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Revision as of 22:34, 22 December 2011 edit18.111.89.185 (talk) →Trait reconstruction← Previous edit Revision as of 09:28, 15 March 2012 edit undoRjwilmsi (talk | contribs)Extended confirmed users, Pending changes reviewers, Rollbackers932,067 editsm →DNA and Protein reconstruction: Journal cites:, added 1 DOI, using AWB (8010)Next edit →
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Originally proposed by Pauling and Zuckerkandl in 1963<ref>{{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| doi =10.3891/acta.chem.scand.17s-0009}}</ref> 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. Originally proposed by Pauling and Zuckerkandl in 1963<ref>{{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| doi =10.3891/acta.chem.scand.17s-0009}}</ref> 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 ] and ] reconstruction allows for the recreation of protein and DNA evolution in the laboratory so that it can be studied directly<ref name="Chang2005">{{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| doi =10.1016/S0076-6879(05)95034-9| pmid =15865989| series =Methods in Enzymology| isbn =9780121828004}}</ref>. 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<ref>{{cite journal| author =Jermann T. M. | 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| pmid =7532788| author-separator =,| display-authors =1| last2 =Opitz| first2 =Jochen G.| last3 =Stackhouse| first3 =Joseph| last4 =Benner| first4 =Steven A.}}</ref><ref>{{cite journal|last=Sadqi|first=Mourad|coauthors=Eva de Alba, Raúl Pérez-Jiménez, Jose M. Sanchez-Ruiz ,Victor Muñoz|title=A designed protein as experimental model of primordial folding|journal=Proc Natl Acad Sci U S A|year=2009|month=January|volume=106|issue=11|pages=4127–4132|doi=10.1073/pnas.0812108106|pmid=19240216|url=http://www.pnas.org/content/106/11/4127.long|pmc=2647338}}</ref>. It also allows insights into the biology and ecology of extinct organisms<ref>{{cite journal| author =Chang B.S. | year =2002| title = Recreating a functional ancestral archosaur visual pigment| journal =Molecular Biology and Evolution | volume =19 | issue =9 | pages =1483–1489| pmid =12200476| author-separator =,| display-authors =1| last2 =Jönsson| first2 =K| last3 =Kazmi| first3 =MA| last4 =Donoghue| first4 =MJ| last5 =Sakmar| first5 =TP}}</ref>. 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<ref>{{cite journal| author =Zhang C. | 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| pmid =12949110| pmc =193770| author-separator =,| display-authors =1| last2 =Zhang| first2 =M.| last3 =Ju| first3 =J.| last4 =Nietfeldt| first4 =J.| last5 =Wise| first5 =J.| last6 =Terry| first6 =P. M.| last7 =Olson| first7 =M.| last8 =Kachman| first8 =S. D.| last9 =Wiedmann| first9 =M.}}</ref> and primate gene sequences<ref>{{cite journal| author =Krishnan N.M. | 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| pmid =15229290| author-separator =,| display-authors =1| last2 =Seligmann| first2 =H| last3 =Stewart| first3 =CB| last4 =De Koning| first4 =AP| last5 =Pollock| first5 =DD}}</ref>. Ancestral ] and ] reconstruction allows for the recreation of protein and DNA evolution in the laboratory so that it can be studied directly<ref name="Chang2005">{{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| doi =10.1016/S0076-6879(05)95034-9| pmid =15865989| series =Methods in Enzymology| isbn =9780121828004}}</ref>. 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<ref>{{cite journal| author =Jermann T. M. | 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| pmid =7532788| author-separator =,| display-authors =1| last2 =Opitz| first2 =Jochen G.| last3 =Stackhouse| first3 =Joseph| last4 =Benner| first4 =Steven A.}}</ref><ref>{{cite journal|last=Sadqi|first=Mourad|coauthors=Eva de Alba, Raúl Pérez-Jiménez, Jose M. Sanchez-Ruiz ,Victor Muñoz|title=A designed protein as experimental model of primordial folding|journal=Proc Natl Acad Sci U S A|year=2009|month=January|volume=106|issue=11|pages=4127–4132|doi=10.1073/pnas.0812108106|pmid=19240216|url=http://www.pnas.org/content/106/11/4127.long|pmc=2647338}}</ref>. It also allows insights into the biology and ecology of extinct organisms<ref>{{cite journal| author =Chang B.S. | year =2002| title = Recreating a functional ancestral archosaur visual pigment| journal =Molecular Biology and Evolution | volume =19 | issue =9 | pages =1483–1489| pmid =12200476| author-separator =,| display-authors =1| last2 =Jönsson| first2 =K| last3 =Kazmi| first3 =MA| last4 =Donoghue| first4 =MJ| last5 =Sakmar| first5 =TP | doi=10.1093/oxfordjournals.molbev.a004211}}</ref>. 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<ref>{{cite journal| author =Zhang C. | 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| pmid =12949110| pmc =193770| author-separator =,| display-authors =1| last2 =Zhang| first2 =M.| last3 =Ju| first3 =J.| last4 =Nietfeldt| first4 =J.| last5 =Wise| first5 =J.| last6 =Terry| first6 =P. M.| last7 =Olson| first7 =M.| last8 =Kachman| first8 =S. D.| last9 =Wiedmann| first9 =M.}}</ref> and primate gene sequences<ref>{{cite journal| author =Krishnan N.M. | 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| pmid =15229290| author-separator =,| display-authors =1| last2 =Seligmann| first2 =H| last3 =Stewart| first3 =CB| last4 =De Koning| first4 =AP| last5 =Pollock| first5 =DD}}</ref>.
In summary, ancestral reconstruction allows for the study of evolutionary pathways, ], and functional divergence of the evolutionary past. For a review of biological and computational techniques of ancestral reconstruction see Chang ''et al.''<ref name="Chang2005" />. For criticism of ancestral reconstruction computation methods see Williams P.D. ''et al.''<ref>{{cite journal| author = Williams P.D. | 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| pmid = 16789817| pmc = 1480538| author-separator = ,| display-authors = 1| last2 = Pollock| first2 = David D.| last3 = Blackburne| first3 = Benjamin P.| last4 = Goldstein| first4 = Richard A.}}</ref>. In summary, ancestral reconstruction allows for the study of evolutionary pathways, ], and functional divergence of the evolutionary past. For a review of biological and computational techniques of ancestral reconstruction see Chang ''et al.''<ref name="Chang2005" />. For criticism of ancestral reconstruction computation methods see Williams P.D. ''et al.''<ref>{{cite journal| author = Williams P.D. | 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| pmid = 16789817| pmc = 1480538| author-separator = ,| display-authors = 1| last2 = Pollock| first2 = David D.| last3 = Blackburne| first3 = Benjamin P.| last4 = Goldstein| first4 = Richard A.}}</ref>.

Revision as of 09:28, 15 March 2012

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It has been suggested that this article be merged with Paleogenetics. (Discuss) Proposed since May 2011.

Trait reconstruction

Ancestral reconstruction is widely used to infer the ecological, phenotypic, or biogeographic traits associated with ancestral nodes in a phylogenetic tree. Methods for ancestral reconstruction include parsimony, maximum likelihood, and Bayesian inference.

DNA and Protein reconstruction

Originally proposed by Pauling and Zuckerkandl in 1963 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. 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. It also allows insights into the biology and ecology of extinct organisms. 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 and primate gene sequences.

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.. For criticism of ancestral reconstruction computation methods see Williams P.D. et al..

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. and Froenicke et al. . .

Recently, researchers have developed computational methods to reconstruct the ancestral karyotype by taking advantage of comparative genomics. See refs. Murphy et al. and Ma et al. .

See also

Notes and references

  1. Pauling L. and Zuckerkandl E. (1963). "Chemical paleogenetics, molecular restoration studies of extinct forms of life". Acta chemica Scandinavica. 17 (89): 9–16. doi:10.3891/acta.chem.scand.17s-0009.
  2. ^ Chang S.W.; Ugalde J.A.; Matz M.V. (2005). "Applications of Ancestral Protein Reconstruction in Understanding Protein Function: GFP-Like Proteins". Methods in Enzymology. Methods in Enzymology. 395: 652–670. doi:10.1016/S0076-6879(05)95034-9. ISBN 9780121828004. PMID 15865989.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  3. Jermann T. M.; et al. (1995). "Reconstructing the evolutionary history of the artiodactyl ribonuclease superfamily". Nature. 374 (6517): 57–59. doi:10.1038/374057a0. PMID 7532788. {{cite journal}}: Unknown parameter |author-separator= ignored (help)
  4. Sadqi, Mourad (2009). "A designed protein as experimental model of primordial folding". Proc Natl Acad Sci U S A. 106 (11): 4127–4132. doi:10.1073/pnas.0812108106. PMC 2647338. PMID 19240216. {{cite journal}}: Unknown parameter |coauthors= ignored (|author= suggested) (help); Unknown parameter |month= ignored (help)
  5. Chang B.S.; et al. (2002). "Recreating a functional ancestral archosaur visual pigment". Molecular Biology and Evolution. 19 (9): 1483–1489. doi:10.1093/oxfordjournals.molbev.a004211. PMID 12200476. {{cite journal}}: Unknown parameter |author-separator= ignored (help)
  6. Zhang C.; et al. (2003). "Genome Diversification in Phylogenetic Lineages I and II of Listeria monocytogenes: Identification of Segments Unique to Lineage II Populations". Journal of Bacteriology. 185 (18): 5573–5584. doi:10.1128/JB.185.18.5573-5584.2003. PMC 193770. PMID 12949110. {{cite journal}}: Unknown parameter |author-separator= ignored (help)
  7. Krishnan N.M.; et al. (2004). "Ancestral sequence reconstruction in primate mitochondrial DNA: compositional bias and effect on functional inference". Molecular Biology and Evolution. 21 (10): 1871–1883. doi:10.1093/molbev/msh198. PMID 15229290. {{cite journal}}: Unknown parameter |author-separator= ignored (help)
  8. Williams P.D.; et al. (2006). "Assessing the Accuracy of Ancestral Protein Reconstruction Methods". PLoS Computational Biology. 2 (6): e69. doi:10.1371/journal.pcbi.0020069. PMC 1480538. PMID 16789817. {{cite journal}}: Unknown parameter |author-separator= ignored (help)CS1 maint: unflagged free DOI (link)
  9. Wienberg, J.; et al. (2004). "The evolution of eutherian chromosomes". Curr Opin Genet Dev. 14 (6): 657–666. doi:10.1016/j.gde.2004.10.001. PMID 15531161.
  10. Froenicke, L.; et al. (2006). "Are molecular cytogenetics and bioinformatics suggesting diverging models of ancestral mammalian genomes?". Genome Res. 16 (3): 306–310. doi:10.1101/gr.3955206. PMC 1415215. PMID 16510895.
  11. Murphy; W. J.; et al. (2005). "Dynamics of mammalian chromosome evolution inferred from multispecies comparative maps". Science. 309 (5734): 613–617. doi:10.1126/science.1111387. PMID 16040707. {{cite journal}}: Unknown parameter |author-separator= ignored (help)
  12. Ma, J.; et al. (2006). "Reconstructing contiguous regions of an ancestral genome". Genome Res. 16 (12): 1557–1565. doi:10.1101/gr.5383506. PMC 1665639. PMID 16983148.


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