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RESEARCH ARTICLE
Integrative Taxonomic Approach for
Describing a New Cryptic Species of Bush
Frog (Raorchestes: Anura: Rhacophoridae)
from the Western Ghats, India
H. Priti
1,2☯
, Rekha Sarma Roshmi
1,2
, Badrinath Ramya
3
, H. S. Sudhira
3,4
, G. Ravikanth
1
,
Neelavara Anantharam Aravind
1
, Kotambylu Vasudeva Gururaja
3,4☯
*
1Suri Sehgal Centre for Biodiversity and Conservation, Royal Enclave, Ashoka Trust for Research in
Ecology and the Environment, Sriramapura, Jakkur Post Office, Bengaluru, India, 2Manipal University,
Manipal, India, 3Research and Development Center, Gubbi Labs LLP, II Cross Extension, Gubbi, India,
4Science Media Center, Gubbi Labs LLP, WS-5, I Floor, Entrepreneurship Center, Society for Innovation
and Development, Indian Institute of Science Campus, Bengaluru, India
☯These authors contributed equally to this work.
*gururaja@gubbilabs.in (KVG)
Abstract
A new cryptic species of bush frog Raorchestes honnametti sp. nov. is described from the
south-eastern part of the Western Ghats, India. This newly described species belongs to
the Charius clade and is morphologically similar to other clade members—R.charius and R.
griet. Therefore, an integrative taxonomic approach based on molecular and bioacoustic
analysis along with morphology was used to delimit the new species. Raorchestes honna-
metti sp. nov., is currently known only from Biligiri Rangaswamy Temple Tiger Reserve, a
part of Biligiri Rangaswamy horst mountain range (a mountain formed due movement of two
faults) formed during the Late Quaternary period (1.8–2.58 Ma). Discovery of cryptic spe-
cies from a highly speciose and well-studied genus Raorchestes hints at the possible exis-
tence of several more cryptic species in this genus. We discuss the possible reasons for
crypsis and emphasize the need for continued systematic surveys of amphibians across
the Western Ghats.
Introduction
Cryptic species are morphologically similar and difficult to distinguish from their closest con-
geners [1]. Studies have shown that cryptic species are common and many of them go unde-
tected when studied solely on the basis of morphological evidence. In recent years, molecular
genetic techniques and bioacoustics have helped in the discovery of cryptic anurans [2,3].
Identifying cryptic species is of paramount importance not only for biodiversity conservation
but also to understand processes of evolution and biogeography [1,4].
The Western Ghats of India is known for high diversity of amphibians with 220 species
recorded. Along with high diversity, many studies have also suggested presence of high number
PLOS ONE | DOI:10.1371/journal.pone.0149382 March 2, 2016 1/21
OPEN ACCESS
Citation: Priti H, Roshmi RS, Ramya B, Sudhira HS,
Ravikanth G, Aravind NA, et al. (2016) Integrative
Taxonomic Approach for Describing a New Cryptic
Species of Bush Frog (Raorchestes: Anura:
Rhacophoridae) from the Western Ghats, India. PLoS
ONE 11(3): e0149382. doi:10.1371/journal.
pone.0149382
Editor: Ulrich Joger, State Natural History Museum,
GERMANY
Received: June 24, 2015
Accepted: February 1, 2016
Published: March 2, 2016
Copyright: © 2016 Priti et al. This is an open access
article distributed under the terms of the Creative
Commons Attribution License, which permits
unrestricted use, distribution, and reproduction in any
medium, provided the original author and source are
credited.
Data Availability Statement: All relevant data are
within the paper and its Supporting Information files.
All nucleotide sequence files are available from the
GenBank database (accession numbers KT151650,
KT151651, KT151652, KT151653).
Funding: The authors received no specific funding
for this work.
Competing Interests: The authors have declared
that no competing interests exist.
of cryptic species in the Western Ghats. Using molecular techniques, Nair et al [5] carried out a
study on endemic genus Indirana, and demonstrated high cryptic diversity among them. Simi-
larly, two new genera in the family Rhacophoridae were discovered, in a cryptic genus Polype-
dates [6]. Using bioacoustics and molecular techniques, cryptic species were discovered from
widely distributed genera like Euphlyctis (2 species, [7]) and Fejervarya (4 species, [8]).
The genus Raorchestes belongs to family Rhacophoridae. It includes bush frogs with adult
size ranging from 10 mm to 50.5 mm. They are distinguished by the presence of transparent/
translucent vocal sac and the absence of vomerine teeth. Adults are nocturnal and lack free
swimming larvae [9]. There are 59 valid species in the genus Raorchestes [10], of which 50 spe-
cies are from the Western Ghats, 4 from Eastern Himalaya, 1 from Eastern Ghats and 4 species
from China, Myanmar and Vietnam. Bee et al [11] indicated the possible existence of several
undescribed cryptic species in the genus Raorchestes. However, till date, there is no published
literature about cryptic species from this genus. Here we describe a new cryptic bush frog spe-
cies from south eastern region of the Western Ghats. The description is based on an integrative
taxonomic approach involving morphology, molecular techniques and bioacoustics. We dis-
cuss the possible reason for cryptic speciation and the need for more detailed studies on cryptic
species of Western Ghats.
Materials and Methods
Ethics statement
Fieldwork and sampling was carried out in the Biligiri Rangaswamy Temple Tiger Reserve
(BRTTR) of Karnataka, with due permission from the Director, BRTTR dated 10 October
2012. Tissue sampling was carried out under the strict supervision of local foresters and used
solely for scientific research. Minimum samples were collected (six individuals) as required for
the study and the sampling do not in any way affect effect the population of this species. Field
Permit issued by Principal Chief Conservator of Forests and Chief Wildlife Warden, Karnataka
State Forest Department.
Nomenclatural acts
The electronic edition of this article conforms to the requirements of the amended Interna-
tional Code of Zoological Nomenclature, and hence the new names contained herein are avail-
able under that Code from the electronic edition of this article. This published work and the
nomenclatural acts it contains have been registered in ZooBank, the online registration system
for the ICZN. The ZooBank LSIDs (Life Science Identifiers) can be resolved and the associated
information viewed through any standard web browser by appending the LSID to the prefix
“http://zoobank.org/”. The LSID for this publication is: urn:lsid:zoobank.org:pub:93347FEF-
6BF8-40A2-9EEB-2F2C743E70FC. The electronic edition of this work was published in a jour-
nal with an ISSN, and has been archived and is available from the following digital repositories:
PubMed Central, LOCKSS.
Study area
The study was carried out in BRTTR (Biligiri Rangaswamy hill range; latitude: 11°–12.15°N,
longitude: 77°–77.2667°E, altitude: 600–1800 m amsl). Specimens were collected from shola
forests (shola forests are a type of forest in the valleys of a mountain separated by montane
grasslands) in Honnametti (11.8987° N, 77.1741° E, 1659 m amsl) and Dodda Sampige
(11.9473° N, 77.1836° E, 1142 m amsl) within BRTTR (Figs 1and 2). The reserve got its name
“Biligiri”from the white cliff on which the temple of Lord Rangaswamy is situated. This tiger
New Cryptic Bush Frog from the Western Ghats
PLOS ONE | DOI:10.1371/journal.pone.0149382 March 2, 2016 2/21
reserve is located to the east of the Western Ghats in Karnataka State. The total area of the tiger
reserve is 540 km
2
. The landscape is very heterogeneous and undulating. The annual rainfall,
received mainly during the southwest monsoon, ranges from 600 mm at the base to 3000 mm
at the hilltop. The variation in temperature ranges from 8°C to 25°C. The wide range of cli-
matic conditions as well as altitudinal variations within the small area has resulted in varied
forest types like scrub forest, dry deciduous, moist deciduous, riparian, evergreen, sholas and
Fig 1. Biligiri Rangaswamy Temple Tiger Reserve and sampling sites of Raorchestes honnametti sp. nov. (blue circles). Maps were generated using
QGIS1Pisa Ver. 2.10. Data was sourced from www.gadm.org for administrative boundary of India and Shuttle Radar Topography Mission (SRTM) 90 m
database (http://srtm.csi.cgiar.org) for elevation.
doi:10.1371/journal.pone.0149382.g001
New Cryptic Bush Frog from the Western Ghats
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grasslands [12]. The extent of the major forest types represented as percent of total area is as
follows: deciduous (moist and dry) = 61.1%, scrub = 28.2%, grassland = 3.4%, evergreen = 6.5%
and high altitude sholas = 0.8% [13].
Specimen collection
Six adult calling males were collected in October 2012. Specimens collected were euthanized
and fixed in 5% formalin for 24h and preserved in 70% alcohol. Thigh muscle tissue samples
for genetic analysis were collected before fixing the specimen. Color of live specimens and nat-
ural history notes were recorded at the type locality during multiple visits. Specimens were
deposited in the Bombay Natural History Society (BNHS) museum, Mumbai.
Genetic analysis
For DNA extraction, we followed the method described in Vences et al [14]. A small amount of
thigh muscle tissue was excised from the holotype for extraction. The PCR amplification and
sequencing of 16S rRNA and ND1 genes (subunit of NADH dehydrogenase) were done follow-
ing Palumbi et al [15] and Bossuyt et al [16] respectively. The amplified products were sent to
Amnion Sequencing services, Bangalore, India. The sequences were checked manually using
program Chromas lite 2.01 (http://www.technelysium.com.au/chromas_lite.html). The
sequences were aligned using MAFFT algorithm [17] and manually corrected in MEGA 5.10
software [18] and deposited in GenBank (Accession numbers, KT151650–KT151653). The
final dataset consisted of 1032 base pairs. 16S and ND1 genes of 49 valid species of the genus
Raorchestes endemic to the Western Ghats [19,20,21] were used in phylogenetic analysis.
Fig 2. Type locality of Raorchestes honnametti sp. nov.–a high altitude shola forest at Honnametti in BRTTR.
doi:10.1371/journal.pone.0149382.g002
New Cryptic Bush Frog from the Western Ghats
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GenBank accession numbers for 16S rRNA and ND1 genes of 49 valid species used in the
molecular analysis are given in S1 and S2 Tables, respectively. The phylogenetic analyses were
performed using Maximum likelihood (ML) algorithm and Bayesian inference methods. The
ML analysis was executed in raxmlGUI v1.3 [22] with GTR+G model selected as the best-fit
nucleotide substitution model in jModel test [23] for 1000 bootstrap replicates. The Bayesian
analysis was performed in MrBayes 3.2.4 [24]. The combined data set of 16S and ND1 parti-
tioned as separate gene fragments were used for the analysis with TIM2+I+G and TPM3uf+I
+G selected as best fit models for 16S and ND1 genes respectively in jModel test. The Markov
chain Monte Carlo analysis for the dataset was run for 50 million generations and trees were
sampled every 500 cycles. The convergence of the runs was analyzed by assessing the split fre-
quency standard deviations (<0.001) and potential scale reduction factor (PSRF ~1.0). The
first 10% of the sampled trees were discarded as burn-in and remaining samples were used to
generate majority rule consensus tree. For estimating the genetic divergence, uncorrected pair-
wise genetic distance between the species was calculated in MEGA 5.10.
Morphology
The new species was compared with all valid species of Raorchestes both from published litera-
ture and through examination of type specimens deposited in India (S3 Table). After the phylo-
genetic analysis, initial morphological comparisons were made with the members of the
Charius clade. Raorchestes thodai [25] from Western Ghats lacked genetic data and was mor-
phologically compared with the new species. Similarly, other non-Western Ghats species of
Raorchestes, namely, R.terebrans from Eastern Ghats [26], R.annandalii [27], R.manipurensis
[28], R.sahai [29] and R.shillongensis [30] from Eastern Himalayas; R.gryllus [31], R.long-
chuanensis [32,33,34], R.menglaensis [32,35] and R.parvulus [36] from Myanmar, Vietnam
and South-China were also compared morphologically with the new species. Morphological
comparisons were made with synonymised species based on their original description, namely,
R.emeraldi [21], R.montanus [37,38,39] and R.neelanethrus [40] to verify the availability of
those names to the new species. Morphological measurements were taken using a Mitutoyo
1
digital slide calliper to the nearest 0.1 mm. Measurement and terminology follows Biju and
Bossuyt [20] and Gururaja et al [41]. Abbreviations used are as follows: snout–vent length
(SVL); head width, at the angle of the jaws (HW); head length, from the rear of the mandible to
the tip of the snout (HL); inter upper eyelid width, i.e. the shortest distance between the upper
eyelids (IUE); maximum upper eyelid width (UEW); snout length, measured from the tip of
the snout to the anterior orbital border of the eye (SL); eye length, i.e. the horizontal distance
between the bony orbital borders of the eye (EL); internarial distance, i.e. least distance between
the inner margins of nares (IN); nostril–snout distance, i.e. distance between middle of nostril
and tip of snout (NS); eye to nostril distance, i.e. distance between anterior-most point of eye
and middle of nostril (EN); tympanum–eye distance, i.e. anterior rim of tympanum to poste-
rior of eye (TYE); distance from the rear of the mandible to the nostril (MN); distance from the
rear of the mandible to the anterior orbital border of the eye (MFE); distance from the rear of
the mandible to the posterior orbital border of the eye (MBE); distance between anterior corner
of eyes, i.e. the shortest distance between the anterior orbital borders of the eyes (IFE); distance
between posterior corner of eyes, i.e. the shortest distance between the posterior orbital borders
of the eyes (IBE); largest tympanum diameter (TYD); forelimb length, measured from the
elbow to the base of the outer palmar tubercle (FLL); hand length, measured from the base of
the outer palmar tubercle to the tip of the third finger (HAL); thigh length (TL); shank length
(ShL); foot length, measured from the base of the inner metatarsal tubercle to the tip of the
fourth toe (FOL); distance from the heel to the tip of the fourth toe (TFOL); disc width on
New Cryptic Bush Frog from the Western Ghats
PLOS ONE | DOI:10.1371/journal.pone.0149382 March 2, 2016 5/21
fingers I, II, III and IV (FD I, II, III and IV); width of finger I, II, III and IV measured at the
base of the disc (FW I, II, III and IV); lengths of fingers I, II, III and IV measured from base of
proximal subarticular tubercle to fingertip (FL I, II, III and IV); tibia width, i.e. width of tibia at
its widest region (TW); disc width on toes I, II, III, IV and V (TD I, II, III, IV and V); width of
toes I, II, III, IV and V (ToW I, II, III, IV and V) measured at the base of disc; length of toes I,
II, III, IV and V measured from base of proximal subarticular tubercle to tip of toe (ToL I, II,
III, IV and V); length of inner metatarsal tubercle (IMT); distance from distal edge of metatar-
sal tubercle to maximum incurvature of web between fourth and fifth toe (MTFF); distance
from distal edge of metatarsal tubercle to maximum incurvature of web between third and
fourth toe (MTTF); distance from maximum incurvature of web between fourth and fifth toe
to tip of fourth toe (FFTF); distance from maximum incurvature of web between third and
fourth toe to tip of fourth toe (TFTF). Intercalary ossification, which is the cartilaginous struc-
ture between distal and penultimate phalanges in fingers and toes was observed. The presence
of an intercalary ossification can be noticed without anatomical sectioning as a glandular pro-
jection between phalanges [42]. We carried out linear discriminant analysis (LDA) using R v.
3.1.3 [43] and R Studio v. 0.98.1102 (http://www.rstudio.com/) on morphological data. The
data was converted as ratio of SVL and tested for normality. Eight morphological characters
viz., HW, HL, UEW, SL, HAL, TL, ShL and FOL were subjected to LDA to get a linear combi-
nation of these characters to discriminate R.charius,R.griet and R.honnametti. To identify
multivariate differences among species MANOVA was performed and Tukey HSD post-hoc
test was used for pairwise comparison of characters.
Advertisement call recording and analysis
Call recordings were made using Olympus stereo digital voice recorder (LS-11) for R.charius
and R.honnametti. Calls of R.griet were recorded using Canon EOS 600D. Calls with less back-
ground noise were manually selected from different individual call records and were analysed
using Audacity Ver.1.3 (Beta) and Raven Pro 1.5. Nineteen calls from 3 individuals of R.hon-
nametti; 20 calls from 4 individuals of R.charius and 8 calls from 1 individual of R.griet were
selected for further analysis. Duration, inter-call interval duration, dominant frequency and
number of pulses of each call was recorded. Call terminology was based on Kok and Kalamand-
een [44]. Air temperature and relative humidity were recorded using TFA digital Thermo-
Hygrometer. We used Welch t-test in R v.3.1.3 to compare the means of call characteristics
between two species, assuming normal distribution of call samples with unequal variance and
sample size.
Results
Genetic analysis
The molecular data analysis suggested that Raorchestes honnametti sp. nov. belonged to the
‘Charius clade’[21] comprising of R.charius and R.griet The uncorrected pairwise genetic dis-
tance (Mean ± SD) between R.honnametti and R.charius is 4.14 ± 0.14% and between R.hon-
nametti and R.griet is 6.47 ± 0.17%. Fig 3 shows the result of ML tree with a strong bootstrap
support (100%) for the R.honnametti and R.charius. Hence, the morphological comparisons
are made only with the closest relatives of the species, i.e. R.charius and R.griet. The overall
genetic divergence of 50 species, including R.honnametti for the combined dataset of 16S
rRNA and ND1 genes ranges from 2 to 32% (S4 Table).
New Cryptic Bush Frog from the Western Ghats
PLOS ONE | DOI:10.1371/journal.pone.0149382 March 2, 2016 6/21
Fig 3. Maximum Likelihood tree for 50 Raorchestes species from the Western Ghats biodiversity hotspot and an outgroup Rhacophorus
malabaricus.Numbers above and below the nodes indicate Bayesian Posterior Probabilities and Maximum Likelihood Bootstrap values >50, respectively.
Asterisk (*) indicates values <50.
doi:10.1371/journal.pone.0149382.g003
New Cryptic Bush Frog from the Western Ghats
PLOS ONE | DOI:10.1371/journal.pone.0149382 March 2, 2016 7/21
Raorchestes honnametti sp. nov. Gururaja, Priti, Roshmi and Aravind
urn:lsid:zoobank.org:act:071B913C-BB18-4E6A-97C6-6BA2621F8D6E
Suggested common name. Honnametti bush frog.
Holotype: BNHS 5941, an adult male collected by authors from Strobilanthus shrubs at
0.48m above ground at Honnametti, on 13
th
October 2012 at 20:20 h from Biligiri Rangaswamy
hills (11.8987° N, 77.1741° E, 1659 m amsl).
Paratypes: BNHS 5942, BNHS 5943, BNHS 5945 and BNHS 5946, male individuals col-
lected by authors in Honnametti, collection date and place same as holotype. BNHS 5944, a
male collected by authors on 14
th
October 2012 at 19:45 h Dodda Sampige (11.9473° N and
77.1836° E, 1142 m amsl).
Diagnosis:Raorchestes honnametti belongs to the genus Raorchestes as they are relatively
small sized frogs (15–45 mm), active in night, vomerine teeth absent, transparent/translucent
vocal sac while calling and direct development without free swimming tadpoles. It is a small
sized adult (male: 21.7–24.8 mm, n = 6); snout longer than the horizontal diameter of eye;
groin uniform light brown with 3–4 yellow blotches; both anterior and posterior part of thigh
uniform light brown with small round to oval shaped yellow blotches and relatively short hind
limbs ShL/SVL ratio <0.5. It belongs to the Charius clade and morphologically similar to R.
charius and R.griet.
Description of holotype: A small sized frog (SVL = 24, Fig 4A–4H,Table 1, all measurements
in mm), head wider than long (HW = 8.0; HL = 7.4), snout oval in dorsal view and in profile
rounded. Snout longer than or equal to eye (EL = 3.2; SL = 3.6). Canthus rostralis rounded,
loreal region slightly concave. Interorbital space flat, almost equal to upper eyelid width and
internarial distance (IUE = 2.5; UEW = 2.1; IN = 2.2). Internarial distance between posterior
margins of eyes 1.7 times that of anterior margins (IFE = 4.3; IBE = 7.2). Nostrils oval, without
flap, closer to tip of snout than to eye (NS = 1.4; EN = 2.0). Weak symphysial knob. Pineal ocel-
lus absent. Tympanum indistinct, oval, closer to eye (TYD = 1.4), 2.3 times in eye length.
Supratympanic fold distinct from back of eye to shoulder. Median sub-gular vocal sac with a
pair of openings at the base of lower jaw. Tongue bifid, chordate, sparsely granular. Lingual
papilla absent. Eyes moderately large (EL = 3.2), protruding, pupil horizontal.
Fore limb length shorter than hand length (FLL = 5.1; HAL = 7.1). Relative lengths of fin-
gers I<II<IV<III (FL I = 1.9; FL II = 2.4; FL III = 3.2; FL IV = 2.5). Finger tips with well-devel-
oped discs (FD I = 0.7, FD II = 0.9, FD III = 1.1, FD IV = 1.2; FW I = 0.6, FW II = 0.4, FW
III = 0.6, FW IV = 0.6) with circum marginal grooves, grooves fold upwards, giving bifid
appearance in dorsal view, intercalary ossification distinct between penultimate and distal pha-
langes. Dermal fringe weak, on both sides of the fingers. Webbing between fingers absent. Sub-
articular tubercles distinct (finger: i = 1, ii = 1, iii = 2, iv = 1) rounded and pre–pollex tubercle
oval, distinct. Supernumerary tubercles present. Nuptial pad absent.
Hind limbs long, do not overlap or touch when folded at right angles to body. Shank 4.2
times longer than wide (ShL = 10.6; TW = 2.5), shorter than thigh length (TL = 11.3) and lon-
ger than foot length (FOL = 10.0). Heel to tip of fourth toe (TFOL = 16.4) 3.1 times longer than
fourth toe length (ToL IV = 5.3). Relative toe length I<II<IIIV<IV (ToL I = 1.9; ToL
II = 2.0, ToL III = 3.2; ToL IV = 5.3; ToL V = 3.8). Toes with well develop discs at tip (TD
I = 0.8, TD II = 0.8, TD III = 0.8, TD IV = 1.0, TD V = 1.0; ToW I = 0.5, ToW II = 0.5, ToW
III = 0.6, ToW IV = 0.7, ToW V = 0.6). Webbing moderate (MTTF = 5.1, MTFF = 6.4,
TFTF = 5.7, FFTF = 4.7). First toe (ToL I = 1.9) 1.9 times the length of inner metatarsal tubercle
(IMT = 1.0). Outer metatarsal tubercle absent, supernumerary tubercles and tarsal tubercle
present (toe: i = 1, ii = 1, iii = 2, iv = 3, v = 2).
New Cryptic Bush Frog from the Western Ghats
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Skin: Entire dorsum, snout and upper eyelid with very small horny spines, mid-dorsum
dense with small horny spines; dorsal part of forelimbs, thighs and shanks smooth; throat,
Fig 4. Holotype (BNHS 5941) of Raorchestes honnametti sp. nov. a-b—Live specimen; c—ventral view; d—dorsal view; e—ventral view of hind limb; f—
ventral view of forelimb; g—lateral profile of head; h—Schematic view of webbing in hind limb.
doi:10.1371/journal.pone.0149382.g004
New Cryptic Bush Frog from the Western Ghats
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Table 1. Morphometric data of Raorchestes honnametti sp. nov. (Holotype and paratypes). Measurements in mm.
Characters BNHS 5941
Holotype
BNHS 5942
Paratype
BNHS 5943
Paratype
BNHS 5944
Paratype
BNHS 5945
Paratype
BNHS 5946
Paratype
Mean ±SD
Sex Male Male Male Male Male Male
SVL 24.0 24.8 23.9 23.4 25.0 21.7 23.8 ±1.2
HW 8.00 8.2 8.5 8.4 8.3 8.7 8.4 ±0.2
HL 7.4 7.2 7.1 7.1 7.1 7.3 7.2 ±0.1
IUE 2.5 3.2 3.2 3.5 3.2 3.6 3.2 ±0.4
UEW 2.1 1.9 2.0 2.0 1.8 2.1 2.0 ±0.1
SL 3.6 3.6 3.7 3.1 3.3 3.9 3.5 ±0.3
EL 3.2 3.3 3.1 3.1 3.3 2.8 3.1 ±0.2
MN 5.6 5.9 5.8 5.7 5.9 6.1 5.8 ±0.2
MFE 6.0 4.6 4.5 4.5 4.3 4.4 4.7 ±0.6
MBE 2.5 2.1 2.2 2.1 2.2 2.1 2.2 ±0.2
IN 2.2 2.4 2.4 2.0 2.5 2.4 2.3 ±0.2
IFE 4.3 4.2 4.0 4.1 4.3 5.3 4.4 ±0.5
IBE 7.2 7.0 7.4 7.5 7.6 7.9 7.4 ±0.3
NS 1.4 1.6 1.5 1.3 1.5 1.4 1.5 ±0.1
EN 2.0 2.2 2.3 1.7 1.9 2.1 2.0 ±0.2
TYD 1.4 1.7 1.2 1.3 1.6 1.1 1.4 ±0.2
FLL 5.1 5.1 5.4 5.0 6.1 4.7 5.2 ±0.5
HAL 7.1 7.6 7.5 6.8 7.1 6.8 7.2 ±0.3
FD1 0.7 0.7 0.7 0.7 0.7 0.6 0.7 ±0.0
FD2 0.9 0.9 0.7 0.9 0.9 0.8 0.9 ±0.1
FD3 1.1 1.3 1.1 1.2 1.0 1.2 1.2 ±0.1
FD4 1.2 1.1 1.0 1.2 1.1 1.0 1.1 ±0.1
FW1 0.6 0.5 0.5 0.5 0.4 0.5 0.5 ±0.1
FW2 0.4 0.5 0.5 0.6 0.6 0.5 0.5 ±0.1
FW3 0.6 0.5 0.6 0.7 0.7 0.7 0.6 ±0.1
FW4 0.6 0.6 0.5 0.6 0.7 0.6 0.6 ±0.1
FIL 1.9 1.9 1.9 1.7 1.7 1.7 1.8 ±0.1
FIIL 2.4 2.3 2.4 2.3 2.2 2.1 2.3 ±0.1
FIIIL 3.2 4.4 3.8 3.6 4.5 3.9 3.9 ±0.5
FIVL 2.3 3.1 3.6 3.1 3.9 3.2 3.2 ±0.5
FL 11.3 11.5 11.4 10.3 11.9 11.9 11.4 ±0.6
ShL 10.6 10.9 11.3 10.3 10.9 10.7 10.8 ±0.3
TW 2.5 1.9 2.6 2.3 2.5 3.1 2.5 ±0.4
FOL 10.2 10.6 10.9 8.8 10.3 9.8 10.1 ±0.7
TW1 0.5 0.5 0.5 0.5 0.6 0.6 0.5 ±0.1
TW2 0.5 0.5 0.5 0.6 0.5 0.6 0.5 ±0.1
TW3 0.6 0.5 0.6 0.6 0.6 0.6 0.6 ±0.0
TW4 0.7 0.6 0.6 0.6 0.8 0.7 0.7 ±0.1
TW5 0.6 0.6 0.7 0.6 0.8 0.8 0.7 ±0.1
TD1 0.8 0.7 0.7 0.8 0.8 0.6 0.7 ±0.1
TD2 0.8 0.9 0.8 0.7 0.8 0.7 0.8 ±0.1
TD3 0.8 0.7 0.9 0.9 0.7 0.7 0.8 ±0.1
TD4 1.0 1.0 1.0 1.1 0.8 0.9 1.0 ±0.1
TD5 1.0 1.1 1.0 1.1 0.8 1.0 1.0 ±0.1
IMT 1.0 1.1 0.9 1. 0.9 0.8 1.0 ±0.1
TFOL 16.4 11.1 17.5 15.1 16.9 16.2 15.5 ±2.3
(Continued)
New Cryptic Bush Frog from the Western Ghats
PLOS ONE | DOI:10.1371/journal.pone.0149382 March 2, 2016 10 / 21
chest, belly, lower flanks and ventral sides of forelimbs and thighs granular; chest with larger
granules; no dorso lateral fold,
Colour in life: Dorsum light grey with two dark grey concave stripes behind eyes to groin;
light brown stripe between eyes demarcates triangular light grey snout, limbs barred, brown
band from snout passing through loreal, mid iris and tympanic region till end of supratympa-
nic fold. Iris golden above and light golden below, horizontally separated by brown band; dor-
sal side of forelimbs and hind limbs with dark grey cross bands. A triangular white spot on the
tip of the snout. Venter uniform cream white, vocal sac yellow translucent with granular grey
spots. Webbing cream white. Groin uniform light brown with 3–4 yellow blotches, both ante-
rior and posterior part of thigh uniform light brown with small round to oval shaped yellow
blotches.
Colour in preservative: Dorsum light grey, dorsal side of forelimbs and hind limbs with faint
cross bands. Venter uniform cream white, vocal sac with granular grey spots. Webbing cream
white. Groin uniform pale brown with 3–4 cream white blotches, both anterior and posterior
part of thigh uniform pale brown with small round to oval shaped cream white blotches.
Etymology: Named after the locality of holotype–Honnametti. Honnametti is treated as an
invariable noun in apposition to the generic name.
Variation: Details of the morphometric variations observed in 6 individuals is provided in
Table 1. The dorsum colouration varied from light grey to dark brown. A triangular white spot
on the tip of the snout are seen in couple of individuals. Flanks light grey to dark brown, yellow
blotches in the groin varies both in numbers (2 to 5) as well as in size. Variations included dis-
tinct cross bands on both forelimbs and hind limbs.
Comparison: Molecular data suggested that Raorchestes honnametti belonged to the Charius
clade within the Western Ghat endemic species of Raorchestes and hence initial morphological
comparisons were made only with R.charius and R.griet.Raorchestes charius differs from R.
honnametti in following characters: adult size (R.charius: 27.2–31.4 mm vs R.honnametti:
21.7–24.8 mm), snout length (R.charius: 3.5–4.3 mm vs. R.honnametti: 3.1–3.9 mm) shorter
or sub-equal to eye vs. snout length longer than eye (R.charius: 3.5–4.4 mm vs. R.honnametti:
2.8–3.3 mm), groin brownish black with yellow blotches vs. groin brown with 3–4 yellow
blotches; posterior surface of thighs uniform brownish black with large yellow blotches vs. both
anterior and posterior surface of thighs light brown with small round-oval shaped yellow
blotches. Raorchestes griet differs from R.honnametti in following characters: adult size (R.
griet: 19.7–22.4 mm vs. R.honnametti: 21.7–24.8 mm), snout length (R.griet: 2.4–2.7 mm vs.
Table 1. (Continued)
Characters BNHS 5941
Holotype
BNHS 5942
Paratype
BNHS 5943
Paratype
BNHS 5944
Paratype
BNHS 5945
Paratype
BNHS 5946
Paratype
Mean ±SD
Sex Male Male Male Male Male Male
TIL 1.9 2.0 1.8 1.8 1.7 1.7 1.8 ±0.1
TIIL 2.0 2.2 2.0 1.9 2.0 2.1 2.0 ±0.1
TIIIL 3.2 3.3 3.3 3.0 3.2 3.0 3.2 ±0.1
TIVL 5.3 5.5 5.6 4.4 6.3 5.0 5.4 ±0.6
TVL 3.8 4.1 3.0 3.5 4.3 3.9 3.8 ±0.5
MTFF 6.4 5.6 5.9 5.1 5.4 6.0 5.7 ±0.5
MTTF 5.1 4.7 4.5 4.2 4.4 5.2 4.7 ±0.4
TFTF 5.7 5.6 5.9 4.6 5.9 4.6 5.4 ±0.6
FFTF 4.7 5.7 5.1 4.9 4.8 4.5 5.0 ±0.4
doi:10.1371/journal.pone.0149382.t001
New Cryptic Bush Frog from the Western Ghats
PLOS ONE | DOI:10.1371/journal.pone.0149382 March 2, 2016 11 / 21
R.honnametti: 3.1–3.9 mm) shorter than eye vs. longer than eye (R.griet: 2.4–2.8 mm vs. R.
honnametti: 2.8–3.3 mm), groin light brown with minute white marbling vs groin brown with
3–4 yellow blotches; posterior surface of thighs dark brown with some light brown spots vs.
both anterior and posterior surface of thighs light brown with small round-oval shaped yellow
blotches. Fig 5 shows LDA plot between three species. There is an overlap between R.honna-
metti and R.charius.Raorchestes griet, however, forms a distinct cluster. Factor loading for axis
1 and 2 are given in S5 Table. MANOVA did not result in significant differences between the
three species (F
2,16
= 1.61, p = 0.17). Tukey’s HSD post-hoc test also did not exhibit significant
differences in pairwise comparison of characters except for SL in R.griet and R.honnametti
(Q = 4.73, p = 0.012); TL in R.griet and R.charius (Q = 3.83, p = 0.041) and TL in R.honna-
metti and R.griet (Q = 5.03, p = 0.008).
Morphological comparisons of R.honnametti with R.thodai and with non-Western Ghats
species of Raorchestes are given in S6 Table.Raorchestes honnametti differed from these conge-
ners. Similarly, morphological comparison with synonymised species showed that earlier
names were not available for the new species.
Advertisement call analysis: Calls of R.honnametti were recorded on 13 October 2012,
20:15h, Air Temperature 18.03 ± 0.12°C, Relative Humidity 79 ± 1% at Honnametti, 11.8987°
N, 77.1741° E, 1659 m amsl; calls of R.charius were recorded on 5 July 2013; 18:20hr; Air Tem-
perature: 20.74 ± 0.21°C; Relative Humidity: 86.67 ± 1.16%, at Honey Valley,12.2312° N,
75.6558° E, 1033 m amsl and calls of R.griet were recorded on 29 August 2014; 19:30h at Mun-
nar; Air Temperature and Relative Humidity not recorded. Advertisement calls of these species
greatly resemble each other (Figs 6,7and 8; Tables 2and 3). Phonetically, the advertisement
call sounds like ‘treenk.....treenk.....treenk...’, however they vary in number of pulses, call
duration, inter-call interval duration and dominant frequency. Table 2 provides detail on call
characteristics of R.honnametti,R.charius and R.griet. Calls of R.honnametti had 6–9 pulses
(Mean ± SE, 6.4 ± 0.18) in each call. Average dominant frequency was 2635.9 ± 11.75 Hz, Call
Fig 5. Linear discriminant analysis of morphometric data of the Charius clade members.
doi:10.1371/journal.pone.0149382.g005
New Cryptic Bush Frog from the Western Ghats
PLOS ONE | DOI:10.1371/journal.pone.0149382 March 2, 2016 12 / 21
duration was 0.1 ± 0.003 s, inter-call interval duration of a lone individual was 6.3 ± 0.31 s and
in the presence of multiple calling individuals, inter-call interval duration was 2.45 ± 0.02 s.
Calls of R.charius had 13–18 pulses in each call. Average dominant frequency was
2478.57 ± 12.56 Hz; Call duration was 0.09 ± 0.004 s; inter call duration was 2.51 ± 0.09 s in the
presence of multiple calling individuals. Calls of R.griet had 13–15 pulses in each call. Average
dominant frequency was 3699.88 ± 9.51 Hz, Call duration was 0.09 ± 0.0007 s, and inter-call
interval duration was 5.22 ± 0.2 s in the presence of multiple calling individuals. Welch t-test
showed significant differences in dominant frequency, call duration and number of pulses of
all the three species (Table 3).
Natural history:Raorchestes honnametti sp. nov. is known only from Biligiri Rangaswamy
hills and is one of the very common frogs in that landscape. It is found in shola forests, ever-
green forests, semi-evergreen forests and around human habitations. Individuals were found
calling in an open area within Ageratina adenophora (Asteraceae) and Strobilanthus bushes.
Some individuals were also found on tree saplings in the understory. Individuals call at a
perched height between 0.48–1.00 m from ground. Call starts at around 6 pm and goes till
early morning. During monsoon (June to September), individuals call almost throughout the
day except on days with heavy rains or dry days. Other anuran species like Pseudophilautus sp.,
Fig 6. Advertisement call spectrogram of Raorchestes charius.a. Amplitude, b. Spectrogram, c. Amplitude of a single call and d. Spectrogram of a single
call.
doi:10.1371/journal.pone.0149382.g006
New Cryptic Bush Frog from the Western Ghats
PLOS ONE | DOI:10.1371/journal.pone.0149382 March 2, 2016 13 / 21
Hylarana sp., Fejervarya sp., Duttaphrynus melanostictus,Microhyla sholigari,M.ornata,M.
rubra and Euphlyctis cyanophlyctis co-occur with R.honnametti in Biligiri Rangaswamy hills.
Conservation
There are no immediate threats from human activities to this newly described species as Biligiri
Rangaswamy hills is a tiger reserve and enjoys high level of protection. However, in the last one
decade, a significant area of the Reserve has been taken over by highly invasive species like Lan-
tana camara (Verbenaceae) and Ageratina adenophora (Asteraceae). On subsequent visits, we
have seen several calling males of R.honnametti on Lantana and Ageratina bushes, indicating
that this species might have adapted to the presence of these invasive species. However, a sys-
tematic research needs to be undertaken to assess the impact of invasive species on R.
honnametti.
Discussion
The bush frogs of the genus Raorchestes are distributed across India, southern China, Myanmar
and Vietnam. India harbours 55 of these species, with 50 species distributed in the Western
Fig 7. Advertisement call spectrogram of Raorchestes griet.a. Amplitude, b. Spectrogram, c. Amplitude of a single call and d. Spectrogram of a single
call.
doi:10.1371/journal.pone.0149382.g007
New Cryptic Bush Frog from the Western Ghats
PLOS ONE | DOI:10.1371/journal.pone.0149382 March 2, 2016 14 / 21
Ghats. With the addition of R.honnametti the total number of species in genus Raorchestes
stands at 60. Discovery pattern shows that 42 species of Raorchestes were described in last 15
years (Fig 9), indicating that there may be many more species to be described from the Western
Ghats and needs a continued systematic surveys of amphibians across the region. Such patterns
Fig 8. Advertisement call spectrogram of Raorchestes honnametti sp. nov. a. Amplitude, b. Spectrogram, c. Amplitude of a single call and d. Spectrogramof
a single call.
doi:10.1371/journal.pone.0149382.g008
Table 2. Acoustic characteristics of R.charius (N = 21), R.griet (N = 8) and R.honnametti (N = 20).
Features R.charius R.griet R.honnametti
Dominant Frequency (Hz) Mean ±SE (Range) 2478.57±12.56 (2346–
2541)
3699.88±9.51 (3634–
3746)
2635.9±11.75 (2536–
2736)
Call duration (s) Mean ±SE (Range) 0.09±0.004 (0.06–0.14) 0.086±0.001 (0.081–
0.089)
0.1±0.003 (0.006–0.121)
Number of pulses Mean ±SE (Range) 15.14±0.26 (13–18) 13.38±0.16 (13–15) 6.4±0.179 (6–9)
Inter-call interval duration (s) Mean ±SE (Range) 2.51±0.09 (1.88–3.47) 5.22±0.2 (4.31–6.82) 2.45±0.023 (2.32–2.55)
Inter-call interval duration (s) with single male calling Mean ±SE
(Range)
- - 6.3±0.31 (3.94–8.07)
doi:10.1371/journal.pone.0149382.t002
New Cryptic Bush Frog from the Western Ghats
PLOS ONE | DOI:10.1371/journal.pone.0149382 March 2, 2016 15 / 21
in discovery further strengthen our expectations that not only morphologically distinct species,
but also many cryptic species are waiting to be discovered from the Western Ghats.
Multivariate analysis of morphological data using LDA showed an overlap between R.char-
ius and R.honnametti individuals while R.griet formed a distinct cluster. MANOVA and
Tukey’s HSD post-hoc tests on morphological data did not show significant differences
between R.charius,R.griet and R.honnametti, except for SL and TL. This validates our obser-
vations on morphological similarities between the three species and hence morphological
Table 3. Welch t-test to compare means of call characteristics of R.charius,R.griet and R.honnametti.Value in parenthesis indicates level of signifi-
cance (P).
R.charius Dominant
frequency
R.charius Call
duration
R.charius
Pulse #
R.griet Dominant
frequency
R.griet Call
duration
R.griet Pulse
#
R.griet Dominant
frequency
-61.4468 (0.0001)
R.griet Call duration 0.1797 (0.8559)
R.griet Pulse # 4.7724
(0.0001)
R.honnametti Dominant
frequency
-9.0426 (0.0001) 54.4185 (0.0001)
R.honnametti Call
duration
-1.805 (0.078) 2.6189 (0.015)
R.honnametti Pulse # 27.4138
(0.0001)
21.7459
(0.00001)
doi:10.1371/journal.pone.0149382.t003
Fig 9. Species discovery pattern in the genus Raorchestes in India till 2014.
doi:10.1371/journal.pone.0149382.g009
New Cryptic Bush Frog from the Western Ghats
PLOS ONE | DOI:10.1371/journal.pone.0149382 March 2, 2016 16 / 21
characters alone cannot distinguish cryptic species. Tools like bioacoustics and molecular
genetic technique can be a better aid in describing a cryptic species through integrated taxo-
nomic approach. Studies have shown that a bioacoustic character like call dominant frequency
has a highly significant negative relationship with body size in anurans [45]. A similar signifi-
cant negative relationship was exhibited among the Charius clade members between dominant
frequency (DF) and body size (SVL) (Pearson’s correlation coefficient, r = -0.74, p = 0.0004).
External factors like temperature, relative humidity and altitude influence advertisement call
characteristics [46]. Due to lack of data, we did not analyze the effect of external factors on
advertisement call characteristics of Charius clade members.
Biju and Bossuyt [20] through their study on genus Raorchestes showed that R.charius,R.
griet and R.coonoorensis formed a distinct clade. Recently, Vijayakumar et al [21] revised the
Charius clade which involved only R.charius and R.griet, with R.coonoorensis forming a sepa-
rate clade basal to the Charius clade. From our study, the Charius clade now includes R.char-
ius,R.griet and R.honnametti with R.charius and R.honnametti forming sister taxa, while R.
griet remains basal to the other two. The distribution range of these three species is restricted
to separate regions of Western Ghats. According to the present distribution (Fig 1), R.charius
is found in Bababudangiri to Brahmagiri hill ranges of central Western Ghats. It is 169 km
Fig 10. Elevation profile of hill ranges in and around BRT Tiger Reserve. Faults within Biligiri Rangaswamy hill ranges are shown with dash lines. Maps
and elevation profile were generated using QGIS1Pisa Ver. 2.10. Data was sourced from www.gadm.org for administrative boundary of India and Shuttle
Radar Topography Mission (SRTM) 90 m database (http://srtm.csi.cgiar.org) for elevation.
doi:10.1371/journal.pone.0149382.g010
New Cryptic Bush Frog from the Western Ghats
PLOS ONE | DOI:10.1371/journal.pone.0149382 March 2, 2016 17 / 21
north-west from R.honnametti and 251 km north from R.griet distribution. R.griet is found in
Munnar and Valparai regions of southern Western Ghats below Palghat Gap. It is 169 km
south west from R.honnametti, whereas R.honnametti (from this study) is found only in Bili-
giri Rangaswamy hills, south east of the Western Ghats. Absence of R.charius and R.griet in
Biligiri Rangaswamy hills indicates that each of the three species has a smaller non-overlapping
geographical range.
Studies understanding cryptic speciation signify the need to understand role of historical
and biogeographical processes. The phenomenon of morphological stasis and genetic diver-
gence in cryptic species could be because of recent speciation events owed to climatic oscilla-
tions and geographic barriers [47]. Biju and Bossuyt [20], stated that species of genus
Raorchestes showed a high level of local endemism and emphasized the role of isolated hilly
regions as a major reason for restricted species distribution. Studies understanding the diver-
gence in frog lineages indicate that not just mountains but ecology, climatic conditions, forest
types and rivers can act as barriers [48,49,50]. Raorchestes honnametti is a nocturnal, arboreal
and a direct developing frog. Though detailed ecological study on R.honnametti is warranted,
above mentioned ecological factors could have acted as barriers resulting in speciation of R.
honnametti. The geological studies on Biligiri Rangaswamy hills suggest that it is a horst moun-
tain formed due to the movement of Kollegal fault running N-NE to S-SW direction (Fig 10)
and might have formed recently during late Quaternary period (1.80 to 2.58 Ma) along the
eastern borders of Mysore Plateau [51]. The underlying rocks date back to 3.6 Ga of Dharwad
Craton. This uplift of Biligiri Rangaswamy hills–Male Mahadeshwara hills and subsequent iso-
lation of Biligiri Rangaswamy hills from Niligiris due to Moyar Gorge could be one of the rea-
sons for diversification of R.honnametti from R.charius and R.griet.
The restricted distribution of R.honnametti could also be due to the present day disjunct
distribution of evergreen forests in Biligiri Rangaswamy hills. Studies have shown that such for-
ests of India got restricted due to variation in climatic conditions (Miocene and Quaternary
period) and anthropogenic factors resulting in a disjunct distribution of species [52]. Molecular
dating can further help in understanding the diversification in R.honnametti as well its other
clade members. Nevertheless, the discovery of R.honnametti opens up interesting evolutionary
questions on cryptic species and studies understanding ecological and evolutionary mecha-
nisms can help in appreciating the conserved morphology of such cryptic species.
Supporting Information
S1 Table. GenBank accession numbers for 16S rRNA gene of 49 species of Raorchestes and
Rhacophorus malabaricus compared in the study.
(XLSX)
S2 Table. GenBank accession numbers for ND1 gene of 49 species of Raorchestes and Rha-
cophorus malabaricus compared in the study.
(XLSX)
S3 Table. Details of type materials and voucher specimens examined.
(XLSX)
S4 Table. Genetic divergence (in percentage) matrix of 50 species of Raorchestes and an
outgroup Rhacophorus malabaricus.
(XLSX)
S5 Table. Linear Discriminant Analysis factor loadings for Axis 1 and Axis 2.
(XLSX)
New Cryptic Bush Frog from the Western Ghats
PLOS ONE | DOI:10.1371/journal.pone.0149382 March 2, 2016 18 / 21
S6 Table. Morphological comparison of R.honnametti with R.thodai and with non-West-
ern Ghats species of Raorchestes.
(DOCX)
Acknowledgments
We thank Vijay Mohan Raj, IFS, Chief Conservator of Forests and Executive Director (Project
& Business Development), Jungle Lodges and Resorts for the permissions provided during his
tenure as Field Director of BRTTR in 2012. We thank Lingaraja S.S., IFS, Field Director, BRT
Tiger Reserve for the support. We thank all the Range Forest Officers and field staff of BRT
Tiger Reserve for the active support during the field visit. We thank Dinesh K.P. for specimen
verification. We thank Ramit Singal for the call records of Raorchestes griet from Munnar. The
authors also thank ATREE field station staff and field assistants for their help during the field
work at Biligiri Rangaswamy hills. We thank Madhukara Putty and Seshadri K.S. for language
corrections in the revised manuscript. We thank Ulrich Joger and an anonymous reviewer for
the critical comments on the manuscript.
Author Contributions
Conceived and designed the experiments: KVG HP NAA. Performed the experiments: KVG
HP NAA. Analyzed the data: KVG HP NAA RSR BR. Contributed reagents/materials/analysis
tools: KVG HP NAA RSR BR GR HSS. Wrote the paper: KVG HP NAA RSR GR HSS BR.
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