How scientists study Evolution?

DNA Molecule
A [[KW]] DNA [[/KW]] molecule consists of a ladder, formed of sugars and phosphates, and four nucleotide bases: adenine (A), thymine (T), cytosine (C), and guanine (G). The genetic code is specified by the order of the nucleotide bases, and each gene possesses a unique sequence of base pairs. Scientists use these base sequences to locate the position of genes on chromosomes and to construct a [[KW]] map [[/KW]] of an organism’s genome.

With advances in molecular biology in the last few decades, researchers seek evolutionary clues at the smallest level: within the molecules of living organisms. Despite the enormous variety of form and function seen in living things, the underlying genetic code—the molecular building material of life—displays a striking uniformity. Almost all living organisms have DNA, and in each case it consists of different pairings of the same building blocks: four nucleotide bases called adenine, thymine, guanine, and cytosine. Using different combinations of these bases, DNA directs the assembly of amino acids into functional proteins. The same uniform code operates within all living things.
 
Genetic Mapping
This gel scan showing the arrangement of chromosomes within a [[KW]] cell [[/KW]] enables scientists to take a closer look at the genetic makeup of each individual. By comparing the genetic makeup of different species, researchers can determine how they are related.
Perkin Elmer/Applied Biosytems Division

These molecules contain more than the master plan for living organisms—each is a record of an organism’s evolutionary history. By examining the makeup of such molecules, scientists gain insights into how different species are related. For example, scientists compare the protein cytochrome c from different species. In closely related species, the proteins have amino-acid sequences that are very similar, perhaps varying by one or a few amino acids. More distantly related organisms generally have proteins with fewer similarities. The more distant the relationship, the less alike the proteins.
The idea that species become genetically more different as they diverge from a common ancestor laid the groundwork for the concept of the molecular clock. Scientists know that, statistically, neutral mutations tend to accumulate at a regular rate, like ticks of a clock. Therefore, the number of molecular differences in a shared molecule is proportional to the amount of time that has elapsed since the species shared a common ancestor. This calculation has provided new knowledge of the evolutionary relationship between modern apes and modern humans. The molecular [[KW]] clock [[/KW]] concept is controversial, however, and has caused much disagreement between evolutionary scientists who study molecules and those who study fossils. This disagreement arises particularly when the molecular clock time estimates do not agree with the estimates derived from studying the fossil record.