6.1 Homologs Are Descended from a Common Ancestor

Exploring evolution biochemically often means searching for homology between molecules, because homologous molecules, or homologs, evolved from a common ancestor. Paralogs are homologous molecules that are found in one species and have acquired different functions through evolutionary time. Orthologs are homologous molecules that are found in different species and have similar or identical functions.

6.2 Statistical Analysis of Sequence Alignments Can Detect Homology

Protein and nucleic acid sequences are two of the primary languages of biochemistry. Sequence-alignment methods are the most powerful tools of the evolutionary detective. Sequences can be aligned to maximize their similarity, and the significance of these alignments can be judged by statistical tests. The detection of a statistically significant alignment between two sequences strongly suggests that two sequences are related by divergent evolution from a common ancestor. The use of substitution matrices makes the detection of more-distant evolutionary relationships possible. Any sequence can be used to probe sequence databases to identify related sequences present in the same organism or in other organisms.

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6.3 Examination of Three-Dimensional Structure Enhances Our Understanding of Evolutionary Relationships

The evolutionary kinship between proteins may be even more strikingly evident in the conserved three-dimensional structures. The analysis of three-dimensional structure in combination with the analysis of especially conserved sequences has made it possible to determine evolutionary relationships that cannot be detected by other means. Sequence-comparison methods can also be used to detect imperfectly repeated sequences within a protein, indicative of linked similar domains.

6.4 Evolutionary Trees Can Be Constructed on the Basis of Sequence Information

Evolutionary trees can be constructed with the assumption that the number of sequence differences corresponds to the time since the two sequences diverged. Construction of an evolutionary tree based on sequence comparisons revealed approximate times for the gene-duplication events separating myoglobin and hemoglobin as well as the α and β subunits of hemoglobin. Evolutionary trees based on sequences can be compared with those based on fossil records. Horizontal gene transfer events can manifest as unexpected branches on the evolutionary tree.

6.5 Modern Techniques Make the Experimental Exploration of Evolution Possible

The exploration of evolution can also be a laboratory science. In favorable cases, PCR amplification of well-preserved samples allows the determination of nucleotide sequences from extinct organisms. Sequences so determined can help authenticate parts of an evolutionary tree constructed by other means. Molecular evolutionary experiments performed in the test tube can examine how molecules such as ligand-binding RNA molecules might have been generated.