Thursday, July 17, 2014

As the crow forks

We had our work on crows (The genomic landscape underlying phenotypic integrity in the face of gene flow in crows) published in the journal Science. Very interesting interpretations of the work ranging from it being proof for evolution to reasoning for human assortative mating in a political context have been presented. It has also been covered by the Swedish Radio, Der Spiegel (a popular German weekly) and few other offline sources.

A well written description of the science that puts the work in a broader context is also available.[It should also be noted that a description of another paper about the human polymorphic inversion 17q21 from the same author was a useful resource while looking at the ancestral state of our fixed differences.]

The whole genome was scanned for differences in DNA sequence content between carrion and hooded crows using 60 crows. While most of the genome is the same, small regions of the genome do show differences in DNA sequence and gene expression. These differences in DNA sequence are localized to specific regions of the genome. Infact all 81 of 82 fixed differences that we find are within a 2 megabase region. 

Snapshots of a region of the genome with fixed differences seen between hooded and carrion crow sequencing reads provides a very visual idea of how these fixed differences "look". Each of the boxes in the figure is a sequencing read (from the bam file) mapped to the reference genome. Positions which differ from the reference genome have the actual base that differs from the reference in each read.

Below figure shows the sequencing reads from one crow from Poland. Note that all the positions are similar to the reference genome. All 30 hooded crow individuals (from Sweden and Poland) look exactly like this at this base.

The next figure shows the sequencing reads from one crow from Germany at the same position as the hooded crow above. However, the blue box has "C" written in all its reads. At this position the Carrion crow has a base that is different from the Hooded crow reference genome. All the 30 carrion crows (from Spain and Germany) have this "C" base at this position.

Similar to the above position, we identify 81 other sites that show such a "fixed difference". The rest of the genome seems to be extremely similar between the carrion and hooded crows.