Fig. 1. Maximum likelihood phylogram of some species of caprimulgiform and apodiform birds plus outgroups. RAG-1 branch lengths are drawn to scale. Dashed lines indicate taxa or clades of taxa with high GC3 content. Circles on branches indicate inferred phylogenetic position of deletion events; numbers in circles indicate number of base pairs deleted.

Fig. 2. Majority rule consensus tree for some caprimulgiform and apodiform species of birds plus four outgroups, based on likelihood bootstrap of RAG-1 sequences. Bootstrap proportions are shown for those nodes occurring in greater than 50% of replicates for maximum likelihood (above branch) and logdet (below branch) analyses. Solid brackets and bold names indicate taxa traditionally classified in the order Apodiformes or five families in the order Caprimulgiformes. Background shading indicates biogeographic occurrence of three major groups within the family Caprimulgidae, with an estimate of the number of species-level taxa in two of the groups (Cleere, 1999). Generic name abbreviated for eight species in the nominate genus Caprimulgus.

Fig. 3. Distributions of individual heterozygosity for the RAG-1 exon for some species in four higher taxa of birds.

Fig. 4. Distribution of GC content at the RAG-1 exon for some caprimulgiform, apodiform, and outgroup species of birds. Distribution envelopes also shown for some species in the order Charadriiformes and the family Falconidae.

Fig. 5. Scatter of observed heterozygosity versus GC3 content for the RAG-1 exon for 25 species of caprimulgiform birds. Open circles indicate clade of Old World species of Caprimulgidae in Fig. 2. Least-squares linear regression line is indicated.

Fig. 6. Comparative topologies of RAG-1 character-based phylogeny (this report) and DNA-DNA hybridization distance-based phenogram (Sibley and Ahlquist, 1990) for nine taxa in the Caprimulgidae shared between studies. Arrows indicate positions switched between results. Solid nodes are concordant; open nodes conflict. The most basal node is uninformative: it only demonstrates monophyly of the family.

Taxonomy, specimen information, and GenBank accessions

Potential causes of elevated heterozygosity in exon sequences