DOI: 10.5061/dryad.jm63xsjhc
title: Hierarchical heuristic species delimitation under the multispecies coalescent model with migration

description: The multispecies coalescent (MSC) model accommodates genealogical
 fluctuations across the genome and provides a natural framework for
 comparative analysis of genomic sequence data from closely related species
 to infer the history of species divergence and gene flow. Given a set of
 populations, hypotheses of species delimitation (and species phylogeny)
 may be formulated as instances of MSC models (e.g., MSC for one species
 versus MSC for two species) and compared using Bayesian model selection.
 This approach, implemented in the program bpp, has been found to be prone
 to over-splitting. Alternatively heuristic criteria based on population
 parameters (such as population split times, population sizes, and
 migration rates) estimated from genomic data may be used to delimit
 species. Here we develop hierarchical merge and split algorithms for
 heuristic species delimitation based on the genealogical divergence index
 (𝑔𝑑𝑖) and implement them in a python pipeline called hhsd. We characterize
 the behavior of the 𝑔𝑑𝑖 under a few simple scenarios of gene flow. We
 apply the new approaches to a dataset simulated under a model of isolation
 by distance as well as three empirical datasets. Our tests suggest that
 the new approaches produced sensible results and were less prone to
 over-splitting. We discuss possible strategies for accommodating
 paraphyletic species in the hierarchical algorithm, as well as the
 challenges of species delimitation based on heuristic criteria.
description: The data are analyzed using our new python pipeline called
 HHSD.
description: # Contents --- ## BPP\_files\_SI BPP Files needed to reproduce the
 analyses in the theory and methods section --- ## Empirical\_Giraffe
 Control files and empirical data for conducting hierarchical heuristic
 species delimitation on complex of five Giraffe populations. ### Original
 publication: Alice Petzold, Alexandre Hassanin, A Comparative Approach for
 Species Delimitation Based on Multiple Methods of Multi-Locus DNA Sequence
 Analysis: A Case Study of the Genus Giraffa (Mammalia,Cetartiodactyla),
 PLOS ONE, Volume 15, Issue 2, February 2020, Pages e0217956.
 [https://doi.org/10.1371/journal.pone.0217956](https://doi.org/10.1371/journal.pone.0217956). Data published at: [https://osf.io/9wv86/](https://osf.io/9wv86/) ### Folder contents: * `Imap_Giraffe.txt` Imap file * `MSA_Giraffe` MSA * `cf_giraffe_merge.txt` hhsd control file for merge analysis * `cf_giraffe_split.txt` hhsd control file for split analysis --- ## Empirical\_Milksnake Control files and empirical data for conducting hierarchical heuristic species delimitation on a complex of seven Milksnake populations, and exploring five potential alternative delimitations of two populations. ### Original publication: E Anne Chambers, David M Hillis, The Multispecies Coalescent Over-Splits Species in the Case of Geographically Widespread Taxa, Systematic Biology, Volume 69, Issue 1, January 2020, Pages 184–193, [https://doi.org/10.1093/sysbio/syz042](https://doi.org/10.1093/sysbio/syz042) Data published at: [https://doi.org/10.5061/dryad.7hs34mj](https://doi.org/10.5061/dryad.7hs34mj) ### Folder contents: * `cf_milksnake_merge.txt` hhsd control file for merge analysis * `cf_milksnake_split.txt` hhsd control file for split analysis * `Imap_Lampropeltis.txt` Imap file * `MSA_Lampropeltis` MSA --- ## Empirical\_Milksnake\_Eastwest control files and empirical data for conducting species delimitations on the 5 alternative East-West splits of milksnake populations. Original publication is the same as above ### Folder contents: * `EW.sh` bash script for running hhsd analyses for the 5 alternative splits. * `trigentalt.txt` sequence alignment * `trigent{n}alt.Imap.txt` for n in the range 1-5, each represents an alternative mapping of individuals to populations * `cf_milksnake_EW.txt` hhsd control file --- ## Empirical\_Sunfish Control files and empirical data for conducting hierarchical heuristic species delimitation on complex of five six Sunfish populations. ### Original publication: Daemin Kim, Bruce H Bauer, Thomas J Near, Introgression and Species Delimitation in the Longear Sunfish Lepomis megalotis (Teleostei: Percomorpha: Centrarchidae), Systematic Biology, Volume 71, Issue 2, March 2022, Pages 273–285, [https://doi.org/10.1093/sysbio/syab029](https://doi.org/10.1093/sysbio/syab029) Data published at: [http://dx.doi.org/10.5061/dryad.dbrv15f05](http://dx.doi.org/10.5061/dryad.dbrv15f05) ### Folder contents: * `Imap_sunfish.txt` Imap file * `MSA_sunfish` MSA * `cf_sunfish_merge.txt` hhsd control file for merge analysis * `cf_sunfish_split.txt` hhsd control file for split analysis --- ## Mathematica\_hhsd Mathematica files needed to reproduce the calculations and plots in the theory and methods section ## Simulated\_ABCD Control file and simulated data for demonstrating the basic behaviour and control of the program. ### Folder contents: * `MyImap.txt` Imap file * `MySeq` MSA * `cf_sim_merge.txt` hhsd control file for merge analysis * `cf_sim_split.txt` hhsd control file for merge analysis --- ## Simulated\_XABCD Control file and simulated data for demonstrating behaviour with paraphyletic species ### Original publication: Adam D Leaché, Tianqi Zhu, Bruce Rannala, Ziheng Yang, The Spectre of Too Many Species, Systematic Biology, Volume 68, Issue 1, January 2019, Pages 168–181, [https://doi.org/10.1093/sysbio/syy051](https://doi.org/10.1093/sysbio/syy051) Data published at: [https://doi.org/10.5061/dryad.t66gq81](https://doi.org/10.5061/dryad.t66gq81) ### Folder contents: * `starting_imap.text` Imap file * `sequences.txt` MSA * `simulated_merge_analysis.txt` hhsd control file for merge analysis * `simulated_split_analysis.txt` hhsd control file for split analysis --- ## Version History: * 08-09-2024: Revision 1: * Added new folders corresponding to the theoretical bpp and mathematica analyses in the accepted version of the paper. * updated all `hhsd` control files to correspond with updates to the the syntax of the`gdi_threshold` parameter. * 13-09-2023: * Original Upload.