Horizontal gene transfer (HGT) involves the acquisition of genetic material from a donor organism and its incorporation into the genome of the recipient, without the two organisms being in a parent-offspring relationship. Genes, gene fragments and even operons can be transferred across broad taxonomic boundaries and this can contribute to genetic novelty of a genome. Hence, the genealogical history of a genome cannot be portrayed simply as a lineal descent from a common ancestor that existed in some distant past because a lineage can trace its ancestry from a myriad of sources, both living and extinct. In this dissertation, I present three different cases of HGT: transfers between close relatives, between distantly related taxa and from ancient lineages. The focus of this dissertation is on aminoacyl-tRNA synthetases, a group of enzymes that play an integral role in the translation machinery. Phylogenetic analyses of these enzymes indicate that HGT has played an important role in their evolutionary histories. In some cases, the transferred genes acquired from distant relatives endow the recipient with novel metabolic processes and physiological capacities, and can therefore result to topologies that conflict with the organismal tree. However, in most instances, a bias to transfer genes with closely related partners will maintain and strengthen similarity within groups. Looking at the overall Tree/Net of Life, we therefore see that microbial lineages and relationships are shaped by both HGT and shared ancestry.
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