A new lizard species in the genus Xantusia from Arizona

2001. Papentfuss, T. J., J. R. Macey, and J. A. Schulte. A New Lizard

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Natural History Museum
The University of Kansas

12 October 2001 Number 23:1-9
2 A New Lizard Species in the Genus Xantusia from Arizona
: By
Z THEODORE J. PAPENFUuSS', J. ROBERT MACEY? AND JAMES A. SCHULTE II?
a ‘Museum of Vertebrate Zoology, University of California, Berkeley, California 94720, USA
@ asiaherp@uclink4. berkeley.edu
a * Department of Comparative Genomics, Joint Genome Institute and Lawrence Berkeley National Laboratory, 2800 Mitchell
s 3 Drive, Walnut Creek, California 94598-1631, USA. jrmacey@Ibl.gov
aa 3 Department of Biology, Box 1137, Washington University, St. Louis, Missouri 63130, USA
a9 P Su § d
Sie schulte@biology.wustl.edu
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ABSTRACT Three species of lizards in the genus Xantusia occur in Arizona: X. vigilis, X. arizonae and
a new species described here, X. bezyi. Previous workers have suggested that only a single species of
Xantusia is found in Arizona with some populations living in yucca-type plants and others specializ-
ing in granite rock habitats. Recognition of the three species is based on previously reported allozyme
data, new mitochondrial DNA sequence data (1716 aligned sites, 59 parsimony informative), and
morphological differences. Phylogenetic analysis of mitochondrial DNA sequences among the three
species of Xantusia that occur in Arizona indicate that X. arizonae and X. vigilis are sister taxa with the
exclusion of X. bezyi. Genetic differentiation between mitochondrial DNA sequences suggests that
species in Arizona are 5—6 million years old.

Key Words: Reptilia; Squamata; Xantusiidae; Xantusia; new species; systematics; phylogenetics; mito-
chondrial DNA; Arizona.

© Natural History Museum, The University of Kansas ISSN No. 1094-0782

2 SCIENTIFIC PAPERS, NATURAL History MUSEUM, THE UNIVERSITY OF KANSAS

INTRODUCTION

The lizard genus Xantusia currently consists of five
species: X. bolsonae in Durango, Mexico, X. henshawi in
southern California and Baja California Norte, Mexico, X.
riversiana on three of the California Channel Islands, X.
sanchezi in southwestern Zacatecas, Mexico, and X. vigilis
with seven subspecies occurring in California, Nevada,
Utah, and Arizona in the United States and in Baja Cali-
fornia, Sonora, Durango, and Zacatecas in Mexico (Bezy
and Flores Villela, 1999).

Xantusia arizonae was described by Klauber (1931) from
the vicinity of Yarnell in Yavapai County, Arizona. The liz-
ards were found under flakes of granite boulders in a habi-
tat similar to that of X. henshawi in southern California.
Xantusia arizonae was diagnosed as being similar in lepi-
dosis and partly in color and pattern to X. vigilis but with
a body form more like that of X. henshawii but with rela-
tively longer limbs and a more flattened head and body
than X. vigilis. At the time of Klauber’s (1931) discovery,
the nearest known localities for Xantusia were for X. vigilis,
some 250 km northwest in the eastern Mojave Desert.

For the next 35 years Xantusia arizonae was treated as
a full species (Savage, 1963; Stebbins, 1954, 1966). Stebbins
(1954) in his key to the species of Xantusia, distinguished
X. arizonae from X. vigilis with the former having more
subdigital lamallae on the fourth toe (25-28 versus 18-21)
and more dorsal granular scales at midbody (43-50 ver-
sus 33-40).

Additional populations of granite-adapted lizards
have been found in Arizona along the southwestern edge
of the Colorado Plateau across a 300-kilometer region from
near Valentine in Mojave County to the Superstition Moun-
tains in Pinal County. Yucca-dwelling populations assigned
to X. vigilis are also known from Arizona. Populations of
X. vigilis and X. arizonae have been found within 50 km of
each other in Yavapai County, Arizona. At one site near
Tonto National Monument in Gila County, Arizona, Bezy
(1967b) found both granite- and yucca-dwelling Xantusia
together. There is an ecologically based morphological gra-
dient froma “granitoform” to a “yuccaform” morphotype
(Bezy, 1967b).

Bezy (1967b) noted that the “granitoform” occurred
in two widely separated places, the southwestern edge of
the Mogollon Rim of Arizona and the western foothills of
the southern Sierra Nevada of California. The latter had
just been described as X. vigilis sierrae (Bezy, 1967a). Bezy

(1967b) found extensive morphological gaps between the
most divergent populations of “granitoform” versus
“yuccaform,” but in all characters examined, these gaps
were spanned by the ranges of variation of morphologi-
cally intermediate populations. He recommended that X.
arizonae be treated as a subspecies of X. vigilis. This taxo-
nomic arrangement was generally accepted (Crother et al.,
1986; Stebbins, 1985; Webb, 1970).

In their discussion on species relationships Bezy and
Sites (1987:288) concluded: “Before phylogenetic relation-
ships among the species of Xantusia can be fully assessed
with allozymes, additional data for populations of X. vigilis
are needed, as the genetic and cladistic diversity within
this apparently paraphyletic taxon is at least as great as
among the presently recognized species units.” Bezy and
Sites (1987) reported data for three presumptive popula-
tions of X. vigilis arizonae which consistently appeared in
three separate positions on their phylogenetic trees.

We present new mitochondrial DNA evidence and
examine previously reported allozyme data (Bezy and
Sites, 1987) to ascertain phylogenetic relationships and the
extent of differentiation among populations of Xantusia
occurring in different ecological habitats in Arizona. Un-
der the phylogenetic species concept (Cracraft, 1989), these
data suggest the occurrence of more than one species in
Arizona. We conclude that three species of Xantusia occur
in Arizona. They are X. vigilis, X. arizonae, and the new
species described here. This new species lives in crevices
in granite boulders (Fig. 1). It was previously regarded as
a population of X. arizonae (Bezy and Sites, 1987).

ACKNOWLEDGMENTS

Scientific collecting permits were issued by the Cali-
fornia Department of Fish and Game and the Arizona
Game and Fish Department. David B. Wake provided use-
ful advice and discussions on the use of mitochondrial
DNA sequence data as an important diagnostic character
in species’ descriptions. Karen Klitz made figures 5, 6, and
7. This work is LBNL-48468 and was partially performed
under the auspices of the U.S. Department of Energy by
the University of California, Lawrence Berkeley National
Laboratory under contract No. DE-AC03-76SF00098. This
work was supported by grants from the National Science
Foundation (DEB-9726064 to Allan Larson, J.R.M and TJ.P.;
predoctoral fellowship to J.A.S.).

MATERIALS AND METHODS

Museum numbers and localities for voucher speci-
mens from which DNA was extracted, and GenBank ac-
cession numbers are presented below. Museum numbers
and localities for voucher specimens examined morpho-
logically are listed in the species description. Institutional

codes are: KU = Natural History Museum, University of
Kansas; MVZ = Museum of Vertebrate Zoology, Univer-
sity of California at Berkeley. Localities of voucher speci-
mens are reported exactly as recorded in museum records
and therefore may be expressed either in English or met-

New SPECIES OF XANTUSIA 3

Fig. 1.

ric units. Measurements were taken using dial calipers (to
the nearest 0.1 mm). The description of scale characters
follows the standard terminology used by Savage (1963)
and Bezy and Flores Villela (1999). Photos of live Xantusia
were taken on granite from the localities where they were
collected.

Tissues were collected and directly stored in freezers
(-80 C) until used. Four samples of Xantusia were se-
quenced: X. henshawi, MVZ 229092, AF404750, elev. 3000
ft., NW 1/4 Sec. 36, T. 6S., R.5 E., junction of Carrizo Road
and Highway 74, 12.2 miles south of Palm Desert on High-
way 74, Riverside County, California; X. bezyi, MVZ 232604,
AF404751, elev. 914 m, 33° 49.48’ N, 111° 28.55’ W, NE1/4
Sec. 31, T. 6 N., R. 9 E., 5.7 km south (by Highway 87) of
Sunflower, Maricopa Coounty, Arizona; X. arizonae, MVZ
230599, AF404752, 1.5 miles south (airline) of Yarnell,
Yavapai County, Arizona; X. vigilis, MVZ 228254, U71328
(Macey et al., 1997), elev. 5800 ft., SW 1/4 Sec. 14, T. 8 N.,

Type locality of X. bezyi, elev. 948 m, 33° 49.48’ N, 111° 28.55’ W, NE 1/4 Sec. 31, T. 6 N., R.9 E., 5.6 km S (by Highway 87) of Sunflower,
Maricopa County, Arizona.

R. 12 E., Granite Mountains Plateau, Granite Mountains,
San Bernardino County, California.

The mitochondrial gene region of ND1 (subunit one of
NADH dehydrogenase), tRNA", RNAS", tRNA™*, ND2,
tRNA, tR NAA? tRNAAS tRNA&Ss, tRNA®*, and COI (sub-
unit one of cytochrome c oxidase) was sequenced. Sequenc-
ing protocols follow Macey et al. (1997) except that cycle-
sequencing reactions were run on an ABI Prism Big Dye Ter-
minator DNA Sequencing Kit (Perkin-Elmer) with a dena-
turation at 95°C for 15 sec, annealing at 50°C for 1 sec, and
extension at 60°C for 4 min for 35-40 cycles. Sequencing re-
actions were run on Long Ranger sequencing gels for 5-12
hours at 38-40°C and ABI 373 or MJ Research Basestation
sequencers. The four sequences were aligned as 1716 sites
(59 parsimony informative). A single gap was placed after
the following positions in each sequence to obtain the align-
ment used in phylogenetic analyses: X. henshawi, 84, 1344,
1496, 1608; X. bezyi, 1544; X. arizonae, 1543; and X. vigilis, 1543.

4 ScrentiFIC PAPERS, NATURAL History Museum, THE UNIVERSITY OF KANSAS

Phylogenetic relationships were estimated using
PAUP beta 4.0b3a (Swofford, 2001). Bootstrap
resampling was used to assess support with 1000 repli-
cates using exhaustive searches. The decay index was
calculated by running searches that retained subopti-
mal trees using exhaustive searches. Alternative phy-

logenetic hypotheses were evaluated with the Wilcoxon
signed-ranks test using the two-tailed probabilities
(Felsenstein, 1985; Templeton, 1983). The allozyme
analysis on the number of fixed differences between
samples of Xantusia was derived from Table 2 in Bezy
and Sites (1987).

DESCRIPTION OF NEW SPECIES

Xantusia bezyi, new species

Holotype.—Museum of Vertebrate Zoology, MVZ
232604. An adult male from 33° 49.48’ N, 111° 28.55’ W, NE

Sunflower, elev. 948 m, Maricopa County, Arizona, USA;
found under an exfoliating granite slab on November 3,

1/4 Sec. 31, T.6 N., R.9 E., 5.6 km S (by Highway 87) of 2000 by Theodore J. Papenfuss.

Fig. 2.
that of X. arizonae, (Fig. 4).

Adult male Xantusia bezyi, MVZ 232608, SVL 53.1 mm. Note that the color pattern is more similar to that of X. henshawi (Fig. 3) than to

New SPECIES OF XANTUSIA 5

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Fig. 3. Xantusia henshawi, MVZ 232630, SVL 58.3 mm, from 33° 31.18’ N, 116° 52.18’ W, 3.2 km SSE (by Wilson Valley Road) of junction with
Sage Road, elev. 815 m, Riverside County, California.

Fig. 4. Xantusia arizonae, MVZ 232578, SVL 52.9 mm, from Yarnell, Yavapai County Arizona.

6 SCIENTIFIC PAPERS, NATURAL History Museum, THE UNIVERSITY OF KANSAS

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Fig. 5. Dorsal midbody color pattern. Above: Xantusia arizonae,
MVZ 73829. The dark blotches seen here and in figure 4 consist of 4-12
individual dark granular scales. Below: X. bezyi holotype, MVZ 232604.
The dark blotches seen here and in figure 2 consist of 3-28 individual
dark granular scales.

Paratypes.—Ten specimens. MVZ 232605-232607;
from the type locality. MVZ 232608-232611, 232571; KU
290503-04 from 33° 51.10’ N, 111° 28.28’ W, NW 1/4 Sec.
29, T.6N.,R.9 E., 2.9 km S (by Highway 87) of Sunflower,
elev. 1085 m, Maricopa County, Arizona, USA.

Diagnosis.—A moderately large (to about 58 mm
snout-vent length) species of Xantusia that is similar in
size and morphology to X. arizonae. It differs from the
latter in allozymes, mitochondrial DNA, and color pat-
tern. The dorsal blotches of adults (Fig. 2) are more simi-
lar to the pattern in X. henshawi (Fig. 3) than to the pat-
tern in X. arizonae (Fig. 4). The individual large dark
dorsal blotches contain 3-28 granular scales versus 4—
12 in X. arizonae (Fig. 5) and there is a proportionally
greater distance from the anterior margin of the eye to
the tip of the snout (Fig 6). The new species differs from
X. vigilis by its larger size, mottled coloration, more than
41 rows of dorsal granular scales and more than 26
lamellae under the fourth toe. It differs from X. bolsonae,
X. riversiana, and X. henshawi in having 12 longitudinal
rows of ventral scales rather than 14-16 rows. These
characters are in addition to substantial differences in
allozymes and mitochondrial DNA.

Dorsal views of heads. Left: Xantusia arizonae, MVZ 73829.

Fig. 6.
Right: X. bezyi holotype, MVZ 232604.

Description of holotype.—Measurements (in mm):
Snout-vent length 54; tail length 68 (complete); head length
from tip of snout to gular fold 19.8; head width 8.2; fourth
toe length, 7.4. Dorsal surface of head: rostral broader than
high, followed in order by two nasals in contact medially,
two prefrontals, a median prefrontal, two frontals in con-
tact medially, large interparietal separating parietals, and
two postparietals in contact medially. Lateral surface of
head: nostril bordered by rostral, first supralabial, nasal,
and postnasal; anterior loreal, posterior loreal, three
loreolabials, four preoculars, four suboculars, five
supraoculars, four postoculars, six supralabials, and three
pretemporals. Ventral surface of head: mental followed by
six pairs of infralabials, four pairs of post mentals, and first
pair in contact; gular scales 35 along midline between first
pair of post mentals and gular fold. Body surface: dorsal
granular scales around body at the 16th transverse row of
ventrals 43; ventral scales in 12 longitudinal rows at mid-
body; transverse rows of ventral scales between gular fold
and vent 33; femoral pores on right leg 9, on left leg 11;
fourth toe lamellae, 26.

Color pattern in life: dorsal surface of the body with
black blotches consisting of 3—28 individual granular scales
on a background of cream to tan granular scales; tail col-
oration similar with black blotches consisting of 1-10 an-
nuli; dorsal surface of head brown with black spots; sides
of body similar to dorsal with interspersed white speck-
ling extending to the base of tail; ventral surface of head,

New SPECIES OF XANTUSIA 7

body, and tail cream to tan. Color pattern in preservative
is like that in life except the background color of the head
is dark and pale gray as opposed to brown.

Variation in paratypes.—The paratypes approximate
the holotype in general morphology, pattern, and colora-
tion. The number of femoral pores is 7-11 (x = 8.9) per leg.
One specimen (MVZ 26415) lacks femoral pores. The num-
ber of dorsal granular scales around the body at the 16th
transverse row of ventrals is 41-47 (x = 44.1). The number
of lamellae under the fourth toe is 26-28 (x = 27.0.

Habitat and distribution.—The two known localities
for Xantusia bezyi are in the vicinity of Sunflower at the
edge of the Sub-Mogollon Colorado Plateau in an ecotone
between the Arizona Upland Subdivision of the Desert
Scrub Formation and the Semidesert Grassland of the
Grassland Formation (Brown and Lowe, 1980). All indi-
viduals were found under pieces of exfoliating rock in
granite outcrops (Fig. 1). Suitable habitat is present for
about 30 km southwest of Sunflower along Highway 87
toward the Rio Verde. The type locality of X. arizonae is
125 km northwest of Sunflower (Fig. 7). Bezy (1967b) re-
ported “granitoform” Xantusia from 30 km southeast of
Sunflower in the vicinity of Tonto National Monument.

Etymology.—This species is named for Robert L. Bezy

in recognition of his lifelong studies on lizards of the fam-
ily Xantusiidae.

Map of Arizona showing the type locality for Xantusia
arizonae (solid circle) and the type locality for X. bezyi (triangle).

Fig. 7.

MOLECULAR VARIATION AMONG XANTUSIA

Allozymic variation.—The 28 variable allozymic loci
reported by Bezy and Sites (1987) among species of
Xantusia and Lepidophyma were reexamined. Three popu-
lations that Bezy and Sites (1987) referred to as X. vigilis
arizonae belong to three distinct species. The northwestern
population (Mojave County) is X. vigilis and has only two
fixed differences from other populations of X. vigilis. The
sample of X. arizonae from the type locality (Yarnell,
Yavapai County) has eight fixed differences from X. bezyi
(Maricopa County) and 5-7 from populations of X. vigilis
(Table 1). Xantusia bezyi has 9-10 fixed differences from
populations of X. vigilis. These differences suggest genetic
discontinuity between groups of populations here sug-
gested to represent distinct species on the level typically
observed between recognized species (for examples in liz-
ards see de Queiroz, 1992; Macey et al., 2000; Sites et al.,
1988).

Mitochondrial DNA sequence data.— The mitochon-
drial gene region of ND1 (subunit one of NADH dehydro-
genase), tRNA", tRNAS", tRNA™*, ND2, tRNA™, tRNA*®,
tRNA", tRNAs, tRNA®5*, and COI (subunit one of cyto-
chrome c oxidase) is reported inTable 2. A single most par-
simonious tree (length = 371 steps) produced from phylo-

genetic analysis of mitochondrial DNA sequences and
rooted with Xantusia henshawi shows X. vigilis and X.
arizonae to be monophyletic with the exclusion of X. bezyi
(Fig. 8). The shortest alternative tree showing X. vigilis and
X. arizonae as non-monophyletic is rejected by using the
Wilcoxon signed-ranks test with the two-tailed probabili-
ties [Felsenstein, 1985; Templeton, 1983; n = 45; T_ = 345, P
< 0.025; alternative tree (X. henshawi, ((X. bezyi, X. arizonae),
X. vigilis)), L = 386].

Table 1. Pairwise comparisons of Nei (1978) distances (above diagonal)
and fixed allozymic differences (below diagonal) among six populations
of Xantusia reported in Bezy and Sites (1987). In Bezy and Sites (1987), X.
henshawi is Population 2, X. bezyi is Population 3 of X. v. arizonae, X. arizonae
is Population 1 of X. v. arizonae. Populations 1 and 2 of X. vigilis are num-
bered the same here as in Bezy and Sites (1987) as X. v. vigilis. Population
3 of X. vigilis is X. v. arizonae Population 2 in Bezy and Sites (1987).

Species 1 2 3 4 5 6
1. X. henshawi — 0.32 0.40 0.32 0.38 0.36
2. X. bezyi 11 _— 0.29 0.27 0.32 0.36
3. X. arizonae 11 8 — 0.19 0.31 0.28
4. X. vigilis-1 9 9 5 a 0.10 0.07
5. X. vigilis-2 10 10 7 D = 0.07
6. X. vigilis-3 8 9 6 2 2 —

8 ScreNTIFIC PAPERS, NATURAL History Museum, THE UNIVERSITY OF KANSAS

Table. 2. Pairwise comparisons of DNA sequences between species of Xantusia.
Percentage sequence divergence is shown above the diagonal and the number of
base substitutions between sequences is shown below the diagonal.

Species 1 2 3 4

1. X. henshawi a 12.98% 13.91% 13.62%
2. X. bezyi 222 — 7.70% 7.59%
3. X. arizonae 238 132 — 6.47%
4. X. vigilis 233 130 111 —

The region sequenced has been found to evolve in
a clock-like manner among a wide range of vertebrates
with a consistent rate of change per lineage per million
years [Fish 0.65% (Bermingham et al., 1997); hynobiid
salamanders 0.64% (unpublished data of the authors);
frogs of the genus Bufo 0.69% (Macey et al., 1998b); liz-
ards of the genus Laudakia 0.65% (Macey et al., 1998a);
lizards of the genus Teratoscincus 0.57% (Macey et al.,
1999b)].

Pairwise percent sequence divergence between
Xantusia bezyi, X. arizonae, and X. vigilis ranges from
6.47% to 7.70%. Using the pairwise rate of 1.3% change
per million years, X. bezyi, X. arizonae, and X. vigilis are
estimated to have diverged 5-6 million years ago. The
amount of sequence divergence among these three spe-
cies of Xantusia is consistent with sequence divergences
observed among other species of lizards, salamanders,
and frogs (Table 3). Furthermore, we estimate that these

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S 5
a = r =
= Ss = 3
ob iS
aS) & v Ss
5 3 S =
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99
15

Fig. 8. The single most-parsimonious tree found from an exhaus-
tive search of the 1716 (59 informative) aligned mitochondrial DNA sites
showing the root relative to Xantusia henshawi. The tree has a length of -
371 steps; the bootstrap value is above the branch and the decay index is
below the branch in boldface type.The shortest alternative topology re-
quires 15 extra steps (the decay index) and is statistically rejected (P <
0.025) applying the conservative two-tailed probability (Felsenstein, 1985)
of the Wilcoxon signed ranks test (Templeton, 1983).

three species diverged from X. henshawi at least 10 mil-
lion years ago. This suggests that the genus dates at
least to the Miocene.

Table 3. Comparative pairwise sequence divergences between species of amphibians and reptiles. Sequence divergences are calculated for the same
segment of mitochondrial DNA spanning from the ND1 gene to the COI gene. Bufonid frogs include only the first half of this segment (from the ND1

gene to the ND2 gene).
Pairwise
sequence
Family Genus Taxa compared divergences Reference
Bufonidae Bufo B. andrewsi and B. gargarizans 6.0-6.9% Macey et al. (1998b)
Ranidae Rana Rana aurora, R. cascadae, and
R. muscosa 7.0-8.4% Macey et al. (2001)
Salamandridae Salamandra S. infraimmaculata and S.
salamandra 7.4-7.5% Weisrock et al. (2001)
Agamidae Laudakia L. caucasia and L. erythrogaster 4.2-5.3% Macey et al. (1998a)
Anguidae Elgaria E. kingii to the clade containing
E. multicarinata, E. panamintina,
and E. paucicarinata 4.8-5.9% Macey et al. (1999a)
Gekkonidae Teratoscincus T. przewalskii and L. roborowskit 6.5% Macey et al. (1999b)

New SPECIES OF XANTUSIA 9

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