Code and data for: A putative bacterial ecocline in Klebsiella pneumoniae

This repository contains the code and data used in the preprint:

A putative bacterial ecocline in Klebsiella pneumoniae
Siqi Liu, Sarah L. Svensson, Daniel Falush
bioRxiv (2025)
https://doi.org/10.1101/2025.01.20.633859

SLiM simulation models

All simulations were implemented in SLiM v4.0.1 using a non-Wright–Fisher (nonWF) framework, as described in the Methods section of the preprint.
The repository contains four main simulation models corresponding to the scenarios analysed in the manuscript:

1. Modeling clonal haploid bacteria with horizontal gene transfer

File: simu_Modeling clonal haploid bacteria with HGT

This model simulates a single panmictic population of clonal haploid bacteria evolving neutrally, with horizontal gene transfer (HGT) of varying tract lengths. It is used to characterize baseline genetic variation generated by mutation and recombination alone.

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2. Linear stepping-stone model

File: simu_A linear stepping-stone model

A spatially structured linear stepping-stone model with 10 subpopulations connected by nearest-neighbour migration. This model is used to examine how restricted gene flow along an ecological or geographical gradient generates population structure.

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3. Selective model

File: simupops_Unfitness_1kb.slim (and related files)

This model introduces diversifying selection on a quantitative trait derived from the difference between two mutation types. Fitness increases with distance from the population mean trait value, favouring individuals with extreme phenotypes.

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4. Refined selective model

File: simupops_Unfitness_gamma.slim
Extended genome version (5 Mb): simu_refinedselectivemodel.slim
Extended genome + multiple HGT events: simupops_5Mb.slim

This model extends the selective framework by assigning locus-specific selection coefficients drawn from a Gamma distribution, allowing heterogeneity in mutational effects. A 5 Mb genome version is used to better approximate the size and structure of a real Klebsiella pneumoniae genome.

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Heterogeneity models

Models exploring recombination-rate and mutation-rate heterogeneity across the genome are located in the revision/ directory.
These simulations are described in the Methods of the preprint.

Software

The analyses and simulations in this repository were performed primarily using:

• SLiM v4.0.1 (non-Wright–Fisher framework)
• R (for PCA, variant loading calculations, and visualization)

All additional software tools and parameters used for genome processing, phylogenetic reconstruction, and population genomic analyses are described in detail in the Methods section of the preprint.