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Further research and more work in this field of immunobiology needs to take place to address the questions still brewing.
The evolution of viruses and bacterial infections has caused the adaptive immune system to become more responsive and effective in terminating more various types of invaders.
With the continued development and evolution of technology and the expansion of the processes that evolutionary biologist use, I am confident that the answers to these questions can some day be resolved.
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Scientists have come to the astonishing conclusion that the jawless fish that lived 500 million years ago possessed an alternate form of adaptive immunity comprised of variable lymphocyte receptors that was strikingly similar to the system in jawed fish.
DIFFERENCE:
VS
Antibodies in the jawed AIS were used for antigen recognition
The jawed fish that lived 500 mya possessed an adaptive immune system that protected and prevented the growth of pathogen growth by using:
Variable lymphocyte receptors (VLR) in the jawless AIS used for antigen recognition
The first jawed fish that walked on land from water carried the RAG-based AIS and passed it on as an inheritable traits to its offspring, and eventually reptiles, and then us. We as mammals share essentially the same immune system as those jawed fish. When it comes down to it, the development of antibodies that protect vertebrates against the increasing diversity of invaders is the primary example of the evolution of the adaptive immunity system.
Bartl, Simon. "Did the Molecules of Adaptive Immunity Evolve from the Innate Immune System?" Oxford Journals. Oxford University Press, 6 Jan. 20002. Web. 05 June 2016. <http://icb.oxfordjournals.org/content/43/2/338.full>.
Boundless. "Whole-Genome Duplication - Boundless Open Textbook."Boundless. Boundless Biology, 26 May 2016. Web. 05 June 2016. <https://www.boundless.com/biology/textbooks/boundless-biology-textbook/evolution-and-the-origin-of-species-18/evolution-of-genomes-127/whole-genome-duplication-509-13089/>.
Dehal, Paramvir. "Two Rounds of Whole Genome Duplication in the Ancestral Vertebrate." PLOS Biology:. Public Library of Science, 6 Sept. 2005. Web. 05 June 2016. <http://journals.plos.org/plosbiology/article?id=10.1371%2Fjournal.pbio.0030314>.
Flajnik, Martin F., and Masanori Kasahara. "Origin and Evolution of the Adaptive Immune System: Genetic Events and Selective Pressures."Nature Reviews. Genetics. U.S. National Library of Medicine, 04 Jan. 2010. Web. 04 June 2016. <http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3805090/>.
Fugmann, Sebastian D. "The Origins of the RAG Genes – from Transposition to V(D)J Recombination." Seminars in Immunology. U.S. National Library of Medicine, 04 Feb. 2010. Web. 04 June 2016. <http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2823946/>.
Herrin, Brantley R. "Alternative Adaptive Immunity in Jawless Vertebrates."Alternative Adaptive Immunity in Jawless Vertebrates. The Journal of Immunology, 10 May 2010. Web. 04 June 2016. <http://www.jimmunol.org/content/185/3/1367.full>.
Janeway, Charles A., Jr. "Evolution of the Adaptive Immune Response."National Center for Biotechnology Information. U.S. National Library of Medicine, 23 Mar. 2001. Web. 05 June 2016. <http://www.ncbi.nlm.nih.gov/books/NBK27108/>.
Lee, Jie-Oh. "Structural Diversity of the Hagfish Variable Lymphocyte Receptors*." Structural Diversity of the Hagfish Variable Lymphocyte Receptors. The Journal of Biological Chemistry, 17 Nov. 2006. Web. 05 June 2016. <http://www.jbc.org/content/282/9/6726.long>.
Provides organisms with redundant alleles that can evolve freely with little selection pressure
The duplicated genes can undergo neofunctionalization or subfunctionalization which could help the organism adapt to the new environment or survive different stress conditions
The RAG transposon and other genes that are important in maintaining the AIS that were dormant in the jawless fish species, became active during the speciation of the jawed fish from the jawless
Allows an organism to produce RAG protein/enzymes that changes the genes to fit the antigen it is defending against appropriately.
Allow antibodies to recognize various antigens by mutating their DNA and changing super fast
The evolution of viruses and bacterial infections has caused the adaptive immune system to become more responsive and effective in terminating more various types of invaders.