Abstract
Horizontal transmission of genetic material is a common phenomenon in nature and occurs via hybridization between sexually reproducing animals, horizontal gene transfer between asexually reproducing bacteria, and homologous recombination among mobile genetic elements. These processes can complicate inference of a single, vertical evolutionary history for a group of organisms (i.e. a phylogenetic tree) due to incongruent phylogenetic histories across different regions of the genome. Although this incongruence can complicate phylogenetic inference, its distribution can be used to reconstruct the historical patterns of migration and gene flow within and between species. Here, we reconstructed and explored the genomic architecture of such patterns between the ow subspecies of red-tailed chipmunks (Tamias ruficaudus) using inference of demographic history based on summary statistics, as well as large-scale phylogenomic analyses from low-coverage, whole-genome resequencing data. We show that hybridization across the genome is currently ongoing in two disjunct contact zones that differ in age. We find that signals of hybridization are more prevalent in the autosomes than sex chromosomes, the genomic architecture of introgression differs between the two contact zones, and introgression is far more prevalent in the younger contact zone.
We also examine the interplay between vertical and horizontal transmission between the subgroups of the IncP-1 group of plasmids, which are widely thought to diversify though horizontal transmission. We identify a set of “backbone genes” which are highly functional and well conserved across subgroups, and demonstrate evolution primarily through vertical inheritance, with little recombination between subgroups.
This work, although focused on two disparate systems, demonstrates the importance of horizontal transfer of genetic material, and how we can account for it in our inferences of vertical evolutionary history.