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Background: The Indian Tectonic Plate split from Gondwanaland approximately 120 MYA and set the Indian subcontinent on a ~ 100 million year collision course with Eurasia. Many phylogenetic studies have demonstrated the Indian subcontinent brought with it an array of endemic faunas that evolved in situ during its journey, suggesting this isolated subcontinent served as a source of biodiversity subsequent to its collision with Eurasia. However, recent molecular studies suggest that Eurasia may have served as the faunal source for some of India's biodiversity, colonizing the subcontinent through land bridges between India and Eurasia during the early to middle Eocene (~35-40 MYA). In this study we investigate whether the Draconinae subfamily of the lizard family Agamidae is of Eurasian or Indian origin, using a multi locus Sanger dataset and a novel dataset of 4536 ultraconserved nuclear element loci. Results: Results from our phylogenetic and biogeographic analyses revealed support for two independent colonizations of India from Eurasian ancestors during the early to late Eocene prior to the subcontinent's hard collision with Eurasia. Conclusion: These results are consistent with other faunal groups and new geologic models that suggest ephemeral Eocene land bridges may have allowed for dispersal and exchange of floras and faunas between India and Eurasia during the Eocene.
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RES E A R C H A R T I C L E Open Access
The Eurasian invasion: phylogenomic data
reveal multiple Southeast Asian origins for
Indian Dragon Lizards
Jesse L. Grismer
, James A. Schulte II
, Alana Alexander
, Philipp Wagner
, Scott L. Travers
, Matt D. Buehler
Luke J. Welton
and Rafe M. Brown
Background: The Indian Tectonic Plate split from Gondwanaland approximately 120 MYA and set the Indian
subcontinent on a ~ 100 million year collisio n course with Eurasia. Many phylogenetic studies have demonstrated
the Indian subcontinent brought with it an array of endemic faunas that evolved in situ during its journey,
suggesting this isolated subcontinent served as a source of biodiversity subsequent to its collision with Eurasia.
However, recent molecular studies suggest that Eurasia may have served as the faunal source for some of Indias
biodiversity, colonizing the subcontinent through land bridges between India and Eurasia during the early to
middle Eocene (~3540 MYA). In this study we investigate whether the Draconinae subfamily of the lizar d family
Agamidae is of Eurasian or Indian origin, using a multi locus Sanger dataset and a novel dataset of 4536
ultraconserved nuclear element loci.
Results: Results from our phylogenetic and biogeographic analyses revealed support for two independent
colonizations of India from Eurasian ancestors during the early to late Eocene prior to the subcontinents hard
collision with Eurasia.
Conclusion: These results are consistent with other faunal groups and new geologic models that suggest
ephemeral Eocene land bridges may have allowed for dispersal and exchange of floras and faunas between India
and Eurasia during the Eocene.
Keywords: Agamidae, Draconinae, Eocene, Eurasia, India, Faunal exchanges, Landbridges
The collision of the Indian subcontinent (ISC) into
Eurasia caused the formation of some of the worlds
most iconic deserts and mountain ranges, dramatically
changing Asian climates, while simultaneously sculpting
its biodiversity. Much interest has centered on investi-
gating the evolutionary and geological processes that
have influenced the origins and diversification of the
ISCs unique biotas ([1]; and references therein). Phylo-
genetic studies of birds, dipterocarp trees, terrestrial
gastropods, crabs, freshwater fish, and certain groups of
amphibians, suggests these lineages originated on the
ISC and were a source of biodiversity for regions of Asia
and areas as far west as Africa after the Indian Plate split
off from Gondwanaland [27]. However, a suite of
phylogenetic studies across a variety of other taxa sug-
gest an alternative biogeographic hypothesis postulating
Eurasia as the ancestral source of diversity for the ISC.
In these groups Asian lineages dispersed to, and success-
fully colonized, the subcontinent before its hard collision
with Eurasia 2530 MYA [812].
The previous lack of geologic models describing the
fine scale events of the final 50 million years of the ISCs
collision, left researchers with no mechanistic explan-
ation for the striking differences between these two ISC
faunal origin hypotheses. Fortunately, newer models are
available that take into account continental connections
between the approaching ISC and areas of mainland
* Correspondence:
Department of Ecology and Evolutionary Biology and Biodiversity Institute,
University of Kansas, Dyche Hall, 1345 Jayhawk Blvd., Lawrence, KS
66045-7561, USA
Full list of author information is available at the end of the article
© 2016 Grismer et al. Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0
International License (, which permits unrestricted use, distribution, and
reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to
the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver
( applies to the data made available in this article, unless otherwise stated.
Grismer et al. BMC Evolutionary Biology (2016) 16:43
DOI 10.1186/s12862-016-0611-6
Asia prior to the ISCs collision with Eurasia [1315].
Acton [13] and Ali and Aitchison [15] hypothesized that
between 3455 MYA (middle Eocene-late Eocene), India
was connected to Eurasia via land-bridges with Sumatra,
and then along what is now the Thai-Malay Peninsula
and Burma (which would have been one land mass
during this time). Two recent studies have recovered
phylogenetic support for these Eocene land bridges and
hypothesized that these pre-collision continental con-
nections would have allowed for faunal exchanges be-
tween the ISC and Eurasia as the ISC continued
northward [7, 16]. We present data from a diverse radi-
ation of Indian and Southeast Asian lizards that provide
an additional model system, with largershould be large
not "larger" amounts of generic diversity of Indian line-
ages and Asian lineages, to test for phylogenetic supp ort
for these Eoc ene land bridges, which we refer to as the
Eocene Exchange Hypothesis (EEH).
The Draconinae is a subfamily within the lizard family
Agamidae that contains 27 genera and 199 species [17]
comprising approximately 50 % of total Agamid diver-
sity. Members of the Draconinae collectively range
throughout mainland Asia (Indochina), Sundaland,
India, and Sri Lanka (Fig. 1). Draconinae lizards are di-
urnal omnivores exhibiting a range of arboreal and
terrestrial life styles and are some of the dominant mem-
bers of diurnal lizard communities throughout South
and Southeast Asia [18, 19]. To date, only two studies
have investigated the phylogenetic relationships within
the Draconinae. However, both were part of broader sys-
tematic studies on the entire Agamidae family [20, 21].
Moodys [20] dissertation included 60 extant taxa, was
based on 122 morphological characters, and included
data from 18 fossils. This work was the first study to
hypothesize a Eurasian origin for the Indian draconine
lineages. Macey et al. [21] was the first study to provide
a molecular phylogeny for the Agamidae (including Dra-
coninae), and included an analysis of 72 taxa and one
mitochondrial gene. This analysis demonstrated that
mainland Asian agamids were paraphyletic with respect
to Indian and Sri Lankan lineages. However, multiple
deeper nodes within the Draconinae were characterized
by poor support, resulting in ambiguous relationships
[21]. The authors then used a series of parsimony
methods to suggest that these problema tic areas of the
draconine phylogeny, along with a lack of biogeographic
signal, were likely due to an Indian-Asian faunal ex-
change just after the hard collision, 2025 MYA. Subse-
quent reviews of Indian-Eurasian collision regarded the
biogeographical interpretations of Macey et al. [21] with
skepticism due to the poorly supported relationships
within the Draconinae ([22]; and references therein).
Since Moody [20] and Macey et al. [21], new Draconinae
genera have been discovered, and previously unsampled
rare genera have been collected, providing additional gen-
etic material for reanalysis of draconine relationships. The
lower per-base cost of next-generation sequencing has also
led to the development of genomic methods extend-
ing the number of genetic markers that have limited
the phylogenetic resolution in previous studies. Here,
we generate a genomic data set of 4536 nuclear loci
derived from ultraconser ved elements (UCEs), along
with traditional Sanger sequencing data , to resolve
the problematic relationships within the Draconinae
reported by Macey e t al. [21]. With the addition of
new ta xa, and genomic sequence -capture data, a na-
lyzed in combination with newly developed geological
models, we are poised to reinterpret the biogeo-
graphic origins of Indian and Southeast A sian draco-
nine lineages. Spe cifically, we tested (1) Moodys [20]
pre-collision hypothesis ve rsus Macey et al. [21] post-
collision hypothesis for the origins of Indian lineages;
and (2) suggest that a conclusion in favor of M oodys
[20] pre-collision hypothesis would show phylogenetic
support for the Eocene land bridge connections pro-
posed by Acton [13] and Atchison et al. [14]. We
term this the Eocene Exchange Hypothesis (EEH).
DNA extraction, Sanger mitochondrial and nuclear DNA
sequence data collection
Genomic DNA was extracted from muscle or liver tissue
samples on loan form La Sierra University, Villanova
University, the California Academy of Sciences, the
Zoologisches Forschungsmuseum Alexander Koenig,
and the Chicago Field Museum. Extractions were pre-
formed using a DNeasy tissue kit (Qiagen, Inc.) and se-
quenced for the mitochondrial and nuclear genes, ND2
(primers from [21]) and RAG-1 (primers from [23]), re-
spectively, using standard PCR and Sanger sequencing pro-
tocols. We edited the sequences and aligned them within
Geneious Pro 5.0.4 (, [24]) and
these new sequence data were combined with existing data
from [21] and [23] (Additional file 1: Table S1). In total, the
dataset included 17 of the 26 draconine genera, including
all but two of the Indian genera (Psammophilus and Cory-
phophylax). H yrdosaurus and Physignathus were not in-
cluded as their phylogenetic affinities are with other agamid
lineages outside of the Draconinae [21]. At least three spe-
cies (or individuals if the genus was monotypic) per genus
were sampled, for a total of 44 individuals. ND2 and RAG-
1 were selected as they are the most frequently sequenced
markers across acrodont lizards and therefore provide max-
imum taxonomic coverage. We used these markers to pre-
liminarily place new genera in a phylogenetic context, and
as a guide tree in our selection of genera for UCE develop-
ment to resolve problematic relationships. No experimental
research was carried out on these animals in this study.
Grismer et al. BMC Evolutionary Biology (2016) 16:43 Page 2 of 11
Ultraconserved elements (UCE) data collection
To resolve the problematic areas in the phylogeny from
the Sanger data (pink nodes : Fig. 2a), we selected 24 in-
dividuals representing 12 genera (underlined taxon
names in Fig. 2) from across four species groups (brown
nodes: Fig. 2a) for ultaconserved element (UCE) enrich-
ment. Sequence-capture data collection followed a modi-
fication of the approach outlined by Faircloth et al. [25].
Briefly, we fragmented genomic DNA with a Covaris S220
ultrasonicator (Covaris , Inc.), and prepared Illumina
libraries using KAPA library preparation kit s (Kapa
Biosystems) and custom sequence tags unique to each
sample [26]. Libraries were pooled into groups of 8
taxa and enriched for 5060 UCE loci (5472 probes).
We amplified enriched pools with a limited-cycle PCR
(18 cycles) and sequenced final libraries on a partial
Ilumina HiSeq 2000 lane. Reads were quality filtered using
the Illumiprocessor [27] wrapper for Trimmomatric [28],
and assembled into contigs using Trinity [29]. Where
alternate alleles differing by less than 5 % sequence diver-
gence (or two nucleotide positions, whatever was greater)
were present in a sample for any given UCE locus, Trinity
retained the allele supported by the largest number of
reads. We used PHYLUCE v. 1.4 (Faircloth et al. [25, 30])
to match contigs to UCE loci and generated two align-
ments in MAFFT [31]: one containing no missing loci
across all individuals (complete) and another containing
data for at least 75 % of taxa per locus (75 % complete),
which returned alignments of 1114 loci and 4536 loci,
Phylogenetic and biogeographic analyses
Sanger data
We first used Bayesian analyses with MrBayes 3.2.2 [32] of
the ND2 and RAG-1 datasets independently in the con-
text of the entire Agamidae to ensure that Draconinae was
monophyletic. Once monophyly and lack of conflict be-
tween loci was established, we concatenated the two gene
Fig. 1 Map showing the distribution of Draconin ae and the four biogeographic area (differently-colored borders) used in ancestral
range reconstructions
Grismer et al. BMC Evolutionary Biology (2016) 16:43 Page 3 of 11
partitions for subsequent analyses. We used uniform
priors in MrBayes 3.2.2 and partitioned the dataset by
locus and codon within each locus for just the members
Draconinae sub-family. We then assigned the GTR+ Γ
substitution model for each partition and used three
chains (two hot and one cold), and carried out 100 million
generations, sampled every 10,000 generations. Due to the
risk of substitution saturation, we performed analyses in-
cluding and excluding the third codon position for the
ND2 alignment. Convergence between chains, likelihood
scores, and estimate sample size (ESS) values were evalu-
ated using Tracer 1.6 [33] In order to obtain a reliable root
age for divergence-time estimates within Draconinae, we
expanded our ND2 and RAG-1 datasets to include data
from all acrodont lineages. We analyzed this expanded
dataset using eight acrodont fossils (Additional file 2:
Table S2) within a Bayesian framework in BEAST 2.3 [34]
using the fossilized-birth-death model [35, 36]. The
fossilized-birth-death process provides a model for the
distribution of speciation times, tree topology, and distri-
bution of lineages sampled before the present, and treats
the fossil observations as part of the prior on node time
estimates. We used the root age for the Draconinae result-
ing from this analysis (85 MYA) as a minimum-age cali-
bration for the root of the Draconinae for subsequent
time of divergence estimates within the Draconinae clade.
Sequence-capture data
We performed likelihood analyses in RAxML v.8.1.20
[37] on concatenated datasets for the incomplete (4536
loci) and complete (1114 loci) matrices, using the GTR+ Γ
substitution model, and ran 100 fast bootstrap replicates.
Fig. 2 a Bayesian analysis (in MrBayes) of ND2 and RAG-1 data, with black dots denoting nodes with posterior probabilities above 0.95. Brown
nodes indicate four well-supported species groups (14; see text for details) and pink nodes identify poorly supported relationships among these
species groups. Underlined taxon names are genera selected for UCE enrichment. b Multi-species coalescent (species tree) from the species tree
estimation using average coalescence times STEAC analysis, using the complete matrix of 1114 UCE loci. Black dots denote nodes with 100
bootstrap support. Brown nodes indicate the four species groups (Group 2 = brown circle; see text for discussion). Blue nodes identify problematic
nodes recovered in Likelihood analysis of the Sanger dataset, resolved with sequence-capture data
Grismer et al. BMC Evolutionary Biology (2016) 16:43 Page 4 of 11
In addition to the concatenated analysis, maximum likeli-
hood gene trees were constructed for each of the UCE loci
included in the complete matrix using Phyluce with
RAxML v.8.1.20 [37], under default settings. Phyluce and
RAxML were also used to generate gene trees for 500
multi-locus bootstraps [38]. Custom R-scripts (R v3.2.0; R
Core Team 2015) and the R library Phybase [39] were
then used to infer the STEAC [40] summary species tree
for the original and bootstrapped data.
Grafted phylogeny and divergence dating
Using 85 MYA as a minimum age limit for the ancestor
of the Draconinae, divergence dates for subclades were
estimated in BEAST 2.3 using the ND2 and RAG-1
datasets with linked clock and tree models. We applied
Birth-Death tree priors and constrained the relationships
to match the results from the analyses of the UCE loci
(blue nodes: Fig. 2b) and let the relationships within
each species group be estimated by the BEAST analyses.
We used a relaxed uncorrelated lognormal clock model
and an exponential prior for the mean rate of each parti-
tion. Default values were used for all other priors, and
the analysis was run for 150 million generations sam-
pling every 12,000 generations, with chain stationarity,
and ESS values were evaluated in Tracer 1.6. The first
25 % of trees were discarded as burn-in and the max-
imum clade credibility tree with median node heights
was summarized using TreeAnnotator 2.3 [34]. We con-
verted our alignments to fasta format using seqmagick
( . Then, with
the estimate for divergence betwee n Mantheyus and
other draconine species of 85MYA , we estimated the
TMRCA of sub clades based on pairwise Hamming
distances [41] between UCE loci (with a sequence sat-
uration correc tion of 0.95) calculated through fas -
tphylo [42], assuming a naïve strict clock. We carried
out the calculations using a custom R-script [43]. Any
loci where subgroup divergence times exceeded those
of the calibration time were discarde d due to the like-
lihood of incomplete lineage sorting and/or excessive
rate variation. Using the same methods, we then esti-
mated the time to most recent common ancestor
(TMRCA) of the Draco + Ptyctolaemus and spe cies
group 14 clades using the estimated age of the Non-
Mantheyus clade. The estimate of the TMRCA of
species group 14 was then used to age the split be-
tween Acanthosaura and Pseudocal ates (species group
1), and the ancestor of spe cies groups 2/3/4. The spe-
cies group 2/3/4 TMRCA estimate was then used to
age the split between Salea and Calotes (species
group 2 and 3), and the ancestor of spe cies group 4.
Finally, the estimate for the TMRCA of species group
4 was used to obtain an estimate of the TMRCA of
Certaophora/Ly riocephalus/Cophotis.
Ancestral area reconstructions were performed using
likelihood and Bayesian methods in LAGRANGE within
the program RA SP 3.0 [44], and in RevBayes 10.10 [45]
respectively. Taxa were assigned to their biogeographic
zone (Fig. 1) based on their modern day distributions
and RevBaye s re constructions were visualized using
Philippines is not classified as part of Sundaland how-
ever, w e included taxa from this archipelago in the
Sundalan d biogeog raph ic are a because the entire Philippine
agamid fauna is Sundaic in origin.
Sanger mitochondrial and nuclear data phylogenetic
The B ayesian analyses of the combined Sanger dataset
recovered new relationships that have not been reported
in any previous study (Fig. 2a). Mantheyus was recov-
ered as sister to the remaining Draconinae. The next
lineage to diverge was a well-supported clade containing
Draco, and Ptyctolaemus (Fig. 2a). Lastly, there were
four well-supported species groups (brown nodes :
Fig. 2a). The relationships within each of these species
groups were well supported. However, the relationships
between the species groups were poorly resolved and
characterized by short branches (pink nodes: Fig. 2a). As
the resolution of the relationships between the species
groups is vital for testing hypotheses of Indian or
Eurasian origins, repr esentatives of the taxa from each
of these species groups were included in a phylogenetic
reconstruction from analyses of UCE data.
Sequence-capture data phylogenetic analyses
There were 4536 loci with data for at least 75 % of
the n = 23 individuals included in this study. These loci
had an average length of 644.7 bp (S.D. = 249.7 bp), of
which an average of 10.5 % of sites (S.D. = 20.0 %) were
parsimony informative. The average amount of missing
data per locus was 23.6 % (S.D. = 19.4 %), including both
missing individuals (up to 25 % of individuals at each
locus) and shorter sequence lengths for individuals that
were present (Additional file 3: Table. S3). All analyses of
the sequence-capture data were successful in resolving the
problematic relationships recovered from the Sanger data
(blue nodes; Fig. 2b) and recovered each of the four spe-
cies groups within the Draconinae, with high support
(brown nodes; Fig. 2b), consistent with the results from
the Sanger datasets.
Biogeographic analyses, divergence dating, and
ancestral areas
Both of the methods employed to estimate ancestral
ranges (LAGRANGE and RevBayes analyses) returned
comparable estimates of ancestral areas, however, the
Grismer et al. BMC Evolutionary Biology (2016) 16:43 Page 5 of 11
RevBayes reconstructions were more conservative. Given
the short branch lengths leading to some of the deeper
nodes in our phylogeny, the RevBayes reconstructions
are a better reflection of geology at the times of these
nodes. Therefore only the RevBayes reconstructions are
discussed. The grafted BEAST time-tree (Fig. 3a) was
concordant with the phylogenies derived from the Se-
quence capture data and Sanger data (Fig. 2). The
BEAST time-tree (Fig. 3) indicated the most recent com-
mon ancestor (MRCA) for the Draconinae originated
approximately 92 MYA in mainland Asia ~30 million
years after the ISC broke off Gondwanaland. The MRCA
for Draco and it s relatives most likely originated in
mainland Asia 53 MYA and diverged from the other
mainland Asian and Sundaic lineages around 69 MYA
from a mainland Asian ancestor. The three remaining
species groups appear to have diversified from one an-
other rapidly between 5159 MYA, most likely from a
mainland Asia ancestor that existed approximately 59
MYA. The Indian endemic Salea (Species group 2) rep-
resents the first invasion of India (D#1: Fig. 3a), having
diverged from a mainland Asian ancestor it shared with
Calotes (Species group 3) approximately 56 MYA
(Fig. 3a). The MRCA for Acanthosaura and Psuedoca-
lotes (species group 1) was estimated at 56 MYA with a
high probability that this ancestor originated in either
mainland Asia or Sundaland (where both genera pres-
ently occur). Within this species group, we recovered
support for a second invasion of India and Sri Lanka,
with the ancestor of Sitana and Otocryptis originating
from a predominantly Sundaic ancestor between 5127
MYA (D#2: Fig. 3a). Lastly, the MRCA for the Sri Lan-
kan and Sundaland radiations (species group 4) origi-
nated around 51 MYA in Sundaland or Sri Lanka
(Fig. 3a). Within species Group 4, Aphaniotis, Broncho-
cela , and Gonocephalus appear to have diverged from
one another 42 MYA and form the sister line age to the
Sri Lankan genera Lyriocephalus, Cophotis, and Cerato-
phora (Fig. 3a). The Sri Lankan lineages diverged from
one another 28 MYA. We obtained these timing esti-
mates for key divergences and dispersal events using
Sanger data (as they were available for a broader taxo-
nomic sample, including key fossils in comparison with
the UCE data) in BEAST, with the topology constrained
by the results from UCE data. We then crosschecked
these estimates using the minimum divergence time for
Draconinae of 85 MYA, and sequence divergence among
UCE loci between clades of interest. This method is some-
what cruder than the BEAST estimates because it cannot
account for among lineage rate variation. However, the es-
timates obtained using this approach were broadly com-
parable with results or our Bayesian analysis performed in
BEAST (Fig. 4), offering support for our timing of key dra-
conine dispersal events in Southeast Asia.
In this study, we utilized unprecedented sampling of the
Draconinae, both in taxonomic diversity and genetic
markers, to give fresh biogeographic insight into the ori-
gins of the Indian and Southeast A sian Draconinae line-
ages. In particular, the thousands of loci generated using
sequence-capture and next-generation sequencing were
successful in reso lving previously problematic relation-
ships within the Draconinae (brown nodes: Fig. 2). Using
the fully resolved UCE phylogeny to constrain the top-
ology of our Sanger dataset, we generated a grafted
Bayesian time tree (Fig. 3a), which supported the hy-
pothesis that there were at least two independent
colonization events of India by Southeast Asian lineages
during the Eocene. These results favor Moodys [20] pre-
collision hypothesis with the estimated times of the
Eurasian invasions in accordance with the Eocene land
bridges proposed by Acton, [13] and Ali and Aitchison
[14]. These hypothesized land bridges would have con-
nected areas of Eurasia (now Sundaland and the Thai-
Malay peninsula) and the ISC before its collision, and
are the likely conduits for terrestrial faunal exchange
and range expansion in the lineages leading to to-
days Indian subcontinent endemics Salea, Sitana,
and Otocr yptis.
The Eocene exchange hypothesis
The first Draconinae invasion into India consisted of a
lineage represented today by the endemic genus Salea,
which descended from a mainland Asian ancestor that
also gave rise to the Indochinese genus Calotes. This
colonization event most likely resulted from an early
Eocene land-bridge connection or an over-water dis-
persal event just prior to the ISCs conne ction with
Sundaland (Eura sia) 5055 MYA (Fig. 3b). Given t he
sedentary and arboreal natural histories of extant dra-
conine species , we feel the former hypothesis is more
likely than the latter, although we acknowledge the
possibility of both. We expe ct a broader sampling
within this clade of Southea st Asian, and especially
Indian, species will provide a better e stimate o f the
ancestral area at this node (Salea + Calotes:Fig.3a).
The second dispersal event into India occurred with
the divergence of the Indian and Sri Lankan endemics
Sitana and Otocryptis from an ancestor most likely
found in Sundaland durin g the middle Eocene. This
colonization of the Indian subcontinent most likely
was facilitated via a la nd bridge that connected the
ISC with Sumatra and the Thai-Malay peninsula at 48
MY A. Additionally, the lineage sister to Sitana and Oto-
cryptis, Japalura, and Pseudocalotes, is Phoxophrys (Fig. 3a).
This genus is endemic to the lowland forests of Borneo and
Sumatrafurther supporting an India-Sundaland (Eurasia)
connection via Sumatra and the southern portion of the
Grismer et al. BMC Evolutionary Biology (2016) 16:43 Page 6 of 11
Fig. 3 (See legend on next page.)
Grismer et al. BMC Evolutionary Biology (2016) 16:43 Page 7 of 11
Thai-Malay Peninsula during the middle Eocene. These in-
dependent colonization events not only support Moodys
[20] pre-collision biogeographic hypothesis, but also give
additional phylogenetic support for Eocene land bridges
postulated by Acton, [13] andAliandAitchison[14].Our
results contribute to a growing body of literature demon-
strating the possibility of floral and faunal exchange be-
tween India and Eurasia during the Eocene, before the
ISCs hard collision 2025 MY A (e.g. freshwater crabs: [7];
rhacophorid tree frogs: Li et al. [16]). Given the ecology of
these organisms, and of the draconine species sampled
here, we feel that it is less likely Eocene faunal exchanges
occurred as the result of over water dispersal events. It is
unclear whether the Eocene land bridges were two separate
spatial/temporal features, versus possibly the same entity,
just changing position as the ISC progressed northward. In
either case, their existence may have provided continental
connections between Southeast Asia and India during the
Fig. 4 Box-and-whisker plots, showing results of our analysis using our UCE_divergence_timing R script (minimum, 25 % quartile, 75 % quartile,
maximum) with a minimum estimate for the age of Draconinae of 85 MYA used to calibrate the ages of the Non-Mantheyus clade. For
subsequent subgroups, the estimated age of the clades were contained within this calibration point. For each groups divergence timing
estimate, only loci that appeared clock-like (ingroup age estimate did not exceed the calibration age) were used. Percentages of loci that were
clock-like versus non-clock-like (likely affected by rate variation or incomplete lineage sorting), and loci with missing data for outgroups (sister
species of the groups of interest) are shown in pies above box-and-whisker plots (see key). Clades with red arrows show slow-downs relative to
their outgroups i.e. average cumulative branch lengths leading to ingroup taxa from the ingroup/outgroup node are shorter than those leading
to the outgroups (this appears to be correlated with underestimates of divergence times using the naïve strict clock method), clades with green
arrows show rate speed-ups relative to their outgroups i.e. average cumulative branch lengths leading to ingroup taxa are longer than those
leading to the outgroups. Bayesian estimates of divergences times performed in BEAST are shown as small blue diamonds, for comparison
(See figure on previous page.)
Fig. 3 a Time-calibrated Bayesian analysis of ND2 and RAG-1 data, with black dots denoting nodes with posterior probabilities above 0.95,
followed by the estimated divergence time for each node in MYA. Pink circles ident ify nodes where topology w as constrained based on
Likelihood and s pecies tree an alyses of UCE data (Fig. 2B). Brown circ les indicate the four species groups. Biogeographic distributions of
con temporary samples follow area coding depic ted in Fig. 1, with probabilit y of areas a t ances tral nodes from our Bay esian analysis in
RevBayes. Infe rred dispersal events into Indi a are labeled D#1 and D#2, resulting in Indian or Indian/Sri Lankan Salea, Sitana, and Otocryptis.
b Hypothesized position of the ISC and an early Eocene land bridge allowing for the first inferred dispersal event (D#1 in a) from Eurasia into India,
5055 MYA. c. Hypothesized position of the ISC and a middle-late Eocene land bridge allowing for the second first inferred dispersal event (D#2 in a)
from Eurasia into India between 3550 MYA (paleomaps modified from Klaus et al. [7])
Grismer et al. BMC Evolutionary Biology (2016) 16:43 Page 8 of 11
Eocene, which could have allowed for terrestrial exchanges
between these areas. These results collectively represent a
broad-scale pattern of faunal exchange between the ISC
and areas of Eurasia before its collision with Asia, at least
partially facilitated by land bridges, which we term the
Eocene Exchange Hypothesis. Furthermore, we believe
the reoccurring and somewhat subjective disagreement be-
tween the Indian vs. Asian origins hypotheses [212, 16],
have simply identified opposing perspectives of a broad
geographic and temporal conduit of opportunity for faunal
exchange between India and Eurasia. Future studies would
benefit from an attempt to empirically focus on the timing
and direction of faunal exchange between these biogeo-
graphic regions, rather than a prevalence of one scenario
over the other.
Revision of the age of draconinae
Our estimate for the age of Draconinae is significantly
older than those previously published in broad scale
squamate phylogenetic studies (most recently [47]). Our
older estimates are largely due to our consideration of
the acrodont fossils, Mimeosaurus and Priscagama,as
leiolepids rather than stem agamids, following Estes
et al. [48]. These fossils have had a rather turbulent his-
tory of classification, with various studies suggesting
Mimeosaurus was allied with the Chameleonidae [49];
then hypothesized to be located along the branch lead-
ing to Leiolepis and Uromystax [20]; and lastly united
with Priscagama in an extinct subfamily, Priscagaminae
[50], considered to be a stem lineage of Leiolepis and
Uromystax [51].
This confusion has persisted because when Mimeo-
saurus and Pr iscagama were first d escribed, the con -
temporary genera Leiolepis and Uromystax were still
included within the family Agamidae and demonstrated to
be the sister group to the remaining agamids [20] (this re-
lationship has been further confirmed with molecular data
[21, 23, 52, 53]. However, Estes et al. [48] removed Leiole-
pis and Uromystax from the Agamidae and placed them
in their own family (the Leiolepidae), and this taxonomy
has not been followed by subsequent studies. Thus, the
acrodont fossils of Priscagama and Mimeosaurus have
been consistently considered as stem fossils for all aga-
mids and not their sister group, Leiolepis and Uromystax.
We followed the taxonomy of Estes et al. [48] and consid-
ered Mimeosaurus and Priscagama as stem leiolepids and
not stem agamids. It was this placement that lead to our
older estimates of Draconinae origins (8592 MYA).
However, this estimate is consistent with the ages of new
amber agamid fossils being described out of Indochina
and previous studies on Iguanian lizards ([54]; Bauer et al.,
unpublished data; personal communicat ion with JLG
and PW). We re commend that researchers continue
to follow the taxonomy of [48] with the re cognition
of the Leiolepidae as a distinct family and the place-
ment of priscagamine fossils a s stem to Leiolepis and
Uromystax, as suggested in the original descriptions
of these fossils [20, 50, 51].
The use of additional taxa, sequence-capture data, and
newer geological modelsall data not available to previ-
ous studies on Draconinaeresulted in novel and well-
resolved relationships, leading to new biogeographic
insights in this unique subfamily of lizards. Using these
biogeographic insights and a broad comparison with pre-
vious biogeographic literature, we propose the Eocene Ex-
change Hypothesis, and the simple but well supported
assumption that land bridges may have facilitated a broad-
scale pattern of faunal exchange between the ISC and
areas of Eurasia before its collision with Asia during the
Eocene. We expect that with additional sampling of Indian
and mainland Asian species, some factors that may have
biased our biogeographic interpretations within the
Draconinae to (i.e., Indian extinction events), can be eval-
uated. In addition, sampling of additional draconine spe-
cies will allow us to test more fine-scaled hypotheses
concerning dispersal and diversification within this group.
Our phylogenomic analysis add to a growing body of
knowledge addressing the effects of the ISCs collision on
biogeography and offers new ideas to be tested by future
Additional files
Additional file 1: Table S1. List of all the species and their associated
localities used in this study. (XLSX 56 kb)
Additional file 2: Table S2. List of all the fossil calibrations, their ages,
and their associated references, used in this study. (DOCX 72 kb)
Additional file 3: Table S3. Per locus metrics for the UCE sequence
capture data. (XLSX 289 kb)
ISC: Indian subcontinent; EEH: Eocene Exchange Hypothesis; MYA: million
years ago.
Competing interests
The authors declare that they have no competing interests.
Authors contributions
JLG, SLT, AA, LJW, and MDB carried out the molecular genetic studies and
participated in the sequence alignment. JLG, JAS, RMB, PW participated in
the design of the study. JLG carried out the analyses and drafted the
manuscript. All authors read and approved the final manuscript.
For tissues, we thank Bryan L. Stuart, Aaron Bauer, L. Lee Grismer, Jens
Vindum (CalAcad.) Jimmy McGuire (MVZ), Funding provided by Clarkson
University and NSF through its post-doctoral fellowship program and grants
(DEB-9726064, DEB-9982736, and DEB-0451832). For field assistance we thank
Indraneli Das and for assistance with UCE pipeline we thank Carl H. Oliveros.
Grismer et al. BMC Evolutionary Biology (2016) 16:43 Page 9 of 11
Author details
Department of Ecology and Evolutionary Biology and Biodiversity Institute,
University of Kansas, Dyche Hall, 1345 Jayhawk Blvd., Lawrence, KS
66045-7561, USA.
Department of Biology, Clarkson University, 8 Clarkson
Avenue, Postdam, NY 13699, USA.
Zoologisches Forschungsmuseum
Alexander Koenig Adenauerallee 160, D-53113 Bonn, Germany.
Received: 17 December 2015 Accepted: 8 February 2016
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Grismer et al. BMC Evolutionary Biology (2016) 16:43 Page 11 of 11
... Studies have shown the survival of amphibian and plant lineages after the Deccan volcanism in south India and Sri Lanka followed by their dispersal across Eurasia after the Indian-Eurasian collision (Conti & al., 2002;Bossuyt & al., 2006). Yet the exact time of the first terrestrial land connection is actively debated (Beck & al., 1995;Acton, 1999;Schettino & Scotese, 2005;Aitchison & al., 2007;Ali & Aitchison, 2008;Najman & al., 2010;Clementz & al., 2011;Aitchison & Ali, 2012;Van Hinsbergen & al., 2011, 2012aGrismer & al., 2016;Hu & al., 2016). In a recent hypothesis, the Indian plate had at least two contact events with Eurasia, the initial one as early as 55 Ma and the final collision occurring between 35 and 20 Ma (Aitchison & al., 2007;Ali & Aitchison, 2008;Van Hinsbergen & al., 2012a,b;Grismer & al., 2016). ...
... Yet the exact time of the first terrestrial land connection is actively debated (Beck & al., 1995;Acton, 1999;Schettino & Scotese, 2005;Aitchison & al., 2007;Ali & Aitchison, 2008;Najman & al., 2010;Clementz & al., 2011;Aitchison & Ali, 2012;Van Hinsbergen & al., 2011, 2012aGrismer & al., 2016;Hu & al., 2016). In a recent hypothesis, the Indian plate had at least two contact events with Eurasia, the initial one as early as 55 Ma and the final collision occurring between 35 and 20 Ma (Aitchison & al., 2007;Ali & Aitchison, 2008;Van Hinsbergen & al., 2012a,b;Grismer & al., 2016). According to Aitchison & al. (2007) and Ali & Aitchison (2008) India brushed up against Sumatra and collided with the Dazhuqu Arc (intra-oceanic arc), around 55 Ma in the Neo-Tethys Ocean, eventually moving closer to Eurasia until its final collision, around 34 Ma. ...
... The DEC analysis also showed dispersal from India to mainland Asia (37.6 Ma) before the collision of the Indian plate with Eurasia. Similar dispersal events were reported in the case of lizards, and it was also speculated that there were land bridges between India and mainland Asia during two time periods, i.e., 55-50 Ma and 50-35 Ma (Grismer & al., 2016). The dipterocarps after reaching Asia via both former (temporary land bridges) and later (after collision) dispersal events diversified probably additionally fueled by the uplift of the Tibetan plateau and favourable climatic conditions (Morley, 2000(Morley, , 2012Klaus & al., 2016). ...
It has been hypothesized that most Asian tropical lineages have originated in Gondwana with the Indian subcontinent playing a crucial role in the dispersal of ancestral Gondwanan taxa. The disjunct distribution of dipterocarps and the fossil record in India support the Gondwana hypothesis. This is the first comprehensive study addressing the evolutionary and biogeographic relationships of dipterocarps in the Indian subcontinent to test the Gondwana hypothesis. A Bayesian phylogenetic tree of the Dipterocarpaceae family including the Indian counterparts corroborates the monophyly of subfamilies/tribes and shows new biogeographic affinities. Molecular dating reveals the Cretaceous origin of Dipterocarpaceae. Diversification of major lineages occurred during the Pliocene‐Miocene epochs. The DEC analysis ascertains the Gondwanan origin and dispersal route from the Madagascar (Africa)‐India‐Sri Lanka‐Seychelles block to Eurasia. The biogeographic analysis suggests early vicariance followed by an out‐of‐India dispersal of Dipterocarpaceae. Three dispersal events from India to the remainder of Asia at 47.6 Ma, 42.53 Ma and 37.6 Ma are identified. There probably was a biotic interchange between India and mainland Asia via Sumatra following the collision of the Indian plate with Eurasia. Molecular dating and dispersal events coincide with the geological events. During the Miocene, uplift of the Himalayan‐Tibetian plateau induced climatic variation, which seems to have resulted in the extinction of major Indian dipterocarp lineages and reverse dispersal into India. Hopea‐Shorea, one of the earliest diverged lineages, originated in Southeast Asia. The establishment of Southeast Asian monsoon climate may have favoured allopatric speciation and diversification of Southeast Asian lineages also resulting in further dispersal into India.
... It is important to note that within many clades outlined earlier in "morphological" trees, the same patterns of phylogenetic relationships are nevertheless preserved. The monophyly of agamid lizards and individual evolutionary lines considered in the system of acrodont lizards in the status of subfamilies has been confirmed: Agaminae, Amphibolurinae, Draconinae, Hydrosaurinae, Leiolepidinae, Uromastycinae (Macey et al., 2000;Ananjeva, 2004;Pyron et al., 2013;Grismer et al., 2016). ...
... These lizards are found in the montane rainforests of northeastern Thailand and eastern Laos. Molecular phylogenetic analysis of Draconinae proper confirmed the hypothesis of Macey (Macey et al., 2000) on the evolutionary lines within acrodont squamate reptiles, as well as the special position of the clade Manthyeus (Fig. 1), which with high reliability represents a sister group in relation to all other repre-sentatives of the subfamily (Schulte et al., 2004;Pyron et al., 2013;Grismer et al., 2016). ...
... 5;Cao et al., 2017). This portion of Sundaland remained subaerial throughout the tectonic evolution of Southeast Asia, was covered with perhumid rainforests since at least the middle Eocene, and became a major center of origin for a vast number of clades of plants and animals (De Bruyn et al., 2014;Grismer et al., 2016;Morley, 2018, and references therein), including Cyrtodactylus (see below). ...
... Approximately 38.1 mya, ancestor A12 diverged in Indochina, giving rise to the Indochinese ancestor A14 and the ancestor of the triedrus group (A13) which dispersed to the India-Sri Lanka region at a time when the Indian subcontinent was adjacent to Indoburma and Indochina (Acton, 1999;Köhler & Glaubrecht, 2007;Aitchison, Ali & Davis, 2007;Ali & Aitchison, 2008: Fig. 5). This invasion route to Indian-Sri Lanka from what was probably southern Indochina (being there is no evidence of this group ever occupying Indoburma), via a relatively narrow over-water dispersal or land bridge, has been hypothesized for a number taxonomic groups (e.g., (Klaus et al., 2010) [crabs]; (Li et al., 2013) [rhacophorid frogs]; J. (Grismer et al., 2016) [draconine lizards]; (Garg & Biju, 2019) [microhylid frogs]; (Gorin et al., 2020) [microhylid frogs]). Given the extensively greater sampling of Cyrtodactylus here and the increased use of tectonic data, this scenario does not support long distance over-water dispersal scenarios across the Bay of Bengal proposed by Wood Jr et al. (2012) andAgarwal et al. (2014) nor does it support the scenario of Grismer & Davis (2018) that Sundaland was colonized by an ancestor of the Indian subcontinent. ...
Full-text available
The gekkonid genus Cyrtodactylus is the third largest vertebrate genus on the planet with well over 300 species that range across at least eight biogeographic regions from South Asia to Melanesia. The ecological and morphological plasticity within the genus, has contributed to its ability to disperse across ephemeral seaways, river systems, basins, land bridges, and mountain ranges—followed by in situ diversification within specific geographic areas. Ancestral ranges were reconstructed on a mitochondrial phylogeny with 346 described and undescribed species from which it was inferred that Cyrtodactylus evolved in a proto-Himalaya region during the early Eocene. From there, it dispersed to what is currently Indoburma and Indochina during the mid-Eocene—the latter becoming the first major center of origin for the remainder of the genus that seeded dispersals to the Indian subcontinent, Papua, and Sundaland. Sundaland became a second major center of radiation during the Oligocene and gave rise to a large number of species that radiated further within Sundaland and dispersed to Wallacea, the Philippines, and back to Indochina. One Papuan lineage dispersed west to recolonize and radiate in Sundaland. Currently, Indochina and Sundaland still harbor the vast majority of species of Cyrtodactylus .
... 44.9 mya in Deepak, Ruane & Gower, 2019), and likely reflects the ancient faunal exchange between the Indian Subcontinent and the Sundaland via a land bridge which existed during the early and middle Eocene (Ali & Aitchison, 2008;Morley, 2018). Similar patterns were reported, for example, in Draconinae agamid lizards (Grismer et al., 2016a), and Microhylinae narrow-mouth frogs (Garg & Biju, 2019;Gorin et al., 2020). In particular, the assumptive vicariance between Pareinae and Xylophiinae and the distribution patterns of the two subfamilies remarkably resembles the divergence pattern between microhylid genera Micryletta (widely distributed across the Southeast Asia) and Mysticellus (restricted to southern peninsular India), which was dated as 39.7-40.6 mya (Garg & Biju, 2019). ...
... Therefore, the general direction of diversification in Pareinae was likely from the tropical continental margins of Sundaland to a nontropical Asian landmass. Starting with at least middle Eocene, Sundaland was covered with perhumid rainforests and became a major source of mainland Asian lineages for a vast number of taxa of plants and animals (see De Bruyn et al., 2014;Grismer et al., 2016a;Morley, 2018, and references therein). Examples include the stream toad genus Ansonia (Grismer et al., 2016b), the litter toads Leptobrachella (Chen et al., 2018), and the breadfruit genus Artocarpus . ...
Full-text available
Slug-eating snakes of the subfamily Pareinae are an insufficiently studied group of snakes specialized in feeding on terrestrial mollusks. Currently Pareinae encompass three genera with 34 species distributed across the Oriental biogeographic region. Despite the recent significant progress in understanding of Pareinae diversity, the subfamily remains taxonomically challenging. Here we present an updated phylogeny of the subfamily with a comprehensive taxon sampling including 30 currently recognized Pareinae species and several previously unknown candidate species and lineages. Phylogenetic analyses of mtDNA and nuDNA data supported the monophyly of the three genera Asthenodipsas , Aplopeltura , and Pareas . Within both Asthenodipsas and Pareas our analyses recovered deep differentiation with each genus being represented by two morphologically diagnosable clades, which we treat as subgenera. We further apply an integrative taxonomic approach, including analyses of molecular and morphological data, along with examination of available type materials, to address the longstanding taxonomic questions of the subgenus Pareas , and reveal the high level of hidden diversity of these snakes in Indochina. We restrict the distribution of P. carinatus to southern Southeast Asia, and recognize two subspecies within it, including one new subspecies proposed for the populations from Thailand and Myanmar. We further revalidate P. berdmorei , synonymize P. menglaensis with P. berdmorei , and recognize three subspecies within this taxon, including the new subspecies erected for the populations from Laos and Vietnam. Furthermore, we describe two new species of Pareas from Vietnam: one belonging to the P. carinatus group from southern Vietnam, and a new member of the P. nuchalis group from the central Vietnam. We provide new data on P. temporalis , and report on a significant range extension for P. nuchalis . Our phylogeny, along with molecular clock and ancestral area analyses, reveal a complex diversification pattern of Pareinae involving a high degree of sympatry of widespread and endemic species. Our analyses support the “upstream” colonization hypothesis and, thus, the Pareinae appears to have originated in Sundaland during the middle Eocene and then colonized mainland Asia in early Oligocene. Sundaland and Eastern Indochina appear to have played the key roles as the centers of Pareinae diversification. Our results reveal that both vicariance and dispersal are responsible for current distribution patterns of Pareinae, with tectonic movements, orogeny and paleoclimatic shifts being the probable drivers of diversification. Our study brings the total number of Pareidae species to 41 and further highlights the importance of comprehensive taxonomic revisions not only for the better understanding of biodiversity and its evolution, but also for the elaboration of adequate conservation actions.
... To control for these factors, we repeated our analyses on closely related, arboreal, nongliding, 'control' clades predominantly from Southeast Asia (the agamid Diploderma compared to Draco, the sciurid Callosciurinae compared with Pteromyini and the rhacophorid genus Philautus compared with the gliding frogs). These 'control' groups have comparable clade sizes and crown ages as our gliding groups [11,[35][36][37][38]. We test if similar patterns of diversification persist in the gliding and non-gliding clades. ...
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The repeated evolution of gliding in diverse Asian vertebrate lineages is hypothesized to have been triggered by the dominance of tall dipterocarp trees in the tropical forests of Southeast Asia. These dipterocarp forests have acted as both centres of diversification and climatic refugia for gliding vertebrates, and support most of their extant diversity. We predict similarities in the diversification patterns of dipterocarp trees and gliding vertebrates, and specifically test whether episodic diversification events such as rate shifts and/or mass extinctions were temporally congruent in these groups.We analysed diversification patterns in reconstructed timetrees of Asian dipterocarps, the most speciose gliding vertebrates from different classes (Draco lizards, gliding frogs and Pteromyini squirrels) and compared them with similar-sized clades of non-gliding relatives (Diploderma lizards, Philautus frogs and Callosciurinae squirrels) from Southeast Asia. We found significant declines in net-diversification rates of dipterocarps and the gliding vertebrates during the Pliocene–Pleistocene, but not in the nongliding groups. We conclude that the homogeneity and temporal coincidence of these rate declines point to a viable ecological correlation between dipterocarps and the gliding vertebrates. Further, we suggest that while the diversification decay in dipterocarps was precipitated by post- Miocene aridification of Asia, the crises in the gliding vertebrates were induced by both events concomitantly.
... By eliminating the need to include morphological characters, which cannot always be obtained for taxa of interest, the unresolved FBD tree potentially allows the inclusion of large amounts of fossil occurrence data. Bayesian tip dating on unresolved FBD trees has been performed for a range of organisms, including mammals (Gavryushkina et al. 2014;Heath et al. 2014;Law et al. 2018;Presslee et al. 2019), reptiles (Card et al. 2016;Grismer et al. 2016), fishes (Arcila et al. 2015), insects (Economo et al. 2018;O'Reilly and Donoghue 2020;Bossert et al. 2022), and plants (Grimm et al. 2015;Saladin et al. 2017). Although fossil sampling has been shown to have an impact on estimates of divergence times (O'Reilly and Donoghue 2020), the potential effects of diversified sampling of extant taxa have not been examined in detail for Bayesian tip dating on unresolved FBD trees. ...
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Evolutionary timescales can be inferred by molecular-clock analyses of genetic data and fossil evidence. Bayesian phylogenetic methods such as tip dating provide a powerful framework for inferring evolutionary timescales, but the most widely used priors for tree topologies and node times often assume that present-day taxa have been sampled randomly or exhaustively. In practice, taxon sampling is often carried out so as to include representatives of major lineages, such as orders or families. We examined the impacts of different densities of diversified sampling on Bayesian tip dating on unresolved fossilized birth-death (FBD) trees, in which fossil taxa are topologically constrained but their exact placements are averaged out. We used synthetic data generated by simulations of nucleotide sequence evolution, fossil occurrences, and diversified taxon sampling. Our analyses under the diversified-sampling FBD process show that increasing taxon-sampling density does not necessarily improve divergence-time estimates. However, when informative priors were specified for the root age or when tree topologies were fixed to those used for simulation, the performance of tip dating on unresolved FBD trees maintains its accuracy and precision or improves with taxon-sampling density. By exploring three situations in which models are mismatched, we find that including all relevant fossils, without pruning off those that are incompatible with the diversified-sampling FBD process, can lead to underestimation of divergence times. Our reanalysis of a eutherian mammal data set confirms some of the findings from our simulation study, and reveals the complexity of diversified taxon sampling in phylogenomic data sets. In highlighting the interplay of taxon-sampling density and other factors, the results of our study have practical implications for using Bayesian tip dating to infer evolutionary timescales across the Tree of Life.
... The approach used here involved ultraconserved elements (UCEs; Faircloth et al. 2012). Use of UCEs has resolved evolutionary relationships on both recent and ancient timescales (Smith et al. 2014;Meiklejohn et al. 2016), among squamate reptiles generally (Leaché et al. 2014;Grismer et al. 2016) and iguanians specifically (Streicher et al. 2016), thus making these markers a good choice for investigating both population-level and higher-level divergences. Because UCEs are conserved for vast periods of evolutionary time, they provide conserved priming sites throughout the tetrapod genome. ...
The genus Cyclura includes nine extant species and six subspecies of West Indian Rock Iguanas and is one of the most imperiled genera of squamate reptiles globally. An understanding of species diversity, evolutionary relationships, diversification, and historical biogeography in this group is crucial for implementing sound long-term conservation strategies. We collected DNA samples from 1-10 individuals per taxon from all Cyclura taxa (n = 70 ingroup individuals), focusing where possible on incorporating individuals from different populations of each species. We also collected 1-2 individuals from each of seven outgroup species of iguanas (Iguana delicatissima; five Ctenosaura species) and Anolis sagrei (n = 12 outgroup individuals). We used targeted genomic sequence capture to isolate and to sequence 1,872 loci comprising of 687,308 base pairs (bp) from each of the 82 individuals from across the nuclear genome. We extracted mitochondrial reads and assembled and annotated mitogenomes for all Cyclura taxa plus outgroup species. We present well-supported phylogenomic gene tree/species tree analyses for all extant species of Cyclura using ASTRAL-III, SVDQuartets, and starBEAST methods, and discuss the taxonomic, biogeographic, and conservation implications of these data. We find a most recent common ancestor of the genus 9.91 million years ago. The earliest divergence within Cyclura separates C. pinguis from a clade comprising all other Cyclura. Within the latter group, a clade comprising C. carinata from the southern Lucayan Islands and C. ricordii from Hispaniola is the sister taxon to a clade comprising the other Cyclura. Among the other Cyclura, the species C. cornuta and C. stejnegeri (from Hispaniola and Isla Mona) form the sister taxon to a clade of species from Jamaica (C. collei), Cuba and Cayman Islands (C. nubila and C. lewisi), and the eastern (C. rileyi) and western (C. cychlura) Lucayan Islands. Cyclura cychlura and C. rileyi form a clade whose sister taxa are C. nubila and C. lewisi. Cyclura collei is the sister taxon to these three species combined.
... Even though this phylogeny includes only approximately 33% of the currently recognized species diversity of Oligodon, the samples used in the analysis come from across the geographic range of this genus. Recent studies have shown that extant reptile lineages that have representatives in both South and Southeast Asia have patterns of complex historical faunal exchange between these two regions (e.g., Kraus et al. 2010Kraus et al. , 2016Grismer et al. 2016. Additional sampling of Oligodon from South Asia, particularly the Western Ghats and Northeast India, will likely shed more light on the phylogenetic relationships and biogeographic history of these lesser-known colubrid snakes. ...
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We report the rediscovery of Oligodon melaneus 112 years after its original description and document the third, and only non-type, specimen for the species. The new specimen was found 267 km east of the type locality (Tindharia, West Bengal state) from Assam state, India. We designate a lectotype for the species, and provide an extended description of a freshly collected male specimen. Phylogenetic analyses of 16s and cytb mitochondrial genes provide support for O. melaneus being closely related to the widespread South Asian endemic O. arnensis.
Insularity provides ample opportunities for species diversification. Sri Lanka is home to a large diversity of species, many of which are endemic but morphologically similar to species found in southern India, due to recent speciation events, suggesting a complex evolutionary history. However, in some taxa although morphological diversity has been noted, the genetic level variations are minimal. Among the wide-ranging horseshoe bats such a phenomenon is noted. In this study, we used bioacoustics, morphometric and molecular data to evaluate the relationships between the taxa of lesser woolly horseshoe bats in the India and Sri Lanka. Our study reveals that the two taxa—Rhinolophus beddomei Andersen, 1905 and here we have validated the existing subspecies from peninsular India and R. sobrinus Andersen, 1918 from Sri Lanka are genetically very close to R. perniger Hodgson, 1843. Currently the taxa—beddomei and sobrinus are recognized as subspecies of Rhinolophus beddomei Andersen, 1905. We provide a detailed description of the taxa beddomei and sobrinus as the original descriptions are limited in nature.
We review morphology of Sunda Shelf Gonocephalus with an emphasis on Sumatran and Javan species. At least 15 species and subspecies inhabit Peninsular Malaysia, Sumatra, Java, Borneo, and adjacent smaller continental islands. Following analysis of external morphology, we provide a dichotomous key to Sunda Shelf Gonocephalus and resolve two taxonomic problems with this group of lizards. Three populations of Gonocephalus doriae on Borneo, Peninsular Malaysia, and Sumatra are recognized as subspecies, because they lack concordance of multiple morphological differences and have low genetic divergence in a 556 base-pair fragment of the 16S rRNA gene. Described as new herein, G. doriae brevis from Aceh and North Sumatra differs from G. d. abbotti and G. d. doriae in usually having more scales around midbody and a relatively shorter tail with fewer dark bands. Though previously reported as lost, a syntype of G. d. doriae (MSNG 29152) is designated as lectotype, illustrated, and described. Also described as new, G. inauris from high elevations of the Bukit Barisan Range of Bengkulu, Sumatra, is a species of the G. megalepis Group differing from all congeners in having 7/6 (vs. 8–19) loreals separating the last canthal and supralabials, 8/8 (11–27) infraorbitals, and 58 (73–153) scales around midbody. In this new species, distinctly enlarged suboculars broadly contact its supralabials, whereas 1–4 lorilabials separate the suboculars and supralabials in congeners. High genetic divergence in the new species mirrors its high level of morphological divergence.
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Upper Cretaceous deposits at Ukhaa Tolgod and adjacent localities in the Mongolian Gobi Desert have yielded a large number of superbly preserved lizard specimens, including representatives of several new taxa (described in this paper) and important supplementary material of several previously poorly known taxa. Study of these specimens gives important insight into the taxonomic diversity and systematics of the Late Cretaceous lizard fauna of the Gobi Desert. A preliminary survey indicates that the lizard assemblage from Ukhaa Tolgod and adjacent localities consists of some 30 species in four higher groups (Iguania, Gekkota, Scincomorpha, and Anguimorpha). The iguanians are documented by eight species, including three species newly recognized in this paper. The Scincomorpha are the most diverse group, represented by as many as 14 species including three new and II previously known species. The Anguimorpha are nearly as diverse as the Iguania, while the Gekkota is the least diverse group with a single species documented in the assemblage. The scincomorphs include forms that are highly specialized for burrowing life-styles, interpreted from their cranial morphology as possibly analogous to extant species. The anguimorphs include phylogenetically important basal members of several major anguimorph clades. The paleoecological significance of these lizards cannot be overlooked. According to tooth morphology, most lizards are predatory in terms of habit, while true herbivorous species are rare. Most specimens are preserved as skulls articulated with mandibles, but virtually complete skeletons in situ are quite common. Delicate parts of the skull, such as the braincase and ear ossicles, are undistorted and the surfaces of the bones show no sign of sand abrasion. These observations indicate not only relatively quick burial but also burial under relatively mesic climatic conditions with low-energy water involved during the taphonomic process.
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Squamate reptiles (lizards and snakes) are a pivotal group whose relationships have become increasingly controversial. Squamates include >9000 species, making them the second largest group of terrestrial vertebrates. They are important medicinally and as model systems for ecological and evolutionary research. However, studies of squamate biology are hindered by uncertainty over their relationships, and some consider squamate phylogeny unresolved, given recent conflicts between molecular and morphological results. To resolve these conflicts, we expand existing morphological and molecular datasets for squamates (691 morphological characters and 46 genes, for 161 living and 49 fossil taxa, including a new set of 81 morphological characters and adding two genes from published studies) and perform integrated analyses. Our results resolve higher-level relationships as indicated by molecular analyses, and reveal hidden morphological support for the molecular hypothesis (but not vice-versa). Furthermore, we find that integrating molecular, morphological, and paleontological data leads to surprising placements for two major fossil clades (Mosasauria and Polyglyphanodontia). These results further demonstrate the importance of combining fossil and molecular information, and the potential problems of estimating the placement of fossil taxa from morphological data alone. Thus, our results caution against estimating fossil relationships without considering relevant molecular data, and against placing fossils into molecular trees (e.g. for dating analyses) without considering the possible impact of molecular data on their placement.
A new asexual species of Leiolepis is described from Binh Chau – Phuoc Buu Nature Reserve, Xuyen Moc district Ba Ria-Vung Tau Province, Vietnam to where it is believed to be endemic. Leiolepis ngovantrii sp. nov. differs from all sexual species of Leiolepis by lacking males and from all asexual species by having nine rows of enlarged keeled scales across the forearm and 37–40 subdigital lamellae beneath the fourth toe. Phylogenetic inference based on 700 base pairs of the mitochondrial ND2 region, placed L. ngovantrii sp. nov. among the currently described asexual species and was used to assess the maternal ancestors of the remaining asexual species. Both maximum parsimony and maximum likelihood analyses recovered L. guttata as the maternal ancestors of L. guentherpetersi, L. boehmei, and L. ngovantrii sp. nov., and L. boehmei as the maternal ancestor to L. triploida.
A new asexual species of Leiolepis is described from Binh Chau - Phuoc Buu Nature Reserve, Xuyen Moc district Ba Ria-Vung Tau Province, Vietnam to where it is believed to be endemic. Leiolepis ngovantrii sp. nov. differs from all sexual species of Leiolepis by lacking males and from all asexual species by having nine rows of enlarged keeled scales across the forearm and 37-40 subdigital lamellae beneath the fourth toe. Phylogenetic inference based on 700 base pairs of the mitochondrial ND2 region, placed L. ngovantrii sp. nov. among the currently described asexual species and was used to assess the maternal ancestors of the remaining asexual species. Both maximum parsimony and maximum likelihood analyses recovered L. guttata as the maternal ancestors of L. guentherpetersi, L. boehmei, and L. ngovantrii sp. nov., and L. boehmei as the maternal ancestor to L. triploida.