H. Ragg, T. Lokot, P.-B. Kamp, W. R. Atchley, and A. Dress:

Vertebrate serpins: construction of a conflict-free phylogeny by combining exon-intron and diagnostic site analyses.

Mol. Biol. Evol., 18:577--584, 2001.
A combination of three independent biological features, genomic organization, diagnostic amino acid sites, and rare indels, was used to elucidate the phylogeny of the vertebrate serpin (serine protease inhibitor) superfamily. A strong correlation between serpin gene families displaying (1) a conserved exon-intron pattern and (2) family-specific combinations of amino acid residues at specific sites suggests that present-day vertebrates encompass six serpin gene families which evolved from primordial genes by massive intron insertion before or during early vertebrate radiation. Introns placed at homologous positions in the gene sequences in combination with diagnostic sequence characters may also constitute a reliable kinship indicator for other protein superfamilies.