Hi Murtaza,

Conserved regions are composed of several nucleotide sites that have remained identical between two sequences (for example, from different populations). These are particularly important for detecting homologous sites. Ultra-conserved regions has also been used as point for comparison across divergent taxa, so analyses can focus on the variable regions that flanks them (Faircloth et al. 2012). In fact, variable regions within the genome are usually used to study the processes involved in lineages differentiation. A good example are the 'genomic islands of speciation' (e.g. Marques et al. 2016).

There are different software that can show you the conserved/variable sites. I personally like MEGA (https://www.megasoftware.net/), which also highlights their positions together with its proportion within the sequences.

Faircloth BC. et al. 2012. Ultraconserved elements anchor thousands of genetic markers spanning multiple evolutionary timescales. Syst Biol 61:717-726

Marques DA. et al. 2016. Genomics of rapid incipient speciation in sympatric threespine stickleback. PLoS Genet 12.2: e1005887.

Hello Carlos!

Thanks for your feedback and instructions. I will search out the mentioned references.

Hi Murtaza,

Carlos Spano gave a very useful explanation.

I just wanted to add that both highly variable and conserved regions can be extremely useful in phylogenetic studies. In fact, while highly variable regions can be used to determine variation between species (or even between population within the same species), more conserved gene regions can be informative at a higher systematic level.

For example, in order to understand the relationships between different families or superfamilies you might prefer to use slowly evolving genes (more conserved). In recent times, in fact, in order to better understand the evolutionary history that originated a species (or a group of species) it's becoming more and more common to use a wide set of genes, possibly including (at least in animals) both mitochondrial genes (such as COI or NADH, generally highly variable) and nuclear genes (such as EF-1alpha, generally more conserved).

In addition to the software suggested by Carlos, also Geneious can help you highlighting conserved/variable regions. It's not a free software but it offers a free trial period! (https://www.geneious.com/academic/)

Hope this helps,

Francesco