406 SYSTEMATIC ZOOLOGY VOL. 38

SCHUMACHER, C. F. 1817. Essai d'un nouveau sys-teme des habitations des vers testaces. Copenhagen.

SCOPOLI, G. A. (I. A.) 1777. Introductio ad historiamnaturalem, sistens genera lapidum, plantarum, etanimalium, hactenus detecta, caracteribus, essen-tialibus donata, in tribus divisa, subinde ad legesnaturae. W. Gerle, Prague.

SMITH, H. M., AND R. B. SMITH 1977. Synopsis of theherpetofauna of Mexico. Volume V. Guide to Mex-ican amphisbaenids and crocodilians. John John-son, North Bennington, Vermont.

SMITH, M. A. 1931. The fauna of British India, in-cluding Ceylon and Burma. Volume 1. Loricata,Testudines. Taylor and Francis Ltd., London.

STEJNEGER, L. 1907. Herpetology of Japan and adja-cent territory. Bull. U.S. Natl. Mus., 5B:l-577.

STEJNEGER, L., AND T. BARBOUR. 1917. A check list of

North American amphibians and reptiles. HarvardUniversity Press, Cambridge.

STEJNEGER, L., AND T. BARBOUR. 1923. Second edition.STEJNEGER, L., AND T. BARBOUR. 1933. Third edition.STEJNEGER, L., AND T. BARBOUR. 1939. Fourth edition.STEJNEGER, L., AND T. BARBOUR. 1943. Fifth edition.

Bull. Mus. Comp. Zool. 93:xix + 260 pp.STRICKLAND, H. E. 1842. Series of propositions for

rendering the nomenclature of zoology uniformand permanent. British Assn. Adv. Sci., London.

TAYLOR, E. H. 1968. The caecilians of the world.University of Kansas Press, Lawrence.

WERMUTH, H. 1953. Systematik der rezenten Kro-kodile. Mitt. Mus. Berlin, 29(2):275-514.

Received 24 April 89; accepted 16 June 89

Syst. Zool, 38(4):406-407, 1989

The Retention Index and Homoplasy Excess

JAMES S. FARMS

Department of Ecology and Evolution, State University of New York,Stony Brook, New York 11794;

Department of Entomology, American Museum of Natural History,Central Park West at 79th St., New York, New York 10024;

Department of Biology, City College, City University of New York

Hennig86, a microcomputer program forphylogenetic analysis released in 1988(discussed in detail by Platnick, 1989; Fitz-hugh, 1989) summarizes the fit of characterdata to phylogenetic trees by both the con-sistency index (of Kluge and Farris, 1969)and the retention index. The latter, whichis the complement of the distortion coef-ficient (of Farris, 1973), is defined as

r = (g - s)/(g - m).

Here s is the number of steps required bythe tree, g is the greatest number of stepsthat may be required of the data by anytree, and m is the number of steps in thedata (cf. Seberg, 1989; Farris, 1989). Theprogram includes facilities for evaluatingthese statistics for multistate as well as bi-nary characters, and for both additive andnonadditive character codings.

Archie (1989) objected to the consistencyindex, advocating instead what he termed

the "homoplasy excess ratio maximum."The method (the same as that of Farris,1973) that he described for evaluating thelatter is applicable only to binary data, butotherwise that measure (see his equation4, p. 260) is identical to the retention index.His novel terminology is somewhat mis-leading, since that index attains its maxi-mum value when there is no homoplasy.

Archie based his preference on the ob-servation, drawn from analyses of severaldata sets, that the consistency index tendedto decrease with increasing numbers of ter-minal taxa. In some of those analyses heemployed "generalized gap coding," amethod of his own (Archie, 1985) that hasrecently been criticized by Chappill (1989;see also Farris, 1990) as introducing statis-tically nonsignificant differences into cod-ed data. But the same trend had been notedby Sanderson (1989; cf. Sanderson andDonoghue, 1989), and in any case it is hard-

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ly a startling finding. The consistency in-dex is inversely proportional to the lengthof a tree. Other things being equal, addingterminals to a tree would be expected toproduce an increase in length.

Archie's conclusion from that trend ismore questionable, for there is nothing tobe gained by rejecting either index. It is asimple matter to compute both, as is doneby Hennig86. While both indices measureextent of homoplasy, their interpretationsdiffer somewhat, and each has its appli-cations. The consistency index assesses ho-moplasy as a fraction of the characterchange on a tree, and so the frequency withwhich states arise in parallel. Applied tosingle characters, it is particularly usefulin character weighting (cf. Carpenter, 1988;Sundberg, 1989). The retention index re-flects the degree to which similarities ap-parent in the data can be retained as ho-mologies on a tree. It has the usefulproperty of being insensitive to inclusionof autapomorphies in data. These pointsare discussed in more detail by Farris (1989).

REFERENCES

ARCHIE, J. W. 1989. Homoplasy excess ratios: Newindices for measuring levels of homoplasy in phy-logenetic systematics and a critique of the consis-tency index. Syst. ZooL, 38:253-269.

ARCHIE, J. W. 1985. Methods for coding variablemorphological features for numerical taxonomicanalysis. Syst. ZooL, 34:326-345.

CARPENTER, J. M. 1988. Choosing among equally par-simonious cladograms. Cladistics, 4:291-296.

CHAPPILL, J. A. 1989. Quantitative characters in phy-logenetic analysis. Cladistics, 5:217-234.

FARRIS, J. S. 1973. On comparing the shapes of taxo-nomic trees. Syst. Zool., 22:50-54.

FARRIS, J. S. 1989. The retention index and the re-scaled consistency index. Cladistics, 5:417-419.

FARRIS, J. S. 1990. Phenetics in camouflage. Cladistics(in press).

FITZHUGH, K. 1989. Cladistics in the fast lane. Jour.New York Ent. Soc, 97:234-241.

KLUGE, A. G., AND J. S. FARRIS. 1969. Quantitativephyletics and the evolution of anurans. Syst. ZooL,18:1-32.

PLATNICK, N. I. 1989. An empirical comparison ofmicrocomputer parsimony programs, II. Cladistics,5:145-162.

SANDERSON, M. J. 1989. Confidence limits on phy-logenies: The bootstrap revisited. Cladistics, 5:113-130.

SANDERSON, M. J., AND M. J. DONOGHUE. 1989. Pat-terns of variation in levels of homoplasy. Evolution(in press).

SEBERG, O. 1989. The seventh annual meeting of theWilli Hennig Society. Cladistics, 5:183-191.

SUNDBERG, P. 1989. Phylogeny and cladistic classi-fication of the paramonostiliferous Family Plecto-nemertidae (Phylum Nemertea). Cladistics, 5:87-100.

Received 11 November 1989; accepted 18 November 1989

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