urillus) of the New World tropics (fig. 2.3). A sound expla-
nation for the phylogenetic positions of these two lineages
requires a more complex biogeographic scenario.
Phylogenetic Position of Rodents among Eutherians
With the advent of improved molecular techniques and the
development of analytical methods that accommodate mo-
lecular data and increased taxon sampling, nagging ques-
tions regarding the origin and evolution of mammals, espe-
cially eutherians, have received increased attention from
molecular systematists. In particular, these studies have fo-
cused primarily on ordinal level relationships (Honeycutt
and Adkins 1993; Graur et al. 1996; Douzery and Huchon
2004; Waddell, Cao, et al. 1999; Stanhope et al. 1998; Mad-
sen et al. 2001; Murphy et al. 2001a, b; Scally et al. 2001;
Huchon et al. 2002; Waddell and Shelley 2003). The phy-
logenetic position of rodents among the eutherian radiation
has received considerable attention, especially with respect
to two major issues, the monophyly of and sister-group to
Rodentia.
Defining the order Rodentia
The order Rodentia represents an assemblage of species
characterized by diversity in morphology, physiology, ecol-
ogy, and many other biological attributes. Nevertheless, all
rodents share derived characteristics associated with the
dentition, skull, soft anatomy, postcranial skeleton, and jaw
(Luckett and Hartenberger 1993; Hartenberger 1998). In
rodents, several features of the dentition and jaw mecha-
nism accommodate a dual jaw action that enhances both
gnawing and chewing over the cheekteeth. These include:
(1) a pair of continually growing incisors with enamel re-
stricted to the labial surface and dentine on the lingual sur-
face, thus allowing for continual sharpening (Jacobs 1984);
(2) the loss of canines and a diastema separating the inci-
sors from the cheekteeth; (3) a zygomasseteric system char-
acterized by specializations of the masseter muscles and in-
fraorbital foramen (Marivaux et al. 2004).Question of rodent monophyly
In his classification of mammals, Gregory (1910; p. 323)
noted that members of the order Rodentia had dentition
“so striking and representative of the order” that recogni-
tion of “the modern conception of the group was reached
much more rapidly than was the case in other orders.” Luck-
ett and Hartenberger (1985; p. 690) confirmed Gregory’s
(1910) notion of Rodentia by stating, “Virtually every as-
pect of comparative biology examined in this volume, from
paleontological to molecular, corroborates monophyly of
the order Rodentia, in relation to other Eutheria.” Given
these statements pertaining to rodent monophyly and the
features diagnostic of the order, it is rather surprising that
some molecular phylogenetic studies failed to find support
for rodent monophyly (Graur et al. 1991, 1992; Li et al.
1992; D’Erchia et al. 1996; Reyes et al. 1998; Reyes et al.
2000). In all of these studies, rodents appeared either para-
phyletic or polyphyletic with two unrelated groups: a clade
containing hystricognath rodents, glirids, and sciurids, and
another clade containing the family Muridae. The molecu-
lar markers supporting rodent polyphyly or paraphyly are
inconsistent in the placement of the two rodent clades.
Amino acid sequences from multiple nuclear genes and
the inclusion of small numbers of taxa (Graur et al. 1991,
1992; Li et al. 1992) place guinea pigs (hystricognaths) at
the base of the eutherian tree, followed by a separate line-
age represented by the family Muridae and other orders of
eutherian mammals. Based on the analysis of amino acid
sequences of genes derived from whole mitochondrial ge-
nomes (D’Erchia et al. 1996; Arnason et al. 1997; Reyes
et al. 1998; Reyes et al. 2000; Arnason et al. 2002), the
Muridae resides at the base of the eutherian radiation, fol-
lowed by a clade containing hystricognaths, sciurids, and
glirids that is sister to other eutherians. The problem with
the “mitogenomic” approach is that the placement of ro-
dent clades varies with the taxa included and the phyloge-
netic method used. For instance, Lin et al.’s (2002) analysis14 Chapter Two
Figure 2.3 Phylogeny of the major groups of the family Sciuridaebased on
Mercer and Roth (2003) and Steppan et al. (2004). Numbers at specific nodes
represent divergence times in millions of years.