Skip to main content
bioRxiv
  • Home
  • About
  • Submit
  • ALERTS / RSS
Advanced Search
New Results

Jointly Modeling Species Niche and Phylogenetic Model in a Bayesian Hierarchical Framework

View ORCID ProfileSean W McHugh, View ORCID ProfileAnahí Espíndola, Emma White, Josef Uyeda
doi: https://doi.org/10.1101/2022.07.06.499056
Sean W McHugh
1Biological Sciences, Virginia Tech
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Sean W McHugh
  • For correspondence: sean.mchugh4@gmail.com
Anahí Espíndola
2Department of Entomology, Plant Sciences Building 3138, 4291 Fieldhouse Dr., University of Maryland, College Park, MD 20742-4454, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Anahí Espíndola
Emma White
1Biological Sciences, Virginia Tech
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Josef Uyeda
1Biological Sciences, Virginia Tech
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Data/Code
  • Preview PDF
Loading

ABSTRACT

When studying how species will respond to climatic change, a common goal is to predict how species distributions change through time. Environmental niche models (ENMs) are commonly used to estimate a species’ environmental niche from observed patterns of occurrence and environmental predictors. However, species distributions are often shaped by non-environmental factors–including biotic interactions and dispersal barriers—truncating niche estimates. Though a truncated niche estimate may accurately predict present-day species distribution within the sampled area, this accuracy decreases when predicting occurrence at different places and under different environmental conditions. Modeling niche in a phylogenetic framework leverages a clade’s shared evolutionary history to pull species estimates closer towards phylogenetic conserved values and farther away from species specific biases. We propose a new Bayesian model of phylogenetic niche estimation implemented in R called BePhyNE (Bayesian environmental Phylogenetic Niche Estimation). Under our model, species ENM parameters are transformed into biologically interpretable continuous parameters of environmental niche optimum, breadth, and tolerance evolving as a multivariate Brownian motion. Through simulation analyses, we demonstrate model accuracy and precision that improve as phylogeny size increases. We also demonstrate our model on eastern United States Plethodontid salamanders and recover accurate estimates of species niche, even when species occurrence data is lacking and entirely informed by the evolutionary model. Our model demonstrates a novel framework where niche changes can be studied forwards and backwards through time to understand ancestral ranges, patterns of environmental specialization, and estimate niches of data-deficient species.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • Remove tracked changes I erroneously left in (SWM)

  • https://github.com/sean-mchugh/BePhyNE

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.
Back to top
PreviousNext
Posted July 11, 2022.
Download PDF
Data/Code
Email

Thank you for your interest in spreading the word about bioRxiv.

NOTE: Your email address is requested solely to identify you as the sender of this article.

Enter multiple addresses on separate lines or separate them with commas.
Jointly Modeling Species Niche and Phylogenetic Model in a Bayesian Hierarchical Framework
(Your Name) has forwarded a page to you from bioRxiv
(Your Name) thought you would like to see this page from the bioRxiv website.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
Jointly Modeling Species Niche and Phylogenetic Model in a Bayesian Hierarchical Framework
Sean W McHugh, Anahí Espíndola, Emma White, Josef Uyeda
bioRxiv 2022.07.06.499056; doi: https://doi.org/10.1101/2022.07.06.499056
Reddit logo Twitter logo Facebook logo LinkedIn logo Mendeley logo
Citation Tools
Jointly Modeling Species Niche and Phylogenetic Model in a Bayesian Hierarchical Framework
Sean W McHugh, Anahí Espíndola, Emma White, Josef Uyeda
bioRxiv 2022.07.06.499056; doi: https://doi.org/10.1101/2022.07.06.499056

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
  • Tweet Widget
  • Facebook Like
  • Google Plus One

Subject Area

  • Evolutionary Biology
Subject Areas
All Articles
  • Animal Behavior and Cognition (4373)
  • Biochemistry (9561)
  • Bioengineering (7075)
  • Bioinformatics (24800)
  • Biophysics (12581)
  • Cancer Biology (9929)
  • Cell Biology (14306)
  • Clinical Trials (138)
  • Developmental Biology (7938)
  • Ecology (12085)
  • Epidemiology (2067)
  • Evolutionary Biology (15965)
  • Genetics (10910)
  • Genomics (14716)
  • Immunology (9850)
  • Microbiology (23597)
  • Molecular Biology (9463)
  • Neuroscience (50757)
  • Paleontology (369)
  • Pathology (1537)
  • Pharmacology and Toxicology (2675)
  • Physiology (4003)
  • Plant Biology (8646)
  • Scientific Communication and Education (1506)
  • Synthetic Biology (2388)
  • Systems Biology (6417)
  • Zoology (1345)