Nothing in Biology Makes Sense: Making sense of gene tree conflict across an entire genome

The only illustration in The Origin of Species. Image via Wikimedia Commons.

This week at Nothing in Biology Makes Sense, I discuss my latest research paper, which has just been published online ahead of print in Systematic Biology. In it, my coauthors and I use a genome-wide data set to reconstruct relationships among a couple dozen species in the genus Medicago—a data set that proved to be kind of a challenge.

Using that data, we identified some 87,000 individual DNA bases that varied among the sampled species—single-nucleotide polymorphisms, or SNPs. That’s not a lot in terms of actual sequence data—but considering that every one of those 87,000 SNPs is a variable character, and that most of them were probably spread far enough across the genome to have independent evolutionary histories, it contains many more independent “gene trees” than most DNA data sets used to estimate phylogenies.

To learn how we tackled all those gene trees, and what we found when we did, go read the whole thing.◼