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The Platypus Is Not a Rodent: DNA Hybridization, Amniote Phylogeny and the Palimpsest Theory

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The Platypus Is Not a Rodent: DNA Hybridization, Amniote Phylogeny and the Palimpsest Theory The platypus is not a rodent: DNA hybridization, amniote phylogeny and the palimpsest theory John A. W. Kirsch1* and Gregory C. Mayer1,2 1The University of Wisconsin Zoological Museum, 250 North Mills Street, Madison,WI 53706, USA 2Department of Biological Sciences, University of Wisconsin-Parkside, Kenosha,WI 53141, USA We present DNA-hybridization data on 21 amniotes and two anurans showing that discrimination is obtained among most of these at the class and lower levels. Trees generated from these data largely agree with conventional views, for example in not associating birds and mammals. However, the sister relation- ships found here of the monotremes to marsupials, and of turtles to the alligator, are surprising results which are nonetheless consistent with the results of some other studies. The Marsupionta hypothesis of Gregory is reviewed, as are opinions about the placement of chelonians. Anatomical and reproductive data considered by Gregory do not unequivocally preclude a marsupial^monotreme special relationship, and there is other recent evidence for placing turtles within the Diapsida. We conclude that the evidential meaning of the molecular data is as shown in the trees, but that the topologies may be in£uenced by a base- compositional bias producing a seemingly slow evolutionary rate in monotremes, or by algorithmic artefacts (in the case of turtles as well). Keywords: Chelonia; Crocodilia; Eutheria; Marsupialia; Marsupionta; molecular evolution `Unyielding factualists have so set the style in taxonomy relationships continue to be debated, `everyone knows' and morphology that, if their assertions were accepted, that the latter result cannot be correct. hardly any known type of animal could possibly have The orthodox view of the phylogeny of mammals been derived even from any known past group.' regards monotremes (the living `Prototheria') as the Gregory (1947, p. 34) sister-group to marsupials + placentals (together, the extant `Theria'). Evidence that the therians are more closely related to each other than to monotremes includes 1. INTRODUCTION a wide range of anatomical and physiological features In connection with a DNA-hybridization investigation (Lillegraven 1975; Vaughn 1986; Carroll 1988; Starck into the phylogeny of several avian orders, which success- 1995; Rougier et al. 1996). A minority opinion, that fully used the alligator as an out-group (Bleiweiss et al. monotremes and certain marsupials might be each 1995), we conducted some additional hybridization other's nearest relatives, was promoted by Gregory experiments using lizards and mammals in which we (1934, 1947, 1951). Gregory's inference of a monotreme^ found that all four of these amniote groups could be marsupial taxon resulted from application of his `palimp- discriminated. Encouraged by these results, we decided sest' theory of phylogenetic inference (see also Camp to explore the ability of the hybridization technique to 1923; Broom 1924; Colbert & Mook 1951). Noting resem- distinguish the deeper branches of tetrapod phylogeny, blances between living monotremes and the Australasian and perhaps the limits of the technique, by carrying out diprotodontian marsupials, Gregory proposed that mono- a series of further hybridizations among representatives tremes were derived relatively recently from the latter, of the amniote classes and two out-group anurans. As invoking truncation of development as one possible expla- shown herein, we found that discrimination was main- nation for the monotreme habit of egg-laying and some tained over the entire group, with recovered relationships other features. His hypothesis was later endorsed (in a that were, in general, at least plausible. Thus, frogs were more general form, with monotremes sister to all clearly separated from the amniotes, predicted terminal marsupials) by Ku« hne (1973, 1977) on the basis of sister-pairs were supported at high bootstrap percentages, supposedly similar tooth-replacement patterns in marsu- and there was no evidence of a bird^mammal clade. At pials and monotremes. Monotreme fossils discovered the same time, we observed two notable departures from since Gregory's papers were written (Archer et al. 1985, expectation: that turtles were placed among diapsids, 1993; Pascual et al. 1992; Flannery et al. 1995) are up to close to the alligator exclusive of birds; and that the repre- twice the inferred age of diprotodontians (Kirsch et al. sentative monotreme was sister to the marsupial instead of 1997; Springer et al. 1997), and thus falsify the speci¢c to a combined marsupial^placental group. While turtle point of divergence argued by Gregory, but not a mono- treme^marsupial sister-group relationship. It is such a more general a¤nity that is supported by our own *Author for correspondence ([email protected]). results. Phil. Trans. R. Soc. Lond. B (1998) 353, 1221^1237 1221 & 1998 The Royal Society 1222 J. A.W. Kirsch and G. C. Mayer DNA hybridization and amniote phylogeny Along with the monotreme^marsupial clade indicated A phylogenetic tree was generated from the data of table by our data, our most surprising ¢nding is the placement 1 (after symmetrization by the method of Sarich & Cronin of the turtles within the Diapsida as sister-group to the (1976) and subsequent re£ection of the distances to Python alligator. Turtles have generally been thought to be regius) by the FITCH program for generating additive among the earliest branches of the amniote tree (e.g. trees in Felsenstein's (1993) PHYLIP package, version Ga¡ney 1980), but whereas a proposed association of 3.5c, varying the input order 100 times and using the turtles with diapsids as a whole is not entirely without subreplicate and global branch-swapping options. The precedent in the literature (Goodrich 1916), the suggestion Cavalli-Sforza & Edwards (1967) least-squares option of special relationship to crocodilians has, to our know- (p0) was also used, as the correlation of standard devia- ledge, only rarely been mooted (Bishop & Friday 1987; tions with distance (r0.15) was not signi¢cant. Goodman et al. 1987; Hedges et al. 1990). Because of these The tree was validated both by bootstrapping on the two unlikely relationships (turtles with crocodilians and replicate measurements (Krajewski & Dickerman 1990) monotremes with marsupials), we hesitated to present our and by jackkni¢ng on taxa (Lapointe et al. 1994). For the results, yet for two general reasons we believe it is worth bootstrap, each pseudoreplicate matrix was separately considering them now. symmetrized and missing reciprocals then re£ected. We First, there is additional recent evidence that calls the employed the jackknife for weighted trees of Lapointe et orthodox views into question, or is at least consistent with al. (1994), performing all possible single and multiple our results. New anatomical analyses (Rieppel & deBraga deletions of taxa (7813) and expressing the result as a 1996) question the received views of turtle relationships, least-squares tree calculated from the average pathlengths and place chelonians amongst the Diapsida. In addition, observed over all jackknife pseudoreplicates, while also Janke et al. (1996, 1997) present trees based on complete noting discrepancies in the `range consensus' (the strict coding sequences of the mitochondria indicating that consensus of trees based on the minimum and maximum marsupials and the platypus (a monotreme) are more pathlengths recovered). closely related to each other than the former are to placen- To test whether the results from the 12Â13 matrix might tals, a result the authors interpret as evidence for a be due to sparse taxonomic sampling among mammals, monotreme^marsupial clade (similar to the Marsupionta we `sutured' the completed data of table 1 with information of Gregory (1947) in content but not structure). on nine additional mammals from the 21-taxon set of The second reason relates to possible algorithmic, comparisons reported in Kirsch et al. (1997). Three labels sampling or biochemical biases, which require serious (of Chaetophractus villosus, Didelphis virginiana, and Tachy- consideration in the larger context of the interpretation of glossus aculeatus) were held in common between these any molecular systematic results. One of these biases is the added experiments and the 12Â13 matrix, and we esti- familiar long-branch attraction problem (Felsenstein 1978), mated the missing cells (37%) in the sutured 22-taxon a di¤culty exacerbated by the rather few exemplars of matrix by the additive-reconstruction method of Landry major taxa that have been compared for relationship in et al. (1996). The resulting ¢lled matrix was then used to many studies (e.g. D'Erchia et al. 1996): species-poor trees generate a FITCH tree, which was validated by the jack- may have strong support for nonetheless untrue relation- knife. Because in this instance it was computationally ships, and use of di¡erent exemplars of the same taxa impractical to carry out all possible deletions (ca. 4.2 may produce inconsistent topologies (Philippe & million), we employed the alternative strategies of Douzery 1994). Another type of bias, only recently appre- performing 1000 random deletions sampled proportion- ciated, may result from base-compositional e¡ects (e.g. ately, and of successive deletions of all single, all double, Loomis & Smith 1992; Pettigrew 1994). etc., deletions until the average-consensus topology stabil- Thus, inthis paper wetake a fresh lookatthe evidence and ized (see Lapointe et al. (1994) for rationalization
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