skip to main content

Title: Integrating herbarium specimen observations into global phenology data systems
Premise of the Study

The Plant Phenology Ontology (PPO) was originally developed to integrate phenology observations of whole plants across different global observation networks. Here we describe a new release of thePPOand associated data pipelines that supports integration of phenology observations from herbarium specimens, which provide historical and modern phenology data.

Methods and Results

Critical changes to thePPOinclude key terms that describe how measurements from parts of plants, which are captured in most imaged herbarium specimens, relate to whole plants. We provide proof of concept for ingesting annotations from imaged herbarium sheets ofPrunus serotina, the common black cherry. We then provide an example analysis of changes in flowering timing over the past 125 years, demonstrating the value of integrating herbarium and observational phenology data sets.


These conceptual and technical advances will support the addition of phenology data from herbaria, but also could be expanded upon to facilitate the inclusion of data from photograph‐based citizen science platforms. With the incorporation of herbarium phenology data, new historical baseline data will strengthen the capability to monitor, model, and forecast plant phenology changes.

more » « less
Author(s) / Creator(s):
 ;  ;  ;  ;  
Publisher / Repository:
Wiley Blackwell (John Wiley & Sons)
Date Published:
Journal Name:
Applications in Plant Sciences
Medium: X
Sponsoring Org:
National Science Foundation
More Like this
  1. Premise

    Herbarium specimens have been used to detect climate‐induced shifts in flowering time by using the day of year of collection (DOY) as a proxy for first or peak flowering date. Variation among herbarium sheets in their phenological status, however, undermines the assumption thatDOYaccurately represents any particular phenophase. Ignoring this variation can reduce the explanatory power of pheno‐climatic models (PCMs) designed to predict the effects of climate on flowering date.


    Here we present a protocol for the phenological scoring of imaged herbarium specimens using an ImageJ plugin, and we introduce a quantitative metric of a specimen's phenological status, the phenological index (PI), which we use inPCMs to control for phenological variation among specimens ofStreptanthus tortuosus(Brassicaceeae) when testing for the effects of climate onDOY. We demonstrate that includingPIas an independent variable improves model fit.


    IncludingPIinPCMs increased the modelR2relative toPCMs that excludedPI; regression coefficients for climatic parameters, however, remained constant.


    Our protocol provides a simple, quantitative phenological metric for any observed plant. IncludingPIinPCMs increasesR2and enables predictions of theDOYof any phenophase under any specified climatic conditions.

    more » « less
  2. Abstract Aim

    High‐elevation plants are disproportionally affected by climate change. As temperatures rise, the amount of available alpine habitat in the Rocky Mountains will decrease resulting in potential local extinctions of plant species. In addition to the direct effects of climate‐driven habitat loss, alpine plants must also respond to indirect effects, such as changes in disturbance regimes. One notable shift is the increase of wildfire frequency in regions where fire was previously rare or absent, including the alpine. We hypothesized that direct climatic changes compounded with increased wildfire frequency will reduce the future suitable habitat of high‐elevation plants more than if climate was considered alone.


    Rocky Mountain Floristic Region, western North America.


    Saxifraga austromontana(Saxifragaceae), a wildflower endemic to high elevations of the Rocky Mountain Floristic Region.


    Our approach integrated historical herbarium records, field surveys, remote sensing, species distribution models, historic wildfire data, and predictive models.


    Our results indicate wildfire has significantly reduced the abundance and increased the likelihood of extirpation forS. austromontana. Increased fire frequency compounded with direct climatic changes will likely reduce the range of the species by approximately 43% by 2050 compared to 38% due to climate alone, under a moderateCO2emissions scenario. The influence of wildfire varies regionally. For instance, the Middle Rockies will likely lose 74% of its suitable habitat of which 16% may be lost due to fire, while other regions, such as the northern range, will be less negatively affected by direct and indirect effects.

    Main Conclusions

    Our evidence that increased wildfire frequency will compound the impacts of climate change on alpine taxa in North America led to the development of a new, general hypothesis on the fundamental interaction between direct and indirect effects of climate change on species range reductions.

    more » « less
  3. Premise

    The ability to sequence genome‐scale data from herbarium specimens would allow for the economical development of data sets with broad taxonomic and geographic sampling that would otherwise not be possible. Here, we evaluate the utility of a basic double‐digest restriction site–associatedDNAsequencing (ddRADseq) protocol usingDNAs from four genera extracted from both silica‐dried and herbarium tissue.


    DNAs fromDraba,Boechera,Solidago, andIlexwere processed with a ddRADseq protocol. The effects ofDNAdegradation, taxon, and specimen age were assessed.


    Although taxon, preservation method, and specimen age affected data recovery, large phylogenetically informative data sets were obtained from the majority of samples.


    These results suggest that herbarium samples can be incorporated into ddRADseq project designs, and that specimen age can be used as a rapid on‐site guide for sample choice. The detailed protocol we provide will allow users to pursue herbarium‐based ddRADseq projects that minimize the expenses associated with fieldwork and sample evaluation.

    more » « less
  4. Premise

    We take an integrative approach in assessing how introgression and Pleistocene climate fluctuations have shaped the diversification of the coreLentagoclade ofViburnum, a group of five interfertile species with broad areas of sympatry. We specifically tested whether flowering time plays a role in maintaining species isolation.


    RAD‐seq data for 103 individuals were used to infer the species relationships and the genetic structure within each species. Flowering times were compared among species on the basis of historical flowering dates documented by herbarium specimens.


    Within each species, we found a strong relationship between flowering date and latitude, such that southern populations flower earlier than northern ones. In areas of sympatry, the species flower in sequence rather than simultaneously, with flowering dates offset by ≥9 d for all species pairs. In two cases it appears that the offset in flowering times is an incidental consequence of adaptation to differing climates, but in the recently diverged sister speciesV. prunifoliumandV. rufidulum, we find evidence that reinforcement led to reproductive character displacement. Long‐term trends suggest that the two northern‐most species are flowering earlier in response to recent climate change.


    We argue that speciation in theLentagoclade has primarily occurred through ecological divergence of allopatric populations, but differences in flowering time were essential to maintain separation of incipient species when they came into secondary contact. This combination of factors may underlie diversification in many other plant clades.

    more » « less
  5. Premise of the Study

    Polyploidy, or whole genome duplication (WGD), is common in plants despite theory suggesting that polyploid establishment is challenging and polyploids should be evolutionarily transitory. There is renewed interest in understanding the mechanisms that could facilitate polyploid establishment and explain their pervasiveness in nature. In particular, premating isolation from their diploid progenitors is suggested to be a crucial factor. To evaluate how changes in assortative mating occur, we need to understand the phenotypic effects ofWGDon reproductive traits.


    We used literature surveys and a meta‐analysis to assess howWGDaffects floral morphology, flowering phenology, and reproductive output in plants. We focused specifically on comparisons of newly generated polyploids (neopolyploids) and their parents to mitigate potential confounding effects of adaptation and drift that may be present in ancient polyploids.

    Key Results

    The results indicated that across a broad representation of angiosperms, floral morphology traits increased in size, reproductive output decreased, and flowering phenology was unaffected byWGD. Additionally, we found that increased trait variation afterWGDwas uncommon for the phenotypic traits examined.


    Our results suggest that the phenotypic effects on traits important to premating isolation of neopolyploids are small, in general. Changes in flowering phenology, reproductive output, and phenotypic variation resulting fromWGDmay be less critical in facilitating premating isolation and neopolyploid establishment. However, floral traits for which size is an important component of function (e.g., pollen transfer) could be strongly influenced byWGD.

    more » « less