MOLECULAR TRACES AND EVIDENCE OF EVOLUTION

Year 2014, Volume: 77 Issue: 2, 31 - 36, 30.01.2014

Selen Güçlü Gülşah Albayrak Asuman Deveci , Abdullah Ekmekçi

https://doi.org/10.18017/iuitfd.13056441.2015.77/2.31-36

Abstract

Evolution is being investigated with the aid of today’s technological advances. Evolutionary biology researches directly or indirectly may affect today and tomorrow. When evolution is mentioned, even at first Darwin’s Evolutionary Theory and phylogenetic approaches that depend on organisms’ morphological features come to mind, there are also hypotheses that see mutation and genetic drift as the genetic diversity resource in populations. Proofs that support evolution vary from rocks and bones to molecules. As living organisms’ genome sequences and proteins that are involved in common mechanisms are discovered through DNA sequence analysis, it has been answered to these questions in molecular level like what is the origin of the living organisms, which living organism is relative with another, which organisms share the common ancestor. The hypotheses like origin of the life and evolutionary history are not being able to be explained exactly as the hypothesis testing applications can not be performed in the laboratory. In this review, various theories and hypotheses related with molecular evolution are being discussed with proofs that have been obtained by tracking evolution’s molecular marks in the light of mechanisms that affect gene and genome evolution.

Keywords

mutation, molecular evolution, LUCA

EVRİMİN MOLEKÜLER İZLERİ VE KANITLARI

Abstract

Evrim, günümüzde teknolojinin sağladığı olanaklarla merakla araştırılmaya devam edilen bir konudur. Evrimsel biyolojik araştırmalar, doğrudan ya da dolaylı olarak bugünü ve yarını etkileyebilmektedir. Evrim denildiğinde akla öncelikle gelen türlerin kökeniyle ilgili Darwin’in evrim teorisi ve organizmaların morfolojisini dikkate alan geleneksel filogenetik yaklaşımlar olsa da, mutasyonu ve genetik kaymayı, popülasyonlardaki genetik çeşitliliğin kaynağı olarak gören hipotezler de bulunmaktadır. Evrimi destekleyen kanıtlar kayalardan kemiklere, kemiklerden moleküllere kadar çeşitlilik göstermektedir. DNA dizileme analizleriyle canlıların genom dizilimi ve canlılardaki ortak mekanizmalarda etkili proteinler belirlendikçe canlılığın biyolojik kökeninin nereden geldiği, hangi canlının birbiri ile akraba olduğu, hangi organizmaların ortak atayı paylaştığı sorularına moleküler boyutta yanıt oluşturulabilmektedir. Yaşamın kökeni ve evrimin tarihsel olaylarıyla ilgili hipotezlerin bir kısmı, hipotezi test edecek uygulamaların laboratuvarlarda henüz yapılamaması nedeniyle tam olarak açıklanamamaktadır. Bu derlemede, gen ve genom evrimine etki eden mekanizmalar ışığında moleküler evrim ile ilgili çeşitli teori, hipotezler ve evrimin moleküler izleri takip edilerek elde edilen kanıtlar tartışılmaktadır.

Keywords

mutasyon, moleküler evrim, LUCA

References

• Angers B, Castonguay E, Massicotte R. Environmentally induced phenotypes and DNA methylation: how to deal with unpredictable conditions until the next generation and after. Molecular Ecology 2010;19(7):1283-1295.
• Bada JL. How life began on Earth: a status report, Earth Planet Science Leters 2004;226:1-15.
• Berger SL, Kouzarides T, Shiekhattar R, Shilatifard A. An operational definition of epigenetics. Genes and Development, 2009;23(7):781-783.
• Blöchl E, Keller M, Wächtershäuser G, Stetter ΚΟ. Reactions depending on iron sulphide and linking geochemistry with biochemistry. Proceedings of the National Academy of Science USA 1992;89:81178
• Butlin RK, Tregenza T. Levels of genetic polymorphism: marker loci versus quantitative traits. Philosophical Transactions of the Royal Society B 1998;353(1366):187-198.
• Carroll SB, Grenier J, Weatherbee SD. From DNA to Diversity: Molecular Genetics and the Evolution of Animal Design. 2nd ed., Oxford: Blackwell Publishing, 2005.
• Cech TR, Zaug AJ, Grabowski PJ. In vitro splicing of the ribosomal RNA precursor of Tetrahymena: involvement of a guanosine nucleotide in the excision of the intervening sequence. Cell 1981;27:487-496.
• Corliss JB, Baross JΑ, Hoffman SE. An hypothesis concerning the relationship between submarine hot springs and the origin of life on earth. Oceanologica Acta 1981;4:59-69.
• Crick FHC. The origin of the genetic code. Journal of Molecular Biology 1968; 38: 367–379.
• Dobzhansky T. Nothing in Biology Makes Sense except in the Light of Evolution. National Association of Biology Teachers 1973;35(3):1251
• Forterr P. The two ages of the RNA world, and the transition to the DNA world:a story of viruses and cells. Biochimie 2005; 87(9):793-803.
• Gilbert, W. The RNA world. Nature 1986; 319: 618. Guerrier TC, Altman S. Catalytic activity of an RNA molecule prepared by transcription in vitro. Science 1984;223:285-286.
• Hastings PJ, Lupski JR. Rosenberg SM, Ira G. Mechanisms of change in gene copy number. Nature Reviews Genetics 2009;10(8):551-564 Hazen RM. The Emergence of Chemical Complexity: An Introduction, In: Zaikowski L (ed). Chemical Evolution across Space and Time. ACS Symposium Series; American Chemical Society. Washington, DC, 2008. Heng HHQ. The genome-centric concept: resynthesis of evolutionary theory. BioEssays, DOI: 1002/bies.200800182, March 30, 2009.
• Higuchi R, Bowman B, Freiberger M, Ryder OA, Wilson AC. DNA sequences from the quagga, an extinct member of the horse family. Nature 1984;312:282–284.
• Hofreiter M, Serre D, Poinar HN, Kuch M, Pääbo S. Ancient DNA. Nature Reviews Genetics 2001;2:353-359.
• Hurles M. Gene duplication: the genomic trade in spare parts. PLoS Biol DOI:10.1371/journal.pbio. 0020206, July 13, 2004.
• Johannes F, et al. Assessing the impact of transgenerational epigenetic variation on complex traits. PLoS Genet, DOI:1371/journal.pgen.1000530, June 26, 2009.
• Kimura M. Evolutionary rate at the molecular level. Nature 1968;217:624-626.
• Kimura M, Ohta T. On some principles governing molecular evolution. Proceedings of the National Academy of Sciences of the USA 1974;71(7): 28482
• Kimura M. The neutral theory of molecular evolution: A review of recent evidence. The Japanese Journal of Genetics 1991;66:367-386
• Knight RD, Landweber LF. Rhyme or reason: RNAarginine interactions and the genetic code. Chemistry & Biology 1998;5(9):215-220.
• Knoll AH, Carroll SB. Early animal evolution: emerging views from comparative biology and geology. Science 1999;284(5423):2129-37.
• Koonin EV. Comparative genomics, minimal genesets and the last universal common ancestor. Nature Reviews Microbiology 2003;1:127-136.
• Kurland C.G.(2000), Something for everyone:Horizontal gene transfer in evolution. EMBO Rep. 2000 August 15;1(2):92–95.
• Lazcano A, Miller SL. The origin and early evolution review of life: Prebiotic chemistry, the Pre-RNA world, and time. Cell 1996;85:793-798.
• Marc J, et al. Genomically recoded organisms expand biological functions. Science, DOI: 1126/science.124145918, October 18, 2013.
• Martin W, Russel MJ. On the origins of cells: a hypothesis for the evolutionary transitions from abiotic geochemistry to chemoautotrophic prokaryotes, and from prokaryotes to nucleated cells. Philosophical Transactions of the Royal Society B: Biological 2003;358(1429):59-83.
• McClintock B. The Stability of Broken Ends of Chromosomes in Zea Mays. Genetics 1941;26(2):234–282.
• Miller SL. Production of amino acids under possible primitive earth conditions. Journal of American Chemical Society 1955;77(9):2351-2361.
• Morjan C, Rieseberg L. How species evolve collectively: implications of gene flow and selection for the spread of advantageous alleles. Molecular Ecology 2004; 13(6):1341-1356.
• Ohno S. Sex Chromosomes and Sex Linked Gene. Springer Verlag, Berlin, 1967.
• Ohta T. Role of gene duplication in evolution. Genome 1989;31(1):304-310.
• Orengo CA, Thornton JM. Protein families and their evolution-a structural perspective. Annual Review of Biochemistry 2005;74(1):867-900.
• Orgel LE. RNA catalysis and the origin of life. Journal of Theorotical Biology 1986;123(2):127-49.
• Orgel L. Prebiotic chemistry and the origin of the RNA world. Critical Review of Biochemistry and Molecular Biology 2004;39(2):99-123.
• Oró J, Kamat SS. Amino-acid synthesis from hydrogen cyanide under possible primitive earth conditions. Nature 1961;190:442-443.
• Penny D, Poole A. The nature of the last universal common ancestor. Current opinion in genetics & development 1999;9(6):672-677.
• Pirrotta V, Steller H, Bozzetti MP. Multiple upstream regulatory elements control the expression of the Drosophila white gene. The EMBO Journal 1985;4(13A):3501-3508.
• Poole A, Penny D, Sjöberg BM. Confounded cytosine! Tinkering and the evolution of DNA, Nature Review of Molecular Cell Biology 2001;2:147-151.
• River MC, Lake JA. The ring of life provides evidence for a genome fusion origin of eukaryotes. Nature 2004;431(9):152-155.
• Russell MJ, Hall AJ. The emergence of life from iron monosulphide bubbles at a submarine hydrothermal redox and pH front. Journal of the Geological Society of London,1957; 154: 377-402.
• Saladino R, Crestini C, Costanzo G, DiMauro, E. From Simple Amphiphiles to Protocell Models. In: Walde P (ed). Topics in Current Chemistry, Springer. Berlin/Heidelberg, 2005;29.
• Sawyer SA, Parsch J, Zhang Z, Hartl DL. Prevalence of positive selection among nearly neutral amino acid replacements in Drosophila. Proc Natl Acad Sci USA 2007;104(16):6504-6510
• Schrey AW, et al. The role of epigenetics in evolution: the extended synthesis, Genetics Research International, DOI:10.1155/2012/286164, December 15, 2012.
• Sella G, Ardell DH. The coevolution of genes and genetic codes: Crick's frozen accident revisited. Journal of Molecular Evolution 2006;63(3):297-313. Sievers D, Von Kiedrowski G. Self-replication of complementary nucleotide-based oligomers, Nature 1994;369:221-224.
• Simon FW, et al. A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus. Science 2011; 332(6034):1163-1166.
• Stribling R, Miller SL. Energy yields for hydrogen cyanide and formaldehyde synthesis: the HCN and amino acid concentrations in the primitive ocean. Origins of Life and Evolution of Biospheres 1987;17:261-273.
• Wetterbom A, Sevov M, Cavelier L, Bergström TF. Comparative genomic analysis of human and chimpanzee indicates a key role for indels in primate evolution. Journal of Molecular Evolution 2006;63(5):682-690.
• Vladar HP. Amino acid fermentation at the origin of the genetic code. Biology Direct 2012;7:6.
• Zuckerkandl E, Pauling L. 1965 In: Bryson V, Vogel HJ (ed). Evolving Gene and Proteins. Academic Press, New York, 1965;97-166.