sensitivity to climate</em>". 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 benefited from the increasing availability of digitized herbarium specimens, but issues unique to these data can undermine the findings of such research. One potential 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 discrepancies between recorded and simulated collection sites, as well as error distance itself, affect estimates of phenological sensitivity to climate in specimens of a widespread annual California wildflower. Simulated site deviations led to increasingly weak and non-significant estimates of phenological sensitivity to climate anomalies with increasing location mismatch. However, we found no significant effect of error distance magnitude on estimates of phenological sensitivity. These findings suggest that large error distances among specimens of widely collected plant species may not adversely affect the relationships inferred from trait-climate models. Collection site uncertainty merits further attention as a potential source of noise in herbarium data, especially for research on how plant traits respond to interannual climate variation.
description: See README file. Contact Devin Gamble (dgamble@ucsb.edu) if you have questions about using these data or Rmd files.
description: <em>Nemophila menziesii</em> 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 5 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.