Supplemental Information
Figure S1. A fully bifurcating guide tree for BP&P analysis based on the mtDNA data was difficult to generate
because of weakly supported basal relationships within the southern clade (Fig. 1; Supplemental Figure). To deal
with this problem, we generated the BP&P guide tree based on the fully-resolved (including weakly supported
nodes) ML tree; when bootstrap values were < 70 in this tree, we generated multiple guide trees to of sub-clades to
reflect the uncertainty of these relationships. After analyzing the sub-clades, we combined them into a single-results
figure. Each sub-clade was strongly supported at the base, and because of the way the rjMCMC algorithm evaluates
nested models in BP&P, nodes towards the base of the guide tree will have higher support values (support values
cannot decrease towards the base of the tree). This means that joining these sub-clades had no effect on support
values between sub-clades. Although not depicted, the same method was performed to unite the sub-clades in the
BP&P morphological guide tree.
Figure S2. Results from the AICM model selection in examining the four species-delimitation scenarios in (a) the
simulated data and (b) the eight models tested with the empirical data. Boxplots show upper and lower quartiles,
median values, and outliers (note the y-axis break).
Figure S3a. BACH1 maximum likelihood tree with each individual represented by two alleles (A and B). Support
values at nodes or on branches represent bootstrap proportions. Tip labels denote taxon and location (Sae = S. a.
aeneus, Sbi = S. bicanthalis, Sbr = S. s. brownorum North, Sca = S. s. brownorum South, Sch = S. chaneyi, Ssa = S.
samcolemani, Ssc = S. s. scalaris, Ssl = S. slevini, Sun = S. s. unicanthalis, Ssu = S. a. subniger; AGUA =
Aguascalientes, ARIZ = Arizona, CHIH = Chihuahua, COAH = Coahuila, DURA = Durango, EDDM = Mexico
State, HIDA = Hidalgo, JALI = Jalisco, MICH = Michoacán, MORE = Morelos, NEME = New Mexico, NULE =
Nuevo León, OAXA = Oaxaca, PUEB = Puebla, QUER = Querétaro, SALP = San Luis Potosí, TAMA =
Tamaulipas, VERA = Veracruz).
Figure S3b. EXPH5 maximum likelihood tree with each individual represented by two alleles (A and B). Support
values at nodes or on branches represent bootstrap proportions. Tip labels denote taxon and location (Sae = S. a.
aeneus, Sbi = S. bicanthalis, Sbr = S. s. brownorum North, Sca = S. s. brownorum South, Sch = S. chaneyi, Ssa = S.
samcolemani, Ssc = S. s. scalaris, Ssl = S. slevini, Sun = S. s. unicanthalis, Ssu = S. a. subniger; AGUA =
Aguascalientes, ARIZ = Arizona, CHIH = Chihuahua, COAH = Coahuila, DURA = Durango, EDDM = Mexico
State, HIDA = Hidalgo, JALI = Jalisco, MICH = Michoacán, MORE = Morelos, NEME = New Mexico, NULE =
Nuevo León, OAXA = Oaxaca, PUEB = Puebla, QUER = Querétaro, SALP = San Luis Potosí, TAMA =
Tamaulipas, VERA = Veracruz).
Figure S3c. KIF24 maximum likelihood tree with each individual represented by two alleles (A and B). Support
values at nodes or on branches represent bootstrap proportions. Tip labels denote taxon and location (Sae = S. a.
aeneus, Sbi = S. bicanthalis, Sbr = S. s. brownorum North, Sca = S. s. brownorum South, Sch = S. chaneyi, Ssa = S.
samcolemani, Ssc = S. s. scalaris, Ssl = S. slevini, Sun = S. s. unicanthalis, Ssu = S. a. subniger; AGUA =
Aguascalientes, ARIZ = Arizona, CHIH = Chihuahua, COAH = Coahuila, DURA = Durango, EDDM = Mexico
State, HIDA = Hidalgo, JALI = Jalisco, MICH = Michoacán, MORE = Morelos, NEME = New Mexico, NULE =
Nuevo León, OAXA = Oaxaca, PUEB = Puebla, QUER = Querétaro, SALP = San Luis Potosí, TAMA =
Tamaulipas, VERA = Veracruz).
Figure S3d. NKTR maximum likelihood tree with each individual represented by two alleles (A and B). Support
values at nodes or on branches represent bootstrap proportions. Tip labels denote taxon and location (Sae = S. a.
aeneus, Sbi = S. bicanthalis, Sbr = S. s. brownorum North, Sca = S. s. brownorum South, Sch = S. chaneyi, Ssa = S.
samcolemani, Ssc = S. s. scalaris, Ssl = S. slevini, Sun = S. s. unicanthalis, Ssu = S. a. subniger; AGUA =
Aguascalientes, ARIZ = Arizona, CHIH = Chihuahua, COAH = Coahuila, DURA = Durango, EDDM = Mexico
State, HIDA = Hidalgo, JALI = Jalisco, MICH = Michoacán, MORE = Morelos, NEME = New Mexico, NULE =
Nuevo León, OAXA = Oaxaca, PUEB = Puebla, QUER = Querétaro, SALP = San Luis Potosí, TAMA =
Tamaulipas, VERA = Veracruz).
Figure S3e. NOS1 maximum likelihood tree with each individual represented by two alleles (A and B). Support
values at nodes or on branches represent bootstrap proportions. Tip labels denote taxon and location (Sae = S. a.
aeneus, Sbi = S. bicanthalis, Sbr = S. s. brownorum North, Sca = S. s. brownorum South, Sch = S. chaneyi, Ssa = S.
samcolemani, Ssc = S. s. scalaris, Ssl = S. slevini, Sun = S. s. unicanthalis, Ssu = S. a. subniger; AGUA =
Aguascalientes, ARIZ = Arizona, CHIH = Chihuahua, COAH = Coahuila, DURA = Durango, EDDM = Mexico
State, HIDA = Hidalgo, JALI = Jalisco, MICH = Michoacán, MORE = Morelos, NEME = New Mexico, NULE =
Nuevo León, OAXA = Oaxaca, PUEB = Puebla, QUER = Querétaro, SALP = San Luis Potosí, TAMA =
Tamaulipas, VERA = Veracruz).
Figure S3f. R35 maximum likelihood tree with each individual represented by two alleles (A and B). Support values
at nodes or on branches represent bootstrap proportions. Tip labels denote taxon and location (Sae = S. a. aeneus,
Sbi = S. bicanthalis, Sbr = S. s. brownorum North, Sca = S. s. brownorum South, Sch = S. chaneyi, Ssa = S.
samcolemani, Ssc = S. s. scalaris, Ssl = S. slevini, Sun = S. s. unicanthalis, Ssu = S. a. subniger; AGUA =
Aguascalientes, ARIZ = Arizona, CHIH = Chihuahua, COAH = Coahuila, DURA = Durango, EDDM = Mexico
State, HIDA = Hidalgo, JALI = Jalisco, MICH = Michoacán, MORE = Morelos, NEME = New Mexico, NULE =
Nuevo León, OAXA = Oaxaca, PUEB = Puebla, QUER = Querétaro, SALP = San Luis Potosí, TAMA =
Tamaulipas, VERA = Veracruz).
Figure S4. Maximum likelihood tree inferred from the concatenated nDNA dataset. Each individual is represented
by a single (randomly selected) allele for each locus. Support values at nodes or on branches represent bootstrap
proportions. Bootstrap proportions with an asterisk (*) indicate nodes that received bootstrap proportions < 70 and
Bayesian posterior probabilities > 0.95. Tip labels denote taxon and location (Sae = S. a. aeneus, Sbi = S.
bicanthalis, Sbr = S. s. brownorum North, Sca = S. s. brownorum South, Sch = S. chaneyi, Ssa = S. samcolemani,
Ssc = S. s. scalaris, Ssl = S. slevini, Sun = S. s. unicanthalis, Ssu = S. a. subniger; AGUA = Aguascalientes, ARIZ =
Arizona, CHIH = Chihuahua, COAH = Coahuila, DURA = Durango, EDDM = Mexico State, HIDA = Hidalgo,
JALI = Jalisco, MICH = Michoacán, MORE = Morelos, NEME = New Mexico, NULE = Nuevo León, OAXA =
Oaxaca, PUEB = Puebla, QUER = Querétaro, SALP = San Luis Potosí, TAMA = Tamaulipas, VERA = Veracruz).
Figure S5. Mitochondrial gene tree for the Sceloporus scalaris species group inferred under maximum likelihood,
rooted with S. undulatus. Nodal support values are bootstrap proportions. Individuals amplified for nDNA are
shown in bold. Lineages used in Bayes factor species delimitation are labeled to the right of the tree. Locations for
individual samples are as follows: AGS = Aguascalientes, AZ = Arizona, CHIH = Chihuahua, COAH = Coahuila,
DF = Federal District, DUR = Durango, HID = Hidalgo, JAL = Jalisco, MEX = Mexico State, MICH = Michoacán,
MOR = Morelos, NM = New Mexico, NL = Nuevo León, OAX = Oaxaca, PUE = Puebla, QTO = Querétaro, SLP =
San Luis Potosí, TAM = Tamaulipas, TLAX = Tlaxcala, VER = Veracruz.
Figure S6. Multi-locus nuclear network inferred from the six nuclear genes using the program POFAD (Joly and
Bruneau 2006). Lineages have been colored to match Figure 1, and the network is rooted with the outgroup
Sceloporus clarkii.
Table S1. Sampling localities for each taxon utilized in this study.
Sample
Taxon
Locality (State, Country)
1
S. slevini
Sonoita, Arizona (USA)
2
S. slevini
Cloverdale, New Mexico (USA)
3
S. slevini
Sierra del Nido, Chihuahua (MEX)
4
S. slevini
Creel, Chihuahua (MEX)
5
S. slevini
Mesa de las Navar, Durango (MEX)
6
S. samcolemani
E San Antonio de las Alazanas, Coahuila (MEX)
7
S. samcolemani
Pablillo, Nuevo León (MEX)
8
S. samcolemani
Sierra Concordia, Coahuila (MEX)
9
S. chaneyi
Aserradero, Tamaulipas (MEX)
10
S. chaneyi
Aserradero, Tamaulipas (MEX)
11
S. s. brownorum
Rancho Santa Barbara, Durango (MEX)
12
S. s. brownorum
Sierra Fría, Aguascalientes (MEX)
13
S. s. brownorum
Sierra del Laurel, Aguascalientes (MEX)
14
S. s. brownorum
Sierra del Laurel, Aguascalientes (MEX)
15
S. s. unicanthalis
Guadalajara, Jalisco (MEX)
16
S. s. scalaris
Tapalpa, Jalisco (MEX)
17
S. s. scalaris
Guadalcazar, San Luis Potosí (MEX)
18
S. s. scalaris
Alvarez, San Luis Potosí (MEX)
19
S. s. scalaris
San Jose de Gracía, Michoacán (MEX)
20
S. a. subniger
El Derramadero, Querétaro (MEX)
21
S. a. subniger
Pinal de Amoles, Querétaro (MEX)
22
S. a. subniger
Autódromo del Ángel, Hidalgo (MEX)
23
S. a. subniger
Pinal de Amoles, Querétaro (MEX)
24
S. a. subniger
Nevado de Colima, Jalisco (MEX)
25
S. a. subniger
W Zacapu, Michoacán (MEX)
26
S. a. subniger
Atlacomulco, Estado de México (MEX)
27
S. a. subniger
Los Azufres, Michoacán (MEX)
28
S. a. subniger
Valle de Bravo, Estado de México (MEX)
29
S. bicanthalis
Tianguistengo, Hidalgo (MEX)
30
S. bicanthalis
Las Vigas, Veracruz (MEX)
31
S. bicanthalis
Volcán Iztaccihuatl, Puebla (MEX)
32
S. bicanthalis
Sierra Negra, Puebla (MEX)
33
S. bicanthalis
Llano de las Flores, Oaxaca (MEX)
34
S. a. aeneus
Zempoala, Morelos (MEX)
Table S2. Information for the primers and loci used in this study.
Primer
Name
BACH1f1
BACH1r2
EXPH5f
EXPH5r
KIF24f
KIF24r
NKTRf19
NKTRr18
NOS1f
NOS1r
R35f
R35r
C2LF
C3LR
ND4
Leu
Primer Sequence
5' GAT TTG AHC CYT TRC TTC AGT TTG C 3'
5' ACC TCA CAT TCY TGT TCY CTR GC 3'
5' AAT AAA CTK GCA GCT ATG TAC AAA ACA AGT C 3'
5' AAY CGC CCT TCT GTG AGT GAC CTC T 3'
5' SAA ACG TRT CTC CMA AAC GCA TCC 3'
5' WGG CTG CTG RAA YTG CTG GTG 3'
5' GAT GAC ATG GAG ATY TGY ACT CC 3'
5' CTY CTD GAY CGA CTT CTT GAG TGA CT 3'
5' GTG GGC AGG ATY CAG TGG TCC AAG CT 3'
5' CTG AGA TTC CCT TTG TTA GTG GC 3'
5' GAC TGT GGA YGA YCT GAT CAG TGT GGT GCC 3'
5' GCC AAA ATG AGS GAG AAR CGC TTC TGA GC 3'
5' ATCTGCGGGTCAAACCACAG 3'
5' GCGTGTGYTTGGTGGGTCAT 3'
5' CACCTATGACTACCAAAAGCTCATGTAGAAGC 3'
5' CATTACTTTTACTTGGATTTGCACCA 3'
Fragment
Length (bp)
Source
1,254
Townsend et al. (2008)
965
Portik et al. (2010)
521
Portik et al. (2010)
617
Townsend et al. (2011)
608
D.H. Leavitt (pers.
comm.)
658
Brandley et al. (2011)
828
Bryson et al. (2012)
870
Arévalo et al. (1994)