of an increased number of mitochondrial genomes of ro-
dents found support for rodent monophyly, thus implying
the utility of complete mitochondrial genomes as a marker
with increased taxon sampling. All more recent molecular
studies, employing larger numbers of taxa, increased num-
bers of characters, and multiple nuclear genes, have ob-
tained strong support for rodent monophyly and do not
place rodent lineages at the base of the eutherian radiation
(Madsen et al. 2001; Murphy et al. 2001a, b; Waddell et al.
2001; Delsuc et al. 2002; Waddell and Shelley 2003). Sev-
eral problems may explain the failure of some studies to
find support for rodent monophyly, including the lack of
analytical approaches that adequately correct for rate het-
erogeneity among rodent lineages (Cao et al. 1994; Sulli-
van and Swofford 1997), influence on tree rooting by selec-
tion of an outgroup (Philippe 1997), and simply sampling
artifact in terms of the taxa selected (Philippe 1997; Arna-
son et al. 2002). In addition, many rodent lineages are old
and arose rapidly during the Eocene. Therefore, large num-
bers of both taxa and sequences may be required to split
long branches and obtain support for short and more basal
internodes.
Sister-group of Rodentia
The concept of the order Lagomorpha (rabbits, hares, and
pikas) as the sister-group to rodents has fallen in and out of
favor over the decades since Brandt (1855), and this is re-
flected in different classifications of eutherian mammals, es-
pecially as they relate to the placement of rabbits (Wood
1957). Simpson (1945) recognized the cohort Glires as con-
taining the orders Rodentia and Lagomorpha (rabbits),
whereas McKenna’s (1975) classification placed Rodentia
as incertae sedisin the cohort Epitheria (a group of euthe-
rians containing all orders but Xenarthra), and the order
Lagomorpha was placed in a grandorder Anagalia that in-
cluded the order Macroscelidea (elephant shrews). More re-
cent cladistic analyses based on morphology (Luckett 1985;
Luckett and Hartenberger 1985; Novacek 1985; Landry
1999) provide support for a monophyletic Glires contain-
ing the orders Rodentia and Lagomorpha, and according to
Novacek (1992), this relationship is strongly supported. De-
spite a growing consensus among paleontologists and neon-
tologists for a monophyletic Glires, several molecular stud-
ies using either nucleotide sequences of mitochondrial genes
or amino acid sequences of nuclear-encoding genes failed
to find support for the monophyly of Glires (D’Erichia et al.
1996; Graur et al. 1991; Graur et al. 1996; Misawa and
Janke 2003). These molecular studies have been criticized
for their lack of taxon sampling (Halanych 1998; Lin et al.
2002; Delsuc et al. 2002), the use of inappropriate tree
building methods that do not consider rate heterogeneity
across lineages (Sullivan and Swofford 1997), and an inac-
curate rooting of the eutherian phylogeny (Douzery and
Huchon 2004). In fact, most recent molecular studies, uti-
lizing primarily nucleotide sequences of nuclear genes and
more complex models of sequence evolution, have provided
strong support for the monophyly of Glires to include rab-
bits and rodents (Waddell and Shelley 2003; Madsen et al.
2001; Murphy et al. 2001a, b).Rodent Phylogenetics and ClassificationTraditional classifications of rodents
One of the major dilemmas in rodent taxonomy pertains
to the diagnosis of higher taxonomic categories, specifically
superfamilies and suborders. Traditional classifications have
used variants of two schemes (table 2.1), one based on char-
acteristics of the zygomasseteric system (Brandt 1855) and
the other emphasizing the lower jaw (Tullberg 1899). The
classification using the zygomasseteric system groups rodent
families into three suborders: (1) Sciuromorpha — charac-
terized by a small infraorbital foramen and an expansion of
the masseter muscle on the anterior part of the zygomatic
arch; (2) Hystricomorpha —with an enlarged infraorbital
foramen through which the masseter passes; and (3) Myo-
morpha — displaying an intermediate zygomasseteric sys-
tem characterized by a “keyhole-shaped” infraorbital fo-
ramen penetrated by the masseter muscle. In contrast,
Tullberg (1899) recognized two suborders, Hystricognathi
(angle of lower jaw originating lateral to the plane of the in-
cisor) and Sciurognathi (angle of lower jaw arising below
the incisor). He further divided each suborder into tribes on
the basis of the zygomasseteric system. In general, rodent
families display different combinations of the zygomasse-
teric system and structure of the lower jaw, thus making the
placement of some families difficult (e.g., Anomaluridae,
Castoridae, Ctenodactylidae, Myoxidae, Pedetidae). In ad-
dition, these traits display parallel evolution among unre-
lated families, resulting in the inability to discern between
natural groups derived from a common ancestor and unre-
lated forms sharing similar specializations and life history
strategies (Hartenberger 1985; Jaeger 1988).Relationships among rodent families
“Rodentology, more than any other taxonomic group,
needs the collaboration of different research fields, from
morphology to biochemistry, to determine evolutionary
relationships” (Hartenberger, 1985, p. 25). Unraveling the
evolutionary history of rodents is complicated by at leastRodent Evolution, Phylogenetics, and Biogeography 15