DELINEATE: Species Delimitation

DELINEATE is a package that implements the DELINEATE approach to species delimitation (Sukumaran, Holder, and Knowles, 2020). This approach integrates an explicit model of speciation into the multipopulation coalescent (also known as the “censored” or “multispecies” coalescent) model, to organize a set of population lineages sampled from one or more species into mutually-exclusive and jointly-comprehensive subsets, where each subset of population lineages represents a distinct species.

DELINEATE requires Python 3.7 or greater to run. Package and dependency management is greatly simplified if pip is installed as well.

Installation

Providing you have all the system requirements (see the installation guide), you can use the following command to install or upgrade DELINEATE directly from the package repositories:

python3 -m pip install -U git+https://github.com/jeetsukumaran/delineate.git

Documentation

• Installation
  • Installation or Upgrade
  • System Requirements
  • Library Dependencies
• Basic Concepts
  • “Partitions”
  • The Diversification Process
  • Formation of New Species
  • The Speciation Completion Rate
  • Estimating the Speciation Completion Rate
  • A Different Way of Doing Business
  • Sampling Design
  • Workflow: From Individuals to Populations to Species
• Quick Start
  • Data Requirements
    • Input Data: Population Tree
    • Input Data: Species Assignment Table
  • Running a Species Delimitation Analysis
    • Basic Run
    • Basic Run Output
    • More Options
  • Summarizing the Marginal Probability of Conspecificity and New Species Status for a Subset of Taxa
• A Complete Worked Example: Lionepha
  • (Software Prerequisites)
  • (Data Files)
  • Introduction
  • Background
    • Study Design
    • Data
  • Stage I: Identification of Population Units using the Multipopulation Coalescent Model
    • Candidate Population Units
    • Generating a Guide Tree for Population Delimitation
    • Delimitation of Population Units
  • Stage II. Generating the (Multipopulation Coalescent, Ultrametric) Phylogeny of Populations
  • Stage III. Assignment of Known vs. Unknown Species Identities
  • Stage IV. Delimitation of Species Units
  • Examination and Interpretation of the Results