Data from: Demographically explicit scans for barriers to gene flow using gIMble
Data files
Sep 11, 2023 version files 18.15 GB
Abstract
Identifying regions of the genome that act as barriers to gene flow between recently diverged taxa has remained challenging given the many evolutionary forces that generate variation in genetic diversity and divergence along the genome, and the stochastic nature of this variation. Here we implement a composite likelihood approach for the quantification of barriers to gene flow. This analytic framework captures background selection and selection against locally maladaptive alleles (i.e. genomic barriers) in a model of isolation with migration (IM) as heterogeneity in effective population size (Ne) and effective migration rate (me), respectively. Variation in both effective demographic parameters is estimated in sliding windows via pre-computed likelihood grids. We have implemented genomewide IM blockwise likelihood estimation (gIMble) as a modular tool, which includes modules for pre-processing/filtering of genomic data and performing parametric bootstraps using coalescent simulations. To demonstrate the new approach, we analyse data from a well-studied sister species pair of tropical butterflies with a known history of post-divergence gene flow: Heliconius melpomene and H. cydno. Our analysis uncovers both large effect barrier loci (including well-known wing-pattern genes) and a genome-wide signal of polygenic barrier architecture.
README: Demographically explicit scans for barriers to gene flow using gIMble
https://doi.org/10.5061/dryad.4j0zpc8jc
Description of the data and file structure
This dataset contains data used in the article:
DR Laetsch, G Bisschop, SH Martin, S Aeschbacher, D Setter, K Lohse (2023). Demographically explicit scans for barriers to gene flow using gIMble. PLOS Genetics.
Dataset contains:
- Heliconius melpomene
Hmel2.5
genome assembly FASTA sensu Davey et al. 2017 - VCF file based on BAM files (alignments against
Hmel2.5
of 20 selected Illumina datasets from ENA project PRJEB11772. See Table S1 in manuscript for details) and genome assembly. - Simulation bootstrap replicates (
bootstrap_replicates.tar.gz
)
Sharing/Access information
Comments and requests should be addressed to Dominik R Laetsch (dominik.laetsch at gmail.com).
All data has been generated by us and is free of use. We would appreciate if the paper is cited if appropriate.
Methods
See manuscript: section Materials and Methods, subsection Heliconius Analyses.