The niche through time: Considering phenology and demographic stages in plant distribution models
Data files
Jun 19, 2024 version files 2.78 MB
-
README.md
21.02 KB
-
Zurell_etal_JEcol-2024-0056_DataTable_LitSearch.xlsx
2.76 MB
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.
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 |
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.