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Integrating fossil data in ecological niche models to improve predictions of future habitat of Caribbean corals.

Code ↔ Paper

2 matches between paragraphs of the paper and lines of its authors' code, computed by the harvester (lexical-v1). Click a colored paragraph or line to see its counterpart.

The 2 matches
  1. [1] § METHODS › Ecological niche models ↔ COBI-40-e70323-s014.R, lines 181–239 · score 0.77 · feature classes, cross validation, response curves, binary, sensitivity, likelihood
  2. [2] § METHODS › Environmental data ↔ COBI-40-e70323-s014.R, lines 1415–1428 · score 0.52 · arc minute, Paleo, cell

Paper

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The authors' code

R · 4,467 lines · 236 KB · no license · 2 matches

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Overview

Authors: Claire M Williams1, Fernando Machado‐Stredel2, Rowan C Martindale1, Corinne E Myers3
ORCID iDs: Claire M Williams, Fernando Machado‐Stredel, Rowan C Martindale, Corinne E Myers
  1. Department of Earth and Planetary Sciences, The University of Texas at Austin, Austin, Texas, USA
  2. Department of Biology, The University of New Mexico, Albuquerque, New Mexico, USA
  3. Department of Earth and Planetary Sciences, The University of New Mexico, Albuquerque, New Mexico, USA
Institutions: The University of Texas at Austin (United States); University of New Mexico (United States)
Journal: Conservation biology : the journal of the Society for Conservation Biology, volume 40, issue 5, article e70323
Dates: received 1 June 2025; accepted 16 March 2026; published online 13 May 2026; in print October 2026
Type: Research article · Language: English
License: CC BY-NC
Identifiers: DOI 10.1111/cobi.70323 · PMID 42125997 · PMCID PMC13613574 · OpenAlex W7161027982
Open access: hybrid, a free copy (OpenAlex)
Status: code verified
Categories: none (in silico) (organism), computational (subfield)
Methods: Statistics, Smoothing, state filtering, decompositions, Machine learning
Keywords: Acropora, Caribbean, Colpophyllia, coral reef, Holocene, palaeoecological niche models, Porites, arrecife de coral, Caribe, Holoceno, modelos de nicho paleoecológico, 古生态位模型, 加勒比海, 全新世, 珊瑚礁, 鹿角珊瑚(Acropora), 滨珊瑚(Porites), 有沟珊瑚(Colpophyllia)
MeSH: Anthozoa*, Climate Change*, Conservation of Natural Resources*, Coral Reefs*, Ecosystem*, Fossils*, Models, Biological*, Animals, Caribbean Region, Models, Theoretical (* major topic)
Topic: Species Distribution and Climate Change (Ecological Modeling, Environmental Science), according to OpenAlex
Funding: NIH HHS (DGE 2137420); National Science Foundation (DGE-2137420, DGE‐2137420)
Citations: cited by 1 paper (Europe PMC); 137 references in the paper

Abstract

Ecological niche models (ENMs) are used to assess the abiotic preferences of species by linking their occurrences to the environmental conditions in which they live. We developed a fossil‐informed ENM framework that integrates mid‐Holocene and modern occurrences to test niche stability and reconstruct abiotic niche characteristics for four critical reef‐building Caribbean coral species (elkhorn coral [Acropora palmata], staghorn coral [Acropora cervicornis], boulder brain coral [Colpophyllia natans], and mustard hill coral [Porites astreoides]). Given evidence of niche stability, we used fossil‐improved niche estimates to predict area and location of habitat for future climate scenarios in 2050 and 2100. We built species distribution models with environmental predictors and compared models trained with modern‐only versus combined fossil and modern occurrences to evaluate differences in niche breadth, model performance, and projected habitat distributions under future climate scenarios. Including mid‐Holocene fossil data in ENMs broadened niche estimates, resulting in a larger area of predicted habitat than models based solely on modern data (up to 114,559 km2 more in 2100). Although our models showed that suitable habitats existed for most corals in 2100, the amount declined dramatically (45–100% decrease in area from the present day), there was a significant restriction of lower latitude habitat suitability, and marine protected areas did not overlap the majority of predicted future suitable habitat (8–20% overlap by 2100). Fossil‐informed models expanded niche estimates in environmental space and incorporated environmental conditions not represented in modern data, resulting in broader projections of future habitat. Our results suggest that actions to reduce emissions and expand protected areas in the northern Caribbean are imperative to prevent significant degradation and that using fossil occurrences in niche estimation can improve the reliability of conservation forecasting, an approach that is transferable across taxa and regions.

Reproduced under the paper's license (CC BY-NC), from the paper cited above.

Repository

Its files are read in the Code ↔ Paper reader above, with 2 matches between paragraphs and lines of code.

supp:PMC13613574/COBI-40-e70323-s014.R

License: none: the authors keep all their rights
State: the link answers, verified on 28 September 2026
Evidence: files inventoried
Languages: R (1)
Size: 1 file, 1 script
Software Heritage: not checked
Found in: the supplementary material
Not found: README, license file, CITATION.cff, environment file, tests, continuous integration, documentation
Tools: ggplot2 (1 file), tidyverse (1 file)
Availability: 1 check, the latest on 28 September 2026: the link answers (HTTP 200)
  • 28 September 2026: the link answers (HTTP 200)
1 file, to read at the source

This repository has no license: its authors keep all rights. Read it at the source.

At the source: pmc-oa-opendata.s3.amazonaws.com/PMC13613574.1/COBI-40-e70323-s014.R

Tracing map

Proposed by the machine: these links were found in the paper and verified at the source, without human review. The map will receive a Zenodo DOI once one of the paper's authors has validated it with their ORCID.

What the map holds:

  • 1 repository of the authors' code, each at its verified commit, with its license and how the link was found in the paper;
  • 1 script, each with its path and the digest of its content;
  • 2 matches between paragraphs of the paper and lines of the code (method lexical-v1);
  • neither the text of the paper nor the code itself.

Its JSON (tracing-map.json) is deposited on Zenodo with its DOI once the map is validated.

Data

No dataset and no data link were found in the paper.

Versions

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Version 2, 28 September 2026

  • Publisher: — → Wiley

Version 1, 28 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 4 authors, 18 keywords, 10 MeSH terms, 2 funders, 119 references.

Cite

This paper

Williams, C. M., Machado‐Stredel, F., Martindale, R. C., & Myers, C. E. (2026). Integrating fossil data in ecological niche models to improve predictions of future habitat of Caribbean corals. Conservation biology : the journal of the Society for Conservation Biology, 40(5), e70323. https://doi.org/10.1111/cobi.70323

BibTeX

@article{williams2026integrating,
author = {Williams, Claire M and Machado‐Stredel, Fernando and Martindale, Rowan C and Myers, Corinne E},
title = {{Integrating fossil data in ecological niche models to improve predictions of future habitat of Caribbean corals}},
journal = {Conservation biology : the journal of the Society for Conservation Biology},
year = {2026},
month = may,
volume = {40},
number = {5},
pages = {e70323},
publisher = {Wiley},
issn = {1523-1739},
doi = {10.1111/cobi.70323},
url = {https://doi.org/10.1111/cobi.70323},
pmid = {42125997},
pmcid = {PMC13613574}
}

RIS

TY - JOUR
AU - Williams, Claire M
AU - Machado‐Stredel, Fernando
AU - Martindale, Rowan C
AU - Myers, Corinne E
TI - Integrating fossil data in ecological niche models to improve predictions of future habitat of Caribbean corals
T2 - Conservation biology : the journal of the Society for Conservation Biology
J2 - Conserv Biol
PY - 2026
DA - 2026/05/13
VL - 40
IS - 5
SP - e70323
SN - 1523-1739
PB - Wiley
DO - 10.1111/cobi.70323
UR - https://doi.org/10.1111/cobi.70323
LA - en
ER -

CSL-JSON

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