ZSC035.
fm Page 101 Thursday, June 1, 2000 3:12 PM
Soft anatomy, diffuse homoplasy, and the relationships of
Blackwell Science, Ltd
lizards and snakes
MICHAEL S. LEE
Accepted 25 September 1999
Introduction
It is more than 75 years since Charles Camp produced his
landmark monograph, Classification of the Lizards (Camp 1923),
and more than a decade since Estes et al. (1988) published
the modern successor to that study. Yet, many long-standing
uncertainties remain regarding higher-level relationships
within squamate reptiles (lizards, snakes, and amphisbaenians).
Xantusiids have been allied with either gekkotans (e.g.
Northcutt 1978; Greer 1985a) or lacertiforms (e.g. Estes
et al. 1988; Wu et al. 1996; Evans & Barbadillo 1997).
Gekkotans have been associated with scincomorphs
(Presch 1988; Schwenk 1988) or have been interpreted as
The Norwegian Academy of Science and Letters Zoologica Scripta, 29, 2, April 2000, pp101130
Lee, M. S. Y. 2000. Soft anatomy, diffuse homoplasy, and the relationships of lizards and snakes.
Zoologica Scripta, 29, 101130
Most previous phylogenetic analyses of squamates (lizards and snakes) employing large
character sets have focused on osteology. Soft anatomical traits bearing on this problem
have usually been considered in small subsets. Here, a comprehensive phylogenetic analysis
of squamate soft anatomy is attempted. 126 informative characters are assessed for 23
squamate lineages, representing snakes, amphisbaenians, dibamids, and all the traditionally
recognized families of lizards. The traditionally recognized groupings Iguania, Scleroglossa,
Gekkota, Scincomorpha, Anguimorpha and Varanoidea are corroborated in this analysis.
More controversial taxa are resolved as follows. Xantusiids, amphisbaenians and dibamids
cluster with gekkotans, and snakes are strongly allied with anguimorphs in general, and
varanids in particular. Nearly all these clades are congruent with those found in a recent
comprehensive osteological analysis; the strong support for snake-varanid relationships found
in both studies is particularly notable. This congruence is surprising given that previous
studies of soft anatomy tended to give differing and often heterodox results. These previous
results can be attributed to overrepresentation of misleading characters in small isolated
data sets. Such misleading signals are minimized when data sets are combined. For instance,
the snake-varanid clade is contradicted by many characters, and analyses of particular organ
systems therefore give differing results. However, characters that are incongruent with the
snake-varanid clade also disagree with each other (diffuse homoplasy), rather than forming
coherent support for some particular alternative clade (concerted homoplasy). In a com-
bined analysis these incongruent but diffuse characters cancel each other out to leave a very
strong (and orthodox) phylogenetic signal. These results underscore the view that the raw
amount of homoplasy as revealed by consistency and retention indices is not the only
determinant of phylogenetic signal; the distribution of that homoplasy is also important.
Thus, questioning a phylogenetic hypothesis (e.g. the snake-varanid clade) by identifying
numerous conflicting characters is insufficient the structure of the conflicting characters
should be assessed in a rigorous phylogenetic analysis.
Michael S. Y. Lee. Department of Zoology, University of Queensland, Brisbane, QLD 4072,
Australia. E-mail: mlee@zoology.uq.edu.au
the sister group of scincomorphs plus anguimorphs (Estes
et al. 1988). Inferred relationships within scincomorphs also
differ between studies (Estes et al. 1988; Presch 1988; Evans
& Barbadillo 1997; Evans & Chure 1998), and this diverse
assemblage might not even be monophyletic (Lee 1998).
Within anguimorphs, the relationships between anguids,
xenosaurids, and varanoids are uncertain, with all three
possibilities having some support in recent analyses (Rieppel
1980; Presch 1988; Wu et al. 1996).
In addition to the above problems involving limbed
squamates (lizards), three elongated, limb-reduced taxa
have long defied phylogenetic placement. Estes et al. (1988)
101
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Soft anatomy and squamate phylogeny M. S. Y. Lee
emphasized that relationships of snakes, dibamids and amphis-
baenians could not be resolved in their study, beyond the
probability that each belonged somewhere within sclero-
glossans, the large clade that includes most noniguanian
lizards. Snakes have been allied with either anguimorphs,
burrowing scincomorphs, amphisbaenians, dibamids, or
placed outside lizards altogether; dibamids have been placed
with scincomorphs, gekkotans, amphisbaenians, or snakes,
and amphisbaenians have been associated with lacertoids,
gekkotans, dibamids, or snakes. As discussed in recent
reviews (e.g. Estes et al. 1988; Rieppel 1988; Rage 1992;
Lee 1998; Caldwell 1999), each arrangement has some
character support and current advocates. Some recent work
places snakes with anguimorphs, and amphisbaenians and
dibamids with gekkotans (Lee 1998; Reynoso 1998). However,
these studies have mainly (Reynoso 1998) or entirely (Lee
1998) focused on osteology, and have yet to be corroborated
by a large-scale study of other traits.
All these uncertainties have persisted despite the accumula-
tion of large sets of morphological data from a variety of
systems: osteology (Estes et al. 1988; Wu et al. 1996; Evans
& Barbadillo 1997; Reynoso 1998; Hallermann 1998; Lee
1998; Caldwell 1999), myology (Russell 1988), visceral organs
(Saint Girons 1976; Farrel et al. 1998; Perry 1998), oral
glands (Kochva 1978a); the brain (Northcutt 1978), olfactory
structures (Parsons 1970), cranial cartilages (Hallermann
1998), inner ear (Miller 1968; Wever 1978), hemipenis and
cloaca (Gabe & Saint Girons 1965; Arnold 1984), tongue
and hyoid apparatus (Schwenk 1988, 1993), gamete
ultrastructure ( Jamieson 1995; Oliver et al. 1996), and
behaviour (Stamps 1977; Cooper 1995). Molecular data
might help resolve the problem, but even the most recent
published studies have not yet sampled comprehensively
enough across either taxa or genes to give compelling
results (see Forstner et al. 1995; Macey & Verma 1997).
Despite the uncertainties in squamate phylogeny, and the
variety of informative traits that have been sampled, all
large scale phylogenetic analyses have considered mainly
osteological data (e.g. Estes et al. 1988; Wu et al. 1996;
Evans & Barbadillo 1997; Reynoso 1998; Hallermann 1998;
Lee 1998; Caldwell 1999). This is not because the other
sorts anatomical traits are demonstrably (or perceived to be)
less informative. Rather, it undoubtedly reflects the relative
ease that skeletal data can be gathered for a large number
of taxa, through examination of osteological collections in
museums. In contrast, there are far fewer preparations of
internal soft anatomy, or ultrastructure, in museums such
studies require time-consuming and often destructive pre-
paration of specimens. Studies that have considered soft
anatomical data have tended to focus on different and often
small subsets of characters and, with some exceptions (e.g.
Schwenk 1988, 1993; Jamieson 1995), have rarely employed
102
rigorous numerical methods. These studies have often
yielded incompatible phylogenies: however, such different
outcomes might be expected due to sampling errors inher-
ent in small data sets (e.g. Bull et al. 1993). Here, I attempt
to include in a single comprehensive analysis the phylo-
genetically informative soft anatomical traits that have
been surveyed in a broad range of squamate families, to
ascertain what signal is present in the totality of the non-
osteological data.
Nevertheless, the caveat must be made that any separa-
tion of characters into distinct data sets for analysis might
be subjective and artificial. The assumption of such separ-
ate analyses is that the different sets of traits might evolve
under different rules, i.e. that correlation of characters
within the same data division is stronger than correlation
of characters from different data divisions (e.g. Bull et al.
1993; Miyamoto & Fitch 1995). There is little a priori reason
to expect that such traditional divisions reflect biological
reality (e.g. Nixon & Carpenter 1996; Baker & deSalle
1997; Kluge 1998). Organisms are integrated entities and
evolutionary significant phenonema will usually affect sev-
eral systems (data divisions) simultaneously because of
selection, pleiotropy or developmental constraints. Indeed,
even the widely accepted division between molecular and
nonmolecular (morphological, physiological, ecological)
traits is by no means clear-cut, and there are many char-
acter associations which violate this traditional boundary.
Birds that have morphological and physiological modifica-
tions for flying at high altitudes also have molecular adapta-
tions which enable their haemoglobin to function at lower
oxygen levels, and animals with the morphological and
behavioural adaptations for eating brightly coloured fruits
have corresponding molecular adaptations of their visual
pigments (e.g. Golding & Dean 1998). Aquatic mammals
have repeatedly evolved an excess of arginine residues
(Romero-Herrara et al. 1978), endothermic (warm-blooded)
vertebrates have independently increased GC nucleotide
levels (e.g. Bishop & Friday 1988; Lockhart et al. 1994), and
accelerated morphological evolution is often accompanied
by accelerated molecular evolution (Omland 1997).
In morphology, characters are often classified as osteo-
logical or soft anatomical, but again this division is far
from sharp. For instance, body elongation results in an
increase in the number of vertebrae and ribs (osteology),
elaboration of the axial musculature and rearrangement of
the internal organs (soft anatomy), and reduction of limbs
(osteology and soft anatomy). Even the classification of
certain characters into one or the other category can be sub-
jective: for instance, the width of the parietal skull roof
(osteology) and arrangement of the jaw adductor muscula-
ture (soft anatomy) are intimately related: encroachment
of the jaw adductors onto the dorsal surface of the skull
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ZSC035.fm Page 103 Thursday, June 1, 2000 3:12 PM
results in a narrow parietal roof. Similarly, the presence of
a stapedial foramen (osteology) partly reflects the course of
the stapedial artery (soft anatomy). Nevertheless, it remains
true that most phylogenetically informative morphological
traits are usually classified as either osteological or soft
anatomical. Furthermore, while comprehensive cladistic
data sets of osteological traits have been compiled in several
studies, such is clearly not yet the case for soft anatomical
traits.
This study attempts to fill this gap. However, it should be
emphasized that it is merely a first attempt to evaluate the
large body of soft anatomical traits. As with any large-scale
phylogenetic analysis of morphology, there are undoubtedly
many questionable codings, and relevant characters which
have been omitted altogether. Also, it attempts to review
and draws together existing information: while some char-
acters were rechecked or reinterpreted (as noted in the
relevant character descriptions), many are taken directly
from the primary descriptions in the literature. Often, how-
ever, the latter characters had not been interpreted cladis-
tically before, and individual characters had to be extracted
from general descriptions of anatomical areas. Thus, many
of these characters are new despite having been taken from
existing descriptions. This data set should therefore be
treated as merely a starting point to be supplemented
and (where necessary) corrected in future studies, much
in the same way as the mainly osteological study of
Estes et al. (1988) served as the baseline for almost all
subsequent phylogenetic analyses of squamate osteology
(e.g. Wu et al. 1996; Evans & Barbadillo 1997; Evans &
Chure 1998; Reynoso 1998; Hallermann 1998; Lee 1998;
Lee & Caldwell 2000).
Terminal taxa
The monophyly of the ingroup (Squamata) is highly cor-
roborated by a large suite of derived characters from a
variety of anatomical systems (Gauthier et al. 1988a; Estes
et al. 1988) and by molecular data (e.g. Saint et al. 1998).
Sphenodon, the Tuatara, is the nearest living relative of
squamates, again based on both morphology (e.g. Benton
1984, 1985; Gauthier et al. 1988a; Evans 1988; Carroll &
Currie 1991; Laurin 1991) and most molecular analyses
(e.g. Zardoya & Meyer 1998). The tree was rooted, and
character polarities determined, by comparison with Sphen-
odon. Characters which were not applicable in Sphenodon
were left unpolarized. Ideally, the next outgroup after
Sphenodon should also have been used to help infer polar-
ity. However, there is currently a vigorous debate over the
identity of this second outgroup, i.e. the sister group to
Sphenodon plus squamates (Lepidosauria). The traditional
interpretation is that the sister group to Lepidosauria is
Archosauria (e.g. Gauthier et al. 1988b). However, a recent
The Norwegian Academy of Science and Letters Zoologica Scripta, 29, 2, April 2000, pp101130
M. S. Y. Lee Soft anatomy and squamate phylogeny
morphological study has suggested that the sister group
might be turtles (deBraga & Rieppel 1997; but see re-
analyses by Wilkinson et al. 1997 and Lee 1997) while several
molecular studies suggest instead a turtle-archosaur clade
(Zardoya & Meyer 1998; Hedges & Poling 1999; Kumazawa
& Nishida 1999). As these alternative possible second out-
groups are very different morphologically, it was decided not
to use a second outgroup until this debate is more resolved.
The terminal taxa used in this analysis are very similar to
those used in previous analyses of higher-level squamate
phylogeny and include all the major extant groups of
squamates, conventionally termed families (Table 1). Most
of these terminal taxa are accepted as monophyletic. Thus,
iguanians are here represented as three monophyletic
terminal taxa: Iguanidae, Agamidae, and Chamaeleonidae.
Until recently, two of these terminal taxa were of dubious
monophyly: iguanids and agamids (Estes et al. 1988). Recent
studies, however, provide strong evidence that iguanids
are monophyletic (Macey et al. 1997), and weaker evid-
ence that agamids ( Joger 1991; Macey et al. 1999) are also
monophyletic. Scincids are another diverse terminal taxon
whose monophyly has been questioned (e.g. Rieppel 1984),
but a recent study has upheld their monophyly (Hallermann
1998). The only terminal taxon for which there is no cur-
rent support for monophyly is gekkonids. It is used as a
terminal taxon here but with parentheses, indicating that it
could be either monophyletic (e.g. Estes et al. 1988) or, more
likely, paraphyletic with respect to pygopodids (e.g. Kluge
1987). A more rigorous approach of splitting up gekkonids
into numerous smaller (but demonstrably monophyletic)
groups was not attempted. The demonstrably monophyletic
groups would have to be very small and numerous, since
the position of pygopodids within gekkonids has been
debated (King & Mengden 1990; Kluge 1994). The poor
sampling of many of the characters would have meant that
some of these groups would have consisted almost entirely
of missing data.
Character analysis
Character selection
Most of the soft anatomical characters used in this study
have previously been discussed in the literature, and the
relevant references are cited under each character. Some of
these traits have already been included in explicit numerical
cladistic analyses (Estes et al. 1988; Presch 1988; Schwenk
1988, 1993; Jamieson 1995). However, unlike the osteolo-
gical characters, a large proportion of the soft anatomical
characters have not yet been included in any numerical
phylogenetic analyses, such as many from the hemipenis
(Branch 1982; Arnold 1984), ear (Miller 1966a, 1966b,
1968; Baird 1970; Wever 1978), nasal region (Parsons
1970), histology and urinogenital system (Gabe & Saint
103

104
Zoologica Scripta, 29, 2, April 2000, pp101130
ZSC035.fm Page 104 Thursday, June 1, 2000 3:12 PM
Soft anatomy and squamate phylogeny M. S. Y. Lee
Table 1 The character by taxon matrix compiled in this study. denotes character is not applicable; ? denotes character is unknown but applicable. Multiple possible primitive
states (= polymorphism) in terminal taxa are indicated by the following letters: A denotes states 0 or 1; B denotes states 0 or 2; C denotes states 1 or 2; D denotes states 0, 1 or 2;
E denotes states 1 or 3.
12 3 4 5 6 78 91 11 11 1 1 1 1 12 22 2 22222233333 3 3 3 3 344 4 4 444444 55555555 556 6 6 666 6 6 667777777777 8 8888 8 8 8889999999 9 99 11 1 11 1 1 1 11 1 11 1 11 11 1 1 1 1 1 1 1 1 1
0 12 34 5 6 7 8 90 12 3 45678901234 5 6 7 8 901 2 3 456789 01234567 890 1 2 345 6 7 890123456789 0 1234 5 6 7890123456 7 89 00 0 00 0 0 0 00 1 11 1 11 11 1 1 2 2 2 2 2 2 2
01 2 34 5 6 7 89 0 12 3 45 67 8 9 0 1 2 3 4 5 6
Sphenodon 00 0 0 0 00 00 00 00 0 0 0 0 00 00 0 00000000 0 000 0 0 000000 0000000 000 0 0 000 0 0 000000000000 0000 0 0 000000000 0 00 00 0 00 0 0 0 00 0 0 00 00 0 0 0 0 0 0 0 0
Iguanidae 1 0 A 0 A 0 0 0 A 0 A 0 0 0 0 A 0 A0 0 0 0 0 0 0 0 1 0 1 0 0 0 A 0 0 0 0 1 0 0 A 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 A 1 0 0 0 A 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 A 0 0 1 0 0 0 0 0 0 0 1 1 0 0 1 0 1 1 ? 0 0 0 1 0 2 0 1 0 A 0 0 1 2 0 0 1 2 0 2 1 C 0
Agamidae 1 0 A 0 1 0 0 0 A 0 A 0 0 0 0 0 0 AB 0 0 0 0 0 0 0 1 0 1 0 0 0 A 0 0 1 0 1 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 ? ? 1 1 0 1 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 2 0 0 1 0 0 0 0 0 0 0 1 1 0 0 1 0 A 0 0 0 0 0 1 0 2 0 1 0 A 0 1 1 1 1 ? 1 2 0 1 E 0
Chamaeleonidae 10 0 0 0 00 01 01 00 0 0 2 0 10 00 0 00000010000 0 0 1 0 101 1 ? 000000 0000000 001 0 100 0 0 00000000010 0002 0 0 1000000011 0 0 0A 0 00 0 0 ? 12 0 11 0 02 0 1 0 1 2 1 2 1 2 0
Xantusiidae 01 1 0 1 00 ?0 ?? 00 1 0 0 0 01 11 0 00002101001 0 0 0 010 0 A 001001 02000011 120 1 1 010 0 1 10010010000 0010 1 0 1000000010 1 02 00 ? ?0 0 0 ? 02 0 01 0 02 0 ? ? ? ? ? ? ? ? ?
Gekkonidae 0 0 1 0 A 0 0 0 A 0 0 0 0 0 0 C 1 0 0 0 0 A 1 1 0 1 2 0 0 0 1 0 1 0 0 0 0 0 1 0 0 1 1 2 1 0 1 0 1 1 0 1 1 1 1 0 1 2 0 0 1 0 1 0 0 1 1 0 0 0 0 0 1 0 0 0 0 0 0 1 0 1 0 1 0 0 1 0 0 0 0 1 0 A 0 1 0 A 2 0 0 0 0 0 0 A 0 AA 0 1 0 0 2 0 1 0 0 1 2 0 4 0
The Norwegian Academy of Science and Letters
Pygopodidae 01 1 1 1 1 00 01 00 00 0 A 1 1 0 01 1 11012000100 1 1 A 01 0 1 121010 11011110 120 1 1 010 0 1 10000010000 0010 1 0 1001000010 1 01 11 ? ?0 0 0 0 00 0 0 A 10 02 0 ? 0 2 1 2 1 3 1
Dibamidae 01 1 1 1 1 11 10 01 11 2 1 0 0? ? 0??011????? ? ? ? 0 0? 0 ??0000 0???0?12 ??0 1 1 020 0 1 00000020??0 2010 0 ? 0000001? 2 01 2? ? ?? ? 0 ? 01 0 ? 0 ?? ?? ? ? ? ? ? ? ? ? ?
Amphisbaenia 01 1 1 0 A 11 10 00 11 1 1 ? 10 0? 1 00002100001 1 0 ? ?10 1 010200 000001D 220 0 1 000 0 1 411000200011 0 0010 0 0 200000?11 2 01 20 0 ?0 0 A A 12 0 0 A 0B 12 ? ? ? ? ? ? ? ? ?
Lacertidae 01 1 0 1 00 00 00 00 0 0 0 0 12 11 0 00002100001 0 0 0 1 001 0 0 010001 01000010 120 1 1 010 0 0 311000100010 0 2010 0 0 1000010011 0 01 00 1 00 0 0 0 02 0 10 0 01 01 1 0 0 1 0 2 0 5 0
Teiidae 01 1 0 A 00 01 00 00 0 0 0 0 02 21 0 0000210101 2 101 1 0 020001 0100001A 210 1 1 010 A 0 411000100011 0 1110 0 0 1000101011 0 01 00 A ?0 0 0 0 02 0 00 1 00 1A 1 0 0 2 0 2 0 1 0
Gymnophthalmidae 01 1 A 0 A 00 0? 00 00 0 0 ? 0 02 21 0 ??00210101 2 1?1 1 1 ?????? ??????1? ??? ? 1 010 0 0 411000100011 0 1110 0 0 1000101011 0 ?? 00 0 ?? ? 0 ? 02 0 00 1 0? ?? ? ? ? ? ? ? ? ? ?
Cordylidae 01 1 1 0 1 00 01 0A 00 0 0 0 0 00 01 0 00002101000 0 0 ? 000 A 0 001000 0210?10 110 1 1 010 0 0 100100000010 1 2010 0 0 1100010011 0 01 00 ? ?0 0 0 ? 02 0 00 ? 0? ?? ? ? ? ? ? ? ? ? ?
Scincidae 01 1 1 1 0 0A 00 00 1A 1 0 0 0 00 01 0 0000210102 0 1 000 0 1 001000 0210110 110 1 1 010 0 0 100100000010 1 1010 0 0 1100010011 0 01 00 ? 00 0 0 ? 02 0 01 0 01 11 A A 0 D A 2 A C
Anguidae 01 1 1 A 0 0A 0A 01 0A A 0 0 0 00 0A 0 0010210000A A A 1 000 0 1 010000 0000011 110 A A 011 0 0 20001010000 0010 0 1 1000000011 0 00 00 1 ?A A 0 0 02 0 0A 0 00 02 ? ? ? ? ? ? ? ? ?
Xenosauridae 00 1 0 0 00 ?? 0? 00 0 0 ? 0 00 01 0 00102100000 0 0 1 0?0 0 0 000000 0000??? ??? ? ? 001 0 0 20001010??0 0010 0 1 1000000011 0 ?? 01 1 ?? ? 0 ? 02 0 00 ? 0? ?? ? ? ? ? ? ? ? ? ?
Heloderma 00 1 0 0 00 ?? ?? 00 0 0 ? 0 10 01 0 00102100001 0 0 2 001 1 0 000000 0000?11 ?1? ? ? 011 0 0 31001010000 0010 0 1 1000000011 0 01 02 1 ?1 1 0 2 12 0 00 1 0A 0C ? ? ? ? ? ? ? ? ?
Lanthanotus 00 1 0 0 00 ?? ?? 00 0 0 ? 0 10 01 0 ??102?00000 0 0 2 0?1 0 0 ?00100 0???0??1 ??? ? ? 011 1 0 41101011100 002 210000011 0 1? 01 1 ?? ? ? ? 12 1 00 ? 0? ?? ? ? ? ? ? ? ? ? ?
Varanus 00 1 0 0 00 11 11 00 0 0 0 0 10 21 0 00102100000 0 0 0 2 101 0 0 00010A 0000022 20A 1 1 011 1 0 4110111120 002 210000011 0 11 02 1 11 1 1 2 12 1 10 1 0A 1C 1 1 0 2 0 2 0 1 0
Serpentes 0 A 1 1 1 0 1 1 1 1 1 1 0 A C 1 0 0 0 1 0 0 1 0 2 1 0 0 0 0 0 0 1 2 0 A 0 0 0 0 0 0 0 0 0 0 0 1 2 2 2 1 0 1 A 0 0 A 1 0 4 1 1 0 1 1 1 1 2 0 0 0 2 2 1 0 0 0 0 0 0 1 C 0 1 1 B A 1 1 A 1 0 1 0 0 0 1 0 2 2 0 0 0 1 2 2 1 3 1
ZSC035.fm Page 105 Thursday, June 1, 2000 3:12 PM
Girons 1965; Saint Girons 1976). As there has been a his-
torical tendency to focus on particular organ systems for
phylogenetic purposes, and the present study is inevitably
based on previous work, there is an undoubted bias in terms
of character sampling. The number of well-defined and
sampled tongue characters is striking, and has been due to
the phylogenetic interest in this region (e.g. McDowell
1972; Schwenk 1988). In contrast, the number of visceral
characters is rather paltry, probably due partly to the lack
of previous interest rather than an intrinsic lack of phylo-
genetic information. Many visceral characters, for instance,
have been identified as phylogenetically significant within
snakes (e.g. Underwood 1967; Rossman et al. 1982; Wallach
1985; Cundall et al. 1993), and there seems every reason to
expect that a similar situation will hold within squamates
in general. Thus, characters from organ systems previ-
ously assumed to be phylogenetically useful are well-sampled,
while characters from other systems are probably greatly
under-used. Also, characters that require time-consuming
and destructive sampling will also tend to be examined for
fewer taxa than other characters. It is hoped that the current
study will lead to further work on areas of anatomy that
have been phylogenetically neglected for these and other
reasons.
Characters described in these previous studies were evalu-
ated and, if found valid, included in this analysis. As just
noted, some of these characters have never been explicitly
analysed in a cladistic framework while others have already
been so treated. However, for some of the latter traits, addi-
tional character states were recognized, single characters
were split, or separate characters combined: these changes
are explained under the individual character descriptions.
Where appropriate, I have recoded single multistate charac-
ters with complex (e.g. branching) morphoclines into two
or more simpler (binary or linear multistate) characters,
an approach advocated previously (Lee 1995) and termed
reductive (Wilkinson 1995) or absence/presence (Pleijel
1995) coding. For some characters, the character states
assigned to certain taxa were also changed, either based on
personal observation or published descriptions; these are
also discussed. Some characters traditionally implicated in
squamate phylogeny were rejected for various reasons and
are discussed at the end of the character list. It should be
noted that many characters mentioned in previous studies
were omitted, not because they were problematic, but
because they were not phylogenetically informative here
given the terminal taxa employed. Though they might have
been informative in the original studies, which employed
different terminal taxa, here they were either invariant, or
the derived state did not unequivocally characterize more
than one terminal taxon and was thus equally compatible
with all possible cladograms.
The Norwegian Academy of Science and Letters Zoologica Scripta, 29, 2, April 2000, pp101130
M. S. Y. Lee Soft anatomy and squamate phylogeny
Characters used in previous analyses are cited appro-
priately in the character descriptions. However, for brevity,
commonly cited studies are abbreviated in the character
descriptions as follows:
AXX: character XX in Arnold (1984).
EXX: character XX in Estes et al. (1988).
JXX: character XX in Jamieson (1995).
PXX: character XX in Presch (1988).
SaXX: character XX in Schwenk (1988).
SbXX: character XX in Schwenk (1993).
HXX: character XX in Hallermann (1998).
Character codings
Because of the size and diversity of many of the terminal
taxa (e.g. snakes: nearly 3000 species), many of the charac-
ters are variable within at least some terminal taxa. Here, as
in previous studies (Estes et al. 1988; Frost & Etheridge
1989; Lee 1998), an attempt was made to determine, on the
basis of well-corroborated phylogenetic relationships within
the terminal taxon, which state was primitive (i.e. present in
all basal lineages). This approach has been demonstrated to
yield more accurate phylogenies than formerly widespread
approach of coding taxa as polymorphic without regard for
the distribution or frequency of character states (Wiens
1998a; Bininda-Emonds et al. 1998). However, in order to
identify which state of a polymorphic character is primitive,
this approach requires that basal forms in a terminal taxon
are known, and also that the distribution of the polymorphic
character in these basal forms is also known. In many cases,
poor knowledge of either relationships or character distribu-
tion within the terminal taxon meant that the primitive state
could not be determined. In other cases, variability of the
character across basal forms also meant that the primitive
state could not be determined. In all these equivocal cases,
the terminal taxon was coded with all states which might
conceivably be primitive.
It should also be acknowledged that many of the char-
acters used in this analysis are relatively poorly sampled,
compared to most osteological characters. Many of the
terminal taxa are very diverse, but are coded based on few
(or even one) examined species. The amount of variability
within these diverse terminal taxa will tend to be under-
estimated, and indeed the few species examined might
eventually be found to possess a state neither typical nor
primitive for the group. Nevertheless, the most reasonable
approach is still to code each terminal taxon with the char-
acter state(s) found in the examined species, however, few
but to treat such codings as provisional. However, to
present information in the discussion of each character on
species sampling in all 23 terminal taxa would have extended
this paper severely; this information is contained in the
references cited under each character.
105
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Soft anatomy and squamate phylogeny M. S. Y. Lee
Many of the characters in this analysis are multistate. For
such characters, transformation series are derived that
minimize the amount of evolutionary change between char-
acter states. The extremes in a morphocline were coded as
being derivable from each other only via intermediate stages
(i.e. the transformation from 0 to 2 entails two steps, 0 1
and then 1 2), i.e. they were coded as ordered or additive.
Only characters that formed no clear morphoclines were
unordered. Parsimony-based arguments in favour of this
approach are presented in Wilkinson (1992) and Slowinski
(1993): because such codings discriminate against large
changes within a character (e.g. those between extremes in
a morphocline), they result in cladograms that entail less
overall evolutionary change than cladograms constructed
by coding all multistate characters as unordered. In the
ordered analysis therefore the following multistate char-
acters formed clear morphoclines and were thus ordered:
15, 17, 20, 21, 28, 38, 45, 51, 56, 57, 58, 59, 64, 68, 70, 74,
76, 81, 83, 84, 99, 100, 109, 115, 117, 121, 122, 123. The
specific linear arrangement of character states is discussed
under each individual character. The following multistate
characters did not form unambiguous morphoclines and
were left unordered: 33, 47, 87, 97, 102, 107, 125.
It must be acknowledged that ordering characters accord-
ing to morphoclines entails assumptions, in particular, that
small changes along a morphocline are less likely than large
changes (e.g. Slowinski 1993; Wilkinson 1995). Therefore,
to investigate how heavily the results of the ordered ana-
lysis depended upon ordering of characters and its associ-
ated assumptions, a second analysis was performed. In this
unordered analysis, all characters were treated as unordered.
However, leaving characters as unordered is not more
conservative as it also entails assumptions. The tree is con-
structed under the assumption that all transitions between
character states (regardless of magnitude) are not only
possible but equally likely, which seems at odds with the
neo-Darwinian view that, in general, natura non facit saltum.
Descriptions of soft anatomical characters
External morphology
1. Complex dewlap apparatus (gular fan). Absent (0);
present (1). P25.
2. Cephalic scales. Numerous and small (0); few and
enlarged (1). E147. Some iguanids exhibit state 1, but state
0 appears to be primitive for the group (Estes et al. 1988).
3. Scales in mid-dorsal row. Larger than other dorsal scales
(0); same size as other dorsal scales (1). E146.
4. Dorsal body scales. Mostly small and granular, only a few
isolated large scales at most (0); all large and flat (1). I have
restricted this character to scales on the dorsal surface of
the body, excluding the midline, to avoid correlation with
the previous character. The morphology of the scales on the
106
ventral surface and appendages appears to be much too
labile (variable within most families) to be phylogenetically
informative.
5. Enlarged dorsal body scales. Polygonal (0); cycloid (1).
This represents a modified version of E148 (cycloid scales
absent/present). It cannot be coded in taxa with only small
granular body scales (see previous character). Contrary to
Estes et al. (1988), all pygopodids have cycloid scales (per-
sonal observation).
6. Femoral or preanal pores. Absent (0); present (1). E144.
Estes et al. (1988) listed agamids, pygopodids and lacertids
as variable (but primitively lacking pores), and dibamids
as lacking pores. However, pores are present in all basal
agamids (see Frost & Etheridge 1989), basal pygopodids (Kluge
1974; Greer 1989), basal lacertids (Arnold 1989) and all dibamids
(Greer 1985b, personal observation).
7. Tail length. Long, i.e. more than 38% of snout-vent
length (0); short, e.g. less than 38% of snout vent length (1).
From Greer (1985b).
Cartilaginous structures
8. Inferior alary process of anterior nasal copula. Small (0);
large (1). H131.
9. Apical foramen of anterior nasal copula. Present, copula
perforated by medial branch of ethmoid nerve (0); absent,
medial branch of ethmoid nerve passes ventral to copula (1).
H134.
10. Superior nasal fenestra of parietectal cartilage. Present
(0); absent (1). H133.
11. Course of medial branch of ethmoid nerve. Through groove
on premaxilla (0); through groove on septomaxilla (1). This
represents a modification of character 135 of Hallermann
(1998), who subdivided state 0 into two further states (presence
or absence of apical foramen). This subdivision is not used
here as it is already covered by character 9.
12. Paraseptal cartilage. Well-developed and antero-
posteriorly complete (0); reduced and anteroposteriorly
incomplete, or absent (1). H136. Hallermann (1998) phrases
the derived state of this character as paraseptal cartilage
absent. However, most of the taxa he coded with this state
are acknowledged to possess remnants (or possible remnants)
of the cartilage, and the character has thus here been
modified. As redefined, anguids and varanids both have
state 1.
13. Planum antorbitale of nasal capsule. Complete posteriorly,
separating cavum antorbitale from choanal duct (0); incom-
plete posteriorly, cavum antorbitale continuous with choanal
duct (1). H139 slightly rephrased.
14. Foramen olfactorius leading into ethmoidal region. Small
(0); very large (1). H140.
15. Nasopharyngeal cavity. Nasal passage not separated
from oral cavity (0); nasal passage partially separated from
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ZSC035.fm Page 107 Thursday, June 1, 2000 3:12 PM
oral cavity (1); nasal passage fully separated from oral cavity
(2). H141. This character is ordered according to the
morphocline 012.
16. Interorbital septum. Present (0); absent (1). H142.
17. Commissura sphenethmoidalis connecting nasal capsule
and interorbital septum. Present, complete (0); present, incom-
plete (1); absent (2). H144. Unlike Hallermann (1998), taxa
without an interorbital septum (see previous character) are
here coded as not applicable for this character. This
character is ordered according to the morphocline 012.
18. Processus supraoccipitalis (tectum synoticum). Present
(0); absent (1). H143. This process represents a cartilaginous
flange that extends dorsally from the supraoccipital to
the skull roof. I thus differ from Hallermann in coding
snakes and dibamids, where the supraoccipital is behind
rather than beneath the skull roof, as not applicable for this
character.
19. Epicoracoid cartilage. Extensive, contacting mesos-
capula and usually suprascapula (0); reduced, does not contact
mesoscapula nor suprascapula (1). E114.
Musculature
20. Insertion of adductor mandibulae posterior muscle on
lower jaw. Not extending into Meckels canal (0); extending
slightly into Meckels canal, but lacking median tendon (1);
extending greatly into Meckels canal, with median tendon (2).
This is based on E131, except that the derived state in that
character has been subdivided into states 1 and 2 here. This
character is ordered 012.
21. Origin of pseudotemporalis superficialis muscle of jaws.
Restricted to anterior margin of temporal fenestra (0);
extending posteriorly along entire medial margin of tem-
poral fenestra but not onto supratemporal (1); extending
posteriorly along entire medial margin of temporal fenestra
and onto supratemporal (2). E132. An extra informative
character state (2) identified in Rieppel (1980) has been
added to this character. This character is ordered according
to the morphocline 012.
22. Anterior head of pseudotemporalis profundus muscle of
jaws. Absent (0); present (1). E133.
23. Depressor palpebris inferior muscle of eyelid. Present
(0); absent (1). Amphisbaenians, pygopodids, snakes and
some gekkonids lack this muscle (Underwood 1970).
24. Extracolumellaris muscle of middle ear. Absent (0);
present (1). E135.
25. Meatal closure muscle of tympanum. Absent or vestigial
(0); well-developed and functional (1). Data from Wever
(1978) and Kluge (1987). As this muscle occurs in all basal
gekkonids, absence in some gekkonines is secondary.
26. Geniomyoideus muscle of throat. Absent (0); present (1).
P20. Snakes possess this muscle (McDowell 1972), while
dibamids possess a similar muscle of uncertain homology
The Norwegian Academy of Science and Letters Zoologica Scripta, 29, 2, April 2000, pp101130
M. S. Y. Lee Soft anatomy and squamate phylogeny
(Groombridge 1979a,b; Greer 1985b) and have been coded
as unknown. Contrary to Presch (1988), this muscle is
present in Lanthanotus and Varanus (e.g. Camp 1923;
McDowell 1972; Rieppel 1980; Pregill et al. 1986).
27. Hyoglossus muscle of tongue. Divided into two bundles
only (0); subdivided into multiple bundles (1). Sa15.
28. Intrinsic circular muscle system of tongue. Incomplete
ring (0); complete ring but weakly developed (1); complete
ring and well-developed (2). Sb3. This character has been
ordered according to the morphocline 012.
29. Rectus abdominis lateralis muscle of abdomen. Absent (0);
present (1). E134.
30. Intercostalis ventralis muscle of abdomen with ventral
slips. Present (0); absent (1). Redefined from Presch (1988).
Snakes, coded as unknown in Presch (1988), possess this
muscle (e.g. Gasc 1974, 1981; Cundall 1987).
31. Transversus penis muscle of hemipenis. Well-developed
(0); greatly reduced or absent (1). A12. This, and following
six hemipenial characters, cannot be polarized as they are
not applicable in rhynchocephalians or more distant out-
groups, which lack a hemipenis.
32. Transversus penis muscle of hemipenis. Fibres extend
transversely (0); fibres extend obliquely or longitudinally (1).
A13.
33. Retractores laterales muscles of hemipenis. Anterior and
posterior muscles present (0); single muscle present of
uncertain homology, which might represent the anterior,
posterior, or combined muscle (1); anterior muscle present
only (2). This character is unordered, since different trans-
formation series are possible depending on the homologies
of the single muscle in state 1. It represents a combination
of A25 (both muscles present/single unidentified muscle
present) and A26 (both muscles present/anterior muscle
present). Arnold (1984: 68) noted that scincids have a single,
probably anterior muscle, but a typographic error in the
data table assigned this state to cordylids.
34. Retractores laterales muscles of hemipenis. Widely
separated (0); close together or partially fused (1). A23. This
character cannot be coded in taxa with only a single retractor
lateralis.
35. Retractor lateralis anterior muscle of hemipenis. Originates
lateral to the hemipenis (0); originates dorsal to hemipenis
(1). This character and the following represent a recoding
of A24 (both retractores laterales lateral to hemipenis/one
or both retractores laterales dorsal to penis). The original
coding potentially lumps two very different derived condi-
tions into the same character state, i.e. taxa with only the
anterior, and those with only the posterior retractor lateralis
muscle positioned dorsally will both be coded as sharing
the same derived state. This character is not applicable in
teiids and gymnophthalmids, which lack a clearly identifiable
retractor lateralis anterior (see character 33).
107
ZSC035.fm Page 108 Thursday, June 1, 2000 3:12 PM
Soft anatomy and squamate phylogeny M. S. Y. Lee
Fig. 1 AF. The pituitary gland of various squamates, in sagittal section, illustrating differences in the shape of the distal lobe. Anterior is to
the left. A. Chamaeleonidae (Chamaeleo). B. Gekkonidae (Hemidactylus). C. Amphisbaenia (Trogonophis). D. Teiidae (Cnemidophorus).
E. Varanidae (Varanus). F. Serpentes (Cerastes). All figures are diagrammatic and not to scale. Based on St. Girons (1970).
36. Retractor lateralis posterior muscle of hemipenis. Originates
lateral to hemipenis (0); originates dorsal to hemipenis (1).
This character is not applicable in teiids, gymnophthalmids
and scincids, which lack a clearly identifiable retractor lateralis
posterior (see character 33).
37. Retractor lateralis posterior muscle of hemipenis. Not
situated within hemipenial sheath (0); substantially situated
within hemipenial sheath (1). A35. I have coded iguanids as
possessing state 0 since this condition is found in all but one
of the 10 groups surveyed by Arnold (1984); optimization
on an iguanid cladogram is not yet possible since their rela-
tionships are still poorly resolved (Macey et al. 1997). This
character is not applicable in taxa which lack either a hemi-
penial sheath or a retractor lateralis posterior (see characters 33
and 108).
Brain and nervous system
38. Nucleus sphericus of accessory olfactory bulb. Weakly to
moderately developed, diffuse (0); strongly developed, dis-
crete (1); extremely well-developed, discrete (2). Sb11. This
character has been ordered according to the morphocline
012. Schwenk (1993) coded xantusiids, pygopodids,
anguids, xenosaurids, Lanthanotus, dibamids and gymno-
phthalmids as unknown. However, the nucleus sphericus
is weakly developed in xantusiids (Northcutt 1978: 28), well-
developed in anguids and xenosaurids (Northcutt 1978: 28)
and very well developed in Lanthanotus (Northcutt 1978:
108
29, fig. 6E). Dibamids have a moderately developed
nucleus sphericus (Senn & Northcutt 1973). The condition
in pygopodids is uncertain: Northcutt describes the nucleus
sphericus as slightly more developed than in taxa with
state 0. However, whether it is as well developed as those
with state 1 (lacertids, etc.) was not specified pygopodids
are here coded with both possible states. Also, Northcutt
(1978) used the taxon name teiids to include both (macro)
teiids and gymnophthalmids and examined several species
from both groups. His statement that the nucleus sphericus
is particularly pronounced in teiids (p. 23) is therefore taken
to mean it characterized all examined (macro)teiids and
gymnophthalmids. Gymnophthalmids are here coded with
state 2 rather than as unknown.
39. Brain organization. Lacertomorph pattern (0); draco-
morph pattern (1). P7. Snakes, not coded by Presch (1988),
and dibamids coded as unknown, dibamids and snakes
exhibit the lacertomorph pattern (Senn & Northcutt 1973;
Northcutt 1978).
40. Pituitary gland (see Fig. 1). Distal lobe a regular mass,
lying ventral to intermediate lobe (0); distal lobe greatly
enlarged anteriorly and thin posteriorly, distal lobe there-
fore lies mostly anteroventral to intermediate lobe (1). Data
from Saint Girons (1970).
41. Ulnar nerve in forelimb. Superficial (0); deep (1). E142.
Estes et al. (1988) listed iguanids and lacertids with both
states, state 0 being primitive. Nearly all iguanids have state 0,
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ZSC035.fm Page 109 Thursday, June 1, 2000 3:12 PM
the only two genera with state 1 are highly derived forms
(Frost & Etheridge 1989; Macey et al. 1997). Most basal
lacertids have either the deep position or an intermediate
condition (Arnold 1989); they are here coded with state 1.
Not applicable in taxa without forelimbs.
42. Innervation of muscles of lower leg. Peroneal nerve (0);
interosseous nerve (1). E143. Not applicable in taxa without
limbs.
Ear
43. Internal (quadrate) process of extracolumella. Present (0);
absent (1). E141, P6.
44. Spindle body in cochlear duct. Absent (0); present (1).
Data from Wever (1978).
45. Limbic mound (vestibular lip) of cochlear duct (see Fig. 3).
Absent or very weak (0); distinct, simple ridge (1); large
recurved flange (2). This character is ordered according to
the morphocline 012. Data from Torien (1963); Schmidt
(1964), Miller (1966a, 1966b, 1968), Miller et al. (1967), Baird
(1970) and Wever (1978).
46. Shape of limbus (see Fig. 2). Circular to slightly oval (0);
greatly elongated anteroposteriorly (1). Data from Miller
(1966a, 1966b, 1968), Miller et al. (1967), and Baird (1970).
47. Anteroventral region of limbus. Not intruded by periotic
sac (0); accommodates long posterodorsal projection the
accessory scala tympani from periotic sac (1); accom-
modates short anterior projection from periotic sac (2).
This character does not form an obvious morphocline and
is unordered, since the projections of the periotic sac in
states 1 and 2 have a very different position and orientation.
Data from Miller (1966a, 1966b, 1968), Miller et al. (1967),
and Baird (1970).
48. Basal papilla (see Fig. 2). Does not extend all the way
across limbus, large margin of limbic tissue present at either
end (0); extends almost all the way across limbus, only a
narrow strip of limbic tissue present at one end (1). Data
from Miller (1966a, 1966b, 1968), Miller et al. (1967), and
Baird (1970).
49. Basal papilla (see Fig. 2). Simple continuous strip, not
or only slightly constricted (0); with deep constriction that
almost or completely separates the strip into two por-
tions (1). Data from Schmidt (1964), Miller (1966a, 1966b,
1968), Miller et al. (1967), Baird (1970) and Wever (1978).
Schmidt (1964) reported Varanus with state 0 while Baird
(1970) reported state 1, and Miller (1966a) and Wever
(1978) noted variability; Varanus has therefore been coded
with both states.
50. Basal papilla and membrane (see Fig. 2). Posterodorsal
extremity not tapered (0); posterodorsal extremity tapered (1).
Data from Schmidt (1964), Miller (1966a, 1966b, 1968),
Miller et al. (1967), Baird (1970) and Wever (1978).
51. Restraint system for cilia of hair cells. Cells attached to
The Norwegian Academy of Science and Letters Zoologica Scripta, 29, 2, April 2000, pp101130
M. S. Y. Lee Soft anatomy and squamate phylogeny
tectorial membrane (0); cells attached to tectorial membrane
and inertial bodies (sallets) (1); cells attached to inertial
bodies (sallets and culmen) only (2). E140, P1. This charac-
ter is ordered according to the morphocline 012 and is
correlated with P3 (sallets present/absent) and P4 (culmen
present/absent), which have therefore not been included
here. Information on character states is based on Wever
(1978). Contrary to Presch (1988), amphisbaenians have
a membrane restraint system, not a sallet system (Wever
1978; Estes et al. 1988).
52. Tectorial membrane (see Fig. 3). Present (0); absent (1). P2.
53. Arrangement of inertial bodies and tectorial membrane.
Inertial bodies situated at both ends of tectorial membrane (0);
inertial bodies situated alongside entire length of tectorial
membrane (1). It cannot be coded in taxa lacking either iner-
tial bodies or a tectorial membrane.
54. Otic sac (see Fig. 2a). Small to moderate in size (0);
greatly enlarged (1). Data from Baird (1970).
55. Periotic (perilymphatic) cistern. Not divided into saccu-
lar and cochlear parts (0); fully divided into saccular and
cochlear parts (1). Data from Baird (1970).
Olfactory and vomerolfactory organs
56. Jacobsons organ. Weakly developed (0); moderately
developed (1); extremely well developed (2). This character
has been ordered according to the morphocline 012. This
character is Sb5 with an extra state (2) added: Parsons
(1970) noted how the organ in varanids and snakes is even
more developed than in other scleroglossans. Heloderma
and Dibamus, coded by Schwenk (1993) as unknown,
have recently been shown to have state 1 (Bernstein 1997;
Hallermann 1998).
57. Jacobsons organ opening and choanal groove. Choanal groove
long, reaches opening of Jacobsons organ (0); choanal groove
short, does not reach opening of Jacobsons organ (1);
choanal groove absent (2). H137, Sb8 States 1 and 2 of
Hallermann (1988) have been combined but a new state 2
was added from Schwenk (1993). This character is ordered
according to the morphocline 012. The choanal groove is the
fissure on the soft palate extending between the vomerine
cushion and the choanal fold, and is reduced or lost when the
latter structures fuse. Scincids, lacertids, and cordylids are
assigned state 0 (Bellairs & Boyd 1950; Parsons 1970). Some
teiids and amphisbaenians have state 0 (Bellairs & Boyd 1950;
Parsons 1970; Hallermann 1998; contra Schwenk 1993).
58. Jacobsons organ epithelium. Poorly developed, less than
2.5 receptor cells for each supporting cell (0); intermediate,
between 2.5 and 8 receptor cells for each supporting cell
(1); well-developed, more than 8 receptor cells for each
supporting cell (2). This character has been ordered according
to the morphocline 012. Data taken from Gabe & Saint
Girons (1976) and Cooper (1996a, 1997); the mean value
109
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Soft anatomy and squamate phylogeny M. S. Y. Lee

Fig. 2 A. The inner ear of a typical squamate, with labels indicating important characters described in the text. BT. The limbus and
basal papilla in various lepidosaur groups conventionally ranked as families. B. Sphenodontidae (Sphenodon). C. Iguanidae
(Crotaphytus). D. Agamidae (Agama). E. Chamaeleonidae (Chamaeleo). F. Xantusiidae (Xantusia = Klauberina). G. Gekkonidae
(Cosymbotus). H. Pygopodidae (Lialis). I. Dibamidae (Dibamus). J. Amphisbaenia (Amphisbaena). K. Lacertidae (Acanthodactylus).
L. Teiidae (Cnemidophorus). M. Cordylidae (Cordylus). N. Scincidae (Mabuya). O. Anguidae (Diploglossus). P. Xenosauridae
(Xenosauridae). Q. Helodermatidae (Heloderma). R. Lanthanotidae (Lanthanotus). S. Varanidae (Varanus). T. Serpentes (Pituophis).
All figures are diagrammatic and not to scale. (a) based on Baird (1970); (b)(t) based on Miller (1966a, b, 1968) and Miller et al. (1967).

110 Zoologica Scripta, 29, 2, April 2000, pp101130 The Norwegian Academy of Science and Letters
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M. S. Y. Lee Soft anatomy and squamate phylogeny

Fig. 3 AD. Transverse sections through the cochlear duct of squamates, illustrating differences in the development of the limbic mound,
and presence of the tectorial membrane. Lateral is to the left. A. Iguanidae (Anolis). B. Scincidae (Eumeces). C. Gekkonidae
(Coleonyx). D. Teiidae (Tupinambis). All figures are diagrammatic and not to scale. After Schmidt (1964).

Fig. 4 A, B. The nasal region of squamates, in

lateral aspect, illustrating differences in the
length of the vestibulum. A. Anguidae
(Gerrhonotus). B. Iguanidae (Dipsosaurus).
Figures are diagrammatic and not to scale.
After Parsons (1970).

Fig. 5 AC. The nasal region of various squamates, in dorsal view, illustrating differences in the shape of the conchae. A. Gekkonidae
(Hoplodactylus). B. Varanidae (Varanus). C. Serpentes (Natrix). All figures are diagrammatic and not to scale. After Parsons (1970).

for each family has been used in determining character
states.
59. Olfactory epithelium (see Fig. 4). Poorly developed, less
than 2 receptor cells for each supporting cell (0); intermediate,
between 2 and 4 receptor cells for each supporting cell (1);
well-developed, more than 4 receptor cells for each sup-
porting cell (2). This character has been ordered according
to the morphocline 012. Data taken from Gabe & Saint
Girons (1976) and Cooper (1996a, 1997); the mean value
for each family has been used in determining character states.
It is a quantified version of Sb16 (olfactory epithelium
poorly developed/well-developed).
60. Vestibulum of nasal cavity (see Fig. 4). Short (0); greatly
elongated (1). Data taken from Parsons (1970) and references
therein. Dibamids have a short vestibulum (Hallermann
1998).
61. Conchal shape (see Fig. 5). Central space small or
absent, entire external nasal gland lies lateral to nasal capsule

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Soft anatomy and squamate phylogeny M. S. Y. Lee
(0); central space large, accommodating part of external nasal
gland (1). Data taken from Parsons (1970); dibamids have
state 1 (Hallermann 1998). Chamaeleons lack a well-developed
concha and are coded as not applicable.
62. Size of external nasal gland. Small (0); large (1). Data
from Parsons (1970); dibamids have state 1 (Hallermann 1998).
Oral glands
63. Dental glands (serous glands opening at the base of the
teeth). Absent on both jaws (0); present on both jaws (1).
P8. The descriptions for the states were switched in Presch
(1988), so that iguanians were stated to lack dental glands,
and Sphenodon and scleroglossans to possess them; the
reverse situation is true (Kochva 1978a,b). Dental glands
are absent in all basal modern snakes (Kochva 1978a,b;
Underwood 1997). Discussion of serially sectioned material
of Dibamus (Rieppel 1984, 1988) does not mention these
glands, and they have been tentatively coded as absent.
64. Labial glands (mucous or muco-serous glands open-
ing into the lips). Present on both jaws (0); lost in upper
jaws only (1); lost in both upper and lower jaws (2). This
character has been ordered according to the morphocline
0 12. Modified from P9; the character states as defined
by Presch (1988) were somewhat ambiguous (labial gland
present /incipient upper and lower labial glands/lower labial
glands only) and have been changed. Data taken from Gabe
& Saint Girons (1969), with the modification that agamids
and chamaeleons have state 0 while Lanthanotus and Varanus
have state 1 (Kochva 1978a,b). Snakes have well-developed
upper and lower labial glands (Kochva 1978a,b; Underwood
1997), while dibamids lack both (Rieppel 1988). Presch
(1988) coded xenosaurids with incipient upper and lower
glands, I have followed this but have not been able to locate
the primary reference.
65. Gland of Gabe on lower jaw. Absent (0); present (1). This
character refers to a large distinct seromucous gland on the
lower jaw (Kochva 1978a,b), and is presumably equivalent
to P10 (venom glands absent/present). If this inter-
pretation is correct, then contrary to Presch (1988), both
conditions appear to be present in basal modern snakes.
Scolecophidians lack such glands but aniliids and cylin-
drophids possess a large distinct seromucous gland which
Underwood (1997) terms the inferior rictal gland; despite
a different name it might well be homologous to the Gland
of Gabe. A discussion of serially sectioned material of
Dibamus (Rieppel 1988) does not mention these glands, and
they have been tentatively assumed to be absent.
Tongue and hyoid apparatus
66. Tongue shape. Short and wide (0); long and narrow (1).
Shape is here defined as in Cooper (1996b: Baselong-TL),
i.e. resting length of tongue (excluding tines and posterior
112
limbs) divided by maximum width of tongue (i.e. in the pos-
terior region). Values considered short and wide are < 2,
long and narrow are values > 2. The development of the
tines is scored as a separate character (69). A third state
(values > 3) was considered, but was not added because it
was phylogenetically uninformative, being found only in
Varanus (it is polymorphic in snakes, being absent in
scolecophidians but present in alethinophidians). Data are
taken from Cooper (1996b), McDowell (1972), Schwenk
(1986, 1995), and personal observations.
67. Tongue cross-section. Thick (vertically) in cross-
section and not greatly broadened (0); very flat and broad (1).
This character is a modification of Sa23 (anterior tongue
rounded in cross section with tapering tips/flat and broad
with untapered tips). The second part of the character
(tapering of tips) is correlated with the presence of extended
tines (see character 69) and has been omitted. It is also
related to E138 (cross-section and keratinization of tongue).
Iguanids have been coded as polymorphic rather than with
state 0 because some taxa (e.g. Crotaphytus) have state 1
(Schwenk 1995). Dibamus has a broad tongue (Greer 1985b,
personal observation). Amphisbaenians also have a rather
broad tongue if the extended tines are not considered (e.g.
see Schwenk 1994).
68. Notching of free part of tongue. Not notched (0);
notched less than 10% of total length of tongue (exclud-
ing posterior limbs) (1); notched between 10 and 20% (2);
notched between 20 and 40% (3); notched more than 40%
(4). E137. This character has been ordered according to the
morphocline 01234. The character states are broadly
concordant with the tongue fork score of Cooper (1996b),
i.e. length of forked zone divided by width (rather than
length) of tongue. This character includes Sa22 (tongue tip
not bifurcated/bifurcated). Estes et al. (1988) included a
further character state, tongue notched more than 50%.
However, this state is not cladistically informative as it
occurs uniformly only in one terminal taxon (Varanus).
Most snakes also have this condition but some basal forms
(scolecophidians) have a tongue that is notched less than
50% (McDowell 1972; Wallach, personal communication;
personal observation).
69. Tines of tongue tip. Not drawn out into long, tapering
points (0); drawn out into long, tapering points (1). Sa25.
Though this shape character is admittedly subjective, I
differ from Schwenk (1988) in considering lacertids,
Heloderma and Lanthanotus to have the derived state. Their
tines are long, tapered, and sharply pointed, and appear
more similar in shape to teiids and gymnophthalmids, which
were coded with the derived state by Schwenk (1988), than
to iguanids, scincids and anguids, which were coded with
the primitive state (see illustrations in McDowell 1972;
Schwenk 1994, 1995).
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ZSC035.fm Page 113 Thursday, June 1, 2000 3:12 PM
70. Relationship of tongue to sublingual plicae. Entire tongue
rests above sublingual plicae (0); anterior portion lies
between rather than above sublingual plicae (1). This
corresponds to part of the variable pallet in Cooper
(1996b), which included two traits (position of tongue, and
development of pallets). Data from McDowell (1972) and
Cooper (1996b). Amphisbaenians have state 1 (Schwenk,
personal communication).
71. Foretongue. Not much wider than width of the internal
hyoglossus muscle bundles (0); much wider than width of the
internal hyoglossus muscle bundles (1). Sa16.
72. Foretongue retractability. Foretongue not retractable into
hindtongue (0); foretongue retracts within hindtongue at a
zone of invagination (1). E136; Sa 34.
73. Hindtongue. Fleshy and solid (0); modified into sheath
(1). Sa27. While this character is likely to be partly cor-
related with the previous, they have been treated as separate
because some taxa possess a retractile foretongue but retain
a fleshy, solid hindtongue.
74. Glandular epithelium of tongue. Present on foretongue
and hindtongue (0); lost on hindtongue only (1); lost on
hindtongue and foretongue (2). This character has been
ordered according to the morphocline 012. This represents
Sa20 with an additional state (2). According to Schwenk (1988),
amphisbaenians and dibamids are the only squamates which
completely lack glands on the tongue epithelium. Dibamids
possess some glands deeper within the tongue; however, as they
lack epilthelial glands and the deeper glands are of uncertain
homology (Schwenk 1988), they have been coded with state 2.
75. Taste buds on tongue. Present (0); absent (1). Sb4. The
observation that Varanus and snakes lack lingual taste buds
(Schwenk 1985) has recently been confirmed (Young 1997).
Lingual taste buds are also absent, or at least exceedingly
rare, in Lanthanotus (Schwenk, personal communication).
76. Lingual mucocytes. Present over entire tongue (0); lost
on foretongue but present on hindtongue (1); lost on fore-
tongue and hindtongue (2). This character is ordered
according to the morphocline 012. Lingual mucocytes are
present on only the hindtongue in Lanthanotus, and com-
pletely absent in Varanus and the few snakes so far examined
(Schwenk, personal communication).
77. Lingual mucocytes. Few serous glands, i.e. mostly
muco-serous (0); many serous glands (1). Sa21. Not applicable
in taxa lacking lingual mucocytes (see previous character).
78. Lingual scales. Absent (0); present (1). Sa3.
79. Lingual scale arrangement. Arranged irregularly (0);
arranged in diagonal rows across tongue (1). Sa4. Codings for
this, and the next character are as in Schwenk (1988), except
that taxa without lingual scales (see previous character) are
scored as not applicable.
80. Lingual scale morphology. With smooth posterior edges
(0); with crenulated or irregular posterior edges (1). Sa5.
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M. S. Y. Lee Soft anatomy and squamate phylogeny
81. Dorsal lingual plicae (transverse, imbricate folds across
dorsal tongue surface). Absent (0); present on hindtongue
only (1); present on hindtongue and foretongue (2). E139.
This character also represents a combination of Sa1 (plicae
absent/present on hindtongue) and Sa2 (plicae absent /present
on foretongue). It has been ordered according to the morpho-
cline 012.
82. Ventral lingual plicae (transverse, imbricate folds across
ventral surface of tongue). Absent (0); present on fore-
tongue (1). Sa26 after Harris (1985).
83. Covering of main body of tongue. High-profile papillae
(0); low-profile papillae (1); papillae absent, replaced by
smooth keratinized epithelium (2). Sb2. This character is
a more finely subdivided version of Sa11 (papillae present/
absent) and also overlaps with E138 (cross-section and
keratinization of tongue). This character has been ordered
according to the morphocline 012. To avoid correlation
with character 87, this character refers to the covering of
only the body of the tongue, excluding the tines.
84. Reticulation of tongue papillae. Papillae not reticular
(0); reticular on foretongue only (1); reticular on fore-
tongue and hindtongue (2). This character represents both
Sa6 (reticular papillae present/absent on foretongue) and
Sa7 (reticular papillae present/absent on hindtongue also).
This character has been ordered according to the morpho-
cline 012. This, and the next two characters, have been
rephrased slightly from Schwenk (1988) so as to be not
applicable in taxa without tongue papillae (see previous
character).
85. Shape of tongue papillae. Tops convex, not flat (0); tops
flat (1). Sa8.
86. Pointed epithelial apices on papillae of hindtongue. Absent
(0); present (1). Sa9.
87. Tongue keratinization. Absent (0); keratinous ventral
pallets present on ventral surface of foretongue (1); keratinous
covering present over tines of tongue tip (2). Data from
McDowell (1972), Greer (1985b), Schwenk (1986), Cooper
(1997) and personal observations. Cooper (1997) codes taxa
with state 2 (keratinous tines) as lacking ventral pallets;
however, as the keratinous tine surfaces might represent
modified ventral pallets, they have been coded as a third
state here. Because of uncertainty over the homology between
states 1 and 2, this character is unordered. Amphisbaenians
have state 2 (personal observation and Schwenk, personal
communication).
88. Ventral pallet shape. Does not project laterally, covered
by main body of tongue in dorsal view (0); projects laterally
beyond margins of main body of tongue, and visible in
dorsal view (1). Sa24. Codings are as in Schwenk (1988),
except that the character is treated as not applicable in taxa
lacking ventral pallets (see previous character).
89. Sublingual glands on floor of mouth under free part of
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Soft anatomy and squamate phylogeny M. S. Y. Lee
tongue. Diffuse and irregular in transverse section (0); dense
and round in transverse section (1). Sa29.
90. Sublingual glands on floor of mouth under free part of
tongue. Paired (0); scattered (1). Sa30.
91. Entoglossal process of hyoid. Single continuous cartilage
(0); distal end detached and connected to proximal portion
by ligaments (1). Sa19.
92. Laryngohyoid ligament. Without dorsolateral branches
(0); with dorsolateral branches extending ventral to laryngeal
cartilage (1). Sa18.
93. Hypohyal (Sensu Maclean 1974). Short or absent (0);
long (1). P89. Among taxa not considered by Presch, the
hypohyal is short in dibamids (Rieppel 1981; Greer 1985b)
and absent in snakes (Rieppel 1981). Because the entire
hyoid apparatus in amphisbaenians is small relative to skull
and body size, the hypohyal is long relative to the rest of
the hyoid but short relative to skull and body size (e.g.
Maclean 1974). They are coded as unknown rather than
with state 1.
Eye and orbital structures
94. Eye. Well developed with sharply formed lens and
fully differentiated retinal visual cells, animal very responsive
to light when constructing burrows (0); poorly developed
with vaguely formed lens and incompletely differentiated
retinal visual cells, animal poorly responsive to light when
constructing burrows (1). Amphisbaenians and dibamids
both have poorly developed eyes and are poorly responsive
to light, constructing burrows along the walls of glass
enclosures (Underwood 1970 and personal communication).
In contrast, even the most visually reduced modern snakes,
the blindsnakes (scolecophidians), retain a well-developed
lens and retina with differentiated visual cells, and are highly
responsive to light, avoiding constructing burrows near
walls of glass enclosures (Underwood 1957 and personal
communication). Since all modern snakes retain a well-
developed lens and retina, snakes have been scored with
state 0. Furthermore, at least one blindsnake has large eyes
(Broadley & Wallach 1996).
95. Visual cells of retina. Rods present (0); rods absent (1).
All lizards lack true rods, defined as retinal cells with single
synaptic connection, and rhodopsin, although some have
modified cones that superficially resemble rods (Underwood
1970). This also appears to be the case with amphisbaenians;
the cells in dibamids are too poorly differentiated to determine
the condition (Underwood, personal communication). All
basal modern snakes retain rods, and either have a duplex
(rod and cone) or scolecophidian (rod only) retina. Rods
have been lost, however, in some highly derived snakes
(colubrids).
96. Pupil shape. Vertical (0); round (1). This character is
not applicable in amphisbaenians and dibamids, which have
114
greatly reduced eyes (including pupils). Data taken from
Underwood (1970).
97. Eye covering. Eye exposed, upper and lower eyelids
present (0); eye covered by single transparent spectacle (1);
eye covered by opaque scales (2). This character does not
form an obvious morphocline and is unordered. Both
derived states occur in basal modern snakes (e.g. state 1 in
cylindrophids, xenopeltids and some scolecophidians and
uropeltids, state 2 in most scolecophidians, aniliids, and
some uropeltids). Basal gymnophthalmids and scincids all
have normal eyelids, but a few forms in both groups have
spectacles (Underwood 1970).
98. Lacrimal duct. Single (0); double (1). Data from Bellairs
& Boyd (1950), Parsons (1970), Saint Girons (1976), Pregill
et al. (1986) and Hallermann (1998).
99. Anterior opening of lacrimal duct. Enters oral cavity
directly, near opening of duct of Jacobsons organ (0); enters
duct of Jacobsons organ (1); enters main lumen of Jacobsons
organ (2). This character represents H138 (lacrimal duct
connecting with choanal groove/connecting with duct of
Jacobsons organ) with a new state added. This character
has been ordered according to the morphocline 012. The
character state codings are rather different from that in
Hallermanns data matrix (all squamates apart from anguids
are here coded as possessing states 1 or 2). This interpreta-
tion agrees with Hallermanns statement that the connection
of the lacrimal duct and the duct of Jacobsons organ is a
synapomorphy of Squamata, but inconsistent with his matrix
coding of most lizards with state 0. The codings here are
based on Bellairs & Boyd (1950), Parsons (1970) and refer-
ences therein; while there is some uncertainty, Sphenodon
appears to exhibit state 0 (Parsons 1970). Dibamids and Helo-
derma have recently been reported to have state 1 (Hallermann
1998 p. 412). Chamaeleons are difficult to score because of
the great reduction of Jacobsons organ (Parsons 1970).
Visceral organs and histology
100. Lungs. Subequal in size (0); left lung reduced (1); right
lung reduced (2). State 1 occurs in pygopodids and snakes
(Butler 1895; Underwood 1957, 1967; Wallach 1998) and
state 2 in dibamids (Greer 1985b) and most amphisbaenians,
including basal forms (Butler 1895; Gans 1978; Crook
& Parsons 1980; Perry 1998). In dibamids, the single lung
mass might either represent the left lung alone, or a com-
bined left and right lung where the left is longer and wider
than the right (Greer 1985b; fig. 12); under either inter-
pretation they exhibit state 2. This character is unordered,
since either state 1 and 2 might evolve directly from state 0,
and states 1 and 2 might evolve into each other by a simple
switch in asymmetry.
101. Lungs. Single-chambered (0); partially divided into
numerous chambers by septae (1); multichambered, divided
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ZSC035.fm Page 115 Thursday, June 1, 2000 3:12 PM
fully into numerous chambers (2). This character is ordered
012. Data from Perry (1998); xenosaurids are coded as
0 and 1 in his cladogram (fig. 1.11), are both genera are
described in the text as having septa; thus, only the latter
condition is coded here.
102. Lungs. Without intrapulmonary bronchi or pseudo-
bronchus (0); with intrapulmonary bronchi, one in each
lung (1); with single pseudobronchus between lungs (2).
Data from Perry (1998). As the homologies between the
intrapulmonary bronchi and the pseudobronchus are uncertain,
this character is not ordered.
103. Ventricle of heart. Apex attached to pericardium by
ligamentous gubernaculum cordis (0); apex free from peri-
cardium, gubernaculum cordis absent (1).
104. Fundic glands of stomach. Body of gland consisting of
both mucous (cyanophilic) and serous (erythrophilic) cells
(0); mucous cells lost, body of gland consisting of serous
(erythrophilic) cells only (1). Data from Gabe & Saint
Girons (1972) and Saint Girons (1976).
105. Fundic glands of stomach. Distinct neck cells absent (0);
distinct neck cells present (1). Data from Gabe & Saint
Girons (1972) and Saint Girons (1976). Modern snakes are
polymorphic for this character: alethinophidians possess neck
cells while scolecophidians lack them.
106. Pancreas. Elongated or multilobed (0); compact (1).
Snakes and Varanus are unusual among squamates in
having a compact pancreas (Underwood 1957, 1967). Most
other lizards, and Sphenodon, have an elongated diffuse
pancreas (Guib 1970; Hill 1926). Some amphisbaenians
have an elongated pancreas (Crook & Parsons 1980; contra
Underwood 1957).
107. Main bile salt. Cholic acid (0); allocholic acid (1);
varanid acid (2). Data based on appendices in Haslewood
(1967, 1978). In addition, anguids and lacertids were noted
to have cholic acid (1978 p. 98). Although the condition in
Sphenodon is not known, archosaurs (the second living out-
group) have predominantly cholic acid, so this state has
been coded in the outgroup. Most snakes have cholic acid,
although pythons and related taxa have an autapomorphous
(and cladistically uninformative) pythocholic acid (Haslewood
1967); snakes have therefore been coded with state 0. This
character is unordered, although a study of the chemical
formulae of the three states might reveal a morphocline
(chemocline?).
Circulatory system
108. Carotid duct connecting carotid and systemic arches.
Present (0); absent (1). P23. Contrary to Presch (1988),
the duct is absent in Lanthanotus (McDowell 1972; Estes
et al. 1988). Of taxa not considered by Presch, the duct is
present in dibamids (Greer 1985b) and absent in snakes
(Underwood 1957).
The Norwegian Academy of Science and Letters Zoologica Scripta, 29, 2, April 2000, pp101130
M. S. Y. Lee Soft anatomy and squamate phylogeny
109. Stapedial artery. Passes anterior to stapes (0); passes
through stapes via stapedial foramen (1); passes posterior
to stapes (2). E145. This character has been ordered
according to the morphocline 012.
Cloaca and genitalia
110. Cartilaginous apical horns within hemipenis. Absent (0);
present (1). From Branch (1982). This character and the next
cannot be polarized because rhynchocephalians and other
reptiles lack a hemipenis.
111. Hemipenial sheath. Absent (0); present (1). A19. Of
the taxa examined by Arnold (1984), all basal lacertids have
state 1 and all basal scincids have state 0. They have been
coded with these states, even though one sampled genus in
each family has a different condition.
112. Hypoischium. Well developed (0); vestigial or absent
(1). A1. This character is not applicable in taxa with highly
reduced pelves.
113. Urinary bladder. Present (0); absent (1). P21. Dis-
tribution of this character in lizards is based on Beuchat
(1986). In some cases, some very old references were listed
as contradicting more recent studies: for instance, Shufeldt
(1890) and Cope (1900; cited by Beuchat as 1898) reported
a bladder in Heloderma but Gabe & Saint Girons (1965)
could not locate one. In such instances, the more recent
reference is accepted. Of taxa not discussed in Fox (1986),
dibamids possess a bladder (Greer 1985b), snakes lack one
(Fox 1977; Greer 1997), and amphisbaenians exhibit both
states (Crook & Parsons 1980; contra Presch 1988).
114. Post-cloacal sacs. Absent (0); present (1). A14.
115. Cloacal gland. Discrete ventral gland present in both
sexes (0); discrete gland lost in males but not females (1);
discrete glands lost in both sexes (2). Data from Gabe &
Saint Girons (1965). The glande sbace of Sphenodon is
histologically and positionally similar to the ventral cloacal
gland of squamates and provisionally coded as homologous.
Only males of Heloderma and Varanus were investigated by
Gabe & Saint Girons (1965): glands were present and on
this basis these taxa must exhibit either states 0 or 1. Only
a female teiid was examined, which possessed glands; since
taxa with glands in the female invariably have them in
males, teiids have been provisionally coded with state 0.
This character is ordered according to the morphocline
012, i.e. glands present lost in males only lost in
both sexes.
116. Cloacal glands. Ventral glands a single mass (0);
ventral glands divided into two or more discrete masses (1).
Data from Gabe & Saint Girons (1965). This character is
not applicable in taxa where neither sex possesses ventral
glands (see previous character).
117. Cloacal glands. Discrete dorsolateral glands absent in
both sexes (0); dorsolateral glands present in males only (1);
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Soft anatomy and squamate phylogeny M. S. Y. Lee
dorsolateral glands present in both sexes (2). Data from
Gabe & Saint Girons (1965). Only males of Heloderma
and Varanus were investigated by Gabe & Saint Girons
(1965): glands were present and on this basis these taxa
must exhibit either states 1 or 2. Only a female teiid was
investigated, which lacked glands; teiids have been coded
with either 0 or 1. This character is ordered according to
the morphocline 012.
Spermatozoon
118. Acrosome of spermatozoon. Circular in cross-section (0);
flattened in cross-section (1). J1. Information on all sperma-
tozoon characters is taken from Jamieson (1995), Jamieson
et al. (1996), and Oliver et al. (1996).
119. Perforatorial base plate of spermatozoon. Absent or
indistinct (0); well-developed and distinct (1). J2. Agamids
have been coded as unknown rather than with state 1 because
the presence of a distinct base plate has been acknowledged
to be questionable ( Jamieson 1995 p. 368).
120. Perforatorium. Rod-like, constant diameter through-
out (0); gradually tapering anteriorly (1). Data from Jamieson
(1995) and references therein.
121. Epinuclear translucent space. Absent (0); indistinct and
small (1); distinct and large (2). J5. This character has been
ordered according to the morphocline 012.
122. Midpiece. Short (0); moderate in length (1); long (2).
J6. This character has been ordered according to the morpho-
cline 0 12.
123. Mitochondria of midpiece. Round (0); intermediate
(1); long (2). This character is ordered according to the
morphocline 012. It, and the following, represent a sub-
division of J8 (mitochondria round/intermediate/long and
columnar/long and sinuous).
124. Shape of elongate mitochondria. Straight and columnar
(0); curved and sinuous (1). J8. Not applicable in taxa lacking
elongate mitochondria (see previous character).
125. Dense bodies. Intramitochondrial (0); regular rings
(1); scattered (2); linear series (3); stellate spiral (4); two
groups (5). J9. This character does not form an obvious
morphocline and is unordered.
126. Multilaminar membranes. Absent (0); present (1). J16.
Excluded characters
Certain soft anatomical and behavioural characters employed
in previous analyses of squamates were not included in the
present analysis. Often, it was because the derived state
of the character is present in all the squamates for which
they can be determined. While these characters support
monophyly of squamates, they are uninformative with
respect to relationships within squamates and have not been
included in this cladistic analysis. They include characters
1214, 17, 28, 31 from Schwenk (1988), characters 6, 7, 13,
116
1921 from Schwenk (1993) and characters 4, 11, 14 and 17
from Jamieson (1995).
Many characters used in older studies of snake relation-
ships have been discussed in a detailed review (Rieppel
1988). Some were shown to be uninformative or equivocal
and accordingly have not been used here: these include the
trabeculae cranii cartilages, the retractor pterygoidei muscle,
and adventitious cartilage. The remaining characters dis-
cussed in that review were either included in the above data
matrix, or omitted for the reasons discussed below. Often,
the reason is mainly because (as emphasized in Rieppel
1988) the distribution of character states is at present
extremely poorly known (e.g. for only two or three ter-
minal taxa) or poorly described (e.g. stated to be usually
absent in lizards without further details). When surveyed
rigorously across a more comprehensive range of taxa, such
characters will prove phylogenetically informative.
Metotic fissure. The metotic fissure is subdivided in both
lizards and snakes, but by slightly different developmental
routes in the two groups. Rieppel (1988) interpreted the
patterns as two separate specializations, and thus, as sup-
port for lizard monophyly to the exclusion of snakes.
However, the polarity of this character is indeterminate as
Sphenodon retains an undivided metotic fissure and cannot
be coded. There remains the strong possibility that the lizard
pattern is primitive for squamates and the snake pattern
derived. If so, this character would be uninformative in this
analysis as the derived condition would be an autapomorphy
of a single terminal taxon (snakes).
Nasal septum not connected dorsally. This character was used
by Hallermann (1998) but was not cladistically informative
as the derived state occurred uniformly in only one terminal
taxon (dibamids).
Geniotrachealis muscle. Groombridge (1979a,b) suggested
that varanids and snakes, unlike most squamates, possess a
geniotrachealis muscle. However, he asserted that this must
be convergent (without explanation), and also did not
discuss which lizard taxa were confirmed as lacking the
muscle.
Genioglossus lateralis, constrictor colli, episterno-cleido-mastoideus
and pseudotemporalis profundus muscles. Pregill et al. (1986),
citing Rieppel (1980), suggested that Varanus and Lanthanotus
share a subdivided genioglossus lateralis and a constrictor colli
which covers the first ceratobranchials. Varanoids (Varanus,
Lanthanotus and Heloderma) were said to be characterized by
an episterno-cleido-mastoideus inserting broadly on the parietal.
These traits were absent in other anguimorph lizards. How-
ever, the distribution in other squamates (including snakes)
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ZSC035.fm Page 117 Thursday, June 1, 2000 3:12 PM
was not adequately discussed in either of these studies. An
enlarged anterior head of the pseudotemporalis profundus was
said to characterize Varanus and Lanthanotus. However, this
character is difficult to define as the anterior head is often
continuous with the rest of the muscle, and furthermore,
appears to be enlarged in many other taxa (e.g. pygopodids,
teiids).
Trunk musculature. Rage (1982, 1992) suggested that amphis-
baenians and snakes shared two synapomorphies in the
trunk musculature; Rieppel (1988) reviewed the evidence
and showed that the pattern is not clear-cut, with snakes
showing variability for these traits.
Thymus. The thymus develops from the second and third
pharyngeal pouches in lizards, but from the fourth and fifth
in snakes (Bockman 1970). Rieppel (1988) noted that the
latter condition appears to characterize Sphenodon; if so, the
condition in lizards is derived and would suggest that
snakes lie outside lizards. However, the distribution of this
character within lizards is too poorly known at present
(Bockman 1970 examined only three genera).
Position of heart. The heart appears to be situated more pos-
teriorly in varanids, snakes, amphisbaenians, and dibamids
than in most squamates (Webb et al. 1971; Bellairs 1972;
Greer 1985b; see review in Rieppel 1988). However, the
lizard families which have the normal (anterior) position
of the heart were not specified in these studies, and there is
also the difficulty of standardizing interpretation of the
relative position of the heart in short-bodied and elongate
squamates.
Morphology of heart. Webb et al. (1971) stated that varanids
and snakes share several similarities in heart morphology,
absent in most other squamates. However, they did not specify
in detail which groups were observed to lack these features
the distributions of these characters therefore need to
be further investigated. Similarly, Farrell et al. (1998; see
also MacKinnon & Heatwole 1981) suggested that unlike
most lepidosaurs, the atrium of varanids and some snakes
possess a cortical layer of compact muscle. The characters
distribution needs to be further investigated; if primitively
present in snakes, this would make it another varanid-snake
synapomorphy.
Spleen. It has been suggested that amphisbaenians and
snakes share a synapomorphy of having the spleen embedded
in the pancreas, while the two organs are separated in other
squamates (e.g. Rage 1982; Rieppel 1988). However, the
embedded condition does not uniformly characterize amphis-
baenians: many have the typical squamate condition (Gans
The Norwegian Academy of Science and Letters Zoologica Scripta, 29, 2, April 2000, pp101130
M. S. Y. Lee Soft anatomy and squamate phylogeny
1978; Crook & Parsons 1980). Thus, the derived state of
this character only uniformly characterizes a single terminal
taxon.
Hemipenis. Branch (1982) suggested that varanids and
snakes do not exhibit the seasonal changes in hemipenis
development which occur in most squamates. However, the
distribution of this character in other squamates was not
discussed in detail.
Interrenal cells. Hebard & Charipper (1955) reported major
differences between higher squamate taxa in the arrangement
of the nuclei of the cells of the interrenal cords. However,
these differences are not consistent: the alternative positions
of the nuclei can occur even within the same individuals
and are probably correlated with seasonal cycles (Gabe
1970).
Calyciform duodenal cells. Pregill et al. (1986) suggested that
sero-mucous calyciform duodenal cells are a varanoid
synapomorphy, but did not discuss the distribution of this
character in other squamates in detail.
Short-term colour change ability (metachromatism). Frost
& Etheridge (1989) listed this trait as a synapomorphy of
iguanians, implying that other squamates lack metachromatism.
However, Greer (1989) listed absence of metachromatism
as a synapomorphy of varanids and snakes alone, implying
that other squamates possess it. At least some species from
most squamate families possess varying ability to change
colour, although the rapidity and extent varies greatly (e.g.
Greer 1989). This character needs to be rigorously defined
and resurveyed.
Male combat dance and wrestling. Greer (1989, 1997) listed
this as a synapomorphy of Varanus and snakes. However,
it is only present in some snakes and has not been
recorded in any primitive forms (Carpenter & Ferguson
1977). This character is cladistically uninformative because
the derived state is uniformly present in only one terminal
taxon.
Phylogenetic analysis and results
In both the ordered and unordered analyses (see Terminal
taxa, polarity and character state codings), the branch-and-
bound search of PAUP* (Swofford 1999) was used to find the
most parsimonious trees. In the Parsimony Settings, multistate
taxa were interpreted as uncertainty over the primitive state,
rather than as having multiple states in the ancestral species.
The tree was rooted with the outgroup (Rhynchocephalia).
The support index (Bremer 1988) was calculated using PAUP
commands generated in TreeRot (Sorenson 1996) modified
117
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Soft anatomy and squamate phylogeny M. S. Y. Lee

Fig. 6 The strict consensus of the four most parsimonious trees found in the ordered analysis of the soft anatomical characters (each 312
steps long, consistency index 0.5, retention index 0.6). Clades in common with the unordered analysis (Fig. 7) are indicated with the white
bars, clades in common with a recent osteological analysis (Fig. 8) are indicated with the shaded bars. It will be clear that all three analyses
produced almost identical trees. The first number beside each clade refers to the Bremer support, the second number refers to
bootstrapping frequency.+ found in the unordered analysis of the soft anatomical characters (each 294 steps long, consistency index 0.54,
retention index 0.61) Clades in common with the ordered analysis (Fig. 6) are indicated with white bars, clades in common with a recent
osteological analysis (Fig. 8) are indicated with the shaded bars. The first number beside each clade refers to the Bremer support, thee
second number refers to bootstrapping frequency.

so that all heuristic searches involved 100 rather than 20
random addition sequences. Bootstrapping frequencies
are based on 1000 heuristic searches each with 100 random
addition replicates. Branch-and-bound searches could not
be used for calculating support indices or in bootstrapping
because of time constraints.
In the ordered analysis, four most parsimonious trees were
found, each with a length of 323 steps, a consistency index
of 0.51, and a retention index of 0.62. The strict consensus
of these is shown in Fig. 6. The results of the unordered
analysis were almost identical. Nine most-parsimonious
trees were found. The tree length was slightly shorter (303
steps) but the consistency and retention indices approx-
imately the same (0.54 and 0.61, respectively); this was
to be expected since removing constraints of character-
state order makes multistate characters more likely to be
congruent with any particular phylogenetic arrangement.
The strict consensus is shown in Fig. 7 and is very similar
to that found in the ordered analysis; most clades are present
and with similar levels of support. There are no mutually
incompatible clades between the two analyses. The only
topological differences introduced by relaxing assumptions
of character state order are as follows. Two poorly corrobor-
ated clades are collapsed (Agamidae + Chamaeleonidae, and
Xenosauridae + Varanoidea), while a previous trichotomy is
now resolved weakly in favour of a Lanthanotus + Varanus
clade. Thus, it seems in this study, the effect of character
ordering is minor.
The strength of phylogenetic signal in the soft anatomical
characters (consistency index 0.5154, retention index
0.610.62) is remarkably similar to that in the osteology
(consistency index 0.48, retention index 0.64: Lee 1998);
thus, neither class of characters is inherently better (i.e.
less prone to homoplasy). The nature of the signal is also
highly congruent with that of the osteology. Nearly all the
resolved clades on the strict consensus trees (Figs 6, 7) match

118 Zoologica Scripta, 29, 2, April 2000, pp101130 The Norwegian Academy of Science and Letters
ZSC035.fm Page 119 Thursday, June 1, 2000 3:12 PM
Fig. 7 The strict consensus of the nine most parsimonious trees found in the unordered analysis of the soft anatomical characters (each 294
steps long, consistency index 0.54, retention index 0.61). Clades in common with the ordered analysis (Fig. 6) are indicated with white
bars, clades in common with a recent osteological analysis (Fig. 8) are indicated with the shaded bars. The first number beside each clade
refers to the Bremer support, the second number refers to bootstrapping frequency.
clades discovered in a recent analysis of osteology (Fig. 8).
In many cases, clades present in both analyses were highly
corroborated in at least one data set: Iguania, Scleroglossa,
Gekkota, Annulata (Amphisbaenia + Dibamidae), Lacertoidea,
Teioidea, Varanoidea, and Thecoglossa (Varanidae + Serpentes).
These clades can be treated as especially well corroborated.
The only difference in the two studies concerns scincids
and cordylids. In the soft anatomical tree (Figs 6, 7) scincids
and cordylids form sister-taxa and together group with
lacertoids, forming the traditionally recognized Scincomorpha.
However, the association with lacertoids is very weak, and
the conservative interpretation would collapse this part of
the phylogeny into an unresolved trichotomy: (lacertoids)
(scincids + cordylids) (anguimorphs). In the osteological
tree (Fig. 8) scincids and cordylids form a tichotomy with
anguimorphs, but this clade (Diploglossa) is also only weakly
supported. Again, the most conservative interpretation
would collapse the osteological cladogram into a four-way
polytomy: (lacertoids) (scincids) (cordylids) (anguimorphs).
This conservative arrangement is compatible with the con-
servative soft anatomical tree. Thus, the sole disagreement
between the data sets disappears when only well-corroborated
clades are considered. The conflicting arrangements are
only weakly supported and attributable to sampling error
The Norwegian Academy of Science and Letters Zoologica Scripta, 29, 2, April 2000, pp101130
M. S. Y. Lee Soft anatomy and squamate phylogeny
rather than cohesive and incongruent signals in the two
data sets (e.g. Bull et al. 1993; Page 1995).
The only other difference between the soft anatomical
and osteological trees is that the former is more poorly
resolved, with a basal polytomy within Scleroglossa, and a
polytomy between Varanus, Lanthanotus and snakes. In the
osteological tree, relationships at the base of Scleroglossa
are resolved (albeit weakly), and a Varanus-Lanthanotus
clade is strongly corroborated. These differences therefore
are very minor. Conversely, the agreement between the two
trees is very reassuring. Most of the major groups of limbed
squamates traditionally recognized are identified in both
analyses: Iguania, Acrodonta, Scleroglossa, Scincoidea,
Lacertoidea, Teioidea, Gekkota, Anguimorpha, Varanoidea.
Several areas where there was previously less consensus
are also resolved in similar ways in both analyses. Xantusiids,
a problematic group of uncertain affinities, emerge as related,
albeit weakly, to gekkotans (and thus to dibamids and
amphisbaenians). This view has been suggested before (e.g.
McDowell & Bogert 1954; Hoffstetter 1962; Northcutt 1978;
Greer 1985a; Schwenk 1988). However, the traditional
and currently prevailing view links xantusiids with lacertoids
(e.g. Camp 1923; Estes et al. 1988; Presch 1988; Wu et al.
1996; Evans & Barbadillo 1997). The results of this study
119
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Soft anatomy and squamate phylogeny M. S. Y. Lee

Fig. 8 The strict consensus of the two most parsimonious trees found in a recent analysis of squamate osteology, based on 230 characters
(Lee 1998). Each tree was 580 steps long, consistency index 0.48 retention index 0.64. Clades in common with the ordered analysis of soft
anatomical traits (Fig. 6) are indicated with white bars, clades in common with the unordered analysis (Fig. 7) are indicated with grey bars.
The first number beside each clade refers to the Bremer support, the second number refers to bootstrapping frequency.

suggests that, contrary to this view, the many gekkotan-
xantusiid similarities are probably homologous rather than
convergent. These include the (paedomorphic?) reduction
of many skull bones, a vertical pupil, a transparent spectacle,
broad tongue, eye-licking behaviour, and nocturnal
habits (McDowell & Bogert 1954; Underwood 1970; Greer
1985a; Schwenk 1988; Lee 1998). It is interesting that most
of the skull features, and a broad(ish) tongue, also occur
in amphisbaenians and dibamids. The remaining traits are
not really applicable to these burrowing, almost eyeless
animals. Relationships among basal anguimorphs, how-
ever, remain unresolved: in both the soft anatomical and
osteological studies, xenosaurids and anguids emerge as
successive outgroups to varanoids, but this arrangement is
very poorly supported in both studies.
The relationships of the three problematic groups of
limbless squamates are particularly well-resolved in both
the soft anatomical and osteological studies. In both analyses,
snakes group very strongly with varanids (Varanus and
Lanthanotus) based on traits from all regions of the body.
The soft anatomical traits are listed in the Diagnoses below;
the numerous osteological traits are listed in Lee (1998). This
grouping seems to have as much character support as
many widely accepted morphological groupings (e.g. the
bird-dinosaur clade). Viewed in this context, arguments for
alternative affinities of snakes (reviewed in Rieppel 1988;
Lee 1998) must be seen as special pleading unless they can refute
most of the nested synapomorphies uniting varanids and
snakes, and propose a larger suite of synapomorphies
that coherently support some alternative arrangement. It is
not sufficient to dispute a few of the snake-varanid characters
and mention the existence of some character conflict; a
rigorous phylogenetic analysis must be performed.
Similarly, as in all recent analyses that considered mainly
or entirely osteological data (Estes et al. 1988; Wu et al.
1996; Evans & Chure 1998; Lee 1998; Reynoso 1998;
Hallermann 1998), amphisbaenians and dibamids group
together, an arrangement that has been suggested before
(e.g. Greer 1985b). Thus, amphisbaenians and dibamids
might form a single radiation, and their elongated bodies,
reduced limbs, and extreme fossorial adaptations are homo-
logous. While many of the supporting characters appear
to be correlated with burrowing, at least a few of the soft
anatomical ones appear to be relatively independent (as

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ZSC035.fm Page 121 Thursday, June 1, 2000 3:12 PM
discussed in Diagnoses). However, due to the high levels
of correlation in most of the osteological and soft ana-
tomical characters supporting this clade, it is undoubtedly a
lot less secure than the Bremer support and bootstrap values
indicate. Again as congruent with a recent osteological
study (Lee 1998), the amphisbaenian-dibamid clade in turn
groups with gekkotans and xantusiids. However, it should
be noted that this arrangement is relatively weakly sup-
ported in both studies (Figs 6, 7, 8).
The information from the soft anatomy therefore increases
confidence in the results of a recent comprehensive survey
of osteology (Lee 1998; Lee & Caldnell 2000). The soft
anatomical data, in its totality, produces not only a well-
supported tree, but one that is highly congruent with
osteology. This is an important and surprising result, since
previous analyses of isolated sets of soft anatomical traits
have often produced differing (and often heterodox) results.
Indeed, appreciable character conflict appears to be present,
though not more than in the osteology (see above). The
consistency index in the ordered analysis (0.51) is less than
the expected value of 0.56 for cladistic analyses of 19 taxa
(Sanderson & Donoghue 1996). Yet the resolution of the
tree appears to be much better than expected, with 82% of
clades (141 out of 17) having > 50% bootstrap support, the
threshold level chosen in Sanderson and Donoghues
study. The corresponding figures for the unordered ana-
lysis are a consistencey index of 0.54, and 76% (132 out of
17) clades with > 50% bootstrap support. These figures
(82% and 76%) compare to an average of 48% of clades
with > 50% support in studies for all types of data, and 41%
for morphological studies (Sanderson & Donoghue 1996).
While the relatively high character-to-taxon ratio in this
study might have contributed to such resolution, this is
probably not the only factor, since some of the morpho-
logical studies, and most of the molecular sequence studies,
examined in Sanderson & Donoghue (1996) have even
higher ratios.
The affinities of snakes suggest a probable explanation
for why the phylogenetic signal is strong, despite the less-
than-averge consistency index. Snakes have been grouped
with anguimorphs, and in particular varanids, based on
tongue morphology (McDowell 1972; Schwenk 1988),
vomerolfactory anatomy (Schwenk 1993) and stomach histo-
logy (Gabe & St. Girons 1972 Saint Girons 1972). However,
other soft anatomical traits suggest alternative affinities:
snakes have also been grouped with amphisbaenians based
1
In addition to the 13 clades present in the strict consensus with more than
50% bootstrap support (Fig. 6), a Varanus-Lanthanotus clade is also sup-
ported with a bootstrap of 56%.
2
In addition to the 11 clades present in the strict consensus with more than
50% bootstrap support (Fig. 7), an agamid-chamaeleonid clade is supported
with a bootstrap of 58%, and a xantusiid-gekkotansclade is supported with a
bootstrap of 52%.
The Norwegian Academy of Science and Letters Zoologica Scripta, 29, 2, April 2000, pp101130
M. S. Y. Lee Soft anatomy and squamate phylogeny
on myological and visceral characters (Rage 1982), with
dibamids and feyliniid skinks based on brain characters (Senn
& Northcutt 1973), with pygopodids and lygosomine skinks
based on sperm ultrastructure (Jamieson 1995), with amphis-
baenians and dibamids based largely on cranial cartilages
(Hallermann 1998), or placed outside of all other squamates
based on eye characters (Underwood 1970). However, even
though the traits supporting different relationships for
snakes were all assessed and, if found valid, included in this
analysis, snakes still grouped robustly with varanids.
It appears that in all of these cases of character conflict,
one of the signals is stronger than the others, and remains
discernible in the combined analysis. The other, weaker
signals found in different soft anatomical organs cancel
each other out. As will be apparent from inspection of the
cladograms in Figs 6 and 7, the surviving signal is almost
always the signal that was congruent with the osteological
information. A more extreme hypothetical example is dis-
cussed in Barrett et al. (1991; see also Page 1995; Nixon &
Carpenter 1996), where the true phylogenetic signal is so
weak that it is hidden within two data sets (i.e. is not
apparent when the data sets are analysed separately), and
only emerges in a combined analysis when large numbers
of conflicting characters from the two data sets meet and
cancel each other out.
With the current example, most of the alternative posi-
tions of snakes are supported by only a few traits; often
these are from a single organ system and thus more likely to
be correlated than traits chosen at random. The exception
is the snake-anguimorph clade, which is supported by
numerous characters from the tongue, vomeronasal system
and stomach histology. There appear to be at least as many
conflicting characters, of course. However, these do not
combine to form a coherent signal suggesting a clear
alternative hypothesis (concerted homoplasy). Rather, the
characters contradicting a snake-anguimorph clade also
conflict with each other (diffuse homoplasy). Thus, when
all the evidence is analysed simultaneously, the support
for the snake-anguimorph clade remains discernible because
the numerous conflicting characters tend to nullify each
other. The residual signal from the soft anatomy closely
matches the signal found in the osteology.
This observation is consistent with the empirical results
which show that overall tree support is not closely cor-
related with the amount of homoplasy (e.g. Sanderson &
Donoghue 1989, 1996). In order to evaluate the support for
a clade (or an entire tree), the sheer number of incongruent
characters is not the only important consideration: whether
they are concerted or diffuse is equally important. A clade
supported by 10 characters and contradicted by nine will be
weak if the nine incongruent characters unanimously sup-
port a particular alternative clade; however, it will be strong
121
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Soft anatomy and squamate phylogeny M. S. Y. Lee
if the nine incongruent characters support nine different
clades. While Bremer and bootstrap supports will be much
higher in the first tree, tree lengths and consistency and
retention indices will be identical in both cases. Thus, it
is probably fruitless to seek an overall minimal level
of homoplasy in data sets that must be met in order for
cladistic analyses to yield robust results, or to argue that
particular types of data are better due to lower levels
of homoplasy: data sets with high incongruence can still
yield clear phylogenetic signals, while those with much lower
levels of incongruence can be phylogenetically ambiguous.
Support for the snake-anguimorph clade might be mis-
interpreted as weak if one simply tallies the large number
of conflicting characters. This was the approach taken in
Rieppel (1988), and it was concluded that there were far too
many conflicting characters for snake-anguimorph affinities
to be accepted. However, because the incongruent characters
conflict with each other, support for the snake-anguimorph
clade is actually rather strong. A similar situation also
appears to hold for most other taxa in this analysis. For
many of these squamate families, different soft anatomical
systems suggest different affinities (Estes et al. 1988; Lee
1998), suggesting a large amount of character conflict.
However, in many cases a strong signal emerges from
the combined analysis, indicating that there is a single (presum-
ably real) signal and no coherence in the incongruent
characters.
It is clear that concerted homoplasy is more likely to
mislead than is diffuse homoplasy (e.g. Wilkinson 1991;
Sanderson & Donoghue 1989, 1996; Givnish & Sytsma
1997). However, the suggestion that morphological traits are
more adaptive than molecular traits, and thus more prone
to concerted homoplasy (e.g. Hedges & Maxson 1996;
Givnish & Sytsma 1997) appears premature. All that can be
said is that the adaptiveness of molecular traits is currently
poorly understood, and thus that concerted homoplasy
in molecular traits might be less likely to be detected.
Indeed, recent studies indicate that many molecular traits
are under selection (e.g. Golding & Dean 1998; Chang &
Donoghue 2000) and that large portions of the genome
can evolve cohesively in response to a certain selective
forces (e.g. Naylor & Brown 1998). Furthermore, while it
is undoubtedly true that phenomena such as pleiotropy
and heterochrony can result in concerted homoplasy in
morphological traits, interdependence of sequences due to
constraints of secondary structure, base compositional
bias, hydrophobicity, strand asymmetry and correlated
changes due to gene rearrangments can lead to similar
concerted homoplasy in molecules (e.g. Naylor & Brown
1998; Hassanin et al. 1998; Andrews et al. 1998; Lee 1999).
Finally, a caveat must be made. The phylogeny sup-
ported by the soft anatomy is indeed almost identical to that
122
suggested by osteology. It seems that two sources of informa-
tion are both giving the same signal, and such taxonomic
congruence would increase ones confidence in the results
(Mickevich 1978; Miyamoto & Fitch 1995; Wiens 1998b).
However, the data sets are clearly not independent. As
emphasized above, many traits cannot be neatly classified
into one or the other category, and organismal integration
means that most significant evolutionary phenomena
would affect both systems. There will always be correlation
between, as well as within, osteological and soft anatomical
data sets. As a result, common signals from these sources do
not represent totally independent support for the same
phylogeny, and the common approach of analysing them
separately is suspect. Thus, the argument that the various
sets of soft anatomical traits should not be considered in
isolation, but should be combined into a single analysis,
applies more broadly. Even the entire soft anatomical data
set, or the entire osteological, behavioural, karyotypic or
molecular data sets, should not be considered in isolation, but
should eventually be combined into a single comprehensive
analysis. It is planned to eventually combine the osteological
(Lee 1998; Lee & Caldwell 2000) and soft anatomical data
(this study) with a behavioural and molecular data sets
currently still in preparation. Such a study will hopefully
do much to resolve affinities among squamates.
Soft anatomical diagnoses of squamate clades
The following soft anatomical characters diagnose clades
present in the strict consensus tree of the ordered analysis
(Fig. 6). Most of these clades were also found in the un-
ordered analysis (Fig. 7), and in osteological studies (Lee
1998; Lee & Caldwell 2000). Formal definitions of taxon
names, and osteological synapomorphies, are presented in
the latter studies. Characters listed here are those that
occur under delayed transformation (deltran) optimiza-
tion on the strict consensus tree (Fig. 6); those indicated
by asterisks also occur under accelerated transformation
(acctran) and are thus optimization-independent. The strict
consensus in this situation is only slightly less resolved, and
only slightly longer (331 steps vs. 323 steps), than any of the
most-parsimonious trees. Hence, the patterns of character
evolution are not greatly distorted by optimizing on this
(slightly) suboptimal consensus tree instead on each of the
four shortest trees.
Squamata
*28: Intrinsic circular muscles of tongue form complete ring
(0.5).
*45: Vestibular lip of cochlear duct distinct (0.29).
*61: Nasal concha with large central space (0.33).
*68: Free part of tongue notched (0.33).
*87: Ventral pallets of tongue present (0.5).
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M. S. Y. Lee Soft anatomy and squamate phylogeny

*95: Retina lacking rods (0.5). *56: Jacobsons organ at least moderately developed (1.0).
*96: Pupil round (0.5). *58: Jacobsons organ epithelium with at least 2.5 receptor
*99: Lacrimal duct enters duct of Jacobsons organ (0.67). cells per supporting cell (0.5).
*109: Stapedial artery passes posterior to stapes (0 2, 0.29). *59: Olfactory epithelium with at least 2 receptor cells per
*117: Dorsolateral cloacal glands present at least in males supporting cell (0.5).
(0.29). *62: External nasal gland large (1.0).
*121: Epinuclear space of spermatozoon small (0.33). *64: Labial gland of upper jaw lost (0.4).
*123: Mitochondria of spermatozoon elongated (0 2, *74: Glandular epithelium absent on at least foretongue
0.67). (0.67).
*125: Dense bodies of spermatozoon forming rings (0.83). *83: Tongue papillae low in profile (1.0).

Comments. Since only characters informative (i.e. variable) Nyctisaura

within squamates were considered in this study, the above
characters all optimize as diagnostic of squamates but with
subsequent reversals or further elaborations. Additional
soft anatomical characters, many of them unique and unre-
versed, are discussed in Gauthier et al. (1988a) and Estes
et al. (1988).
Iguania
*1: Dewlap present (1.0).
*30: Intercostalis ventralis muscle absent (1.0).
*39: Dracomorph brain organization (0.33).
*60: Vestibulum of nasal cavity elongated (1.0).
*63: Dental glands present (1.0).
*77: Lingual mucocytes serous and muco-serous (1.0).
*107: Allocholic acid present as main bile salt (0.67).
111: Hemipenial sheath present (0.33).
116: ventral cloacal glands a single mass (0.2).
*119: Perforatorial base plate of spermatozoon well-developed
(1.0).
121: Epinuclear space of spermatozoon large (1 2, 0.33).
124: Mitochondria of spermatozoon sinuous (0.33).
Acrodonta
*37: Retractor lateralis posterior muscle of hemipenis situated
within sheath (1.0).
42: Lower leg innervated by interosseous nerve (0.33).
*84: Reticulate papillae present over entire tongue (0 2, 1.0).
115: Ventral cloacal glands lost from females or from both
sexes (0.25).
*118: Acrosome of spermatozoon flattened in cross-section
(0.33).
Scleroglossa
*2: Cephalic scales few but large (0.33).
*3: Mid-dorsal scales same size as other dorsals (1.0).
*22: Pseudotemporalis profundus muscle of jaw with anterior
head (0.33).
*28: Intrinsic circular tongue muscles form thick ring (1 2,
0.5).
*29: Rectus abdominis lateralis muscle present (0.5).
6: Femoral or preanal pores present (0.25).
*34: Retractor laterales muscles of hemipenis close together
(0.25).
*40: Distal lobe of pituitary gland enlarged anteriorly (1.0).
*59: Olfactory epithelium with over 4 receptor cells per
supporting cell (1 2, 0.5).
*67: Tongue very flat and broad in cross-section (1.0).
*96: Pupil vertical (1 0, 0.5).
*97: Eye with transparent spectacle (0.67).
Gekkota
*17: Connection between nasal capsule and interorbital
septum incomplete (0.67).
*18: Processus supraoccipitalis absent (1.0).
*24: Extracolumellaris muscle of middle ear present (1.0).
*25: Meatal closure muscle of tympanum present (1.0).
*27: Hyoglossus muscle of tongue greatly subdivided (1.0).
*29: Rectus abdominalis lateralis muscle absent (1 0, 0.5).
*32: Transversus penis muscle of hemipenis with longitudinal
fibres (1.0).
43: Internal process of extracolumella absent (0.2).
*44: Spindle body in cochlear present (1.0).
*45: Vestibular lip of cochlear duct enlarged into recurved
flange (1 2, 0.29).
46: Limbus of inner ear greatly elongated anteroposteriorly
(0.33).
*48: Basal papilla of inner ear extends fully across limbus (1.0).
*50: Basal papilla of inner ear with tapered posterior
extremity (1.0).
51: Hair cells of inner ear attached to tectorial membrane
and intertial bodies (0.4).
*53: Inertial bodies situated alongside entire length of
tectorial membrane (1.0).
*54: Otic sac of inner ear greatly enlarged (1.0).
*55: Periotic cistern of inner ear completely divided (0.33).
85: Tongue papillae with flat tops (0.5).
*90: Sublingual glands on floor of mouth scattered (1.0).
*109: Stapedial artery passes through stapedial foramen
(2 1, 0.29).
*114: Post-cloacal sacs absent (1.0).

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Soft anatomy and squamate phylogeny M. S. Y. Lee
*116: Ventral cloacal glands in two or more masses (0.25).
117: Dorsal cloacal glands present in both sexes (1 2, 0.29).
122: Midpiece of spermatozoon of at least moderate length
(0.5).
Comments. This clade is supported by many soft anatomical
characters, particularly related to the auditory system. This
is consistent with the observation that gekkotans have the
most complex vocalizations of squamates, and use sound to
communicate more do than other squamates (e.g. Greer 1989).
Annulata
*4: Enlarged body scales present (0.2).
*7: Tail short (0.5).
*8: Nasal copula with large alary process (0.5).
*9: Parietectal cartilage without superior fenestra (0.5).
*13: Nasal capsule with incomplete planum antorbitale (0.5).
*14: Ethmoid region with large foramen olfactorius (1.0).
15: Nasal passage at least partly separated from oral cavity
(0.4).
*16: Interorbital septum absent (0.5).
*74: Glandular epithelium absent over entire tongue (1 2,
0.67).
*94: Eyes vestigial (1.0).
*97: Eyes covered by opaque scales (1 2, 0.67).
*100: Left lung large, right reduced (0 2, 0.67).
Comments. This clade is corroborated by many characters
which might be functionally related to head-first burrowing
and its correlates of miniaturization, body elongation and
cranial consolidation (4, 7, 8, 14, 16, 94, 97, 100). A similar
situation occurs with the osteological characters (Lee 1998),
hence support for this clade is probably far weaker than
raw numbers of synapomorphies would suggest. However,
unlike the osteological data, at least a few of the soft anatomical
synapomorphies are not obviously correlated with burrowing
(e.g. 9, 13, 15, 74) although detailed functional studies are
needed to confirm this.
Scincomorpha
38: Nucleus sphericus of braincase well-developed (0.5).
51: Hair cells of inner ear attached to tectorial membrane
and inertial bodies (0.4).
*78: Lingual scales present (0.5).
*81: Dorsal lingual plicae present at most on hindtongue (0.4).
Comments. This traditionally recognized clade (e.g. Estes
et al. 1988) is only very weakly supported by the soft anatomy.
However, the conflicting arrangement suggested by the
osteology scincoids grouping with anguimorphs is similarly
weakly supported. The affinities of scincoids are best inter-
preted as unresolved in both studies.
124
Lacertoidea
*20: Adductor mandibulae posterior muscle extending deeply
into Meckels canal (0 2, 0.67).
*21: Pseudotemporalis superficialis muscle extending along
medial margin of temporal fenestra (0.4).
*41: Ulnar nerve deep within forelimb (0.33).
*49: Basal papilla of inner ear with distinct constriction
(0.5).
*68: Tongue notched for at least 20% of length (1 3, 0.33).
*69: Tines of tongue tip long and tapering (0.33).
*70: Tines of tongue tip lie between sublingual plicae
(0.33).
118: Acrosome of spermatozoon flattened in cross-section
(0.33).
Teioidea
*21: Pseudotemporalis superficialis muscle extending along
medial margin of temporal fenestra and supratemporal
(1 2, 0.4).
31: Transversus penis muscle of hemipenis reduced (0.33).
*33: Retractores laterales muscles of hemipenis a single mass
(1.0).
*38: Nucleus sphericus of brain extremely enlarged (1 2,
0.5).
*39: Dracomorph brain organization (0.33).
*42: Lower leg muscles innervated by interosseus nerve
(0.33).
*68: Tongue notched for more than 45% of length (3 4,
0.33).
79: Lingual scales arranged diagonally across tongue (0.5).
*82: Lingual plicae present on ventral surface of foretongue
(1.0).
*91: Entoglossal process of hyoid apparatus separated into
two portions (1.0).
*93: Hypohyal element of hyoid apparatus very long (1.0).
*113: Urinary bladder absent (0.5).
Scincoidea
*4: Dorsal body scales all enlarged (0.2).
31: Transversus penis muscle of hemipenis reduced (0.33).
*45: Vestibular lip of cochlear duct very weak (1 0, 0.29).
*46: Limbus of inner ear greatly elongated (0.33).
*51: Hair cells of inner ear attached to inertial bodies only
(1 2, 0.4).
*52: Tectorial membrane absent (1.0).
*71: Foretongue much wider than hyoglossus muscles (0.5).
*74: Glandular epithelium over entire tongue (1 0, 0.67).
*80: Lingual scales with crenulated posterior edges (1.0).
*88: Ventral pallets project laterally beyond tongue margin
(1.0).
*92: Laryngohyoid ligament with dorsolateral branches
(0.5).
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M. S. Y. Lee Soft anatomy and squamate phylogeny

Comments. The above soft anatomical characters provide strong
evidence for the monophyly of the traditional Scincoidea
(e.g. Estes et al. 1988). Although a recent analysis of
osteology (Lee 1998) raises the question that scincoids and
cordylids might not be closest relatives, the evidence for this
was very weak in both analyses. Thus, the osteological data
is best interpreted as equivocal, and thus not inconsistent
with the current arrangement.
Anguimorpha
*12: Paraseptal cartilage of skull reduced (0.33).
*26: Geniomyoideus muscle of throat present (1.0).
38: Nucleus sphericus of brain well-developed (0.5).
57: Choanal groove on palate short (0.33).
*65: Gland of Gabe present on lower jaw (1.0).
*68: Tongue notched at least 10% of its length (1 2, 0.33).
*72: Foretongue retracts within hindtongue (1.0).
*86: Papillae of hindtongue with pointed epithelial apices
(1.0).
*102: Lungs with intrapulmonary bronchi (0.5).
117: Dorsolateral cloacal glands present in both sexes (1 2,
0.29).
Xenosauridae + Varanoidea
*2: Cephalic scales numerous and small (1 0, 0.33).
*45: Vestibular lip of cochlear duct weakly developed (1 0,
0.29).
*101: Lungs at least partially divided into chambers (0.4).
Varanoidea
*19: Epicoracoid cartilage of shoulder girdle reduced (0.25).
*38: Nucleus sphericus of brain extremely well-developed
(1 2, 0.5).
*41: Ulnar nerve deep within forelimb (0.33).
*68: Tongue notched for at least 20% of its length (2 3, 0.33).
*69: Tines of tongue tip long and tapering (0.33).
104: Fundic glands of stomach with serous cells only (1.0).
105: Fundic glands of stomach with neck cells (1.0).
*108: Carotid and systematic arteries separate, connecting
carotid duct absent (0.33).
113: Urinary bladder absent (0.5).
Thecoglossa
9: Anterior nasal copula without apical foramen (0.2).
10: Parietectal cartilage lacking superior nasal fenestra (0.5).
11: Ethmoid nerve passes through groove on septomaxilla
(1.0).
*56: Jacobsons organ extremely enlarged (1 2, 1.0).
58: Jacobsons organ epithelium with at least 8 receptor cells
per supporting cell (1 2, 0.5).

Table 2 Autapomorphies of terminal taxa, as revealed by deltran optimization in the ordered analysis. Changes which also occur under
acctran optimization are indicated by asterisks. All changes are 01 unless otherwise indicated. The consistency index for each character is
also indicated.

Iguanidae: 101 (0.4), *102 (0.5), 117 (1 2, 0.29)H

Agamidae: 6 (0.25), *123 (2 1, 0.67)
Chamaeleonidae: 9 (0.2), 12 (0.33), *17 (0 2, 0.67), 19 (0.25), *28 (1 0, 0.5), *41 (0.33), *45 (1 0, 0.29), *68 (1 0, 0.33), *108 (0.33), *112 (0.33),
*115 (1 2, 0.25), 117 (1 0, 0.29), *122 (0.5), *125 (1 2, 0.83).
Xantusiidae: 15 (0.4), *20 (0.67), *21 (0.4), *31 (0.33), *45 (1 0, 0.29), 46 (0.33), *49 (0.5), *51 (0 2, 0.4), 57 (0.33), *71 (0.5), 85 (0.5), *99 (1 2, 0.67), 112 (0.33),
*115 (0 2, 0.25), *117 (1 0, 0.29).
Gekkonidae: *2 (1 0, 0.33), *22 (1 0, 0.33), *61 (1 0, 0.33), 102 (0 2, 0.5), 119 (0.5), *121 (1 0, 0.33), 125 (1 4, 0.83).
Pygopodidae: *4 (0.2), 10 (0.2), 23 (0.33), *34 (1 0, 0.25), *35 (0.5), *36 (0.5), *100 (0.67), 101 (0.4), 109 (1 0, 0.29), 121 (1 2, 0.33), 124 (0.33), 125 (1 3, 0.83),
*126 (0 1, 0.5).
Dibamidae: *12 (0.33), *15 (1 2, 0.4), *28 (2 1, 0.5), 57 (0 2, 0.33), *64 (1 2, 0.4), *68 (1 0, 0.33), *81 (0 2, 0.4), 87 (1 0, 0.5), *109 (2 1, 0.29).
Amphisbaenia: *5 (1 0, 0.33), 19 (0.25), 23 (0.33), 35 (0.5), 43 (0.2), *47 (0 2, 0.67), 58 (1 2, 0.5), *61 (1 0, 0.33), *64 (1 0, 0.4), *68 (1 4, 0.33), *69 (0.33),
*70 (0.33), *78 (0.5), 79 (0.5), 87 (1 2, 0.5), *108 (0.33), 116 (0.2), 117 (1 2, 0.29).
Lacertidae: 6 (0.25), *19 (0.25), 34 (0.25), *59 (1 2, 0.5), *81 (1 2, 0.33), 92 (0.5), *102 (0.5), *111 (0.33), 115 (0.25), *125 (1 5, 0.833).
Teiidae: 10 (0.2), 45 (1 2, 0.29), 58 (1 2, 0.5), 116 (0.2), 121 (1 2, 0.33).
Gymnophthalmidae: 5 (1 0, 0.33), *43 (0.2).
Cordylidae: 5 (1 0, 0.33), 6 (0.25), 9 (0.2), *81 (1 2, 0.4).
Scincidae: *13 (0.5), *15 (0.4), *33 (0 2, 1.0), *43 (0.2), 55 (0.33), *112 (0.33), 115 (0.25), 116 (0.2).
Anguidae: *4 (0.2), *43 (0.2), *99 (1 0, 0.67).
Xenosauridae:*64 (1 0, 0.4).
Heloderma: *34 (0.25), *42 (0.33), 101 (1 2, 0.4), 107 (0 2, 0.67).
Lanthanotus: 47 (0.67), 98 (0.5), 110 (0.5).
Varanus: *21 (0 2, 0.4), *39 (0.33), 47 (0.67), 57 (1 2, 0.33), *59 (1 0, 0.5), 73 (0.5), 76 (1 2, 0.67), 98 (0.5), 101 (1 2, 0.4), 107 (0 2, 0.67), 110 (0.5),
*109 (0.33), 116 (0.2), *118 (0.33), *120 (0.33), 121 (1 2, 0.33).
Serpentes: *4 (0.2), *7 (0.5), *8 (0.5), *15 (0 1 & 2, 0.4), *16 (0.5), *22 (1 0, 0.33), *23 (0.33), *36 (0.5), *55 (0.33), 57 (1 2, 0.33), *64 (1 0, 0.4), 73 (0.5),
76 (1 2, 0.67), *95 (1 0), *97 (0 1 & 2, 0.67), *100 (0.67), *109 (2 0, 0.29), *112 (0.25), *122 (0 2, 0.5), 124 (0.33), *125 (1 3, 0.83), *126 (0.5).

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ZSC035.fm Page 126 Thursday, June 1, 2000 3:12 PM
Soft anatomy and squamate phylogeny M. S. Y. Lee
*66: Tongue long, resting length at least twice maximum
width (1.0).
*68: Tongue notched for more than 40% of length (3 4,
0.33).
*70: Tongue tines lie between sublingual plicae (0.33).
*75: Tongue lacking taste buds (1.0).
*76: Lingual mucocytes present at most only on hind-
tongue (0.67).
*83: Main body of tongue lacking papillae (1 2, 1.0).
*87: Tines of tongue tip keratinous (1 2, 0.5).
*89: Sublingual glands under tongue compact and dense (1.0).
103. Heart not attached to pericardium (1.0).
*106: Pancreas compact (1.0).
Comments. As befits its name, this clade is corroborated in
this analysis mainly by tongue-related characters. However,
some other soft anatomical characters support the clade, as
well as numerous osteological traits from diverse regions of
the body (Lee 1998).
Acknowledgements
I thank Garth Underwood, Kurt Schwenk, Van Wallach,
Allen Greer and Glen Shea for discussion and generously
sharing unpublished observations (though errors in this
study remain mine alone), and Michel Laurin, John Scanlon,
and (especially) an anomymous reviewer for detailed and
helpful comments on the entire manuscript. Information
used in this study was gathered with financial assistance of
the Australian Research Council, the Fulbright Foundation,
the Australian Vice-Chancellors Committee, and American
Museum of Natural History.
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