{{Short description|Evolutionary biological process}} '''Reductive evolution''' is a process involving the progressive loss of genes, also known as reductive genomic evolution. This process has occurred across both prokaryotic and eukaryotic organisms, particularly in organisms that live as endosymbionts or parasites.<ref name="Wilcox">{{cite journal |vauthors=Wilcox JL, Dunbar HE, Wolfinger RD, Moran NA |date=June 2003 |title=Consequences of reductive evolution for gene expression in an obligate endosymbiont |journal=Molecular Microbiology |volume=48 |issue=6 |pages=1491–500 |doi=10.1046/j.1365-2958.2003.03522.x |pmid=12791133 |doi-access=free}}</ref><ref name="pmid9717214">{{cite journal |author1-link=Siv G. E. Andersson |author2-link=Charles Kurland |vauthors=Andersson SG, Kurland CG |date=July 1998 |title=Reductive evolution of resident genomes |journal=Trends in Microbiology |volume=6 |issue=7 |pages=263–8 |doi=10.1016/s0966-842x(98)01312-2 |pmid=9717214}}</ref> This was also an evolutionary process, evident in the transformation of symbionts into cell organelles, as seen in the origin of mitochondria and chloroplasts, through the symbiogenesis process.<ref name="pmid9717214" />
== Mechanisms == Two main factors drive gene loss: gene essentiality and environmental variability. When organisms have several genes that perform the same functions, this redundancy makes them dispensable and prone to being lost over time. Environmental changes can also shift which genes are necessary; for instance, a gene in charge of nutrient acquisition may become more expressed in a poor nutrient environment.<ref name="Wilcox" /><ref name=":0">{{cite journal |vauthors=Wolf YI, Koonin EV |date=September 2013 |title=Genome reduction as the dominant mode of evolution |journal=BioEssays |volume=35 |issue=9 |pages=829–37 |bibcode=2013BiEss..35..829W |doi=10.1002/bies.201300037 |pmc=3840695 |pmid=23801028}}</ref><ref name=":1">{{Cite journal |last1=Albalat |first1=Ricard |last2=Cañestro |first2=Cristian |date=July 2016 |title=Evolution by gene loss |url=https://www.nature.com/articles/nrg.2016.39 |journal=Nature Reviews Genetics |language=en |volume=17 |issue=7 |pages=379–391 |doi=10.1038/nrg.2016.39 |pmid=27087500 |issn=1471-0064|url-access=subscription }}</ref> Once the gene is no longer needed, it may accumulate mutations, become non-functional, and eventually be eliminated from the genome through drift or selection.<ref name=":1" /><ref name=":4">{{cite journal |vauthors=Wang M, Yafremava LS, Caetano-Anollés D, Mittenthal JE, Caetano-Anollés G |date=November 2007 |title=Reductive evolution of architectural repertoires in proteomes and the birth of the tripartite world |journal=Genome Research |volume=17 |issue=11 |pages=1572–85 |doi=10.1101/gr.6454307 |pmc=2045140 |pmid=17908824}}</ref>
Another specific mechanism that can promote gene loss through ecological dependency is the black queen hypothesis, where microorganisms rely on extracellular metabolites produced by other symbiotic microbes in their environment. This circumstance makes the microorganisms dependent on one another by reducing, getting rid of the genes responsible for producing their own metabolites. It can also be a from obligate intracellular organisms that reduce their genomes and become dependent on the host to produce metabolites for the organism to use.<ref>{{cite journal |vauthors=Song H, Hwang J, Yi H, Ulrich RL, Yu Y, Nierman WC, Kim HS |date=May 2010 |title=The early stage of bacterial genome-reductive evolution in the host |journal=PLOS Pathogens |volume=6 |issue=5 |doi=10.1371/journal.ppat.1000922 |pmc=2877748 |pmid=20523904 |doi-access=free |article-number=e1000922}}</ref>
== Examples of reductive evolution ==
=== Bacteria === Reductive evolution in symbiont bacteria has been widely studied because their genomes show marked changes compared with their free-living ancestors.<ref name="Wilcox" /> In these organisms, gene loss is primarily driven by a neutral process; the small population sizes inside hosts promote the accumulation of deleterious mutations and leading to the progressive loss of non-essential genes.<ref name="pmid16848891">{{cite journal |vauthors=Delmotte F, Rispe C, Schaber J, Silva FJ, Moya A |date=July 2006 |title=Tempo and mode of early gene loss in endosymbiotic bacteria from insects |journal=BMC Evolutionary Biology |volume=6 |page=56 |doi=10.1186/1471-2148-6-56 |pmc=1544356 |pmid=16848891 |doi-access=free}}</ref>
Both pathogenetic and mutualistic symbiotic bacteria have undergone genome reduction, but they retain different genes according to their ecological roles.<ref name="pmid16848891" /> Pathogenic bacteria retain genes involved in virulence,<ref name="pmid16848891" /> whereas mutualistic endosymbiotic keep genes required for synthesizing nutrients that benefit the host.<ref>{{Cite journal |last1=Sloan |first1=Daniel B. |last2=Moran |first2=Nancy A. |date=December 2012 |title=Genome reduction and co-evolution between the primary and secondary bacterial symbionts of psyllids |journal=Molecular Biology and Evolution |volume=29 |issue=12 |pages=3781–3792 |doi=10.1093/molbev/mss180 |issn=1537-1719 |pmc=3494270 |pmid=22821013}}</ref>
One of the most studied cases is the parasitic bacterium, ''Rickettsia prowazekii'', which has lost so many essential genes that it cannot survive outside its host. Other mutualistic symbioses, such as ''Buchnera aphidicola'' in aphids, and ''Wolbachia'' bacteria in ''Wuchereria bancrofti'' also exhibited genome reduction and have also been widely studied have all been studied and fully sequenced, which is why they are used as examples of reductive evolution.<ref name="Wilcox" />
=== Fungi === Although reduction evolution has been widely studied in bacteria, this process also occurs in fungi, particularly mycorrhizal mutualists. Genomic analyses show that ectomycorrhizal (ECM) fungi have progressively lost many genes specialized in cell wall degradation, known as plant cell wall–degrading enzymes (PCWDEs). Compared with their ancestors, white-rot decayers and brown-rot decayers, ECM fungi retain only about 47% and 77%, respectively.<ref name=":2">{{Cite journal |last1=Kohler |first1=Annegret |last2=Kuo |first2=Alan |last3=Nagy |first3=Laszlo G. |last4=Morin |first4=Emmanuelle |last5=Barry |first5=Kerrie W. |last6=Buscot |first6=Francois |last7=Canbäck |first7=Björn |last8=Choi |first8=Cindy |last9=Cichocki |first9=Nicolas |last10=Clum |first10=Alicia |last11=Colpaert |first11=Jan |last12=Copeland |first12=Alex |last13=Costa |first13=Mauricio D. |last14=Doré |first14=Jeanne |last15=Floudas |first15=Dimitrios |date=April 2015 |title=Convergent losses of decay mechanisms and rapid turnover of symbiosis genes in mycorrhizal mutualists |url=https://www.nature.com/articles/ng.3223 |journal=Nature Genetics |language=en |volume=47 |issue=4 |pages=410–415 |doi=10.1038/ng.3223 |pmid=25706625 |issn=1546-1718|hdl=1942/18722 |hdl-access=free }}</ref>
During the mutualistic association with plants, ECM fungi receive fixed carbohydrates from the host. Because of this nutrient supplementation, they no longer needed the full set of enzymes used by saprotrophic fungi at the same scale; genes focused on the plant cell wall degradation.<ref name=":2" /> However, some retained PCWDEs genes are essential, because they allow the fungi colonization in the apoplast area and acquire nutrients from the soil in inorganic and organic forms.<ref>{{Cite journal |last1=Tunlid |first1=Anders |last2=Floudas |first2=Dimitrios |last3=Op De Beeck |first3=Michiel |last4=Wang |first4=Tao |last5=Persson |first5=Per |date=2022-07-22 |title=Decomposition of soil organic matter by ectomycorrhizal fungi: Mechanisms and consequences for organic nitrogen uptake and soil carbon stabilization |journal=Frontiers in Forests and Global Change |language=English |volume=5 |article-number=934409 |doi=10.3389/ffgc.2022.934409 |bibcode=2022FrFGC...5.4409T |doi-access=free |issn=2624-893X}}</ref>
Besides gene loss, ECM fungi have also evolved new genes that support symbiosis. One example is the family of mycorrhiza-induced small secreted proteins (MiSSPs), which play a key role in establishing and maintaining the symbiotic interaction, as shown in species such as ''Laccaria bicolor''.<ref>{{Cite journal |last1=Plett |first1=Jonathan M. |last2=Daguerre |first2=Yohann |last3=Wittulsky |first3=Sebastian |last4=Vayssières |first4=Alice |last5=Deveau |first5=Aurelie |last6=Melton |first6=Sarah J. |last7=Kohler |first7=Annegret |last8=Morrell-Falvey |first8=Jennifer L. |last9=Brun |first9=Annick |last10=Veneault-Fourrey |first10=Claire |last11=Martin |first11=Francis |date=2014-06-03 |title=Effector MiSSP7 of the mutualistic fungus Laccaria bicolor stabilizes the Populus JAZ6 protein and represses jasmonic acid (JA) responsive genes |journal=Proceedings of the National Academy of Sciences |volume=111 |issue=22 |pages=8299–8304 |doi=10.1073/pnas.1322671111 |doi-access=free |pmc=4050555 |pmid=24847068 |bibcode=2014PNAS..111.8299P }}</ref>
=== Endosymbiotic theory === {{main|Endosymbiotic theory}} Endosymbiotic processes involve reductive evolution as a part of the symbiosis between the endosymbiont and the host, and the endosymbiont transitions into an organelle. Progressively, several genes are transferred from the endosymbiont to the host nucleus, while other unnecessary genes are progressively lost.<ref name="pmid16848891" /> thumb|Serial endosymbiosis Reductive evolution is the central component of the Endosymbiotic Theory, developed by Lynn Margulis.<ref name=":5">{{cite web |last=Margulis |first=Lynn |name-list-style=vanc |title=Endosymbiosis |url=https://evolution.berkeley.edu/evolibrary/article/history_24 |access-date=2019-11-08 |website=evolution.berkeley.edu}}</ref><ref name=":7">{{Cite web |date=11 July 2018 |title=Reductive evolution of microbial genomes |url=https://www.biology.lu.se/research/research-groups/microbial-ecology/research-projects/reductive-evolution-of-microbial-genomes |archive-url=https://web.archive.org/web/20190904164121/https://www.biology.lu.se/research/research-groups/microbial-ecology/research-projects/reductive-evolution-of-microbial-genomes |archive-date=4 September 2019 |access-date=2019-09-30 |website=Department of Biology, Lund University |language=en}}</ref> This theory proposes that mitochondria originated from an alphaproteobacterial endosymbiont that became an organelle within the ancestral archaea.<ref name="Khachane_2007">{{cite journal |vauthors=Khachane AN, Timmis KN, Martins dos Santos VA |date=February 2007 |title=Dynamics of reductive genome evolution in mitochondria and obligate intracellular microbes |journal=Molecular Biology and Evolution |volume=24 |issue=2 |pages=449–56 |doi=10.1093/molbev/msl174 |hdl=10033/19778 |pmid=17108184 |doi-access=free |hdl-access=free}}</ref><ref name="pmid16848891" />
A second major example of reductive evolution through endosymbiosis is the origin of the plastids. Plastids arose from a primary endosymbiosis, when a protist engulfed a photosynthetic cyanobacterium and giving rise to algae and land plants.<ref name=":3">{{Cite journal |last1=Bhattacharya |first1=Debashish |last2=Yoon |first2=Hwan Su |last3=Hackett |first3=Jeremiah D. |date=January 2004 |title=Photosynthetic eukaryotes unite: endosymbiosis connects the dots |journal=BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology |volume=26 |issue=1 |pages=50–60 |doi=10.1002/bies.10376 |issn=0265-9247 |pmid=14696040}}</ref> Secondary endosymbiosis occurs when an eukaryotic alga that already contains a primary plastid is engulfed by another protist. Examples include ''Guillardia'', cryptophyte algae with a plastid obtained from a red alga, and many diatoms that contain chromophyte algae and oomycetes.<ref name=":3" /> Some protists have undergone tertiary endosymbiosis, in which a eukaryote engulfs another eukaryote that has already acquired a secondary plastid. For example, ''Alexandrium'' (Dinoflagellate) contains a plastid derived from a secondary endosymbiotic event.<ref name=":3" /> ===Viruses=== {{main article|Viral evolution}} Despite there being different theories as to how viruses originated, one posits that they may have once been small cells that parasitized larger cells. Over time, genes not required by their parasitism were lost. The bacteria rickettsia and chlamydia are living cells that, like viruses, can reproduce only inside host cells. They lend support to this hypothesis, as their dependence on parasitism is likely to have caused the loss of genes that enabled them to survive outside a cell. This is also called the "degeneracy hypothesis".<ref>{{harvnb|Leppard|Dimmock|Easton|2007|p=[https://archive.org/details/introductiontomo00dimm_306/page/n258 16]}}</ref><ref name="Mahy, p. 24">{{harvnb|Mahy|Van Regenmortel|2009|p=24}}</ref>
A slightly different "symbiogenic model" proposed in 2012 {{#section:Virus world hypothesis|sym}} ==History==
Whole genome sequences over time have served to corroborate the idea of gene loss in some microbes during symbiosis and also in endosymbiosis.<ref>{{Cite journal |last=Moran |first=Nancy A. |date=2002 |title=Microbial Minimalism |url=https://linkinghub.elsevier.com/retrieve/pii/S0092867402006657 |journal=Cell |language=en |volume=108 |issue=5 |pages=583–586 |doi=10.1016/S0092-8674(02)00665-7 |pmid=11893328 }}</ref> This new information, together with new technologies in phylogenomics to reconstruct ancestral lineages, provided sufficient information for model organisms such as ''Rickettsia prowazekii'' and endosymbiotic bacteria related to mitochondria and plastids.<ref name=":0" /><ref>{{Cite journal |last1=Wolf |first1=Yuri I. |last2=Makarova |first2=Kira S. |last3=Yutin |first3=Natalya |last4=Koonin |first4=Eugene V. |date=2012-12-14 |title=Updated clusters of orthologous genes for Archaea: a complex ancestor of the Archaea and the byways of horizontal gene transfer |journal=Biology Direct |volume=7 |issue=1 |pages=46 |doi=10.1186/1745-6150-7-46 |doi-access=free |issn=1745-6150 |pmc=3534625 |pmid=23241446 |bibcode=2012BiDir...7...46W }}</ref> Although fossils help establish the timing of endosymbiotic origins, they cannot directly reveal genome reduction, which is inferred primarily from comparative genomic analyses.<ref name=":7" /><ref name=":2" />
== Gene loss identification ==
There are several methods used to identify which genes have been lost by comparing the genomes of modern organisms with those of their ancestors. Common phylogenetic methods include maximum parsimony (MP) or maximum likelihood (ML).<ref name=":0" /> These methods use patterns to recreate the evolutionary tree of these species and their gene compositions of the ancient forms, as well as the gene losses and gains along the tree branches, which are then compared to identify the similarity between them.
A widely used model species for studying reduction evolution is ''Rickettsia prowazekii,'' an obligate intracellular alphaproteobacterium of some multicellular eukaryotes. Researchers have found through the use of phylogenetic methods that this species has lost between 1254 and 1700 genes in comparison with its ancestor.<ref name=":4" /><ref name=":6">{{Cite journal |last1=Blanc |first1=Guillaume |last2=Ogata |first2=Hiroyuki |last3=Robert |first3=Catherine |last4=Audic |first4=Stéphane |last5=Suhre |first5=Karsten |last6=Vestris |first6=Guy |last7=Claverie |first7=Jean-Michel |last8=Raoult |first8=Didier |date=2007-01-19 |title=Reductive Genome Evolution from the Mother of Rickettsia |journal=PLOS Genetics |language=en |volume=3 |issue=1 |pages=e14 |doi=10.1371/journal.pgen.0030014 |pmid=17238289 |pmc=1779305 |doi-access=free |issn=1553-7404}}</ref><ref>{{cite journal |vauthors=Andersson JO, Andersson SG |date=September 1999 |title=Genome degradation is an ongoing process in Rickettsia |journal=Molecular Biology and Evolution |volume=16 |issue=9 |pages=1178–91 |doi=10.1093/oxfordjournals.molbev.a026208 |pmid=10486973 |doi-access=free}}</ref> The genes that were retained are primarily those required for parasitism, while genes involved in the biosynthesis of amino acids and nucleotides were primarily lost.<ref name=":6" /> This result confirms the genome changes that can be observed in organisms that depend heavily on their host for key metabolites.
== References == {{Reflist}}
==Sources== * {{cite book | vauthors = Leppard K, Dimmock N, Easton A |title=Introduction to Modern Virology |publisher=Blackwell |year=2007 |isbn=978-1-4051-3645-7 |oclc=65207057 }} * {{cite book | veditors = Mahy W, Van Regenmortel MH |title=Desk Encyclopedia of General Virology|publisher=Academic Press |year=2009 |isbn=978-0-12-375146-1 }}
Category:Evolution