Hierarchical heuristic species delimitation under the multispecies coalescent model with migration

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 ..., The data are analyzed using our new python pipeline called HHSD., , # Contents

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## BPP\_files\_SI

BPP Files needed to reproduce the analyses in the theory and methods section

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## 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

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## Empirical\_Milksnake

Control files and empirical data for co...