The physical basis of molecular variation

With the exception of RNA viruses, the hereditary information in all organisms is carried in DNA. Ultimately, differences in any of the molecular markers we study (and of genetically-based morphological, behavioral, or physiological traits) is associated with some difference in the physical structure of DNA, and molecular evolutionists study a variety of its aspects.

Nucleotide sequence

A difference in nucleotide sequence is the most obvious way in which two homologous stretches of DNA may differ. The differences may be in translated portions of protein genes (exons), portions of protein genes that are transcribed but not translated (introns, 5' or 3' untranslated regions), non-transcribed functional regions (promoters), or regions without apparent function.

Sequence organization

Particular genes may differ between organisms because of differences in the position and number of introns. At the whole genome level, there may be differences in the amount and kind of repetitive sequences, in the amount and type of sequences derived from transposable elements, in the relative proportion of G-C relative to A-T, or even in the identity and arrangement of genes that are present.

Imprinting

At certain loci in some organisms the expression pattern of a particular allele depends on whether that allele was inherited from the individual's father or its mother.

Expression

Funcctional differences among individuals may arise because of differences in the patterns of gene expression, even if there are no differences in the primary sequences of the genes that are expressed.

Protein sequence

Because of redundancy in the genetic code, a difference in nucleotide sequence at a protein-coding locus may or may not result in proteins with a different amino acid sequence.

Secondary, tertiary, and quaternary structure

Differences in amino acid sequence may or may not lead to a different distribution of $\alpha$-helices and $\beta$-sheets, to a different three-dimensional structure, or to different multisubunit combinations.

It is worth remembering that in most eukaryotes there are two different genomes whose characteristics may be analyzed: the nuclear genome and the mitochondrial genome. In plants there is a third: the chloroplast genome. The mitochondrial and chloroplast genomes are typically inherited only through the maternal line, although some instances of biparental inheritance are known.