Species to genera: phylogenetic inference in the Hawaiian Drosophilidae

Systematic studies at any taxonomic level require careful planning, even before genes are sequenced or morphological characters scored. Molecular systematists working at the level between species and genera must select gene regions which are suitable for the divergence within the group being examined and decide how many and which ingroup and outgroup taxa to sample in the analysis. This chapter will use studies of the Hawaiian Drosophilidae to illustrate strategies useful in (1) selecting nucleotide sequences for divergences between the levels of species and genera, (2) designing ingroup and outgroup taxon sampling schemes, and (3) performing phylogenetic analysis on data sets with large numbers of taxa and characters.