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The niche through time: Considering phenology and demographic stages in plant distribution models

Cite this dataset

Zurell, Damaris; Zimmermann, Niklaus; Brun, Philipp (2024). The niche through time: Considering phenology and demographic stages in plant distribution models [Dataset]. Dryad. https://doi.org/10.5061/dryad.sn02v6xct

Abstract

Species distribution models (SDMs) are widely used to infer species-environment relationships, predict spatial distributions, and characterise species’ environmental niches. While the importance of space and spatial scales is widely acknowledged in SDM applications, temporal components of the niche are rarely addressed. We discuss how phenology and demographic stages affect model inference in plant SDMs. Ignoring conspicuousness and timing of phenological stages may bias niche estimates through increased observer bias, while ignoring stand age may bias niche estimates through temporal mismatches with environmental variables, especially during times of rapid global warming. We present different methods to consider phenology and demographic stages in plant SDMs, including the selection of causal, spatiotemporally explicit predictors, and the calibration of stage-specific SDMs. Based on a case study with citizen science data, we illustrate how spatiotemporal SDMs provide deeper insights on the coincidence of range and phenological shifts under climate change. The proliferation of digitally available biodiversity and citizen science data increasingly allows considering time explicitly in SDMs. This offers a more mechanistic understanding of plant distributions, and more robust predictions under global change, especially if the reporting of phenological stages and age is facilitated and promoted by relevant data portals.

README: The niche through time: considering phenology and demographic stages in plant distribution models

https://doi.org/10.5061/dryad.sn02v6xct

Description of the data and file structure

Columns from WoS (Web of Science) search – these are identical in both excel sheets

These columns are the standard columns provided as WoS search output. If the entries contain "n/a", then no information was provided by WoS because those items are not applicable. For example, a journal article does not have any entries for book authors.

Column Explanation
Publication Type Type of publication: J .. Journal article
Authors Authors
Book Authors Book Authors
Book Editors Book Editors
Book Group Authors Book Group Authors
Author Full Names Author Full Names
Book Author Full Names Book Author Full Names
Group Authors Group Authors
Article Title Article Title
Source Title Source Title, Journal title
Book Series Title Book Series Title
Book Series Subtitle Book Series Subtitle
Language Language
Document Type Document Type
Conference Title Conference Title
Conference Date Conference Date
Conference Location Conference Location
Conference Sponsor Conference Sponsor
Conference Host Conference Host
Author Keywords Author Keywords
Keywords Plus Keywords Plus
Abstract Abstract
Addresses Addresses
Affiliations Affiliations
Reprint Addresses Reprint Addresses
Email Addresses Email Addresses
Researcher Ids Researcher Ids
ORCIDs ORCIDs
Funding Orgs Funding Organisations
Funding Name Preferred Funding Name Preferred
Funding Text Funding Text
Cited References Cited References
Cited Reference Count Cited Reference Count
Times Cited, WoS Core Times Cited, WoS Core
Times Cited, All Databases Times Cited, All Databases
180 Day Usage Count 180 Day Usage Count
Since 2013 Usage Count Since 2013 Usage Count
Publisher Publisher
Publisher City Publisher City
Publisher Address Publisher Address
ISSN ISSN
eISSN eISSN
ISBN ISBN
Journal Abbreviation Journal Abbreviation
Journal ISO Abbreviation Journal ISO Abbreviation
Publication Date Publication Date
Publication Year Publication Year
Volume Volume
Issue Issue
Part Number Part Number
Supplement Supplement
Special Issue Special Issue
Meeting Abstract Meeting Abstract
Start Page Start Page
End Page End Page
Article Number Article Number
DOI DOI
DOI Link DOI Link
Book DOI Book DOI
Early Access Date Early Access Date
Number of Pages Number of Pages
WoS Categories WoS Categories
Web of Science Index Web of Science Index
Research Areas Research Areas
IDS Number IDS Number
Pubmed Id Pubmed Id
Open Access Designations Open Access Designations
Highly Cited Status Highly Cited Status
Hot Paper Status Hot Paper Status
Date of Export Date of Export
UT (Unique WOS ID) UT (Unique WOS ID)
Web of Science Record Web of Science Record

Additional columns in Sheet Sorted_life_stages

If Q1 and Q2 are answered with NO, then all remaining columns will receive the entry "n/a".

Column Criterion / Question Decision
Q1: Are SDM fitted to plants? (incl. any spatial correlative model) - Yes/No Q1: Are SDM fitted to plants? (i.e. a correlative model is used to fit relationships between spatially explicit occurrence data and environmental covariates; incl. any spatial correlative model) No: exclude paper
Q2 (if Q1=Yes): Are life stages distinguished / explicitly modelled - Yes/No Q2: Are life stages distinguished / explicitly modelled? No: exclude paper
Additional information extracted from included papers
Response Response variable (e.g. occurrence, abundance, biomass)  
(if Q2 = Yes): Which environmental variables? e.g. climate, topographic, edaphic Type of environmental variables considered (e.g. climate, topographic, edaphic)  
(if Q2 = Yes): What is the data source for the plant data? e.g. field measurements, citizen science, remote sensing, etc Data source for the plant data (e.g. field measurements, citizen science, remote sensing)  
(if Q2 = Yes): Taxonomic group, e.g. trees, grass, phytoplankton Taxonomic group (e.g. trees, grass)  
(if Q2 = Yes): spatial extent Spatial extent  
(if Q3 = Yes): spatial resolution Spatial resolution  
(if  Q3 = Yes): temporal extent Temporal extent  
(if Q3 = Yes): temporal resolution Temporal resolution  
(if Q3 = Yes): geographic region Geographic region  
Period 11-year bins (Period 1: 1990-2000, Period 2: 2001-2011, Period 3: 2012-2022)  
Assessor Author initials  
Comments Additional comments  

Additional columns in Sheet Sorted_Phenology

If Q1, Q2 and Q3 are answered with NO, then all remaining columns will receive the entry "n/a". 

Column Criterion / Question Decision
Q1: Are SDM fitted to plants? (incl. any spatial correlative model) - Yes/No Q1: Are SDM fitted to plants? (i.e. a correlative model is used to fit relationships between spatially explicit occurrence data and environmental covariates; incl. any spatial correlative model) No: exclude paper
Q2 (if Q1=Yes): Are phenological stages distinguished / explicitly modelled - Yes/No Q2: Are phenological stages distinguished / explicitly modelled? No: exclude paper
Q3 (if Q1=Yes): Are seasonal occurrence probabilities distinguished / explicitly modelled? - Yes/No Q3: are seasonal occurrence probabilities explicitly modelled? No: exclude paper
Additional information extracted from included papers
Response Response variable (e.g. occurrence, abundance, biomass)  
(if Q2 = Yes): Which environmental variables? e.g. climate, topographic, edaphic Type of environmental variables considered (e.g. climate, topographic, edaphic)  
(if Q2 = Yes): What is the data source for the plant data? e.g. field measurements, citizen science, remote sensing, etc Data source for the plant data (e.g. field measurements, citizen science, remote sensing)  
(if Q2 = Yes): Taxonomic group, e.g. trees, grass, phytoplankton Taxonomic group (e.g. trees, grass)  
(if Q2 = Yes): spatial extent Spatial extent  
(if Q3 = Yes): spatial resolution Spatial resolution  
(if  Q3 = Yes): temporal extent Temporal extent  
(if Q3 = Yes): temporal resolution Temporal resolution  
(if Q3 = Yes): geographic region Geographic region  
Period 11-year bins (Period 1: 1990-2000, Period 2: 2001-2011, Period 3: 2012-2022)  
Assessor Author initials  
Comments Additional comments  

Sharing/Access information

Data was derived from the following sources:

  • Web of Science search was carried out 5-Oct-2023 using the following search criteria:
Topic Search terms
Species distribution model TS=(("species distribut*" OR "habitat distribut*" OR "climat* envelope" OR bioclimat* OR "habitat suitab*" OR niche OR SDM OR ENM OR BEM OR BCM OR HSM) AND (model*))
Taxa TS= (( “plant*” OR “tree*” OR “grass*” OR “herb*” OR “*phyt*” OR “fern*” OR “moss*”) NOT (*vertebrat* OR  animal OR mammal OR bird OR avian OR amphibian OR reptile OR fish OR insect* OR worm))
Search for a) Phenology TS=( “phenol*” OR “seasonal*” )
Search for b) Life stages TS=( “life stage*” OR “ontol*” OR “adult*” OR “juvenil*” OR “regenerat*” OR “demog*”)
Time period PY=(1945-2022)
Document types DT=(Article)
Languages LA=(English)
Web of Science Index Science Citation Index Expanded (SCI-EXPANDED) --1900-present

Methods

We conducted a keyword-based search in the Web of Science to quantify how often temporal components related to phenology and demographic stages are explicitly considered in plant SDMs. A full list of keywords is provided in the Supporting Information Table S1. We used a nested set of keywords to identify all studies that mentioned SDMs (or common synonyms), were focused on plants, and were listing relevant keywords related to phenology or to demographic stages, respectively. The search was carried out on 5-Oct-2023 and was restricted to English-language journal articles in the period 1945-2022 (no studies using SDMs were published before that start year). Overall, we found more than 40,000 articles mentioning SDM and over 10,000 articles in our refined search for plant SDMs, with a strong increase in the number of articles over time. Among these, phenology (or related search terms) was mentioned in 970 articles and demographic stages (or related terms) in 1188 articles, each averaging c. 10% of the plant SDM articles. The search categories phenology and demographic stages, thereby, were largely mutually exclusive.

For each search category, phenology and demographic stages, we assessed a random subset of 300 articles to gain more insights about how these temporal components of the niche were considered in SDMs. To do so, we separated all articles published after 1990 in 11-year bins (1990-2000, 2001-2011, 2012-2022) and aimed at assessing 100 papers per bin and category (phenology vs. demographic stages). As fewer than 100 papers were published in the first time period (1990-2000), we drew slightly more articles from the latter two periods. This resulted in sample sizes of n=28, n=123 and n=149 of publications mentioning phenology in the three 11-year bins, respectively, and n=41, n=130 and n=129 mentioning demographic stages. We then scanned the abstracts for information that the articles indeed fitted plant SDMs and explicitly considered phenology or demographic stages. In cases where the abstract was inconclusive, we also scanned the methods. If the papers fulfilled these search criteria, we extracted additional information from abstract and methods regarding the taxa and region studied, and spatial and temporal scale.

Funding

Swiss Data Science Center , Award: c19-09

Deutsche Forschungsgemeinschaft, Award: ZU 361/3-1