zhongwei/gh-brunoasm-my-claude-skills-bioinfo-skills
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity
Files
c1d9dee646cd34dd9241005b06f1c6ea1e11c4a7
gh-brunoasm-my-claude-skill…/skills/biogeobears/references/biogeobears_details.md
Zhongwei Li c1d9dee646 Initial commit
2025-11-29 18:02:37 +08:00

9.5 KiB
Raw Blame History

BioGeoBEARS Detailed Reference

Overview

BioGeoBEARS (BioGeography with Bayesian and Likelihood Evolutionary Analysis in R Scripts) is an R package for probabilistic inference of historical biogeography on phylogenetic trees. It implements various models of range evolution and allows statistical comparison between them.

Installation

# Install dependencies
install.packages("rexpokit")
install.packages("cladoRcpp")

# Install from GitHub
library(devtools)
devtools::install_github(repo="nmatzke/BioGeoBEARS")

Biogeographic Models

BioGeoBEARS implements several models that differ in their assumptions about how species ranges evolve:

DEC (Dispersal-Extinction-Cladogenesis)

The DEC model is based on LAGRANGE and includes:

  • Anagenetic changes (along branches):

    • d (dispersal): Rate of range expansion into adjacent areas
    • e (extinction): Rate of local extinction in an area

  • Cladogenetic events (at speciation nodes):

    • Vicariance: Ancestral range splits between daughter lineages
    • Subset sympatry: One daughter inherits full range, other subset
    • Range copying: Both daughters inherit full ancestral range

Parameters: 2 (d, e) Best for: General-purpose biogeographic inference

DIVALIKE (Vicariance-focused)

Similar to DIVA (Dispersal-Vicariance Analysis):

  • Emphasizes vicariance at speciation events
  • Fixes subset sympatry probability to 0
  • Only allows vicariance and range copying at nodes

Parameters: 2 (d, e) Best for: Systems where vicariance is the primary speciation mode

BAYAREALIKE (Sympatry-focused)

Based on the BayArea model:

  • Emphasizes sympatric speciation
  • Fixes vicariance probability to 0
  • Only allows subset sympatry and range copying

Parameters: 2 (d, e) Best for: Systems where dispersal and sympatric speciation dominate

+J Extension (Founder-event speciation)

Any of the above models can include a "+J" parameter:

  • j: Jump dispersal / founder-event speciation rate
  • Allows instantaneous dispersal to a new area at speciation
  • Often significantly improves model fit
  • Can be controversial (some argue it's biologically unrealistic)

Examples: DEC+J, DIVALIKE+J, BAYAREALIKE+J Additional parameters: +1 (j)

Model Comparison

AIC (Akaike Information Criterion)

AIC = -2 × ln(L) + 2k

Where:

  • ln(L) = log-likelihood
  • k = number of parameters

Lower AIC = better model

AICc (Corrected AIC)

Used when sample size is small relative to parameters:

AICc = AIC + (2k² + 2k)/(n - k - 1)

AIC Weights

Probability that a model is the best among the set:

w_i = exp(-0.5 × Δ_i) / Σ exp(-0.5 × Δ_j)

Where Δ_i = AIC_i - AIC_min

Likelihood Ratio Test (LRT)

For nested models (e.g., DEC vs DEC+J):

LRT = 2 × (ln(L_complex) - ln(L_simple))
  • Test statistic follows χ² distribution
  • df = difference in number of parameters
  • p < 0.05 suggests complex model significantly better

Input File Formats

Phylogenetic Tree (Newick format)

Standard Newick format with:

  • Branch lengths required
  • Tip labels must match geography file
  • Should be rooted and ultrametric (for time-stratified analyses)

Example:

((A:1.0,B:1.0):0.5,C:1.5);

Geography File (PHYLIP-like format)

Format structure:

n_species [TAB] n_areas [TAB] (area1 area2 area3 ...)
species1 [TAB] 011
species2 [TAB] 110
species3 [TAB] 001

Important formatting rules:

  1. Line 1 (Header):

    • Number of species (integer)
    • TAB character
    • Number of areas (integer)
    • TAB character
    • Area names in parentheses, separated by spaces

  2. Subsequent lines (Species data):

    • Species name (must match tree tip label)
    • TAB character
    • Binary presence/absence code (1=present, 0=absent)
    • NO SPACES in the binary code
    • NO SPACES in species names (use underscores)

  3. Common errors to avoid:

    • Using spaces instead of tabs
    • Spaces within binary codes
    • Species names with spaces
    • Mismatch between species names in tree and geography file
    • Wrong number of digits in binary code

Example file:

5	3	(A B C)
Sp_alpha	011
Sp_beta	010
Sp_gamma	111
Sp_delta	100
Sp_epsilon	001

Key Parameters and Settings

max_range_size

Maximum number of areas a species can occupy simultaneously.

  • Default: Often set to number of areas, or number of areas - 1
  • Impact: Larger values = more possible states = longer computation
  • Recommendation: Set based on biological realism

include_null_range

Whether to include the "null range" (species extinct everywhere).

  • Default: TRUE
  • Purpose: Allows extinction along branches
  • Recommendation: Usually keep TRUE

force_sparse

Use sparse matrix operations for speed.

  • Default: FALSE
  • When to use: Large state spaces (many areas)
  • Note: May cause numerical issues

speedup

Various speedup options.

  • Default: TRUE
  • Recommendation: Usually keep TRUE

use_optimx

Use optimx for parameter optimization.

  • Default: TRUE
  • Benefit: More robust optimization
  • Recommendation: Keep TRUE

calc_ancprobs

Calculate ancestral state probabilities.

  • Default: FALSE
  • Must set to TRUE if you want ancestral range estimates
  • Impact: Adds computational time

Plotting Functions

plot_BioGeoBEARS_results()

Main function for visualizing results.

Key parameters:

  • plotwhat: "pie" (probability distributions) or "text" (ML states)
  • tipcex: Tip label text size
  • statecex: Node state text/pie chart size
  • splitcex: Split state text/pie size (at corners)
  • titlecex: Title text size
  • plotsplits: Show cladogenetic events (TRUE/FALSE)
  • include_null_range: Match analysis setting
  • label.offset: Distance of tip labels from tree
  • cornercoords_loc: Directory with corner coordinate files

Color scheme:

  • Single areas: Bright primary colors
  • Multi-area ranges: Blended colors
  • All areas: White
  • Colors automatically assigned and mixed

Biogeographical Stochastic Mapping (BSM)

Extension of BioGeoBEARS that simulates stochastic histories:

  • Generates multiple possible biogeographic histories
  • Accounts for uncertainty in ancestral ranges
  • Allows visualization of range evolution dynamics
  • More computationally intensive

Not covered in basic workflow but available in package.

Common Analysis Workflow

  1. Prepare inputs

    • Phylogenetic tree (Newick)
    • Geography file (PHYLIP format)
    • Validate both files

  2. Setup analysis

    • Define max_range_size
    • Load tree and geography data
    • Create state space

  3. Fit models

    • DEC, DIVALIKE, BAYAREALIKE
    • With and without +J
    • 6 models total is standard

  4. Compare models

    • AIC/AICc scores
    • AIC weights
    • LRT for nested comparisons

  5. Visualize best model

    • Pie charts for probabilities
    • Text labels for ML states
    • Annotate with split events

  6. Interpret results

    • Ancestral ranges
    • Dispersal patterns
    • Speciation modes (if using +J)

Interpretation Guidelines

Dispersal rate (d)

  • High d: Frequent range expansions
  • Low d: Species mostly stay in current ranges
  • Units: Expected dispersal events per lineage per time unit

Extinction rate (e)

  • High e: Ranges frequently contract
  • Low e: Stable occupancy once established
  • Relative to d: d/e ratio indicates dispersal vs. contraction tendency

Founder-event rate (j)

  • High j: Jump dispersal important in clade evolution
  • Low j (but model still better): Minor role but statistically supported
  • j = 0 (in +J model): Founder events not supported

Model selection insights

  • DEC favored: Balanced dispersal, extinction, and vicariance
  • DIVALIKE favored: Vicariance-driven diversification
  • BAYAREALIKE favored: Sympatric speciation and dispersal
  • +J improves fit: Founder-event speciation may be important

Computational Considerations

Runtime factors

  • Number of tips: Polynomial scaling
  • Number of areas: Exponential scaling in state space
  • max_range_size: Major impact (reduces state space)
  • Tree depth: Linear scaling

Memory usage

  • Large trees + many areas can require substantial RAM
  • Sparse matrices help but have trade-offs

Optimization issues

  • Complex likelihood surfaces
  • Multiple local optima possible
  • May need multiple optimization runs
  • Check parameter estimates for sensibility

Citations

Main BioGeoBEARS reference: Matzke, N. J. (2013). Probabilistic historical biogeography: new models for founder-event speciation, imperfect detection, and fossils allow improved accuracy and model-testing. Frontiers of Biogeography, 5(4), 242-248.

LAGRANGE (DEC model origin): Ree, R. H., & Smith, S. A. (2008). Maximum likelihood inference of geographic range evolution by dispersal, local extinction, and cladogenesis. Systematic Biology, 57(1), 4-14.

+J parameter discussion: Ree, R. H., & Sanmartín, I. (2018). Conceptual and statistical problems with the DEC+J model of founder-event speciation and its comparison with DEC via model selection. Journal of Biogeography, 45(4), 741-749.

Model comparison best practices: Burnham, K. P., & Anderson, D. R. (2002). Model Selection and Multimodel Inference: A Practical Information-Theoretic Approach (2nd ed.). Springer.

Further Resources

Reference in New Issue View Git Blame Copy Permalink