Abstract Detail

Phylogenomics

McKenzie, Patrick [1], Eaton, Deren [2].

Using ipcoal to simulate and visualize genealogies and sequences on species trees or networks.

Despite their popularity in population genetics, coalescent simulations for studying genome-wide patterns are not yet widespread in phylogenetics. We present a new Python package, ipcoal, which offers simple methods for simulating sequences and genealogies on species trees. ipcoal parses a user-supplied species tree or network, along with other parameters like recombination rates and substitution models, to automatically supply complex demographic models to the powerful msprime coalescent simulator. Users can simulate chromosomes or unlinked snps, and ipcoal then makes it easy to access, visualize, and manipulate results interactively and to export results to files for downstream analysis. In real time, we demonstrate the use of ipcoal for teaching concepts related to the multispecies coalescent. In particular, we interactively define simulations that pair species tree topologies with complex substitution models, branch-specific variation in effective population sizes, spatially varying recombination rates, and reticulation events. We show how to easily visualize and access ipcoal outputs, and we take advantage of these features to explore the effects of species tree parameters on distributions of genealogies along chromosomes.

1 - Columbia University, Ecology, Evolution, and Environmental Biology, 1200 Amsterdam Ave., Schermerhorn Ext., New York, NY, 10027, USA
2 - Columbia University, Ecology, Evolution, And Environmental Biology, 1200 Amsterdam Ave. , Schermerhorn Ext. Office 1007, New York, NY, 10027, United States

Keywords:
methods
Multispecies Coalescent
simulation
phylogeny.

Presentation Type: Oral Paper
Session: PHYL3, Phylogenomics III
Location: Virtual/Virtual
Date: Friday, July 31st, 2020
Time: 11:15 AM
Number: PHYL3006
Abstract ID:795
Candidate for Awards:None