Comprehensive leaf size traits dataset for seven plant species from digitised herbarium specimen images covering more than two centuries.

Abstract

Background Morphological leaf traits are frequently used to quantify, understand and predict plant and vegetation functional diversity and ecology, including environmental and climate change responses. Although morphological leaf traits are easy to measure, their coverage for characterising variation within species and across temporal scales is limited. At the same time, there are about 3100 herbaria worldwide, containing approximately 390 million plant specimens dating from the 16th to 21st century, which can potentially be used to extract morphological leaf traits. Globally, plant specimens are rapidly being digitised and images are made openly available via various biodiversity data platforms, such as iDigBio and GBIF. Based on a pilot study to identify the availability and appropriateness of herbarium specimen images for comprehensive trait data extraction, we developed a spatio-temporal dataset on intraspecific trait variability containing 128,036 morphological leaf trait measurements for seven selected species. New information After scrutinising the metadata of digitised herbarium specimen images available from iDigBio and GBIF (21.9 million and 31.6 million images for Tracheophyta ; accessed date December 2020), we identified approximately 10 million images potentially appropriate for our study. From the 10 million images, we selected seven species ( Salix bebbiana Sarg., Alnus incana (L.) Moench, Viola canina L., Salix glauca L., Chenopodium album L., Impatiens capensis Meerb. and Solanum dulcamara L.) , which have a simple leaf shape, are well represented in space and time and have high availability of specimens per species. We downloaded 17,383 images. Out of these, we discarded 5779 images due to quality issues. We used the remaining 11,604 images to measure the area, length, width and perimeter on 32,009 individual leaf blades using the semi-automated tool TraitEx. The resulting dataset contains 128,036 trait records.We demonstrate its comparability to trait data measured in natural environments following standard protocols by comparing trait values from the TRY database. We conclude that the herbarium specimens provide valuable information on leaf sizes. The dataset created in our study, by extracting leaf traits from the digitised herbarium specimen images of seven selected species, is a promising opportunity to improve ecological knowledge about the adaptation of size-related leaf traits to environmental changes in space and time.

Plant phenotyping relevance

デジタル標本画像から葉面積・長さ・幅・周囲長を半自動抽出し、大規模な再利用可能データセットを構築・比較検証しており、植物表現型取得法が中心である。

Code and data availability

The paper's own leaf trait dataset (128,036 records from 11,604 herbarium specimen images) is publicly deposited on Zenodo, and two supplementary CSV files provide image metadata and per-image measurement/exclusion information. No author analysis code with a public URL is provided (Python scripts are mentioned but not)