Diversity and Phylogenetic Implications of CsCl Profiles from Rodent DNAs Christophe Douady,* , ² ,1 Nicolas Carels,* , ‡ Oliver Clay,* , ‡ Franc ¸oisCatzeflis,² and Giorgio Bernardi* , ‡ ,2 * Laboratoire de Ge ´ne ´tique Mole ´culaire, Institut Jacques Monod, Tour 43, 2 Place Jussieu, F-75005 Paris, France; ² E ´ quipe Phyloge ´nie Mole ´culaire, Laboratoire de Pale ´ontologie, Institut des Sciences de l’E ´ volution, UMR5554/UA 327, CNRS, Universite ´ de Montpellier II, Case 064, Place Euge `ne Bataillon, F-34095 Montpellier cedex, France; and ‡Stazione Zoologica Anton Dohrn, Villa Comunale, I-80121 Naples, Italy Received December 13, 1999; revised July 17, 2000 Buoyant density proﬁles of high-molecular-weight DNAs sedimented in CsCl gradients, i.e., composi- tional distributions of 50- to 100-kb genomic frag- ments, have revealed a clear difference between the murids so far studied and most other mammals, in- cluding other rodents. Sequence analyses have re- vealed other, related, compositional differences be- tween murids and nonmurids. In the present study, we obtained CsCl proﬁles of 17 rodent species represent- ing 13 families. The modal buoyant densities obtained for rodents span the full range of values observed in other eutherians. More remarkably, the skewness (asymmetry, mean  modal buoyant density) of the rodent proﬁles extends to values well below those of other eutherians. Scatterplots of these and related CsCl proﬁle parameters show groups of rodent fami- lies that agree largely with established rodent taxon- omy, in particular with the monophyly of the Geomy- oidea superfamily and the position of the Dipodidae family within the Myomorpha. In contrast, while con- ﬁrming and extending previously reported differences between the proﬁles of Myomorpha and those of other rodents, the CsCl data question a traditional hypoth- esis positing Gliridae within Myomorpha, as does the recently sequenced mitochondrial genome of dor- mouse. Analysis of CsCl proﬁles is presented here as a rapid, robust method for exploring rodent and other vertebrate systematics. © 2000 Academic Press Key Words: DNA; phylogeny; ultracentrifugation; ge- nomes; base composition; rodents; vertebrates; Euth- eria; evolution. INTRODUCTION The long, compositionally homogeneous regions of which mammalian genomes consist, the isochores (300 kb on average), belong to a small number of families. Within any isochore family, GC levels 3 of 50- to 100-kb regions, or fragments, vary little (2–3% GC); yet, together these isochore families span a wide GC range, from 30 to 60% (Macaya et al., 1976; Thiery et al., 1976; Cuny et al., 1981; Bernardi et al., 1985; reviewed in Bernardi, 1995, 2000). A buoyant density proﬁle of genomic fragments, ob- tained by analytical ultracentrifugation of total nu- clear DNA to sedimentation equilibrium in CsCl den- sity gradients, yields the distribution of the GC levels of the fragments, since buoyant density and GC of DNA are linearly related (Schildkraut et al., 1962). In the present work, with the knowledge of eukaryotic ge- nomes acquired using sequence-speciﬁc ligands over three decades, we reexamine the potential of screening CsCl proﬁles of total nuclear DNA, without further fractionation or satellite analysis, as a tool for deduc- ing and clarifying mammalian phylogenies. This ap- proach was extensively used in previous work (see Bernardi, 1995, 2000 for reviews). For comparisons between vertebrate species, the ma- jor Gaussian components provide a robust character- ization of a species’ genome. All studies so far indicate that there exists an invariant compositional pattern of a genome or species, independent of the presence or absence of satellite DNA and of molecular weight dif- ferences among DNA samples, that can be deﬁned in terms of the Gaussian components of the CsCl proﬁle’s main band, excluding satellite DNA. It is the set of relative amplitudes (amounts of DNA) and GC con- tents (or buoyant densities, ) of these major compo- 1 Present address: Medical Biology Centre, Biology & Biochemis- try, Queen’s University, 97 Lisburn Road, Belfast BT9 7BL, North- ern Ireland. 2 To whom correspondence should be addressed. E-mail: bernardi@alpha.szn.it. 3 Abbreviations used: GC, molar fraction of guanine and cytosine in DNA; , buoyant density;  0 , modal buoyant density; , mean buoyant density. Molecular Phylogenetics and Evolution Vol. 17, No. 2, November, pp. 219 –230, 2000 doi:10.1006/mpev.2000.0838, available online at http://www.idealibrary.com on 1055-7903/00 $35.00 Copyright © 2000 by Academic Press All rights of reproduction in any form reserved. 219