DOI: 10.5061/dryad.sn02v6xct
title: The niche through time: Considering phenology and demographic stages in plant distribution models

description: 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.
description: 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 <em>c</em>. 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 <em>n</em>=28,
 <em>n</em>=123 and <em>n</em>=149 of publications
 mentioning phenology in the three 11-year bins, respectively, and
 <em>n</em>=41, <em>n</em>=130 and
 <em>n</em>=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.
description: # The niche through time: considering phenology and demographic stages in
 plant distribution models
 [https://doi.org/10.5061/dryad.sn02v6xct](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 |