Phylogenetic relationships within the genus Cinclodes, a group of South American furnariids, were studied using complete sequences of the mitochondrial genes COII and ND3. The 13 species of Cinclodes formed a monophyletic group consisting of three major lineages: (1) the southeastern Brazilian isolate C. pabsti, which was sister to the rest of the genus; (2) a clade of five primarily Patagonian or central Argentine highlands species; and (3) a clade of seven primarily north-central Andean or Pacific species. Biogeographic structure in the Patagonian-Andean taxa was consistent with the deep Patagonian and north-central Andean division previously noted in the similarly distributed genus Muscisaxicola. Evolutionary relationships among Cinclodes species were partially consistent with expectations based on plumage, behavior, and ecology. The phenotypically distinctive C. antarcticus was found to be sister to the widespread C. fuscus in the primarily Patagonian-Argentine clade, and the distinctive C. palliatus to be sister to C. atacamensis in the high Andean-Pacific clade. The central Argentine isolates C. comechingonus and C. olrogi formed a clade with C. oustaleti (olrogi sister to oustaleti, and comechingonus sister to those two) within the Patagonian-Argentine clade. The Pacific marine specialists C. nigrofumosus and C. taczanowskii were sisters within the Andean-Pacific clade and were distantly related to the southern maritime species C. antarcticus. Thus, marine ecological specialization apparently evolved twice within Cinclodes; behavioral and ecological data also support the nonhomology of the two character states. The two exclusively Pacific species were positionally apomorphic within the Andean-Pacific clade; ancestral area analysis indicated that the high Andes were the most likely area of origin for this clade, and that the Pacific coast was occupied secondarily.
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