Compare and contrast how speciation is determined at the population, genetic and epigenetic levels?

Speciation can be discussed in two categories, allopatric and sympatric.

Allopatric speciation means that speciation occured in different regions. The key with allopatric speciation is geographical separation. For example, say you have a squirrel population in a mountain, and over years a canyon forms a physical barrier between the two sides so that what was once one species of squirrel is split up into two different populations on different sides Over time, each population will adapt to its region and eventually speciate.

The isolated populations then undergo genotypic and/or phenotypic divergence as:

(a) they become subjected to dissimilar selective pressures;
(b) they independently undergo genetic drift;
(c) different mutations arise in the two populations.

When the populations come back into contact, they have evolved such that they are reproductively isolated and are no longer capable of exchanging genes.

Sympatric speciation means that one population of one species became two species while in the same geographic region with no physical separation. This usually occurs because different inviduals of the same species begin to occupy a distinct niche and eventually become specifically adapted for that role. Look up African tilapia which is a good example if you want to know more.

At the genetic level, you could use mitochondrial DNA (mtDNA) to determine any difference between closely related species. You could also use the species DNA using various genetic markers to distinguish any similarities and differences.

At the epigenetic level, you could test the DNA for methyl groups or extra methyl groups present on certain bases of the DNA of imprinted genes. These methyl groups are enzymatically added and removed, through the action of special methylases and demethylases. The level of methylation generally correlates with the transcriptional state of a gene: active genes are less methylated than inactive genes. Altered levels of DNA methylation could cause epigenetic changes in gene activity, leading to speciation.