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ORIGINAL ARTICLE
Endemic diversification in the mountains: genetic, morphological,
and geographical differentiation of the Hemidactylus geckos
in southwestern Arabia
JiříŠmíd
1,6
&Mohammed Shobrak
2
&Thomas Wilms
3
&Ulrich Joger
4
&
Salvador Carranza
5
Received: 18 January 2016 /Revised: 8 June 2016 /Accepted: 30 June 2016/Published online: 12 July 2016
#Gesellschaft für Biologische Systematik 2016
Abstract In this study, we provide genetic, morphological,
and geographical comparisons for 11 species of the southwest-
ern Arabian radiation of Hemidactylus geckos, nine of which
are endemic to the region. By using a coalescence-based spe-
cies-tree reconstruction in combination with divergence time
estimations and speciation probability testing, we show that
most of the speciation events occurred in the Pliocene, which
is more recent than previously thought based on calibrations
of concatenated data sets. The current dating indicates that the
changing climate at the beginning of the Pliocene, from hot
and dry to cold and wet, is likely responsible for increased
speciation in Hemidactylus. Analyses of geographic and alti-
tudinal overlap of the species and their morphological differ-
entiation show that most species do not occur in sympatry.
Those that overlap geographically are usually differentiated
by their altitudinal preference, head shape, body size, or their
combination. Our results indicate that the topographically
complex mountains of southwestern Arabia support a signif-
icant radiation of Hemidactylus geckos by allowing multiple
allopatric speciation events to occur in a relatively small area.
Consequently, we describe two new species endemic to the
Asir Mountains of Saudi Arabia, H. alfarraji sp.n.and
H. asirensis sp. n., and elevate two former subspecies of
H. yerburii to a species level, H. montanus and
H. pauciporosus.
Keywords Allopatry .Diversity .Gekkonidae .Radiation .
Species delimitation .Species tree .Speciation
Introduction
Montane areas have been traditionally viewed as bleak envi-
ronments impoverished in terms of biodiversity, especially
when compared to lowland areas of the same region (Fjeldså
et al. 2012). However, recent studies show that montane areas
act as significant reservoirs of species richness that stand out
from the intervening lowlands not only topographically, but
also biologically (e.g., McCormack et al. 2009;Kohlerand
Maselli 2012). This is particularly true for tropical and sub-
tropical mountains that have not been severely affected by
glacial climatic oscillations (e.g., Fjeldså and Rahbek 2006;
Popp et al. 2008; Wollenberg et al. 2008; Pepper et al. 2011).
They are also recognized as areas of high priority for conser-
vation, primarily due to substantial numbers of endemic spe-
cies with narrow distribution ranges easily threatened by ex-
tinction (Myers et al. 2000; Mittermeier et al. 2004).
While most of the Arabian Peninsula isflat and covered by
vast and harsh deserts, the mountain ranges rimming it from
the west and south constitute prominent topographic features
Electronic supplementary material The online version of this article
(doi:10.1007/s13127-016-0293-3) contains supplementary material,
which is available to authorized users.
*JiříŠmíd
jirismd@gmail.com
1
Department of Zoology, National Museum, Cirkusová 1740,
Prague, Czech Republic
2
Biology Department, Faculty of Science, Taif University 888,
Taif, Saudi Arabia
3
Allwetterzoo Münster, Sentruper Straße 315,
48161 Münster, Germany
4
Staatliches Naturhistorisches Museum Braunschweig, Gaußstraße
22, 38106 Braunschweig, Germany
5
Instituteof Evolutionary Biology (CSIC-Universitat Pompeu Fabra),
Passeig Marítim de la Barceloneta 37-49, Barcelona, Spain
6
South African National Biodiversity Institute, Private Bag X7,
Claremont, Cape Town, South Africa
Org Divers Evol (2017) 17:267–285
DOI 10.1007/s13127-016-0293-3
Author's personal copy
that protrude from the surrounding plateaus, in particular, the
Asir Mountains of Yemen and Saudi Arabia, towering up to
over 3000 m, rising from the Tihamah Desert. They form a
broad plateau and, with their rugged topography (Fig. 1), rep-
resent structurally complex habitats and landscape types. The
high elevation of the main ridge and the sharp escarpment
influence the climate in the area significantly. The annual pre-
cipitation in the mountains is as much as six times higher than
in the adjoining lowlands, being a resultof the seasonal south-
western monsoon (also known as Khareef) that drenches the
mountains from June until September (Edgell 2006).
The initial uplift of the mountain ranges began with the
opening of the Red Sea in the Oligocene some 30 million
years ago (Ma) (Bosworth et al. 2005). The mountains rose
further and tilted up to the east during the Miocene (∼15 Ma)
as a result of Arabia’s rifting and volcanism (Bohannon et al.
1989; Davison et al. 1994). The geological evolution of
Arabia has also affected the climate of the region. The climate
fluctuated in cycles from extremely hot and hyper arid at the
beginning of the Miocene to wetter and temperate semi-arid
conditions during the Pliocene, and back to arid conditions in
the Quaternary (Edgell 2006; Huang et al. 2007).
The uniqueness of Southwestern (SW) Arabia’smountain
ranges and its climate is further reflected by the high propor-
tion of endemic species present. It has the richest reptile di-
versity in Arabia (Cox et al. 2012), with 102 species, subspe-
cies, and putative species yet to be described of terrestrial
reptiles currently known to occur in SW Arabia (Sindaco
and Jeremčenko 2008; Sindaco et al. 2013;workinprogress).
Of these, 42 taxa (41 %) are endemic. Geckos (Gekkota) are
represented by eight genera (Bunopus,Cyrtopodion,
Hemidactylus,Stenodactylus,Tropiocolotes, Ptyodactylus,
Pristurus, Trachydactylus), with 26 species representing a
substantial portion of the herpetofauna of this Arabian hotspot
area. The genus Hemidactylus is the most species-rich of all
reptile genera in the area, with ten recognized species and
subspecies. Having undergone numerous taxonomic adjust-
ments within recent years, it is by far the best studied reptile
genus on the Arabian peninsula (Busais and Joger 2011a,b;
Moravec et al. 2011; Carranza and Arnold 2012;Gómez-Díaz
Fig. 1 The extent of the study encompassing the highlands of Yemen and
the Asir Mountains of Saudi Arabia and showing sampling localities from
which material for genetic analyses was used. Elevation profiles at three
sections that show the topography of the region are indicated by the red
lines. (Color figure online)
268 J. Šmíd et al.
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et al. 2012;Šmíd et al. 2013a,b,2015; Vasconcelos and
Carranza 2014). Nine of the ten taxa are part of the Arid clade
of Hemidactylus (Carranza and Arnold 2006), which
underwent major radiation in Arabia subsequent to Arabia’s
separation from the African landmass (Šmíd et al. 2013a). Of
the nine, seven are endemic to SW Arabia (H. adensis Šmíd
et al. 2015;H. jumailiae Busais and Joger, 2011;
H. mandebensis Šmíd et al. 2015;H. saba Busais and Joger,
2011; H. ulii Šmíd et al., 2013; H. yerburii yerburii Anderson
1895; H. y. montanus Busais and Joger, 2011), H. granosus
Heyden, 1827 extends in range to the Sinai Peninsula, and
H. robustus Heyden, 1827 is believed to have been introduced
by humans. These species form two monophyletic groups that
are not closely related (Šmíd et al. 2013a). One is sister to an
African group and the other has an African species nested
within it (H. awashensis Šmíd et al. 2015). All these African
species originated in southern Arabia, and the dating estimates
suggest that the colonization of Africa occurred in the Late
Miocene (Šmíd et al. 2013a), which emphasizes the dispersal
ability of geckos and underscores the close biogeographic
connection between Africa and Arabia.
In this study, we provide novel data on the phylogeny
of all species within the Arid clade of Hemidactylus from
SW Arabia. We reconstruct the phylogeny using a
coalescent-based species-tree estimation and simulta-
neously estimate the divergence times to compare the re-
sults with previously published dates based on
concatenated analyses. The probability of speciation at
each node of our phylogeny is tested in order to assess
the species limits and the credibility of the current taxon-
omy of Hemidactylus.Asaresult,wedescribetwonew
species endemic to the mountains of Saudi Arabia and
elevate two subspecies to species level. Finally, we test
the geographical and altitudinal differentiation, as well as
the morphological niche partitioning in this major endem-
ic radiation of Hemidactylus from SW Arabia.
Materials and methods
Study area
The extent of this study was selected to encompass the major
mountain ranges of SW Arabia—the Yemeni highlands and
the Asir Mountains of Saudi Arabia adjoining to the north. It
forms a strip approximately 400 km in width spanning from
the southwestern corner of the peninsula to Jeddah (roughly
22° of latitude) in the north (Fig. 1).
Material for phylogenetic analyses
New material (67 samples and voucher specimens) was col-
lected during a field trip to Saudi Arabia in May–June 2012.
Additional tissue samples were obtained from collections
listed in Table S1. A total of 108 new samples were combined
with sequences of all species from the Arabian and Socotran
radiations of Hemidactylus, which resulted in a data set of
339 samples.
DNA extraction and sequencing
For the new material and museum samples, genomic DNA
was extracted using commercially available kits.
Concordantly with our previous phylogenetic studies on
Hemidactylus (Carranza and Arnold 2012;Šmíd et al.
2013a,b,2015), we PCR-amplified and sequenced the follow-
ing genes: 12S ribosomal RNA (12S—ca. 425 bp) and
cytochrome b(cytb—1137 or 307 bp, depending on the
amplification success and primers) from the mitochondrial
DNA (mtDNA) and the proto-oncogene mos (cmos—
402 bp), the melanocortin 1 receptor (mc1r—666 bp), and
the recombination activating genes 1 and 2 (rag1—1024 bp,
rag2—408 bp) from the nuclear DNA (nDNA). Primer
sequences and PCR conditions are given elsewhere (Šmíd
et al. 2013a). Both the forward and reverse strands were
sequenced. Chromatograms were checked by eye, and contigs
were assembled and edited in Geneious v.6 (Biomatters Ltd.).
All genes were aligned independently in MAFFT v.7 (Katoh
and Standley 2013) using the Q-INS-i settings for the 12S
alignment and the Bauto^settings for all other genes.
Regions of the 12S alignment containing many indels were
removed with Gblocks (Castresana 2000) with the less
stringent selection applied (Talavera and Castresana 2007),
which resulted in an alignment of 380 bp. All protein-coding
genes were translated to amino acids, and no stop codons were
detected.
Sample details including collection codes, countries of or-
igin, localities, GPS coordinates, and corresponding GenBank
accession numbers are presented in Table S2. Details on the
origin and GenBank accessions of the other Arid clade species
included in the maximum likelihood analysis (see below) that
do not belong to the target groups can be found elsewhere
(Šmíd et al. 2013a).
Phylogenetic analyses
Maximum likelihood of mtDNA data
To reconstruct the phylogenetic relationships of the
SW Arabian Hemidactylus, we performed several
independent analyses on two data sets. To infer the position
of the newly acquired material within the Arabian radiation,
we used all the 339 samples and the two mtDNA genes
concatenated (1517 bp, data set 1). The best-fit model of nu-
cleotide evolution of this data set was identified by
PartitionFinder (Lanfear et al. 2012) under the following
Endemic diversification in the mountains 269
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settings: greedy search, branch lengths linked, only models
available in RAxML evaluated, and BIC selection criterion
applied. The best scheme preferred four independent parti-
tions: 12S,cytb position1, cytb position2, and cytb position3,
with GTR+I+G model suggested for all. A maximum likeli-
hood (ML) phylogenetic analysis of data set 1 was conducted
in RAxML v.7.3 (Stamatakis 2006) using raxmlGUI v.1.2 in-
terface (Silvestro and Michalak 2012). Heuristic search includ-
ed 100 random addition replicates with parameters estimated
independently for each partition and with 100 thorough boot-
strap pseudoreplications. The GTRGAMMA model was used
for all partitions as recommended over the GTRGAMMAI in
the program manual. Identical haplotypes were excluded from
the analysis. Eight individuals representing four species of the
Socotran radiation, which is sister to the Arabian radiation of
the genus (Gómez-Díaz et al. 2012;Šmíd et al. 2013a), were
used to root the tree (H. dracaenacolus—IBES 2604, IBES
3922, IBES 3940; H. granti—IBES 5307, IBES 5626;
H. inintellectus—IBES 5068; H. pumilio—IBES 5021, IBES
5117). By using ML analysis, we identified the monophyletic
groups in which all the SW Arabian species of the
Hemidactylus Arid clade belong—the saba group (consisting
of H. saba,H. granosus,H. ulii, and the two new species
described herein), the robustus group (H. robustus,
H. adensis,H. awashensis,H. mandebensis) as termed in
previous studies (Šmíd et al. 2013b,2015), and the yerburii
group defined here for the first time (H. yerburii yerburii,
H. yerburii montanus,H. yerburii pauciporosus,
H. barodanus,H. granchii,H. jumailiae,H. macropholis).
Intraspecific and interspecific uncorrected pairwise dis-
tances (pdistances) of the 12S and cytb gene fragments were
calculated in MEGA6 (Tamura et al. 2013) using the pairwise
deletion options.
Haplotype networks
Genealogical relationships within the three groups of
Hemidactylus in the four analyzed nuclear markers were
assessed with haplotype networks. Heterozygous positions
were identified based on the presence of two peaks of approx-
imately equal height at a single nucleotide site in both strands
(assessed by eye and Heterozygote Plugin as implemented in
Geneious) and were coded using IUPAC ambiguity codes.
Haplotypes were inferred using PHASE v.2.1 (Stephens
et al. 2001) with the probability threshold set to 0.7.
SeqPHASE (Flot 2010) was employed to convert the input
and output files. Since the presence of distant taxa in the
alignment can strongly affect the results of phasing, the
yerburii group was phased and independent networks were
produced for it separately from the saba and robustus groups,
which were phased together since they are closely related.
Because it has been shown that the presence of missing data
can result in misleading networks (Joly et al. 2007), samples
with sequences much shorter than the rest of the alignment
were removed and the alignment was trimmed to the length of
the shortest sequence. The trimmed alignments had the fol-
lowing lengths: cmos 363 bp and rag1 941 bp for the yerburii
group; rag1 870 bp and mc1r 661 bp for saba and robustus
groups; otherwise, the length was identical to the original (see
above). Haplotype networks were constructed with TCS
v.1.21 (Clement et al. 2000) using statistical parsimony with
95 % connection limit (Templeton et al. 1992) and were visu-
alized with tcsBU (dos Santos et al. 2015).
Species tree
To reliably estimate the divergence times of the studied
Hemidactylus groups (yerburii,robustus,saba), we combined
all 16 species forming these groups in one data set (3924 bp,
data set 2) and performed a multigene coalescent-based spe-
cies tree estimation in *BEAST (Heled and Drummond 2010).
The analysis was performed in BEAST v.1.8 (Drummond
et al. 2012). In total, 124 specimens were used in this analysis
(Table S2). The number of gene copies per species ranged
from 2 to 36 across all genes with the only exception being
rag1, which failed to amplify for H. y. pauciporosus.
BSpecies^need to be defined prior to the species tree analysis,
but since the taxonomy of the Arabian Hemidactylus is very
advanced, we used species and subspecies as defined in pre-
vious studies. The only exception were 14 samples from Saudi
Arabia that formed two isolated clusters within the saba group
as reconstructed by the ML analysis and that were also con-
sidered as two independent Bspecies^for the species tree es-
timation. The probability of their speciation was further tested
(see below). Because the Bayesian time-tree analysis in
BEAST samples the root position from the posterior along
with the rest of the tree topology (Drummond and Bouckaert
2015), we did not use any a priori outgroup to root the tree.
Nuclear markers were imported into BEAUTI after being
phased (see above). Since the species tree estimation assumes
no recombination within loci, we tested all four nDNA genes
for traces of recombination using the RDP, GENECONV, and
MaxChi methods in RDP v.4 (Martin et al. 2010) and no
recombination was detected. Best-fit substitution models for
each gene were identified by AIC selection criterion as imple-
mented in jModelTest v.2.1 (Darriba et al. 2012): 12S and
cytb—GTR+I+G, cmos and rag1—HKY+I, mc1r and
rag2—HKY+I+G. Substitution, clock, and tree models were
unlinked across all partitions. Base frequencies were set to
empirical and the ploidy type of the two mtDNA genes to
mitochondrial. We used a likelihood ratio test (LRT) imple-
mented in MEGA6 to test if the genes studied evolve in a
clock-like manner. The clock-like evolution of all genes was
rejected at a 5 % significance level; a relaxed uncorrelated
270 J. Šmíd et al.
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lognormal clock prior was therefore selected for all of them.
Other prior settings were as follows (otherwise by default):
Yule process tree prior with birth rate uniform (lower 0, upper
1000), random starting trees, GTR base substitution prior uni-
form (0, 100), alpha prior uniform (0, 10), and proportion of
invariable sites uniform (0, 1). The nDNA alignments still
contained some unresolved heterozygous positions after being
phased. In order to account for variability in these heterozygous
positions, we removed the operator on kappa (HKY transition-
transversion parameter), gave it an initial value of 0.5, and mod-
ified manually the xml file by changing the BuseAmbiguities^
parameter to Btrue.^Three individual runs were performed each
of 5 × 10
8
generations with parameters logged every 5 × 10
4
generations. Posterior trace plots, stationarity, convergence,
and effective sample size (ESS) of the parameters were
inspected in Tracer v.1.5 (Rambaut and Drummond 2007).
The tree files resulting from the three runs were combined using
LogCombiner v.1.7 discarding 10 % of each run as burn-in, and
a maximum clade credibility (MCC) tree was produced from
the 27,000 sampled trees using TreeAnnotator v.1.7 (both pro-
grams are part of the BEAST package). Nodes with posterior
probability (pp) values ≥0.95 were considered strongly support-
ed. Original concatenated alignments of data sets 1 and 2 in
FASTA format and Geneious annotated format (compatible
with version 6.0 and later) together with the resulting phyloge-
netic trees (NEWICK format) are available at MorphoBank
under Project 2227 (http://www.morphobank.org/).
Estimation of divergence times
The complete absence of any Hemidactylus fossil record
found in literature (Estes 1983) or in public databases such
as Fossilworks (http://fossilworks.org/)orfosFARbase
(Böhme and Ilg 2003) that could be used as internal calibra-
tion point precludes direct estimation of the time of the speci-
ation events in our phylogeny. We, therefore, used a prior on
the global substitution rates of the same 12S and cytb regions
calculated from a comprehensive phylogenetic study of sev-
eral squamate groups (Carranza and Arnold 2012). These rates
have been corroborated by independent studies of different
taxa that used different calibration points (Metallinou et al.
2012; Sindaco et al. 2012). Specifically, we set a lognormal
prior distribution on the ucld.mean parameters of the 12S and
cytb partitions with mean value = 0.00755 for the 12S and
0.0228 for the cytb and a normal prior distribution on the
ucld.stdev with mean value = 0.00247 for the 12S and
0.00806 for the cytb. The estimated ucld.mean and ucld.stdev
parameters for the nDNA genes were set to have a lognormal
prior distribution with initial value = 0.001, mean = 0,
and stdev = 1 and exponential prior distribution with initial
value = 0.001 and mean = 0.001, respectively.
Topology test
All three currently recognized subspecies of H. yerburii are
part of the same species group as revealed by the ML analysis
of data set 1, yet they do not cluster into a monophyletic group
(Fig. S1). Although Hemidactylus y. yerburii is sister to H. y.
montanus,H. y. pauciporosus forms a well-supported clade
with the other African species (H. barodanus,H. granchii,
H. macropholis). We tested for monophyly of all H. yerburii
subspecies by means of Bayes factor (BF) that compares rel-
ative support of competing hypotheses given the input data
(Kass and Raftery 1995). For the computational demands re-
quired to estimate the marginal likelihood, we confined the
analysis to the yerburii group only. We first generated a spe-
cies tree without any topological constraints using the full set
of genes and settings as described above. Concurrently, we
generated a species tree with the alternative topology inwhich
monophyly of H. y. yerburii,H. y. montanus,a
ndH. y.
pauciporosus was constrained. Marginal likelihood (log) for
each topology was estimated using path sampling (PS) and
stepping-stone sampling (SS) (Baele et al. 2012,2013)as
implemented in BEAST v.1.8, which have been shown to
work well within a multi-species coalescent framework and
to outperform other estimators (Grummer et al. 2014), and BF
was calculated as the difference of log marginal likelihoods of
the unconstrained and constrained trees. The analyses were
run on the CIPRES Science Gateway (Miller et al. 2010).
Speciation probabilities
To test the probability of speciation at each node of our phy-
logeny, we used a Bayesian modeling approach implemented
in Bayesian Phylogenetics and Phylogeography (BPP v.3)
(Rannala and Yang 2003; Yang and Rannala 2010). The meth-
od requires a fully resolved tree as a guide tree from which
subtrees are generated by collapsing or splitting nodes.
Reversible-jump Markov chain Monte Carlo (rjMCMC) algo-
rithm then estimates the posterior distribution for species de-
limitation models and provides a speciation probability for
each node (Leaché and Fujita 2010). BPP has been shown to
perform well even with a relatively small number of loci
(Camargo et al. 2012).
Two groups were analyzed independently: (1) the yerburii
group and (2) the closely related saba and robustus groups.
The guide tree topology was specified using the relationships
inferred by *BEAST. We analyzed two types of data—all
markers (two mtDNA + four nDNA phased) combined and
thenDNA(phased)alone.WerantherjMCMCanalysesfor
10
5
generations with 20 % samples discarded as burn-in.
Following the suggestions of Leaché and Fujita (2010), we
analyzed three combinations of priors for the ancestral popu-
lation size (θ) and root age (τ) with a gamma distribution G(α,
Endemic diversification in the mountains 271
Author's personal copy
β): (1) a relatively large ancestral population size and deep
divergences among species (θ= G(1, 10) and τ=G(1, 10));
(2) a relatively small ancestral population size and shallow
divergences among species (θ= G(2, 2000) and τ=G(2,
2000)); and (3) a relatively large ancestral population size with
shallow divergences among species (θ= G(1, 10) and τ=G(2,
2000)). Each analysis was conducted twice, using reversible-
jump algorithm 0 (with parameter ε= 2) and algorithm 1 (with
parameters α=2 and m =1), respectively (Yang and Rannala
2010). The heredity parameter that allows θto vary among
loci was estimated with a gamma prior G(4, 4), and the locus
rate parameter that allows variable mutation rates among loci
was estimated with a Dirichlet prior (α= 2). The optimal ac-
ceptance proportions were controlled to fall in the interval
(0.15, 0.7) suggested by Yang (2014). Speciation at nodes
with speciation probability values ≥0.95 was interpreted as
strongly supported (Leaché and Fujita 2010).
Geographic and altitudinal overlap
For the paucity of direct field evidence of sympatry/allopatry
in SW Arabian Hemidactylus, we used geographic overlap of
species ranges as a surrogate for this measure. For each spe-
cies, the range was estimated by drawing a convex polygon
around all available localities within the extent of the study
(for a complete list of localities, see Table S2) with the convex
hull function of XTools Pro v.11.1 extension for ArcGIS v.10
with the hull detail level set to 50. Additionally, a 10-km
buffer was added to each hull to account for the uncertainty
associated with the estimate of geographic coordinates of mu-
seum specimens. The exceptions were H. granosus,whichis
known to occur also outside the extent used here and for
which all known records were used; H. robustus, which is
known to be distributed only along the coasts being most
likely a result of having been introduced there by man and
for which the polygon was drawn by hand as a 50–100-km-
wide belt along the coast; and H. saba, which has so far only
been recordedfrom one locality and for which only the 10-km
buffer was drawn. We consider two species to live in sympatry
if at least 10 % of the range of one of them lies within the
range of the other.
To determine pairwise significance of species altitudinal
diversification, we used one-way ANOVA with unequal sam-
ple size honest significant difference (HSD) post hoc test per-
formed in Statistica v.8 (StatSoft Ltd.). For H. granosus dis-
tributed also outside the extent of this study, we used all avail-
able altitudinal data because the species has very shallow pop-
ulation structuring and local adaptation is thus unlikely, while
for H. robustus that has a vast range spanning from Kenya to
Egypt in the northwest and India in the northeast, adaptation to
local conditions is more plausible, especially given its higher
intraspecific genetic diversification, and we therefore used
altitude data only from within the extent of this study.
Altitude data are given in Table S2.
Material for morphological analyses
Morphological analyses were performed on 247 individuals.
The number of individuals ranged from 3 (H. mandebensis,
H. saba, all specimens ever reported for both species) to 94
(H. y. montanus). It is of paramount importance for the taxo-
nomic outcomes of this study that of the 11 SWArabian spe-
cies (9 recognized + 2 described herein), name-bearing type
specimens were examined for nine of them and high-quality
photographs were available for all of them. Apart from that,
additional 68 paratype specimens and one paralectotype were
examined and included in the analyses. The African species
were excluded from the morphological analyses. Only H. y.
pauciporosus measurements were used for a comparison with
H. y. yerburii and H. y. montanus. The list of specimens ex-
amined morphologically including the original morphological
data is shown inTable S2; the list of collection acronyms from
where material was obtained is shown in Table S1. High-
resolution original photographs of 214 vouchered specimens
(totaling in 2891 pictures) of H. jumailiae,H. y. yerburii,H. y.
montanus,H. y. pauciporosus, and the two new species de-
scribed herein were deposited and are available at
MorphoBank. Photographs of most of the other species can
be found at the same repository under the following project
numbers: Project 1006 (H. granosus,H. saba,H. ulii;Šmíd
et al. 2013b), Project1069 (H. granchii;Šmíd et al. 2014), and
Project1172 (H. adensis,H. awashensis,H. mandebensis,
H. robustus;Šmíd et al. 2015).
Morphological analyses
We took the following metric and meristic measurements
using a digital caliper (rounding to 0.1 mm): snout-vent length
(SVL), tail length (TL), head length (HL), head width (HW),
head depth (HD), left eye diameter (E), axilla-groin distance
(AG), number of infralabials (INF) and supralabials (SUP);
contact of uppermost nasals (NASCON); number of
infralabials in contact with anterior postmentals (MENINF);
mutual position of anterior postmentals (MENCON); number
of longitudinal rows of enlarged dorsal tubercles (TUBER);
number of lamellae under the first (1TOE) and fourth (4TOE)
toe of hind legs; and number of preanal pores in males
(PORES). The characters were measured as described in detail
elsewhere (Šmíd et al. 2015).
To test for the morphological differentiation, we compared
features thatare often associated with interspecific disparity in
lizards and that reflect the species ecological niche, such as
prey size or habitat use—body size (represented by SVL) and
head shape (e.g., Vanhooydonck and Van Damme 1999;
Herrel et al. 2001;Losos2009). Head shape was quantified
272 J. Šmíd et al.
Author's personal copy
by means of a principal component analysis (PCA, performed
in Statistica) of the HL, HD, HW, and E variables. The effect
of body size on the headvariables was removed by regressing
them (log
10
-transformed) against log
10
-transformed SVL and
using the residuals as PCA input data. The number of signif-
icant components was determined by the broken-stick model
(Frontier 1976). These components were further tested by un-
equal n HSD post hoc test of factorial MANOVA to determine
the significance of between-species differences. Body size
differences between species were tested by one-way
ANOVA unequal n HSD post hoc test with original, untrans-
formed SVL data used as input. Because sexual dimorphism is
absent in the Arid clade of Hemidactylus in the original metric
values (Carranza and Arnold 2012) as well as in the size-
corrected head proportions (Student’sttest corrected for mul-
tiple comparisons with a Bonferroni correction; data not
shown), we analyzed both sexes together. Meristic characters
and body size variables not employed in the PCA were used
for interspecific comparisons.
Results
Phylogenetic analyses
The ML analysis of the mtDNA data for the 339 individuals
which represented 259 unique haplotypes resulted in the tree
shown in Fig. S1. All Arid clade Hemidactylus species that
occur within the extent of this study fall within three well-
supported groups: (1) the yerburii group (bootstrap support
93) formed by H. y. yerburii,H. y. montanus,H. jumailiae,
and four other species and subspecies from the adjoining
Africa (H. y. pauciporosus,H. barodanus,H. granchii,
H. macropholis); (2) the robustus group (bootstrap 100)
formed by H. robustus,H. adensis,H. awashensis,and
H. mandebensis;and(3)thesaba group (bootstrap 95) formed
by H. saba,H. ulii,H. granosus, and two new species de-
scribed herein. Mean genetic distances of the mtDNA genes
(12S and cytb) between all these taxa are given in Table S3.
In most genes, there is a certain degree of allele sharing
between species in both the yerburii group and the robustus +
saba groups with the only exception of the mc1r network of
the yerburii group, in which all species are clearly separated
and do not share a single allele (Fig. 2b). On the other hand,
networks of cmos and rag2 of both groups and mc1r of the
robustus +saba group show allele sharing between all sister
species. Within the yerburii group, all markers support the
close relationship of H. y. yerburii and H. y. montanus.
All three independent runs of the *BEAST analysis con-
verged with ESS values >200, a critical value recommended
in the BEAST manual indicating adequate mixing of the
MCMC analyses. The *BEAST results are shown in Fig. 2a.
Hemidactylus awashensis was identified as a sister taxon to all
the other species of the robustus group, and the three remain-
ing species were supported to form a clade (pp = 0.97). In the
saba group, the position of H. granosus as sister to the new
species endemic to the Asir Mountains described herein was
supported (pp = 1.0), as well as the sister relationship of the
clade of these two as sister to the new species from Najran also
described herein (pp = 1.0). Otherwise, the deeper phyloge-
netic relationships within this group were not supported.
Within the yerburii group, H. y. yerburii and H. y. montanus
were highly supported as sister taxa (pp = 1.0), closely related
to H. jumailiae (pp = 1.0).
Estimation of divergence times
The basal split within the yerburii group took place 6.6 Ma
(95 % highest posterior density interval (HPD) 5.4–7.9), the
basal split in the robustus group 4.2 Ma (HPD 3.3–5.1), and
that in the saba group 5.6 Ma (HPD 4.6–6.6) (Fig. 2a). The
split between H. y. yerburii and H. y. montanus was dated
back to 1.7 Ma (HPD 1.0–2.5). The split of H. granosus from
one of the new species described herein occurred relatively
recently, 0.9 Ma (HPD 0.4–1.3). These two separated from the
other new species described herein 2.8 Ma (HPD 1.8–3.9).
Topology test
The results ofthe topology test for which the three H. yerburii
subspecies (H. y. yerburii,H. y. montanus,H. y. pauciporosus)
were forced to form a monophyletic group and tested against
our optimal topology from Fig. 2a by means of Bayes factor
indicate that our optimal topology was strongly favored and
that H. y. pauciporosus was decisively excluded from this
clade (log BF >25 in both PS and SS sampling marginal like-
lihood estimations) following the classification by Kass and
Raftery (1995).
Speciation probabilities
Bayesian species delimitation supported with high speciation
probabilities (≥0.95) that all the species analyzed underwent a
speciation event (Fig. 2a). The sole exception was the sister
species pair H. granchii–H. y. pauciporosus that under a large
ancestral population size prior (θ= G(1, 10)) received low
support of the speciation event regardless of root age prior
and the algorithm employed (BPP pp = 0.81 for τ=G(1,10);
BPP pp = 0.83 for τ= G(2, 2000)). Otherwise, all combina-
tions of prior settings, input data types (mtDNA + nDNA vs.
nDNA alone), and algorithm used supported speciation events
in all nodes of the tree. It has been shown that the inclusion of
mtDNA in the Bayesian species delimitation analyses can
influence the results (Burbrink and Guiher 2015); therefore,
we only show and interpret the BPP results of the analyses of
the four nuclear genes.
Endemic diversification in the mountains 273
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Geographic and altitudinal overlap
Ranges of all species estimated by the convex hull and 10-km
buffer functions are presented in Fig. 3. The estimated ranges
of the endemic species cover from over 300 km
2
in H. saba to
79,000 km
2
in H. y. montanus. Out of the 55 available
pairwise comparisons between the 11 SW Arabian species,
only 15 were found to overlap in more than 10 % of ranges
and were therefore considered sympatric under our criteria
(Fig. 4). On the contrary, only 16 species pairs were identified
to be significantly different in their altitudinal preferences by
HSD post hoc test (p< 0.05) (Fig. 4).
Morphological analyses
The first three PCA components were identified as significant
by the broken-stick model. Combined, they accounted for
91.9 % of the variability (PC1 54.9 %, PC2 21.4 %, PC3
15.6 %). The first component mostly corresponded to resid-
uals of head width, the second to residuals of head depth, and
the third to residuals of eye diameter (all log
10
-transformed
against log
10
SVL). The PC1 and PC2 axes show the species
cloud clearly stretched along the narrow-flat (relative to body
size; lower left corner) to broad-high head (relative to body
size; upper right corner) continuum (Fig. S2). Fifteen species
pairs were identified as significantly different in head shape
while 20 species pairs differed significantly in body size
(SVL) by HSD post hoc test (Fig. 4).
Taxonomic implications
Several taxonomic implications for the genus Hemidactylus
stem from our analyses. The three subspecies of H. yerburii
were not recovered as monophyletic in the *BEAST analysis
with H. y. pauciporosus being nested within the other African
species of this clade and sister to H. granchii,fromwhichit
separated 3.3 Ma (HPD 2.1–4.5; Fig. 2a). It also does not
share any allele with either of the two other subspecies
(Fig. 2b). Most of all, the alternative topology in which the
three subspecies were forced to form a monophyletic group
Fig. 2 a Maximum clade credibility (MCC) tree of the ro bustus,saba,
and yerburii groups of the Arabian Hemidactylus resulting from the
*BEAST analysis and inferred using two mtDNA and four nDNA gene
fragments. Posterior probability values ≥0.95 are shown above branches.
The tree isatimetree,thescale at the bottom indicates the age estimates
of the speciation events in millions of years (Ma), and the blue bars
indicate 95 % HPD intervals. Numbersinsquareboxesshow speciation
probabilities for each node as inferred by BPP based on the nDNA data
set under the following combinations of ancestral population size and root
age priors (top to bottom): large ancestral population and deep diver-
gences among species, small ancestral population and shallow
divergences among species, and large ancestral population and shallow
divergences among species. African species that do not occur within the
extent of this study but are closely related to the Arabian species dealt
with herein are in grey.Thebackground coloration indicates changes in
historical climatic conditions in Arabia from extremely hot and arid in the
Miocene to wetter and humid throughout most of the Pliocene and then
back to hyper arid in the Quaternary. bNuclear allele networks of the four
analyzed nuclear loci. Circle sizes are proportional to the number of
alleles. Small empty circles represent mutational steps. Colors correspond
to those given after species names. The dashed line separates the two data
sets for whichnetworks were drawn independently. (Color figure online)
274 J. Šmíd et al.
Author's personal copy
was not supported by the BF test. Based on all these results,
we conclude that H. y. pauciporosus is a full species,
Hemidactylus pauciporosus Lanza, 1978. It should be noted
that the only specimen of H. pauciporosus available for ge-
netic analyses to date (CAS 227511) was in previous publica-
tions (Carranza and Arnold 2012;Gómez-Díazetal.2012;
Šmíd et al. 2013a)misidentifiedasH. macropholis and that
the true H. macropholis appeared for the first time in Garcia-
Portaetal.(2016). The absence of support of the speciation
between H. pauciporosus and H. granchii under the assump-
tion of large ancestral population sizes is further discussed
below.
The status of H. y. montanus is also reassessed. It was
reconstructed as sister to H. y. yerburii in the *BEAST analy-
sis performed here as well as in all analyses of concatenated
data performed elsewhere (Busais and Joger 2011b;Šmíd
et al. 2013a;Garcia-Portaetal.2016). Although the two taxa
share some alleles in three out of the four studied loci
(Fig. 2b), their split that was dated to occur 1.7 Ma (HPD
1.0–2.5) was well supported under all tested scenarios (BPP
pp = 1.0 in all cases; Fig. 2a). They furthermore differ signif-
icantly in their altitudinal distribution and head shape (Figs. 4,
S2). All these multiple lines of evidence strongly support the
elevation of H. y. montanus to full species status,
Hemidactylus montanus Busais and Joger, 2011.
The two isolated lineages obtained in the ML analysis with-
in the saba group (Fig. S1) and composed of the new material
from Saudi Arabia were confirmed to be closely related to
H. granosus by the *BEAST analysis. The common ancestors
of these three species diverged consecutively 2.8 Ma (HPD
1.8–3.9) and 0.9 Ma (HPD 0.4–1.3). Especially the latter di-
vergence occurred relatively recently, yet the speciation prob-
abilities of both nodes under all tested population size and
between-species divergence depth scenarios were strongly
Fig. 3 Sampling sites and distributional ranges estimatedby the Convex
Hull function with an additional 10-km buffer of all SW Arabian Arid
clade Hemidactylus species. For detailed information on the localities,
GPS coordinates, altitude, GenBank accessions, and voucher codes of
all specimens, see Table S2. The range of H. granosus was estimated
based on all localities reported for the species, i.e., even those located
outside the range of this study; the range of H. robustus was drawn by
hand as a 50–100-km-wide belt along the coast based on known
distribution of the species
Endemic diversification in the mountains 275
Author's personal copy
supported (BPP pp =1.0 in all cases; Fig. 2a). As a result of
the molecular differentiation and also the presence of obvious
morphological differences, we describe the two new lineages
endemic to Saudi Arabia as new species.
Hemidactylus alfarraji sp. n.
Synonymy. Hemidactylus yerburii in: Arnold (1980,1986);
Carranza and Arnold (2006,2012); Moravec et al. (2011).
Holotype. NMP 75269 (sample code HSA35, Fig. 5), adult
male, Saudi Arabia, Najran Province, 32 km W of Najran
(17.529° N, 43.827° E, 1969 m a.s.l.), May 24, 2012, collect-
ed by S. Carranza, M. Shobrak, and T. Wilms, MorphoBank
M390464–M390480.
Paratypes. NMP 75270 (sample code HSA36,
MorphoBank M390450–M390463), IBES 10303 (HSA43,
MorphoBank M390355–M390366), adult females; IBES
10266 (HSA37, MorphoBank M390434–M390449), IBES
10295 (HSA41, MorphoBank M390379–M390392), adult
males; all paratypes have the same collection data as the
holotype.
Other material examined. Seven other specimens in total;
see Table S2 for details. Juveniles were used for genetic
analyses only. Specimens from BMNH were used only for
analyses of morphological characters.
Etymology. The species epithet Balfarraji^is a genitive
Latin noun to honor Dr. Saud Al Farraj for his life-long ded-
ication and contribution to the herpetology of Saudi Arabia,
raising public awareness of biodiversity protection and contri-
bution to education at all school levels.
Diagnosis. A species of the Arabian radiation of the Arid
clade of Hemidactylus characterized by (1) medium size with
a maximum recorded SVL 57.8 mm (48.7–57.8 in males,
45.4–52.6 in females); (2) long, wide, and robust head clearly
distinct from the neck, particularly in males (HL = 24–29 % of
SVL; HW = 10.3 ± 0.4 mm st. dev. in males, 9.1 ± 0.9 mm in
females); (3) uppermost nasals always separated by a small
median scale; (4) large anterior postmentals in wide mutual
contact and in contact with the first and second infralabial; (5)
7–9 infralabials and 8–11 supralabials; (6) dorsum with 14–16
longitudinal rows of enlarged, strongly keeled, conical tuber-
cles; (7) males with invariably 4 preanal pores; (8) 7–8lamel-
lae under the first toe and 10–12 lamellae under the fourth toe;
(9) enlarged tile-like subcaudals; and (10) brownish-beige col-
oration with distinct dark bands starting behind nostrils and
crossing the eyes to the ear openings, dorsum with slightly
Fig. 4 a Pairwise comparisons of the geographical, altitudinal, and
morphological overlap of the 11 Hemidactylus species occurring in SW
Arabia. For each species pair, all criteria in which the two species differ
are given. Four differential factors were tested: sympatry/allopatry,
difference in preferred altitude, head shape difference, and size
difference. Cells outlined in red indicate species pairs that do not differ
in any of the tested criteria. bComparison of body size (expressed as
snout-vent length) of the 11 species. cComparison of the altitudinal
distribution of the 11 species. In both band c, mean values are shown
(central line) together with the standard deviation (box), and minimum
and maximum values (whiskers) and species are sorted equally. (Color
figure online)
276 J. Šmíd et al.
Author's personal copy
visible X-shaped dark markings (most distinct in juveniles)
formed by dark tubercles, and intact tail with 10–11 intensely
dark bands on a beige background, becoming paler towards
the tail tip so the dark bands are most contrasting at the end of
the tail.
Differential diagnosis. Hemidactylus alfarraji sp. n. is not
significantly different in body size and head shape from its
closest relatives, H. granosus and the new species endemic to
the Asir Mountains described below, although it is seemingly
the biggest of the three species (Fig. 4). It is significantly
distinct from these species by the following characters: the
number of infralabials in H. alfarraji sp. n. (8.5± 0.5, range
7–9) is higher than in H. granosus (7.4 ± 0.4, 7–8) and the new
species endemic to the Asir Mountains (7.7 ± 0.5, 7–9) (one-
way ANOVA F
(2, 47)
= 17.849, p< 0.001). The number of
supralabials is also higher in H. alfarraji sp. n. (10.2 ± 0.6,
9–11) than in H. granosus (9.3 ± 0.5, 9–11) and the new spe-
cies endemic to the Asir Mountains (9.4 ± 0.7, 7–11) (one-
way ANOVA F
(2, 47)
= 6.467, p<0.01). Hemidactylus
alfarraji sp. n. has a lower number of preanal pores in males
(invariably four) than H. granosus (5.7 ± 0.8, 4–7) and the
new species endemic to the Asir Mountains have (invariably
six) (one-way ANOVA F
(2, 17)
= 24.663, p< 0.001). From the
new species endemic to the Asir Mountains, it further differs
in having distinctly keeled dorsal tubercles and a higher
number of subdigital lamellae under the first toe (7.1 ± 0.3,
7–8inH. alfarraji sp. n. vs. 6.2 ± 0.4, 5–7 in the latter; ttest
t= 6.247, p< 0.001; Fig. 5). Although the above described
significant differences between the species support their spe-
cies status, the high overlap of scale counts indicates that these
characters are of limited use in species identification.
Comparison of metric and meristic variables with the other
SW Arabian Hemidactylus is given in Table S4.
Description of the holotype. NMP 75269 (sample code
HSA35), adult male with distinctly depressed body. The head
is flattened and very wide in the temporal region. There are
enlarged distinctly keeled dorsal tubercles arranged in 14 lon-
gitudinal rows along the body. Large eyes protrude from the
lateral head outline (in life). Round nostrils are defined by a
large rostral with a pronounced median notch, three subequal
nasals, and the first labial. The uppermost nasals are not in
contact; they are separated by a small inserted pentagonal
scale. The supralabials are 10 (left)/11 (right), the infralabials
8/8. The anterior postmentals are ina wide median contact and
in contact with the first and secondinfralabials and are follow-
ed by paired posterior postmentals on each side. The ear open-
ing is oval. The head is dorsally covered with regularly spaced
round unkeeled tubercles that start at the interorbital level and
Fig. 5 Holotypes and type localities of H. alfarraji sp. n. and H. asirensis
sp. n. aGeneral body habitus of H. alfarraji sp. n. holotype (NMP
75269); bdetail of its head; cdetail of its precloacal region with
preanal pores visible; dlamellae under the toes of left hind limb; etype
locality 32 km W of Najran (1969 m a.s.l.), Najran Province, Saudi
Arabia. fGeneral body habitus of H. asirensis sp. n. holotype (NMP
75271); gdetail of its head; hdetail of the precloacal region with
preanal pores visible; ilamellae under the toes of left hind limb; jtype
locality Al Balhy (2376 m a.s.l.), Asir Province, Saudi Arabia
Endemic diversification in the mountains 277
Author's personal copy
continue onto the neck and body where they form keeled
tubercles. The ventrals are roughly hexagonal and imbricate.
The limbs are slender. The forearms, thighs, and lower legs
have large unkeeled tubercles that are pointed caudally. The
lamellae on the underside of toes are well developed and dis-
tinctly extended towards the toe tips. The lamellae under the
first toe are 7/7, under the fourth toe 11/11. Thumbs are very
short. The tail is complete, longer than SVL (TL/SVL = 1.27)
and with 12 whorls bearing at least six tubercles. Tail whorls
are separated by three to five rows of small scales. The
subcaudals are enlarged and start about 1 cm behind the vent.
There are four preanal pores in a slightly curved line separated
medially by one ventral scale. The tongue was removed for
genetic analyses.
Measurements (in mm): SVL 52.7, TL 66.8, HL 13.3, HW
10.1, HD 4.1, E 3.2, AG 21.6.
Coloration in life. Background is pale grey-buff to beige; a
dark stripe runs from the nostril through the eye to the tempo-
ral region and widens distinctly above the ear. There is a dark
V-shaped marking on top of the nasal region. The enlarged
tubercles on the head are dark. There is a series of dark and
almost round vertebral spots that encompass only two verte-
bral rows of tubercles and the smaller scales between them.
The spots start on the nape, the first four (up to scapulae) are
most distinct, and those from the scapular region to the vent
are less prominent. Some tubercles on flanks, forearms,
thighs, and lower legs are also dark. The ventral side is creamy
white to pinkish. The tail has 11 dark bands that get darker and
more clearly bordered towards the tail tip. They do not extend
onto the ventral side of the tail except for the three most pos-
terior bands.
Morphological variation.Original morphometric and me-
ristic data are provided in Table S2. All specimens are very
similar regarding size, body proportions, and coloration.
Adult male SVL varies from 48.7 to 57.8 mm, in females from
45.4 to 52.6 mm. Paratype IBES 10266 is the only specimen
with seven infralabials (unilaterally). Likewise, paratype IBES
10295 is the only specimen with eight supralabials (unilater-
ally). All examined animals have anterior postmentals in con-
tact with first and second infralabials except BMNH
1992.173, in which anterior postmentals touch only the first
infralabial, being separated from the second infralabial by a
small interstitial granule. Dorsal tubercles form 16 rows in
IBES 10278 and IBES 10302 and 15 in IBES 10303, other-
wise always 14. BMNH 1992.172 is the only specimen with 8
lamellae under the first toe and 12 under the fourth toe.
All specimens generally agree in coloration. The dark dor-
sal tubercles of the juveniles (IBES 10278, IBES 10288) form
three clear X-shaped markings, one on scapulae, one in mid-
dorsum, and one just in front of the pelvic area.
Genetic variation.The level of genetic variability within
H. alfarraji sp. n. is very low, perhaps due to the geographic
proximity of both localities from where material for genetic
analyses was available. Maximum pdistance is 1.1 % in the
12S and 2 % in the cytb. Variability in the nuclear genes is also
rather low, although all loci studied are represented by more
than one allele (Fig. 2b). All rag2 alleles of H. alfarraji sp. n
are private, while in the mc1r and rag1 usually the central
allele is shared with the other new species described herein
and also with H. saba in the cmos.
Distribution and ecology.This new species is endemic to
Saudi Arabia. All known localities lie in the Najran area of
Saudi Arabia by the Yemeni border in a radius of ca. 40 km
(Fig. 3), although it may be more widespread. All the speci-
mens were found during the day inside drainage tunnels under
roads that prevent the roads from flooding during torrential
rains. The tunnels were located at tributary gorge at a rocky
area with scattered Acacia tortolis trees. Otherwise, the vege-
tation cover comprised Indigofera spinosa, Aristida pennei,
and Lycium shawii. Onespecimenwasfoundbetween9and
9:30 at locality 17.599° N 44.205° E, 1364 m a.s.l., with the
air temperature outside the tunnel 30 °C and relative air hu-
midity 29 %; the rest of the specimens were collected between
10:30 and 10:45 at the type locality with the air temperature
outside the tunnel 29.7 °C and relative air humidity 25.3 %.
No searches were conducted during the night for security rea-
sons and because a sandstorm hit the area during the only
night spent at Najran. Future studies of this Saudi endemic
should be directed to obtain more information on its distribu-
tion and ecology.
Hemidactylus asirensis sp. n.
Synonymy. Hemidactylus yerburii in: Arnold (1980,1986);
Carranza and Arnold (2012).
Holotype.NMP 75271 (sample code HSA44, Fig. 5), adult
male, Saudi Arabia, Asir Province, Al Balhy (18.075° N,
43.083° E, 2376 m a.s.l.), May 24, 2012, collected by S.
Carranza,M.Shobrak,andT.Wilms,MorphoBank
M389997–M390014.
Paratypes. NMP 75272 (sample code HSA12,
MorphoBank M390048–M390066), adult male, Saudi
Arabia, Asir Province, 5 km N of Wadi Shora (19.836° N,
41.776° E, 1750 m a.s.l.), May 22, 2012; IBES 10044 (sample
code HSA2, MorphoBank M390067–M390077), adult male,
Saudi Arabia, Makkah Province, 20 km NE of Al Sir (21.259°
N, 40.796° E, 1594 m a.s.l.), May 22, 2012; IBES 10011
(HSA4, MorphoBank M390102–M390120, adult female),
IBES 10341 (HSA7, MorphoBank M389944–M389962,
adult female), IBES 10386 (HSA8, MorphoBank M389919–
M389929, adult female), IBES 10330 (HSA6, MorphoBank
M389978–M389995, adult male), Saudi Arabia, Makkah
Province, 10 km S of Al Sir (21.115° N, 40.599° E, 1696 m
a.s.l.), May 21, 2012; IBES 10221 (sample code HSA52,
MorphoBank M390031–M390047), adult female, Saudi
Arabia, Makkah Province, 7 km S of Ghazaial (20.928° N,
278 J. Šmíd et al.
Author's personal copy
41.123° E, 1453 m a.s.l.), May 25, 2012; IBES 10378 (sample
code HSA53, MorphoBank M389930–M389943), adult fe-
male, Saudi Arabia, Makkah Province, Taif (21.338° N,
40.422° E, 1616 m a.s.l.), May 27, 2012. All paratypes have
the same collectors as the holotype.
Other material examined.Eighteen other specimens in to-
tal; see Table S2 for details. Specimens from BMNH were
used only for analyses of morphological characters.
Etymology. The species epithet Basirensis^is an adjective
which refers to the mountain range where the species is dis-
tributed, the Asir Mountains of Saudi Arabia.
Diagnosis. A member of the Arabian radiation of the Arid
clade of Hemidactylus with the following combination of
characters: (1) medium size with SVL ranging between 43.0
and 48.5 mm in males and 38.3 and 51.1 mm in females; (2)
long and narrow head not wider than the body in its widest
part (HL = 23–28 % of SVL, HW = 7.9 ± 1.3 mm in males,
7.6 ± 1.0 mm in females); (3) large anterior postmentals usu-
ally in wide mutual median contact (96 % of specimens) and
in contact with the first and second infralabial (at least on one
side in 96 % of specimens); (4) uppermost nasals separated by
an inserted scale in 87 % of specimens; (5) 7–9 infralabials
and 7–11 supralabials; (6) dorsum with enlarged tubercles in
12–16 longitudinal rows, the tubercles are not keeled or, if so,
only the vertebral ones; (7) males with6 preanal pores; (8) 5–7
lamellae under the first toe and 9–11 under the fourth toe; (9)
enlarged tile-like subcaudals; (10) beige background colora-
tion with dark blotches in irregular vertebral and paravertebral
rows that form X-shaped markings, head with distinct dark
band from the nostril through eye to the ear, parietal and tem-
poral regions with irregular dark markings which can be ab-
sent in some individuals, tail with 9–12 dark bands that grow
in intensity towards the tail tip, and body underside creamy
whitish.
Differential diagnosis. Hemidactylus asirensis sp. n. differs
significantly from its sister species, H. granosus, in the head
shape; it has shorter and narrower head (HL 10.7 ± 1.3 vs.
12.3 ± 1.1 mm, ttest t=−4.085, p< 0.001; HW 7.8 ± 1.2 vs.
9.3 ± 0.8 mm, ttest t=−4.407, p< 0.001; Fig. S2) and in the
degree of keeling of the dorsal tubercles (H. asirensis sp. n.
has flat unkeeled tubercles while H. granosus strongly
keeled). The two species also differ in the number of lamellae
under toes; H. asirensis sp. n. has 6.2 ± 0.4 (range 5–7) lamel-
lae on the first toe while H. granosus has 7.4 ± 0.5 (7–8) (ttest
t=−8.681, p< 0.001) and 10.1 ± 0.6 (9–11) on the fourth toe
while H. granosus has 11.6 ± 0.7 (10–13) (ttest t=−7.051,
p< 0.001). The differences from H. alfarraji sp. n. are de-
scribed above. A comparison of metric and meristic variables
with the other Hemidactylus species form SWArabia is given
in Table S4.
Description of the holotype. NMP 75271 (sample code
HSA44), adult male with a slender body habitus. The head
is long (HL = 24 % of SVL) and narrow (HW = 8.5 mm).
There are enlarged round dorsal tubercles arranged in 14 lon-
gitudinal rows along the body. Round nostrils are defined by a
large rostral, three subequal nasals, and the first labial. The
uppermost nasals are not in contact. The supralabials are 9/8,
the infralabials 8/8. The anterior postmentals are very long and
in a wide median contact and in contact with only the first
postmentals. The ear opening is kidney-shaped. The head is
dorsally covered with small granules intermixed with irregu-
larly spaced round unkeeled tubercles that start at the interor-
bital level and continue onto the neck and body where they
transform to dorsal tubercles. The ventrals are imbricate in
regular diagonal rows. The forearms, thighs, and lower legs
are covered with round enlarged unkeeled tubercles. The la-
mellae on the underside of toes are well developed. The la-
mellae under the first toe are 6/6, under the fourth toe 9/10.
The tail is original but broken in the middle and almost de-
tached from the rest of the body; it is longer than the body (TL/
SVL = 1.22) and has 11 whorls bearing at least six tubercles.
The tail whorls are separated by four to five rows of small
scales. The subcaudals are enlarged, tile-like, and wider than
long. There are six preanal pores in almost straight line sepa-
rated medially by one inserted ventral scale. The tongue was
removed for genetic analyses.
Measurements (in mm): SVL 45.2, TL 55.2, HL 10.9, HW
8.5, HD 3.8, E 2.5, AG 18.4.
Coloration in life. Background color is beige-brownish; a
dark stripe runs from the nostril through the eye to the tempo-
ral region. The top of head has several isolated and almost
round dark brown spots. There are five clearly visible X-
shaped markings on the dorsum, first on the nape, second in
the scapularregion, two on midbody, last on the sacral region.
The markings continue onto the tail in a form of nine dark
transverse bands that get darker and more clearly bordered
towards the tail tip. The last 7 mm of the tail are brown. The
last four dark tail bands are visible also from the underside.
The tubercles on the dorsum and flanks that do not form the X-
shaped marks are clearly whitish. The venter is uniformly
creamy pinkish.
Morphological variation.Original morphometric and me-
ristic data for all examined specimens are in Table S2. All
examined specimens have seven to eight infralabials with
the exception of the paratypes IBES 10221 and IBES 10386
that both have unilaterally nine infralabials. Paratype IBES
10044 is the only specimen with only 7 (unilaterally)
supralabials; all other specimens have 8–11. In BMNH
1978.905, anterior postmentals are not in contact with each
other. In IBES 10378, IBES 10011, and BMNH 1934.10.20.8,
uppermost nasals are not separated by an inserted scale and are
in narrow (IBES 10378) or broad (IBES 10011, BMNH
1934.10.20.8) contact. Number of lamellae under first toe
varies from six to seven in most specimens but BMNH
1978.907, in which there are only five (unilaterally) lamellae.
The holotype differs from all other examined specimens in
Endemic diversification in the mountains 279
Author's personal copy
that it is the only individual with anterior postmentals in con-
tact with only the first and not the second infralabials.
Color pattern is consistent among all specimens with only
the dark dorsal markings varying in intensity. In some indi-
viduals (IBES 10341, IBES 10386), the dark X-shaped dorsal
markings are fragmented and formed only by isolated dark
blotches.
Genetic variation.There is a certain degree of intraspecific
genetic variation in the mtDNA genes in H. asirensis sp. n.
(Fig. S1)withmaximumpdistance being 3.9 % in the 12S and
5.6 % in the cytb. Consistently with the mtDNA variation, the
four nuclear loci also show some genetic structure. Although
there are some private alleles of H. asirensis sp. n. not shared
with any other species, there is allele sharing with some other
species in all the nuclear loci analyzed. Some mc1r and cmos
alleles are shared with H. granosus and H. alfarraji sp. n.,
cmos also with H. saba. The central and most frequent alleles
are shared with H. alfarraji sp.n.intherag1 and with
H. granosus and even with H. robustus,H. mandebensis,
and H. adensis in the rag2.
Distribution and ecology. This species is endemic to Saudi
Arabia. All nine localities from which H. asirensis sp. n. is
reported here are situated in high altitude areas of the Asir
Mountains in Saudi Arabia with elevations ranging from
1453 to 2376 m. They all lie on the eastern foothills of the
mountain slopes that face the inland Arabian deserts (Fig. 3),
and although it is an arid environment, temperature conditions
are much milder than in the surrounding lowland areas. The
specimens were collected while active at night (18:30–20:30)
and during the day (15:00–15:20) hiding inside drainage tun-
nels under roads that prevent the roads from flooding during
torrential rains. Temperatures on the collection site ranged
between 27.5 and 32.1 °C and the relative air humidity be-
tween 16.1 and 55.5 %. Most of the tunnels were found in
wadis with sandy/gravel substrate in otherwise rocky areas.
The vegetation cover was dominated by Acacia gerrardii and
A. asak in the northern sites and A. tortolis in the southern
sites. Other dominant plant species were Arstida sp.,
Forsskaolea tenacissima,Tamarix aphylla,andJuniperus
procera. This gecko species was widely collected between
1934 and 1935 around and inside Taif city by St John Philby
and later on, in 1978, by John Gasperetti.
Discussion
The mountains of the SW Arabian Peninsula are well known
for their pronounced species richness and high endemism of
reptiles (e.g., Arnold 1987;Gasperetti1988), yet the mecha-
nisms responsible for such diversity have never been investi-
gated. It can be attributed in part to the relative scarcity of data
from this region in combination with incomplete taxonomic
classification of many groups and the lack of robust
phylogenetic knowledge that would form a backbone for such
studies. Hemidactylus is an exception in that it is presently the
best studied Arabian reptile genus with well resolved taxono-
my and reliably reconstructed biogeographic history (Busais
and Joger 2011a,b; Moravec et al. 2011; Carranza and Arnold
2012;Gómez-Díazetal.2012;Šmíd et al. 2013a,b,2015;
Vasconcelos and Carranza 2014). More detailed analyses of
the diversification processes underlying its Arabian radiation
were therefore feasible.
The species tree analysis of the saba,robustus,andyerburii
groups performed here and based on five loci (mtDNA and
four nDNA) supports the topology retrieved earlier from the
analyses of concatenated data sets (Šmíd et al. 2013a). The
only exception is the position of H. awashensis, which is sister
to all other species of the robustus group according to the
species tree analysis, a result concordant with previous studies
(Šmíd et al. 2015;Garcia-Portaetal.2016). It is worth noting
that we performed the coalescent-based species tree estima-
tion because the method is generally superior to concatena-
tion, which can be prone to producing different tree resolution
(Kubatko and Degnan 2007). This is so particularly for trees
with short branching intervals or with conflicting gene trees
(Degnan and Rosenberg 2009; Lambert et al. 2015), as is the
case in the Arabian Hemidactylus (Šmíd et al. 2015). The
biggest difference between the species tree produced here
compared to the previous study, which was based on concat-
enation and employed the same calibration approach based on
mutation rates (Šmíd et al. 2013a), was the divergence dates.
Employing the multigene coalescent-based approach resulted
in a general pattern of more recent divergence times for all
nodes. To be exact, the basal split within the yerburii group
occurred 6.6 Ma (HPD 5.4–7.9) compared to 9.8 Ma (HPD
6.5–13.6) in the concatenated analysis, the basal split in the
robustus group 4.2 Ma (HPD 3.3–5.1) compared to 7.0 Ma
(HPD 4.6–9.8), and in the saba group 5.6 Ma (HPD 4.6–6.6)
compared to 7.0 Ma (HPD 4.3–10.0). The split between H. y.
yerburii and H. y. montanus as dated here took place 1.7 Ma
(HPD 1.0–2.5) compared to 4.0 Ma (HPD 2.5–5.7). The split
of H. granosus from H. asirensis sp. n. occurred relatively
recently, 0.9 Ma (HPD 0.4–1.3). These two separated from
H. alfarraji sp. n. 2.8 Ma (HPD 1.8–3.9). Despite being based
on the same rates for the same genes and implemented with
the same priors (Carranza and Arnold 2012), the dating esti-
mates differed slightly with a general pattern of more recent
mean divergence times for all nodes in the species tree analy-
sis, although the HPD intervals of the two approaches show a
large degree of overlap. The mean difference of dating esti-
mates between the species-tree and gene-tree analyses across
all nodes is 2.5 Ma. This is most likely a result of the fact that
gene divergences do not necessarily have to correspond to the
actual timing of speciation events, but their divergence may be
older than the speciation, and that phylogenies derived from
concatenated data sets for that reason overestimate divergence
280 J. Šmíd et al.
Author's personal copy
times (Edwards and Beerli 2000; McCormack et al. 2011).
Moreover, the presence of shared alleles in all four nDNA
genes studied (Fig. 2b) indicates that incomplete lineage
sorting is widespread among Arabian Hemidactylus. Closely
related yet morphologically different species share alleles at
most of the studied loci. Only the African H. awashensis in the
robustus group has all alleles of all loci private. The presence
of incomplete lineage sorting together with the relatively re-
cent speciation of some of the clades suggest that some of the
species are in a stage of incipient speciation (e.g., H. granosus
and H. asirensis sp. n.) and that they have not yet attained
reciprocal monophyly in individual genes.
The taxonomy of the Arabian Hemidactylus is very ad-
vanced compared to other Arabian reptile genera (e.g.,
Metallinou et al. 2015), although their superficial morpholog-
ical similarity may cast doubts on the validity of the taxa.
Nonetheless, the speciation probabilities estimated by the
BPP analyses under all combinations of ancestral population
sizes and divergence depths among species together with a
careful assessment of some informative morphological char-
acters, such as the preanal pores and the lamellae under the
toes (among others), unequivocally support that speciation has
occurred in all the nodes of the species tree and that all the
recently described species are not a result of taxonomy artifi-
cially inflated by species oversplitting (Zachos 2015).
Speciation was supported even for the most recent split be-
tween H. granosus and H. asirensis sp. n. that occurred only
0.9 Ma (HPD 0.4–1.3) (Fig. 2a). The low support of speciation
for the split between H. granchii and H. pauciporosus re-
ceived under the assumption of a large ancestral population
size prior was most likely caused by having only a single
sample (two alleles of phased nDNA loci) of each available
for the analyses. Since large populations assume larger allelic
variation, having low sample size with low variation of alleles
violates this assumption and results in low support for the
speciation event. The two species diverged relatively long
ago according to our dating results (3.3 Ma with HPD 2.1–
4.5 or 4.7 Ma with HPD 2.7–7.0 according to the alternative
dating; Šmíd et al. 2013a). We presume that adding more
specimens of the two species rather than sequencing more loci
might help to support the speciation, a practice generally rec-
ommended for multilocus coalescent-based approaches
(Hovmöller et al. 2013). Alternatively, the low BPP support
in this node could result from incomplete lineage sorting
(see above) and thus the lack of information in the sequence
data (Zhang et al. 2014). However, because H. granchii and
H. pauciporosus share alleles only in the cmos (Fig. 2b), we
assume the former explanation to be more plausible.
The results ofthe geographical and altitudinal overlap anal-
yses and body size and head shape comparisons clearly show
that either geographical differentiation, morphological niche
partitioning, or the combination of both has accompanied the
speciation history in SW Arabian Hemidactylus.Allopatryis
the most common diversification mechanism. Of the 55
pairwise between-species comparisons, 40 (73 % species
pairs) do not overlap geographically (Figs. 3and4), and in
the cases when two species differ in one attribute only, allop-
atry is the most frequent (68 %; 15 of 22 comparisons).
Interestingly, altitude alone is responsible for differentiation
of only one species pair—H. jumailiae and H. ulii. Given the
complex topography of SWArabia, with the sharp escarpment
rising abruptly from almost sea level up to 2500 m (Fig. 1),
one would expect that altitude plays a more substantial role in
the ecological separation of species. Apparently, not the high
mountains themselves but rather the landscape complexity
and habitat heterogeneity are the most likely factors responsi-
ble for the numerous allopatric speciation events. It can be
assumed that when most of the Hemidactylus species are sep-
arated geographically, an altitudinal shift is not needed. Our
analyses indicate that sympatry is usually accompanied by
either body size or head shape differences. These morpholog-
ical prerequisites are in accord with the character displacement
hypothesis (Brown and Wilson 1956) and have been consid-
ered a prerequisite necessary for the coexistence of closely
related lizard species (Pianka 1986 and references therein).
In Hemidactylus, extreme body size disparities caused by ac-
celerated rates of body size evolution, but not coupled with
head shape differentiation, have been confirmed for sympatric
species of the Socotra Archipelago (Garcia-Porta et al. 2016).
Also, in the mainland species studied here, body size dispar-
ities were found more frequently (36 %; 20 of 55 compari-
sons) than is head shape differentiation (27 %; 15 of 55 com-
parisons). For instance, H. yerburii differs from the five other
species with which it occurs in sympatry by being larger than
the others and H. ulii separates from H. robustus and
H. adensis, with which it is sympatric, solely by head shape
(Fig. 4). Head shape has been indicated to be a good predictor
of bite performance in lizards (Herrel et al. 2001), and it is
usually correlated with specialization for different prey sizes
(Metzger and Herrel 2005). It is therefore possible that H. ulii
feeds on different prey items than do H. robustus and
H. adensis. This however requires further study.
Interestingly, there are three species pairs that do not show
significant differences in any of the tested criteria—
H. robustus and H. adensis,H. robustus and
H. mandebensis, and H. ulii and H. mandebensis (Fig. 4).
Hemidactylus robustus,H. adensis,andH. mandebensis are
closely related species that have diverged relatively recently,
2.8Ma(HPD1.9–3.7). Hemidactylus robustus is a wide-
spread species with an extensive range (see Sindaco and
Jeremčenko 2008). It is assumed to have originated in eastern
Arabia (Oman) as revealed by its high genetic diversity in this
region (Carranza and Arnold 2012;Šmíd et al. 2013a); else-
where, its distribution is limited to coastal areas. A likely
explanation of its morphological similarity and geographical
overlap with H. adensis and H. mandebensis is that
Endemic diversification in the mountains 281
Author's personal copy
H. robustus has been introduced to SW Arabia relatively re-
cently by human-mediated dispersal and its ecological sepa-
ration from the other species has not developed yet. Another
case is the H. ulii–H. mandebensis species pair. Both species
originated in the southwestern corner of the Arabian
Peninsula, and their ranges are most likely not a result of
human-mediated translocations. Yet, they do not show any
significant geographic or morphological differences in any
of the characters studied (Fig. 4). Nevertheless, even seeming-
ly sympatric and phenotypically similar species can co-occur
if they have different microhabitat requirements (Pianka 1969;
Vitt and de Carvalho 1995)andH. ulii and H. mandebensis
can separate out just by microhabitat selection. Unfortunately,
the data currently available do not allow for testing such fine-
scale ecological divergence.
According to the results of the dating analyses presented
here, the intra-Arabian diversification began 6.2 Ma (HPD
5.2–7.3; Fig. 2a)whentherobustus and saba groups separated
and were followed by the separation of H. ulii, which split off
5.6 Ma (HPD 4.6–6.6). Although the divergence estimates for
these two splits were dated as older in the analyses of
concatenated data (9.5 Ma with HPD 6.4–13.3 and 7.0 Ma
with HPD 4.3–10.0, respectively; Šmíd et al. 2013a), the
HPD intervals of the latter were much larger and always over-
lapped with those of the current analyses. For instance, the
HPD interval of the split of H. ulii based on concatenation
encompasses entirely that of the species tree approach.
However, even after taking this uncertainty associated with
divergence dating into account, we can still draw tentative
conclusions on the diversification history of Hemidactylus in
SW Arabia.The onset and subsequent rise of the number of
speciation events appears to be linked with gradual climatic
changes that occurred in Arabia during the Miocene–Pliocene
boundary. The climate of Arabia was extremely dry during the
Late Miocene (∼10–5.5 Ma), and the conditions had changed
dramatically to humid in the Early Pliocene (Edgell 2006;
Huang et al. 2007). Throughout the Pliocene, savannah grass-
lands and woodlands dominated the area until aridity began to
increase again towards the end of the Pliocene and resulted in
hyper arid conditions similar to today in most of the Arabian
mainland (Edgell 2006). The results of the dating analyses
show that the onset of Hemidactylus diversification could be
coincident with the establishment of the SW Arabia monsoon
system 8–4.6 Ma and that most of the speciation events took
place duringthe humid climatic phase between 5.5 and 0.8 Ma
(Fig. 2a). Moreover, SW Arabia is also the area of mainland
Arabia that receives the highest annual precipitation (Edgell
2006). It therefore seems that despite the species of the
Hemidactylus Arid clade generally inhabit extremely arid en-
vironments, temporal and spatial precipitation increase has
been the key factor that triggered its speciation and sustained
its diversity in the Arabian Peninsula. Whether and to what
degree the precipitation-related factors influenced the species
distributions during the Quaternary climatic oscillations re-
mainstobetestedwithapproachessuchaspaleo-
distribution modeling which requires more distributional data
than we have currently available (1–19 unique localities).
By elevating the two former H. yerburii subspecies to spe-
cies ranks, one more species (H. montanus) becomes endemic
to SW Arabia and one (H. pauciporosus) to the Horn of
Africa. Together with the two new species described herein,
this further supports SW Arabia as one of the world’srichest
reptile hotspots. Additionally, detailed phylogenetic analyses
of other Arabian reptile genera that shed light on the biogeo-
graphic history and potential species richness of some wide-
spread taxa have been produced in recent years (Metallinou
et al. 2012,2015; Kapli et al. 2014;dePousetal.2016; Tamar
et al. 2016). They give good grounds for expecting that the
overall reptile diversity of southern Arabia will increase once
their taxonomy is sorted out. This highlights the singularity of
the Eastern Afromontane and Horn of Africa biodiversity
hotspots that extend onto the southwestern part of the
Arabian Peninsula and which represent the richest non-
tropical reptile hotspots (Mittermeier et al. 2004).
Acknowledgements We would like to thank all curators who granted
us access to or provided tissue samples of material housed in their collec-
tions, namely, B. Clarke, E. N. Arnold, and P. D. Campbell (BMNH); J.
Vindum (CAS); R. Sindaco, and G. Boano (MCCI); G. Doria (MSNG);
S. Scali (MSNM); A. Nistri (MZUF); J. Moravec (NMP); S. B. El Din
(SMB); G. Köhler, and L. Acker (SMF). Special thanks are due to T.
Mazuch (TMHC) for providing pictures of the syntype of H. yerburii.
We are thankful to the Deanship of academic research at the Taif
University for funding and issuing collection permit for sampling in
Saudi Arabia (Grant No. 1–433–2108). We thank Omer Baeshen,
Environment Protection Agency, Sana’a, Republic of Yemen, for issuing
the collection permit (Ref 10/2007). The manuscript benefitted from com-
ments of two anonymous reviewers, and the English was significantly
improved by Jessica da Silva and Jody Taft. This work was supported by
the Ministry of Culture of the Czech Republic under grant DKRVO
2016/15, National Museum, 00023272 (JŠ), and grant CGL2015-
70390-P (MINECO-FEDER) (SC).
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