The phylogenetic relationships of a number of flightless and volant rails have been investigated using mtDNA sequence data. The third domain of the small ribosomal subunit (12S) has been sequenced for 22 taxa, and part of the 5′ end of the cytochrome–b gene has been sequenced for 12 taxa. Additional sequences were obtained from outgroup taxa, two species of jacana, sarus crane, spur–winged plover and kagu. Extinct rails were investigated using DNA extracted from subfossil bones, and in cases where fresh material could not be obtained from other extant taxa, feathers and museum skins were used as sources of DNA.
Phylogenetic trees produced from these data have topologies that are, in general, consistent with data from DNA–DNA hybridization studies and recent interpretations based on morphology. Gallinula chloropus (moorhen) groups basally with Fulica (coots), Amaurornis (= Megacrex) ineptus falls within the Gallirallus/Rallus group, and Gallinula (= Porphyrula) martinica is basal to Porphyrio (swamphens) and should probably be placed in that genus. Subspecies of Porphyrio porphyrio are paraphyletic with respect to Porphyrio mantelli (takahe). The Northern Hemisphere Rallus aquaticus is basal to the south–western Pacific Rallus (or Gallirallus) group. The flightless Rallus philippensis dieffenbachii is close to Rallus modestus and distinct from the volant Rallus philippensis, and is evidently a seperate species. Porzana (crakes) appears to be more closely associated with Porphyrio than Rallus. Deep relationships among the rails remain poorly resolved. Rhynochetos jubatus (kagu) is closer to the cranes than the rails in this analysis.
Genetic distances between flightless rails and their volant counterparts varied considerably with observed 12S sequence distances, ranging from 0.3 % (Porphyrio porphyrio melanotus and P. mantelli mantelli) to 7.6 % (Rallus modestus and Rallus philippensis). This may be taken as an indication of the rapidity with which flightlessness can evolve, and of the persistence of flightless taxa. Genetic data supported the notion that flightless taxa were independently derived, sometimes from similar colonizing ancestors. The morphology of flightless rails is apparently frequently dominated by evolutionary parallelism although similarity of external appearance is not an indication of the extent of genetic divergence. In some cases, taxa that are genetically close are morphologically distinct from one another (e.g. Rallus (philippensis) dieffenbachii and R. modestus), whilst some morphologically similar taxa are evidently independently derived (e.g. Porphyio mantelli hochstetteri and P. m. mantelli).