Colonization across the Galápagos Islands by the carpenter bee (Xylocopa darwini) was reconstructed based on distribution of mitochondrial haplotypes (cytochrome oxidase II (COII) sequences) and haplotype lineages. A total of 12 haplotypes were found in 118 individuals of X. darwini. Distributional, phylogenetic and phylogeographic analyses suggest early colonization of most islands followed by historical isolation in two main groups: eastern and central-western islands. Evidence of recurrent inter-island colonization of haplotypes is largely lacking, despite strong flight capability and ecological amplitude of the species. Recent palaeogeographic data suggest that several of the current islands were connected in the past and thus the isolation pattern may have been even more pronounced. A contrast analysis was also carried out on 10 animal groups of the Galápagos Islands, and on haplotype colonization of seven animal and plant species from several oceanic archipelagos (the Galápagos, Azores, Canary Islands). New colonization metrics on the number of potential vs. inferred colonization events revealed that the Galápagos carpenter bee shows one of the most significant examples of geographic isolation.

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