The work I started in 2005 has just been published online.
Genome-wide Detection of Gene Extinction in Early Mammalian Evolution.
Kuraku S & Kuratani S.
Genome Biol Evol. 2011 Nov 17.
My team has been dealing with several examples of lineage-specific gene loss within vertebrates, including Hox14, Bmp16 and Pax4 . These are based on small-scale focus on selected examples of gene loss. The genome-wide assessment is the focus of the article just published. There I stick to gene loss in the early mammalian lineage. In addition to some gene loss already implicated by previous gene-level studies, I have identified many gene losses that require functional dissection.
There are still many questions to be addressed employing molecular phylogenetics.