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Abstract

It is now widely accepted that the process of speciation can occur without the necessity of complete reproductive isolation. Unraveling the genetic basis of genomic barriers and understanding the relative importance of gene flow between divergent evolutionary lineages remains an ongoing challenge. Although advances in sequencing technology have made it possible to extend these studies to the whole genome, the lack of population-level studies that exploit the information contained in linkage disequilibrium along individual chromosomes (haplotype) remains a significant obstacle to understanding how and when introgression occurred, which regions are subject to gene flow and, by contrast, what mechanisms maintain genome integrity. Using a linked-read sequencing method called ‘haplotagging’ (Meier et al., 2021), we were able to reconstruct haplotypes as well as complete mitogenomes on hundreds of diploid samples. Our study focuses on the role of mitochondria as a potential barrier to gene flow in two cryptic species of the brown algae Ectocarpus. Mitochondria, offer unique insights into hybridization, speciation dynamics, and the evolutionary history and genetic diversity of species. We examined the mitochondrial diversity and population-level structure across two geographical hybridization regions.