Topics: Total-Evidence Dating under the Fossilized Birth–Death.
As their name implies, ultraconserved elements (UCEs) are highly conserved regions of organismal genomes shared among evolutionary distant taxa - for instance, birds share many UCEs with humans. UCEs were first described in a wonderful manuscript by Gil Bejerano et al. (2004) from David Haussler’s group and subsequently identified in several classes of organisms outside the group of original taxa ( Siepel et al. 2005 ) used to identify these genomic elements. The 27-way vertebrate genome alignment ( Miller et al. 2007 ) identified additional regions of high conservation.
We have discovered (see Citations ) that we can collect data from UCEs and the DNA adjacent to UCE locations (flanking DNA), and that these data are useful for reconstructing the evolutionary history and population-level relationships of many organisms. Because UCEs are conserved across disparate taxa, UCEs are also universal genetic markers in the sense that the locations (or loci) that we can target in humans are identical, in many cases, to the loci that we can target in ducks or snakes or lizards.
That's an extremely good question, and one to which we do not entirely know the answer ( Dermitzakis et al. 2005 ). UCEs have been associated with gene regulation ( Pennachio et al. 2006 ) and development ( Sandelin et al. 2004 , Woolfe et al. 2004 ) and we generally assume that UCEs must be important by the very nature of their near-universal conservation across extremely divergent taxa. However, gene knockouts of UCE loci in mice resulted in viable, fertile offspring ( Ahituv et al. 2007 ), suggesting that their role in the biology of the genome may be cryptic.