Harvard Forest

Data Archive

HF427

Assessing Plant Phenological Patterns in Tropical Brazil 1901–2020

Related Publications

Data

• hf427-01: phenological data (preview)
• hf427-02: dzi tutorial

Overview

• Lead: Charles Davis, Goia Lyra, Daniel Park, Hongrui Zhang, Renata Asprino, Rogerio Maruyama, Debora Torquato, Benjamin Cook, Junxi Xie, Aaron Ellison
• Investigators:
• Contact: Information Manager
• Start date: 1901
• End date: 2020
• Status: complete
• Location: Brazil
• Latitude: +6 to -33 degrees
• Longitude: -34 to -74 degrees
• Elevation: 1 to 1100 meter
• Datum: WGS84
• Taxa:
• Release date: 2023
• Language: English
• EML file: knb-lter-hfr.427.3
• DOI: digital object identifier
• EDI: data package
• DataONE: data package
• Related links:
• Study type: historical
• Research topic: ecological informatics and modelling; historical and retrospective studies; regional studies
• LTER core area: population studies
• Keywords: climate change, phenology, plant species, precipitation, temperature
• Abstract:

  Phenology is a key biological trait of an organism’s success and is one of the best indicators of its response to recent climate change. Plants are among the most well-studied organisms in this regard, but observational data bearing on this topic are largely restricted to species of the northern hemisphere, mostly from ca. the last three decades. Phenological data from tropical latitudes are especially lacking. Recent research has demonstrated that mobilized online herbarium specimens provide important, albeit mostly neglected, information on plant phenology. Here, we use the web tool CrowdCurio to crowdsource phenological data from nearly 35,000 herbarium specimens representing 260 flowering plant species broadly distributed across tropical Brazil. Our results, spanning 120 years and generated from over 1000 crowdsourcers, clarify numerous aspects of tropical plant phenology. First, they reveal that plant reproductive timing is exceptionally diverse across tropical biomes and taxa. Second, they identify that phenological responses to climate are variable across taxa and biomes. Third, among those species with broad latitudinal ranges, populations from more southern latitudes are significantly more phenologically sensitive to precipitation than those from northern populations. Our results are robust to a variety of confounding factors and span large phylogenetic distances and various life histories. These may represent more global trends in the latitudinal gradient of tropical phenological response with myriad potential ecological and evolutionary consequences.

  This dataset may be used for non-commercial purposes. Please provide the following attribution: Davis, C., Lyra, G., Park, D., Zhang, H., Asprino, R., Maruyama, R., Torquato, D., Cook, B., Xie, J., Ellison, A. 2022. Assessing plant phenological patterns in tropical Brazil 1901–2020. Harvard Forest Data Archive: HF427. Please note that the license we provide does not apply to images linked from the data set. Please check each content provider’s online documentation to see what licenses may be provided and what terms and restrictions they impose.

• Methods:

  Active online and open access links to specimens, images, and metadata are presented from Reflora (https://floradobrasil.jbrj.gov.br/reflora/herbarioVirtual/ConsultaPublicoHVUC/ConsultaPublicoHVUC.do), SpeciesLink (https://specieslink.net/search/), Tropicos (https://www.tropicos.org/home), and NY (http://sweetgum.nybg.org/science/vh/). Scripts are additionally provided for downloading images from Reflora. Here, .DZI image links specified are downloaded and converted to a .JPG file for crowdsourcing. An associated video to demonstrate the conversion is also presented. Finally, the web tool CrowdCurio was used to crowd source phenological data from nearly 35,000 herbarium specimens representing 260 flowering plant species across Brazil. Each specimen was scored across all phenophases (bud, flower, fruit) by an average of three crowdsourcers. To clean metadata, we transformed names to proper case as needed; removed all non-alphabetical characters; completed state and municipality data as needed; and cleaned for obvious incorrect formatting. Only specimens with complete species names, full dates, and state and municipality are included.

  The file named hf427-02-dzi-tutorial.zip includes a text-based step-by-step tutorial on how to download .JPG files using the .DZI links in the csv file; the zipped file also contains a Python script that is used in one of the steps in the tutorial. In addition, the text-based tutorial also contains a link to the video version of the same tutorial.

• Organization: Harvard Forest. 324 North Main Street, Petersham, MA 01366, USA. Phone (978) 724-3302. Fax (978) 724-3595.

• Project: The Harvard Forest Long-Term Ecological Research (LTER) program examines ecological dynamics in the New England region resulting from natural disturbances, environmental change, and human impacts. (ROR).

• Funding: National Science Foundation LTER grants: DEB-8811764, DEB-9411975, DEB-0080592, DEB-0620443, DEB-1237491, DEB-1832210.

• Use: This dataset is released to the public under Creative Commons CC0 1.0 (No Rights Reserved). Please keep the dataset creators informed of any plans to use the dataset. Consultation with the original investigators is strongly encouraged. Publications and data products that make use of the dataset should include proper acknowledgement.

• License: Creative Commons Zero v1.0 Universal (CC0-1.0)

• Citation: Davis C, Lyra G, Park D, Zhang H, Asprino R, Maruyama R, Torquato D, Cook B, Xie J, Ellison A. 2023. Assessing Plant Phenological Patterns in Tropical Brazil 1901–2020. Harvard Forest Data Archive: HF427 (v.3). Environmental Data Initiative: https://doi.org/10.6073/pasta/eb856519e993f084e82677e710ed7bac.

Detailed Metadata

hf427-01: phenological data

1. barcode: specimen’s unique identification number
2. scientific_name: species binomial name of the specimen
3. anonymized_username: anonymized crowdworker username
4. bud: number of buds on the specimen image as reported by the crowdworker (unit: number / missing value: NA)
5. flower: number of flowers on the specimen image as reported by the crowdworker (unit: number / missing value: NA)
6. fruit: number of fruits on the specimen image as reported by the crowdworker (unit: number / missing value: NA)
7. duplicated: whether the specimen entry is used for verified work consistency of the crowdworker
   • FALSE: specimen entry not used for verified work consistency
   • TRUE: specimen entry used for verified work consistency
8. anonymized_hit_id: anonymized Human Intelligent Task identification number
9. consistency_score: composite consistency score of the crowdworker for counting buds, flowers, and fruits in the corresponding set of specimen images following [Park, D. S., Breckheimer, I., Williams, A. C., Law, E., Ellison, A. M. and Davis, C. C. Herbarium specimens reveal substantial and unexpected variation in phenological sensitivity across the eastern United States. Philos. Trans. R. Soc. B 374, 20170394, doi:10.1098/rstb.2017.0394 (2019).] (unit: dimensionless / missing value: NA)
10. bud_consistency_score: consistency score of the crowdworker for counting buds in the corresponding set of specimen images following (Park et al. 2019) (unit: dimensionless / missing value: NA)
11. flower_consistency_score: consistency score of the crowdworker for counting flowers in the corresponding set of specimen images following (Park et al. 2019) (unit: dimensionless / missing value: NA)
12. fruit_consistency_score: consistency score of the crowdworker for counting fruits in the corresponding set of specimen images following (Park et al. 2019) (unit: dimensionless / missing value: NA)
13. family: family of the specimen
14. genus: genus of the specimen
15. municipality: municipality in which the specimen was collected
16. state: state in which the specimen was collected
17. year: year in which the specimen was collected
18. month: month in which the specimen was collected
19. day: day in which the specimen was collected
20. date: date on which the specimen was collected
21. reflora_dzi_url: link to download the .DZI image of the specimen from Reflora
22. specieslink_url: link to download the .JPG image of the specimen from SpeciesLink
23. tropicos_url: link to download the .JPG image of the specimen from the Missouri Botanical Garden
24. ny_url: link to download the .JPG image of the specimen from the New York Botanical Garden

hf427-02: dzi tutorial

• Compression: zip
• Format: Python script, text
• Type: document, script