Species delimitation with DELINEATE and DECRYPT

Lacey Knowles, 28 January 2020



DELINEATE is a program that implements the DELINEATE approach to species delimitation (Sukumaran, Holder, and Knowles, 2019; in revision). This approach integrates an explicit model of speciation into 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.

How to run this activity

  • This activity can be run through the terminal; thus, connect to the Amazon instance via SSH.
  • Navigate to the ~/workshop_materials/28_species_delimitation directory.
  • To use the programs required for this activity, we’ll need to load a particular conda environment. Do so using the following command:
    conda activate spdelimit
  • Follow the instructions on https://jeetsukumaran.github.io/delineate/ (but skip sections “Requirements” and “Installation”), with the following modifications as introduced by Lacey Knowles:
    • Use file constraints1.txt instead of data1.tsv as the input species assignment table file.
    • Use file Dynastes_calib_GeoPop.tre instead of population-tree.nex
    • as the input population tree file.

    • Because the population tree file Dynastes_calib_GeoPop.tre is in Newick format instead of Nexus format, we’ll need to add -f newick to both the delineate-estimate and delineate-check commands.
  • After the activity, deactivate the conda environment with conda deactivate.


DECRYPT is a tool allowing to shed light on systems where cryptic diversity and isolation by distance are two competing hypothesis. DECRYPT can help understanding if the genetic structure detected under the MultiSpecies Coalescent, MSC, could possibly be explained by the intra-species spatial structure.

How to run this activity