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.
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 .