Adaptation of the endosymbiont to the host's lifestyle leads to many changes in the endosymbiont–the foremost being drastic reduction in its genome size. This is due to many genes being lost during the process of metabolism, and DNA repair and recombination. While important genes participating in the DNA to RNA transcription, protein translation and DNA/RNA replication are retained. That is, a decrease in genome size is due to loss of protein coding genes and not due to lessening of inter-genic regions or open reading frame (ORF) size. Thus, species that are naturally evolving and contain reduced sizes of genes can be accounted for an increased number of noticeable differences between them, thereby leading to changes in their evolutionary rates. As the endosymbiotic bacteria related with these insects are passed on to the offspring strictly via vertical genetic transmission, intracellular bacteria goes through many hurdles during the process, resulting in the decrease in effective population sizes when compared to the free living bacteria. This incapability of the endosymbiotic bacteria to reinstate its wild type phenotype via a recombination process is called as Muller's ratchet phenomenon. Muller's ratchet phenomenon together with less effective population sizes has led to an accretion of deleterious mutations in the non-essential genes of the intracellular bacteria. This could have been due to lack of selection mechanisms prevailing in the rich environment of the host.

What is the main alteration in an endosymbiont when it adapts to a host?