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https://www.ncbi.nlm.nih.gov/pubmed/12791133

Article Draft Introduction Reductive Evolution is the process of microorganisms removing genes from their genome. These genes can be inessential to the organism and makes it so the bacteria can reproduce more efficiently https://www.ncbi.nlm.nih.gov/pubmed/12791133. Sometimes bacteria will eliminate essential genes in their genome. This seems counterintuitive because it makes the target organism rely on products produced by other organisms. It can occur, when bacteria found in a free-living state enter a restrictive state, or are absorbed by another organism becoming intracellular. The bacteria will adapt to survive in the restrictive state by altering and reducing its genome to get rid of the nonessential material.[1] An example of this would be the black queen hypothesis where bacteria rely on extracellular metabolites produced by symbiotic bacteria in their environment. The bacteria that is dependent reduce their genome and get rid of the genes responsible for producing the extracellular metabolites. It can also be from obligate intracellular organisms that reduce their genomes and become dependent on the host to produce metabolites for the organism to use.

Genome Sizes of Various Organisms Microorganisms Rickettsia prowazekii

Buchnera aphidicola

History Following reductive evolution, it is suggested that between 180 and 425 million years ago the Rickettsia parasite incident occurred. Many believe that this is event had to have happened later on as the Rickettsia and mitochondria evolved from a common ancestor. With this information, scientists believe that Rickettsia and mitochondria had to have happened at different points in history. Many scientists have been able to use fossils to identify and confirm these endosymbiotic events but, there is a lack of good fossils which makes reductive evolution very difficult.[2]

Article body Reductive Evolution[3] is the basis behind the Endosymbiotic Theory which states that Eukaryotes absorbed other microorganism (Eukaryotes and archea) and kept them around because it was advantageous to do so. The absorbed organisms are said to have then gone through Reductive evolution deleting genes that were deemed nonessential or non-beneficial to the cell in its specific niche. When comparing fossil evidence reductive evolution can be demonstrated.[4]

DNA found in ancient prokaryotic and mitochondria fossils have been found to have higher levels of Cytosine and Guanine compared to the DNA found in the same organism today. Different segments of the genome found to be unfavorable have possibly been removed over time due to deletions of DNA causing the genome to be reduced.[5]

There are a few general models for reductive evolution, there are phases that microorganisms can go through.

The short phase: This is generally a fast phase of reproduction which leads to a greater and more complex genome usually involving mutations. This leads to a longer reductive phase, which means loss of genetic material, or a more direct genome. Basically it means the genome can become simplified and more complex due to random mutations. [6]

Methods There are many methods to help identify if genes have been deleted, two of which are maximum parsimony (MP) or maximum likelihood (ML) patterns are used to recreate the evolutionary tree of these species and their gene compositions of the ancient forms as well as the gene losses and gained along the tree branches which are then compared to each other. There are limitations, however, mostly due to using different models or adding new information which can skew results. Such as using Dollo Parsimony or Weighted Parsimony,

Maximum parsimony (MP)

Maximum likelihood (ML)

Rickettsia prowazekii is an unrestricted microorganism which has been used to demonstrate genome degradation[7] DNA and genome size is not linked to the complexity of an organism. There are some bacteria that have a lot more DNA than a human. This is not yet understood and is referred to as the C-value Enigma or C-value Paradox. To put it simply, the amount of DNA in a haploid genome doesn't relate to the complexity of an organism and can be very different.

References https://www.biology.lu.se/research/research-groups/microbial-ecology/research-projects/reductive-evolution-of-microbial-genomes

Song, Han; Hwang, Junghyun; Yi, Hyojeong; Ulrich, Ricky L.; Yu, Yan; Nierman, William C.; Kim, Heenam Stanley (2010-05-27). "The Early Stage of Bacterial Genome-Reductive Evolution in the Host". PLOS Pathogens. 6 (5): e1000922. doi:10.1371/journal.ppat.1000922. ISSN 1553-7374. PMC 2877748. PMID 20523904.
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"Reductive evolution of microbial genomes". Department of Biology. 2014-04-11. Retrieved 2019-09-30.
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Wang, Minglei; Yafremava, Liudmila S.; Caetano-Anollés, Derek; Mittenthal, Jay E.; Caetano-Anollés, Gustavo (2007-11-01). "Reductive evolution of architectural repertoires in proteomes and the birth of the tripartite world". Genome Research. 17 (11): 1572–1585. doi:10.1101/gr.6454307. ISSN 1088-9051. PMID 17908824.
Andersson, J. O.; Andersson, S. G. (1999-09-01). "Genome degradation is an ongoing process in Rickettsia". Molecular Biology and Evolution. 16 (9): 1178–1191. doi:10.1093/oxfordjournals.molbev.a026208. ISSN 0737-4038.