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Philosophical Transactions of the Royal Society B: Biological Sciences logoLink to Philosophical Transactions of the Royal Society B: Biological Sciences
. 1997 Apr 29;352(1352):429–446. doi: 10.1098/rstb.1997.0031

Flightlessness and phylogeny amongst endemic rails (Aves:Rallidae) of the New Zealand region.

S A Trewick 1
PMCID: PMC1691940  PMID: 9163823

Abstract

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 separate species. Porzana (crakes) appears to be more closely associated with Porphyrio than Rallus. Deep relationships among the rails remain poorly resolved. Rhynochetus 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).

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Selected References

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  1. Bandelt H. J., Dress A. W. Split decomposition: a new and useful approach to phylogenetic analysis of distance data. Mol Phylogenet Evol. 1992 Sep;1(3):242–252. doi: 10.1016/1055-7903(92)90021-8. [DOI] [PubMed] [Google Scholar]
  2. Cabot E. L., Beckenbach A. T. Simultaneous editing of multiple nucleic acid and protein sequences with ESEE. Comput Appl Biosci. 1989 Jul;5(3):233–234. doi: 10.1093/bioinformatics/5.3.233. [DOI] [PubMed] [Google Scholar]
  3. Cooper A., Mourer-Chauviré C., Chambers G. K., von Haeseler A., Wilson A. C., Päbo S. Independent origins of New Zealand moas and kiwis. Proc Natl Acad Sci U S A. 1992 Sep 15;89(18):8741–8744. doi: 10.1073/pnas.89.18.8741. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Cooper A., Rhymer J., James H. F., Olson S. L., McIntosh C. E., Sorenson M. D., Fleischer R. C. Ancient DNA and island endemics. Nature. 1996 Jun 6;381(6582):484–484. doi: 10.1038/381484a0. [DOI] [PubMed] [Google Scholar]
  5. Desjardins P., Morais R. Sequence and gene organization of the chicken mitochondrial genome. A novel gene order in higher vertebrates. J Mol Biol. 1990 Apr 20;212(4):599–634. doi: 10.1016/0022-2836(90)90225-B. [DOI] [PubMed] [Google Scholar]
  6. Edwards S. V., Arctander P., Wilson A. C. Mitochondrial resolution of a deep branch in the genealogical tree for perching birds. Proc Biol Sci. 1991 Feb 22;243(1307):99–107. doi: 10.1098/rspb.1991.0017. [DOI] [PubMed] [Google Scholar]
  7. Gyllensten U. B., Erlich H. A. Generation of single-stranded DNA by the polymerase chain reaction and its application to direct sequencing of the HLA-DQA locus. Proc Natl Acad Sci U S A. 1988 Oct;85(20):7652–7656. doi: 10.1073/pnas.85.20.7652. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Hagelberg E., Clegg J. B. Isolation and characterization of DNA from archaeological bone. Proc Biol Sci. 1991 Apr 22;244(1309):45–50. doi: 10.1098/rspb.1991.0049. [DOI] [PubMed] [Google Scholar]
  9. Hagelberg E., Sykes B., Hedges R. Ancient bone DNA amplified. Nature. 1989 Nov 30;342(6249):485–485. doi: 10.1038/342485a0. [DOI] [PubMed] [Google Scholar]
  10. Hardy C., Callou C., Vigne J. D., Casane D., Dennebouy N., Mounolou J. C., Monnerot M. Rabbit mitochondrial DNA diversity from prehistoric to modern times. J Mol Evol. 1995 Mar;40(3):227–237. doi: 10.1007/BF00163228. [DOI] [PubMed] [Google Scholar]
  11. Hickson R. E., Simon C., Cooper A., Spicer G. S., Sullivan J., Penny D. Conserved sequence motifs, alignment, and secondary structure for the third domain of animal 12S rRNA. Mol Biol Evol. 1996 Jan;13(1):150–169. doi: 10.1093/oxfordjournals.molbev.a025552. [DOI] [PubMed] [Google Scholar]
  12. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol. 1980 Dec;16(2):111–120. doi: 10.1007/BF01731581. [DOI] [PubMed] [Google Scholar]
  13. Kimura M. Estimation of evolutionary distances between homologous nucleotide sequences. Proc Natl Acad Sci U S A. 1981 Jan;78(1):454–458. doi: 10.1073/pnas.78.1.454. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Kocher T. D., Thomas W. K., Meyer A., Edwards S. V., Päbo S., Villablanca F. X., Wilson A. C. Dynamics of mitochondrial DNA evolution in animals: amplification and sequencing with conserved primers. Proc Natl Acad Sci U S A. 1989 Aug;86(16):6196–6200. doi: 10.1073/pnas.86.16.6196. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Lento G. M., Hickson R. E., Chambers G. K., Penny D. Use of spectral analysis to test hypotheses on the origin of pinnipeds. Mol Biol Evol. 1995 Jan;12(1):28–52. doi: 10.1093/oxfordjournals.molbev.a040189. [DOI] [PubMed] [Google Scholar]
  16. McLenachan P. A., Lockhart P. J., Faber H. R., Mansfield B. C. Evolutionary analysis of the multigene pregnancy-specific beta 1-glycoprotein family: separation of historical and nonhistorical signals. J Mol Evol. 1996 Feb;42(2):273–280. doi: 10.1007/BF02198854. [DOI] [PubMed] [Google Scholar]
  17. Neefs J. M., Van de Peer Y., Hendriks L., De Wachter R. Compilation of small ribosomal subunit RNA sequences. Nucleic Acids Res. 1990 Apr 25;18 (Suppl):2237–2317. doi: 10.1093/nar/18.suppl.2237. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Parr R. L., Carlyle S. W., O'Rourke D. H. Ancient DNA analysis of Fremont Amerindians of the Great Salt Lake Wetlands. Am J Phys Anthropol. 1996 Apr;99(4):507–518. doi: 10.1002/(SICI)1096-8644(199604)99:4<507::AID-AJPA1>3.0.CO;2-R. [DOI] [PubMed] [Google Scholar]
  19. Russo C. A., Takezaki N., Nei M. Efficiencies of different genes and different tree-building methods in recovering a known vertebrate phylogeny. Mol Biol Evol. 1996 Mar;13(3):525–536. doi: 10.1093/oxfordjournals.molbev.a025613. [DOI] [PubMed] [Google Scholar]
  20. Saiki R. K., Gelfand D. H., Stoffel S., Scharf S. J., Higuchi R., Horn G. T., Mullis K. B., Erlich H. A. Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science. 1988 Jan 29;239(4839):487–491. doi: 10.1126/science.2448875. [DOI] [PubMed] [Google Scholar]
  21. Sanger F., Nicklen S., Coulson A. R. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A. 1977 Dec;74(12):5463–5467. doi: 10.1073/pnas.74.12.5463. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Simon C., Nigro L., Sullivan J., Holsinger K., Martin A., Grapputo A., Franke A., McIntosh C. Large differences in substitutional pattern and evolutionary rate of 12S ribosomal RNA genes. Mol Biol Evol. 1996 Sep;13(7):923–932. doi: 10.1093/oxfordjournals.molbev.a025660. [DOI] [PubMed] [Google Scholar]
  23. Steadman D. W., Olson S. L. Bird remains from an archaeological site on Henderson Island, South Pacific: Man-caused extinctions on an "uninhabited" island. Proc Natl Acad Sci U S A. 1985 Sep;82(18):6191–6195. doi: 10.1073/pnas.82.18.6191. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Steadman D. W. Prehistoric extinctions of pacific island birds: biodiversity meets zooarchaeology. Science. 1995 Feb 24;267(5201):1123–1131. doi: 10.1126/science.267.5201.1123. [DOI] [PubMed] [Google Scholar]
  25. Taylor P. G. Reproducibility of ancient DNA sequences from extinct Pleistocene fauna. Mol Biol Evol. 1996 Jan;13(1):283–285. doi: 10.1093/oxfordjournals.molbev.a025566. [DOI] [PubMed] [Google Scholar]
  26. Thomas R. H., Schaffner W., Wilson A. C., Päbo S. DNA phylogeny of the extinct marsupial wolf. Nature. 1989 Aug 10;340(6233):465–467. doi: 10.1038/340465a0. [DOI] [PubMed] [Google Scholar]
  27. Trewick S. A., Dearden P. A rapid protocol for DNA extraction and primer annealing for PCR sequencing. Biotechniques. 1994 Nov;17(5):842–844. [PubMed] [Google Scholar]
  28. Walsh P. S., Metzger D. A., Higuchi R. Chelex 100 as a medium for simple extraction of DNA for PCR-based typing from forensic material. Biotechniques. 1991 Apr;10(4):506–513. [PubMed] [Google Scholar]

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