The threespine Stickleback, Gasterosteus aculeatus, is emerging as a model system for studying the molecular basis of morphological variation in vertebrates (Kingsley and Peichel, 2007; Kitano et al., 2008). Many populations of G. aculeatus have colonized freshwater habitats from marine ancestors and rapidly adapted to distinct habitats and resources. This pattern of parallel speciation has attracted the attention of evolutionary biologists as an outstanding system for investigating patterns and mechanisms of adaptive radiation and ecological speciation (Schluter, 2000; Schluter and McPhail, 1992).

A resolved phylogenetic hypothesis for the seven recognized stickleback (Gasterosteidae) species is critical for identifying appropriate contrasts to investigate patterns of adaptive divergence observed in G. aculeatus, and to place diversification of the entire clade in a comparative context. However, phylogenetic relationships appear unresolved in spite of a number of attempts based on morphology (Bowne, 1994; Keivany and Nelson, 2004), behavior (McLennan, 1991, 1993), mtDNA gene sequences (Mattern, 2004), and various combinations of these data types (Mattern and McLennan, 2004; McLennan and Mattern, 2001). To examine the phylogenetic relationships of Gasterosteidae, we performed phylogenetic analyses using DNA sequence datasets that include whole mitochondrial genomes (14,807 bp) and 11 single-copy nuclear genes (8703 bp).