Ancestral reconstruction

DNA and Protein reconstruction

Originally proposed by Pauling and Zuckerkandl in 1963 [cite journal| author =Pauling L. and Zuckerkandl E. | year =1963| title = Chemical paleogenetics, molecular restoration studies of extinct forms of life| journal =Acta chemica Scandinavica | volume =17 | issue =89 | pages =9–16] the reconstruction of ancient proteins and DNA sequences has only recently become a significant scientific endeavor. The developments of extensive genomic sequence databases in conjunction with advances in biotechnology and phylogenetic inference methods have made ancestral reconstruction cheap, fast, and scientifically practical. Ancestral protein and DNA reconstruction allows for the recreation of protein and DNA evolution in the laboratory so that it can be studied directly [cite journal| author =Chang S.W.; Ugalde J.A.; Matz M.V. | year =2005| title = Applications of Ancestral Protein Reconstruction in Understanding Protein Function: GFP-Like Proteins| journal =Methods in Enzymology | volume =395 | pages =652–670] . With respect to proteins, this allows for the investigation of the evolution of present-day molecular structure and function. Additionally, ancestral protein reconstruction can lead to the discoveries of new biochemical functions that have been lost in modern proteins [cite journal| author =Jermann T. M. "et al" | year =1995| title = Reconstructing the evolutionary history of the artiodactyl ribonuclease superfamily| journal =Nature | volume =374 | issue =6517 | pages =57–59| doi = 10.1038/374057a0] . It also allows insights into the biology and ecology of extinct organisms [cite journal| author =Chang B.S. "et al" | year =2002| title = Recreating a functional ancestral archosaur visual pigment| journal =Molecular Biology and Evolution | volume =19 | issue =9 | pages =1483–1489] . Although the majority of ancestral reconstructions have dealt with proteins, it has also been used to test evolutionary mechanisms at the level of bacterial genomes [cite journal| author =Zhang C. "et al" | year =2003| title = Genome diversification in phylogenetic lineages I and II of Listeria monocytogenes: identification of segments unique to lineage II populations| journal =Journal of Bacteriology| volume =185 | issue =18 | pages =5573–5584| doi = 10.1128/JB.185.18.5573-5584.2003] and primate gene sequences [cite journal| author =Krishnan N.M. "et al" | year =2004| title = Ancestral sequence reconstruction in primate mitochondrial DNA: compositional bias and effect on functional inference| journal =Molecular Biology and Evolution| volume =21 | issue =10 | pages =1871–1883| doi = 10.1093/molbev/msh198] . In summary, ancestral reconstruction allows for the study of evolutionary pathways, adaptive selection, and functional divergence of the evolutionary past. For a review of biological and computational techniques of ancestral reconstruction see Chang "et al" [cite journal| author =Chang S.W.; Ugalde J.A.; Matz M.V. | year =2005| title =Applications of Ancestral Protein Reconstruction in Understanding Protein Function: GFP-Like Proteins| journal =Methods in Enzymology | volume =395 | pages =652–670] . For criticism of ancestral reconstruction computation methods see Williams P.D. "et al" [cite journal| author = Williams P.D. "et al" | year =2006| title = Assessing the accuracy of ancestral protein reconstruction methods| journal = PLoS Computational Biology| volume =2 | issue=6| pages =e69| doi = 10.1371/journal.pcbi.0020069] .

Genome reconstruction

At chromosomal level, ancestral reconstruction tries to restore the genome rearrangements happened during the evolution. Sometimes it's also called karyotype reconstruction. Chromosome painting is currently the main experimental technique. See refs. Wienberg "et al" [cite journal| author =Wienberg, J. "et al" | year =2004| title = The evolution of eutherian chromosomes| journal =Curr Opin Genet Dev| volume =14 | issue =6 | pages =657–666| doi = 10.1016/j.gde.2004.10.001] and Froenicke "et al" [cite journal| author =Froenicke, L. "et al" | year =2006| title = Are molecular cytogenetics and bioinformatics suggesting diverging models of ancestral mammalian genomes?| journal =Genome Res| volume =16 | issue =3 | pages =306–310| doi = 10.1101/gr.3955206] . .

Recently, researchers have developed computational methods to reconstruct the ancestral karyotype by taking advantage of comparative genomics. See refs. Murphy "et al" [cite journal| author =Murphy, W. J. "et al" | year =2005| title = Dynamics of mammalian chromosome evolution inferred from multispecies comparative maps| journal =Science| volume =309 | issue =5734 | pages =613–617| doi = 10.1126/science.1111387] and Ma "et al" [cite journal| author =Ma, J. "et al" | year =2006| title = Reconstructing contiguous regions of an ancestral genome| journal =Genome Res| volume =16 | issue =12| pages =1557–1565| doi = 10.1101/gr.5383506] .

Notes and references

ee also

* Origin of life