HyDe: hybridization detection using phylogenetic invariants

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HyDe is a software package that detects hybridization in phylogenomic data sets using phylogenetic invariants. The primary interface for HyDe is a Python module called phyde (Pythonic Hybridization Detection). phyde provides a suite of tools for performing hypothesis tests on triples of taxa to detect hybridization. To ensure that the necessary dependencies for phyde are available, we suggest using a Python distribution such as Miniconda.

To facilitate analyses using the Python module, three scripts are provided to conduct hybridization detection analyses directly from the command line:

  • run_hyde.py: runs a standard hybridization detection analysis on all triples in all directions. Results are also filtered based on whether there is significant evidence for hybridization.
  • individual_hyde.py: tests each individual within a putative hybrid population using a list of specified triples specified.
  • bootstrap_hyde.py: conducts bootstrap resampling of the individuals within the putative hybrid lineages for each specified triple.

These last two scripts need to be given a three column table of triples (P1, Hybrid, P2) that you wish to test:

sp1 sp2 sp3
sp1 sp3 sp4
sp3 sp4 sp5
.
.
.

You can also use a results file from a previous analysis as a triples file. For example, you can use the filtered results from the run_hyde.py script so that you only run analyses on triples that have significant levels of hybridization. If you only have a few hypotheses that you want to test, then you can also pass a triples file to run_hyde.py and it will only test those hypotheses rather than testing everything.

Multithreaded versions of these scripts are also available (run_hyde_mp.py, individual_hyde_mp.py, and bootstrap_hyde_mp.py). Make sure you have the multiprocess module installed before you use them: pip install multiprocess.

Getting help

If you have questions about running HyDe, please feel free to use the gitter chatroom to get help:

Gitter

If you have a problem while running HyDe and you think it may be a bug, please consider filing an issue on GitHub:

HyDe Issues

Features

  • Conduct hypothesis tests using multiple individuals per population.
  • Test each individual within a putative hybrid lineage to assess if hybridization is uniform.
  • Test all possible triples of taxa and process results from within Python.
  • Bootstrap individuals within taxa to assess patterns of hybrid speciation vs. introgression.
  • Visualize the distributions of various quantities (Test Statistic, Hybridization Parameter, D-Statistic) using bootstrap replicates.
  • Calculate the D-Statistic (ABBA-BABA) using site pattern counts returned during a hypothesis test.

Indices and tables