Trait reconstruction

Ancestral reconstruction is widely use 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

Protein

Proteins are biochemical compounds consisting of one or more polypeptides typically folded into a globular or fibrous form, facilitating a biological function. A polypeptide is a single linear polymer chain of amino acids bonded together by peptide bonds between the carboxyl and amino groups of...

 and DNA

DNA

Deoxyribonucleic acid is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms . The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in...

 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

Karyotype

A karyotype is the number and appearance of chromosomes in the nucleus of an eukaryotic cell. The term is also used for the complete set of chromosomes in a species, or an individual organism.p28...

 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

Comparative genomics

Comparative genomics is the study of the relationship of genome structure and function across different biological species or strains. Comparative genomics is an attempt to take advantage of the information provided by the signatures of selection to understand the function and evolutionary...

. See refs. Murphy et al. and Ma et al. .