Life in sediments fosters 'sexual' speciation in the Shewanella baltica complex

This repository contains analyses and data to reproduce our study on how intra- and interspecific differentiation arises in natural microbial populations, focusing on the Shewanella baltica species complex in Baltic Sea sediments. We analyzed 112 genomes from sympatric strains sampled across sediment depths (0–6 cm) at Vaxön, Stockholm archipelago, along with earlier isolates from the same site and allopatric strains from the Stockholm area. Using a reverse-ecology population genomics approach, we identified three cohesive evolutionary lineages (G1, G2, and G3), each showing distinct eco-genomic signatures and extensive gene turnover driven by horizontal gene transfer.