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The Australasian frog family Ceratobatrachidae in China, Myanmar and Thailand: discovery of a new Himalayan forest frog clade

  • Chengdu Institute of Biology CAS

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In an effort to study the systematic affinities and specieslevel phylogenetic relationships of the enigmatic anurans variably assigned to the genera Ingerana or Limnonectes (family Dicroglossidae), we collected new molecular sequence data for five species including four Himalayan taxa, Limnonectes xizangensis, Lim. medogensis, Lim. alpine, Ingerana borealis and one southeast Asian species, I. tasanae, and analyzed these together with data from previous studies involving other ostensibly related taxa. Our surprising results demonstrate unequivocally that Lim. xizangensis, Lim. medogensis and Lim. alpine form a strongly supported clade, the sister-group of the family Australasian forest frog family Ceratobatrachidae. This discovery requires an expansion of the definition of Ceratobatrachidae and represents the first record of this family in China. These three species are distinguished from the species of Ingerana and Limnonectes by the: (1) absence of interdigital webbing of the foot, (2) absence of terminal discs on fingers and toes, (3) absence of circumarginal grooves on the fingers and toes, and (4) absence of tarsal folds. Given their phylogenetic and morphological distinctiveness, we assign them to the oldest available generic name for this clade, Liurana Dubois 1987, and transfer Liurana from Dicroglossidae to the family Ceratobatrachidae. In contrast, Ingerana tasanae was found to be clustered with strong support with the recently described genus Alcalus (Ceratobatrachidae), a small clade of otherwise Sundaic species; this constitutes a new record of the family Ceratobatrachidae for Myanmar and Thailand. Finally, Ingerana borealis clustered with the "true" Ingerana (family Dicroglossidae), for which the type species is I. tenasserimensis.
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Science Press Zoological Research 37(1): 7-14, 2016 7
The Australasian frog family Ceratobatrachidae in
China, Myanmar and Thailand: discovery of a new
Himalayan forest frog clade
Fang YAN1,2,#, Ke JIANG1,2,#, Kai WANG1,3, Jie-Qiong JIN1, Chatmongkon SUWANNAPOOM4,1, Cheng LI5, Jens V.
VINDUM6, Rafe M. BROWN7, Jing CHE1,2,*
1 State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming
Yunnan 650223, China
2 Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Yezin, Nay Pyi Taw 05282, Myanmar
3 Sam Noble Oklahoma Museum of Natural History and Department of Biology, University of Oklahoma, Norman OK 73072-7029, U.S.A.
4 School of Agriculture and Natural Resources, University of Phayao, Phayao 56000, Thailand
5 Imaging Biodiversity Expedition, Beijing 100107, China
6 Department of Herpetology, California Academy of Sciences, California 94118, U.S.A.
7 Biodiversity Institute and Department of Ecology and Evolutionary Biology, 1345 Jayhawk Blvd, University of Kansas, Lawrence KS
66045, U.S.A.
In an effort to study the systematic affinities and species-
level phylogenetic relationships of the enigmatic anurans
variably assigned to the genera Ingerana or
Limnonectes (family Dicroglossidae), we collected new
molecular sequence data for five species including four
Himalayan taxa, Limnonectes xizangensis, Lim.
medogensis, Lim. alpine, Ingerana borealis and one
southeast Asian species, I. tasanae, and analyzed these
together with data from previous studies involving other
ostensibly related taxa. Our surprising results
demonstrate unequivocally that Lim. xizangensis, Lim.
medogensis and Lim. alpine form a strongly supported
clade, the sister-group of the family Australasian forest
frog family Ceratobatrachidae. This discovery requires
an expansion of the definition of Ceratobatrachidae and
represents the first record of this family in China. These
three species are distinguished from the species of
Ingerana and Limnonectes by the: (1) absence of
interdigital webbing of the foot, (2) absence of terminal
discs on fingers and toes, (3) absence of circumarginal
grooves on the fingers and toes, and (4) absence of
tarsal folds. Given their phylogenetic and morphological
distinctiveness, we assign them to the oldest available
generic name for this clade, Liurana Dubois 1987, and
transfer Liurana from Dicroglossidae to the family
Ceratobatrachidae. In contrast, Ingerana tasanae was
found to be clustered with strong support with the
recently described genus Alcalus (Ceratobatrachidae), a
small clade of otherwise Sundaic species; this
constitutes a new record of the family Ceratobatrachidae
for Myanmar and Thailand. Finally, Ingerana borealis
clustered with the “true” Ingerana (family Dicroglossidae),
for which the type species is I. tenasserimensis.
Keywords: Dicroglossidae; Himalaya; Liurana
The frogs of family Ceratobatrachidae (Boulenger, 2009)
comprise a morphologically, developmentally, ecologically,
and biogeographically greatly variable and, thus, unique
clade (Brown et al., 2015). This family is notable for highly
variable body size, direct larval development, and the
ability to inhabit a wide variety of environments that lack
Received: 27 October 2015; Accepted: 15 December 2015
Foundation items: This study was supported by the Ministry of Science
and Technology of China (2014FY210200, 2011FY120200), the
program of Chinese Academy of Sciences (2015CASEABRI002), and
the Animal Branch of the Germplasm Bank of Wild Species of Chinese
Academy of Sciences (the Large Research Infrastructure Funding) to
JC; RMB’s work on the family Ceratobatrachidae has been supported
by the U. S. National Science Foundation (DEB 073199, 0334952,
0743491, 1418895).
#Authors contributed equally to this work
*Corresponding author, E-mail:
standing water-from small oceanic islands, to high-
elevation mossy montane forests (Brown & Alcala, 1982;
Brown et al., 2013; Günther, 2015). Currently, 91 species
are assigned to three genera: Platymantis Günther, 1858,
Cornufer Tschudi, 1838, and Alcalus Brown, Siler, Richards,
Diesmos, and Cannatella, 2015 (AmphibiaWeb, 2015;
Brown et al., 2015; Frost, 2015). These species are
distributed broadly from the South-West Pacific to the
island archipelagos of South Asia, with primary centers of
species diversity in Philippines and Solomon-Bismarck
Archipelago (Brown, 2009; Brown et al., 2013, 2015).
Four species, formerly referred to Southeast Asian frogs
Ingerana (Dubois, 1987), were recently assigned to the family
Ceratobatrachidae based on molecular data (Brown et al.,
2015). The four taxa (I. baluensis, I. mariae, I. rajae, I. sariba)
comprise a monophyletic group now shown to be the sister
group of Ceratobatrachinae (genera Platymantis and
Cornufer). However, “true” Ingerana (based on the
phylogenetic position of the type species, Ingerana
tenasserimensis [Sclater, 1892]) has been shown in multiple
studies to be more closely related to Dicroglossidae (Bossyut
et al., 2006; Wiens et al., 2009). Thus, these four species
were just recently assigned to the new genus Alcalus in the
family Ceratobatrachidae (Brown et al., 2015).
The species in genus Ingerana are small, plump frogs with
flattened and expanded toe and finger tips (Dubois, 1987).
Thirteen species previously have been referred to this genus
on the basis of morphological characters and life history traits.
However, recently its members have been placed in different
genera, and even different families, based on phylogenetic
analysis of molecular data analysis, i.e., A. baluensis, A.
mariae, A. rajae and I. tenasserimensis (Bossuyt et al., 2006;
Frost et al., 2006; Wiens et al., 2009; Brown et al., 2015).
The placement of other Ingerana species was controversial,
and some species were tentatively placed in different genera,
in the absence of accompanying molecular data. For example,
Limnonectes xizangensis was variably assigned to the genera
Cornufer (Hu, 1977), Ingerana (subgenus Liurana) (Dubois,
1987), Platymantis (Fei et al., 1990), Micrixalus (Zhao & Adler,
1993), and finally to Limnonectes (subgenus Taylorana)
(Borah et al., 2013; Frost, 2015). The complex and convoluted
taxonomic placement of several of these species has based
on morphological or reproductive characters. Because the
few key diagnostic characters emphasized by previous
worker are variable, and subject to individual interpretation
they may have mislead previous attempts to determine
systematic affinities of these poorly known frog species.
Here we report the results of a systematic study of five
species variably referred to Limnonectes or Ingerana,
including Lim. xizangensis, Lim. medogensis, Lim. alpine, I.
borealis and I. tasanae. We redistribute them among two
families, according to their phylogenetic affinities, as Liurana
xizangensis, Liu. medogensis, Liu. alpine, and Alcalus
tasanae (family Ceratobatrachidae) and Ingerana borealis
(family Dicroglossidae). These discoveries greatly extend the
westernmost geographic distribution of the primarily
Australasian archipelago family Ceratobatrachidae into
Indochina and China and assign early mainland branching
events in this family to lineages now exclusively represented
by species with restricted ranges in the high-elevation
Himalayan mountains of Tibet.
Four species, Limnonectes xizangensis, Lim. medogensis,
Lim. alpine and Ingerana borealis, were sampled from Medog
(=Motuo), Tibet (=Xizang), PR China (locality 1 in Figure 1,
Table 1). Following the collection of liver tissue samples
(preserved in 95% ethanol), the voucher specimens were
fixed with 10% formalin and then stored in 70% ethanol.
Collection of specimens followed animal-use protocols
approved by the Kunming Institute of Zoology Animal Use and
Ethics Committee. Two more species, I. tasanae and
Occidozyga martensii distributed in Myanmar and Thailand,
were also included. We borrowed their tissue samples from
the collections of the California Academy of Sciences (CAS),
Thailand National History Museum (THNHM), and Field
Museum of Natural History (FMNH) (Figure 1, Table 1).
DNA extraction and sequencing
Total DNA was extracted using standard phenol-chloroform
protocols (Sambrook et al., 1989). One fragment of
mitochondrial DNA of 12S rRNA, tRNA-Val, and 16S rRNA
(12S-16S) was sequenced for all samples using primers
L2519 and 16Sbr (Table 2). Three partial nuclear DNA
sequences of recombination activating gene 1 (Rag1),
tyrosinase (Tyr ) and rhodopsin (Rhod) were sequenced for all
samples using primers included in Table 2. Amplifications
were conducted in a 25 uL volume reaction, involved initial
denaturing step at 94 °C for 5 min; then 35 cycles of
denaturing at 94 °C for 45 sec, annealing at 50 °C or 55 °C for
45 sec, and extending at 72 °C for 45 sec; and a nal
extending step of 72 °C for 7 min. The products were purified
with Gel Extraction Mini Kit (Watson BioTechnologies,
Shanghai, China), then sequenced on an ABI 3730×l DNA
automated sequencer (Applied Biosystems, UK).
For species not sampled by us, the sequences of 12S-16S,
Rag1, Tyr and Rhod were downloaded from GenBank (Table
1). All data were aligned with MUSCLE (Edgar, 2004) and
edited using MEGA 5.05 (Tamura et al., 2011).
Phylogenetic analysis
We estimated phylogenetic relationships using Bayesian
inference (BI) and maximum parimony (MP) using MrBayes
3.1.2 (Ronquist & Huelsenbeck, 2003) and PAUP* 4.0b10a
(Swofford, 2003). Mitochondrial and nuclear sequence
data were analyzed separately. Then a phylogenetic tree
was conducted using the concatenated sequence of all
genes. For BI analysis, the best-fitting nucleotide
substitution models were selected for 12S-16S and each
codon of Rag1, Tyr and Rhod using the Akaike information
criterion in MRMODELTEST v2.3 (Nylander, 2004). The BI
analysis used four Markov chains, with default heating
Zoological Research 37(1): 7-14, 2016 9
Figure 1 Map of sampling sites
Numbers correspond to localities in Table 1.
values, and run for 5 million generations while sampling trees every
1 000 generations. The first 25% sampled trees were discarded as
burn-in, and log-likelihood scores were examined using Tracer v
1.4 (Rambaut & Drummond 2007) to assure convergence
(effective sample size [ESS] values >200). For the MP analysis, full
heuristic tree searches were used, with 1 000 replications, random
addition of sequences and tree-bisection-reconnection (TBR)
branch swapping. Non-parametric bootstrap support was estimated
using 1 000 replicates of full heuristic searches.
Sequence information
Sequencing generated a total of 1 371 base pairs (bp) of 12S-
16S data for Limnonectes alpine and Ingereana tasanae.
Additionally, a part of fragment of 12S-16S was successfully
sequenced for Occidozyga martensii, Lim. xizangensis and I.
borealis. We were unable to collect 12S-16S for Lim.
medogensis. For nuclear sequences of Rag1, 1 100 bp was
successfully sequenced for all samples except for Lim.
medogensis, but we only included 553 bp in subsequent
analyses so as to match Rag1 data sequences available on
GenBank. Sequences of 553 bp Ty r and 316 bp Rhod were
successfully sequenced for all samples. All new generated
sequences were submitted to GenBank (Accession numbers
KU243083-KU243120, Table 1).
Tab le 2 Primers information used for four DNA fragments sequencing
Locus Primer name Sequence (5'-3') Tm Citation
12S-16S L2519 AAACTGGGATTAGATACCCCACTAT 55 Richards & Moore, 1996
16Sbr CCGGTYTGAACTCAGATCAYGT Palumbi et al., 1991
Tyr TYR 1 G TGCTGGGCRTCTCTCCARTCCCA 50 Bossuyt & Milinkovitch, 2000
Phylogenetic relationships
The best-fitting model were TVM+I+G for mitochondrial 12S-
16S, K80+I, TIMef+I and TIMef+I for three codon positions
of Rag1, TVM+I+G, K81+I and GTR+G for three codon
positions of Tyr, SYM+G, TVM+I+G and TIM+G for three
codon positions of Rhod. The phylogenetic analyses based
on nuclear DNA and mtDNA showed similar topologies.
Most recognized families formed monophyletic groups;
however, the monophyly of Dicroglossidae was not
recovered using mtDNA, but highly supported by nuclear
DNA. This possibly is due to the inability of mtDNA
sequence to resolve phylogenetic relationship at deeper
levels (i.e., Kingston et al., 2009), or sparse taxon
sampling in our analysis. The five focal species were
yielded the same topology in both phylogenetic analyses,
so the difference between mtDNA and nuclear DNA
topologies do not affect our taxonomy. The Bayesian tree
resulting from based on concatenated sequence of all
genes is shown in Figure 2. Limnonectes xizangensis, Lim.
medogensis, Lim. alpine and Ingerana tasanae clustered
with species of family Ceratobatrachidae. Three primary
lineages were identified in this family, corresponding to two
Zoological Research 37(1): 7-14, 2016 11
known subfamilies Alcalinae (Clade A) and
Ceratobatrachinae (Calde B), and a new lineage (Clade C),
unsampled in previous phylogenetic estimates (Brown et
al., 2015). Samples of Ingerana tasanae from Thailand and
Myanmar grouped together, and this clade formed a
strongly supported group with Alcalus baluensis and A.
mariae (Clade A). Limnonectes xizangensis, Lim.
medogensis and Lim. alpine formed a monophyletic group
(Clade C), which is strongly supported as related to the
family Ceratobatrachidae. Finally, Ingerana borealis
samples clustered with species in the subfamily
Occidozyginae (Dicroglossidae). This species formed a
clade with I. tenasserimensis (type species of Ingerana),
as the sister group to Occidozyga.
Figure 2 Bayesian inference tree based on concatenated analysis of all genes
Nodal support values are Bayesian posterior probabilities (only 90 are shown) and bootstrap proportions from maximum parsimony analysis (only 70 are
shown). Newly sequenced samples are emphasized with bold text.
Taxonomy of species of Limnonectes and Ingerana, and a
record of a new family for China, Myanmar and Thailand
The three poorly understood species, formerly referred to
Limnonectes and Ingerana from the largely unexplored area
of Himalayan Tibet (Lim. xizangensis, Lim. medogensis and
Lim. alpine), have had unstable taxonomic histories (Frost,
2015) and, until now, unclear systematic affinities. Dubois
(1987) established the genus Ingerana, in which there are two
subgenera Ingerana (Ingerana) and Ingerana (Liurana).
Ingerana xizangensis (formerly Cornufer xizangensis, Hu,
1977) was included in subgenus Ingerana (Liurana) by Dubois
(1987). Fei et al. (1997) identified significant morphological
differences between these two subgenera, including the
presence of lingual papilla on the tongue, the absence of
terminal discs on fingers and toes, and the absence of
circumarginal grooves on fingers and toes in Ingerana
(Liurana), (Figures 3-4). Thus, Liurana was elevated to the
level of genus to include the species Liu. xizangensis, Liu.
Figure 3 Photos of Liurana alpine and Liurana xizangensis in life
(Photos by Kai WANG)
A-D: dorsolateral view; ventral view; ventral view of hand; and ventral
view of foot of Liu. Alpine, respectively; E-H: dorsolateral view; ventral
view; ventral view of hand, and ventral view of foot of Liu. Xizangensis,
Figure 4 Photos of Liurana medogensis (Photos by Kai WANG)
A-C: dorsal view, dorsolateral view, and ventral view (C) in life,
respectively; D: ventral view of hand (above) and foot (below) in
drawing (from Fei et al., 2009).
medogensis, Liu. alpine and Liu. liui (Fei et al., 1997, 2009,
2012; Huang & Ye, 1997). Fei et al. (2009) considered Liurana
to be part of the family Occidozygidae. Subsequently, Fei et al.
(2010) established a new subfamily Liuraninae in the family
Occidozygidae based on morphological data. Frost et al.
(2006) considered Liurana to be a junior synonym of Ingerana
on the basis of the original description and overlapping
character states. Based on available morphological
characters, Borah et al. (2013) placed Liurana in synonymy
with Taylorana (now considered to be a subgenus of
Limnonectes, [Frost, 2015]). Thus, for the last several years,
these species have resided in Limnonectes (Frost, 2015)
pending appropriate phylogenetic analysis to determine of
their systematic affinities.
Based on analysis of multilocus DNA sequence data, Liu.
xizangensis, Liu. medogensis and Liu. alpine are herein
assigned to the family Ceratobatrachidae and represent the
first record of this family in China. In our analysis these
species formed strongly supported monophyletic group,
clustering with members of the Ceratobatrachidae (sensu Brown
et al., 2015). In contrast, species of genus Ingerana (I.
tenasserimensis and I. borealis) and Limnonectes (Lim. limborgi,
Lim. sp.) formed the strongly supported clades in subfamily
Occidozyginae, as showed in previous studies (i.e. Bossuyt et
al., 2006; Wiens et al., 2009; Pyron & Wiens, 2011). Based on
our observations of morphological variation, these three
species likewise are distinguished from the species of
Ingerana and Limnonectes by the: (1) absence of interdigital
webbing of the feet, (2) absence of terminal discs on fingers
and toes, (3) absence of circumarginal grooves on the fingers
and toes, and (4) absence of tarsal folds. All available
evidence supports the recognition of Liu. xizangensis, Liu.
medogensis and Liu. alpine as single taxon, for which Liurana is
the available generic name with priority. We assign Liurana to the
family Ceratobatrachidae. Within Ceratobatrachidae, three
lineages are recognized: Clade A and Clade B (Figure 2)
correspond to previously recognized subfamilies Alcalinae
and Ceratobatrachinae, respectively. The genus Liurana
(Clade C) is equivalent in species content to the subfamily
Liuraninae Fei, Ye and Jiang, 2010, now transfered to the
family Ceratobatrachidae.
Ingerana tasanae is distributed in western and central
peninsular Thailand, and its range possibly extends into
adjacent Tenaserim and Myanmar (Stuart et al., 2008). Our
molecular data clearly place all Ingerana tasanae samples in
the same clade as other members of the genus Alcalus
(Ceratobatrachidae). This constitutes a new record of family
Ceratobatrachidae for Myanmar and Thailand. Our northern
Myanmar samples of A. tasanae is highly divergent from
individuals from southern Myanmar and southern Thailand. It
remains possible that additional taxonomic diversity will be
revealed in the genus Alcalus with accumulation of data and
field studies of these populations.
Previous studies placed I. borealis in the genus
Phrynoglossus (Fei et al., 2009, 2010, 2012), Occidozyga
(Ahmed et al., 2009; Mathew & Sen, 2010), and Ingerana
(Sailo et al., 2009). Based on our molecular data, I. borealis
falls into a strongly supported clade with I. tenasserimensis,
the type species of Ingerana. Thus, our molecular data
support its systematic position within genus Ingerana based
on morphological comparison by Sailo et al. (2009).
New insight from the phylogeny and distribution of
Brown et al. (2015) developed a stable taxonomy for the
family Ceratobatrachidae. Two subfamilies were identified:
Ceratobatrachinae and Alcalinae. Ceratobatrachinae includes
Zoological Research 37(1): 7-14, 2016 13
two large monophyletic radiations, Cornufer and Platymantis.
The species belonging to the subfamily Ceratobatrachinae
have a broad distribution in the south-west Pacific, including
Philippines, Borneo, New Guinea, Admiralty and Bismarck
archipelagos, Solomon Islands, and Fiji. Alcalinae includes
only four species of Alcalus, which are distributed only on the
island archipelagos of Southeast Asia (Sundaland).
Our research identified other four species which we now
transfer to Ceratobatrachidae; this greatly increases the
distribution of the family to the mainland of Southeast Asia
and the Himalayan region (Figure 1). Given our experience
with the unexpected phylogenetic affinities of the species
studied here, we would not be surprised if additional
phenotypically similar taxa are found to belong in
Ceratobatrachidae in the near future. Of particular note,
Ingerana charlesdarwini (Das, 1998), distributed in the
Andaman Islands (India), could very well be the sister lineage
to the remaining lineages in this large and spectacularly
diverse anuran family.
The surprising discovery that the clade Ceratobatrachidae
is broadly distributed from the Himalayas, mainland and
peninsular southeastern Asia, to the southwest Pacific, will
help us to understand the biogeography in this region. The
sister-group relationship of Ceratobatrachinae and Alcalinae,
although not unequivocally supported mirrors the geographic
distribution of these clades. This relationship between
mainland and archipelago species is also seen in the
divergence between the mainland species Alcalus tasanae
and the archipelago species A. mariae and A. baluensis.
Additional, unexpected patterns between mainland and island
taxa may be found with more complete taxon sampling, which
emphasizes the need for additional fieldwork in mainland
southeastern Asia.
We would like to thank Dr. Pi-Peng LI (Shenyang Normal University), Mr.
Tao LIANG, Mr. Duan YOU, and Mr. Ya-Di HUANG, who helped with
fieldwork in Tibet, Prof. Yue-Zhao WANG (CIB), Prof. Yue-Ying CHEN (CIB)
and Prof. Sheng-Quan LI (CIB) for kindly letting us examine specimens
under their care. We also thank the California Academy of Sciences (CAS),
Thailand National History Museum (THNHM), and Field Museum of Natural
History (FMNH) for loan of tissue samples.
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... Within our EP limits, four species have been discovered in southeastern Tibet: Liurana xizangensis (Hu, 1977), Liurana medogensis Fei, Ye & Huang, 1997, Liurana alpina Huang & Ye, 1997and Liurana vallecula Jiang, Wang, Wang, Li & Che, 2019. Mitochondrial and nuclear phylogenetic analyses support an independent origin for all of them (Yan et al., 2016;Jiang et al., 2019b;Xu et al., 2021). The strong divergence at barcoding The only species of this genus, Chrysopaa sternosignata (Murray, 1885), has never been the focus of molecular studies and its phylogeography is, therefore, entirely unknown. ...
... While recent phylogenies seem to agree on the former (e.g. Bossuyt et al., 2006;Wiens et al., 2009;Brown et al., 2015;Yan et al., 2016), the diversification and systematics of this genus have not been thoroughly studied, and it remains unclear which species actually belong to it. Two taxa assigned to Ingerana occur in the EP: Ingerana borealis (Annandale, 1912) and Ingerana reticulata (Zhao & Li, 1984). ...
... Two taxa assigned to Ingerana occur in the EP: Ingerana borealis (Annandale, 1912) and Ingerana reticulata (Zhao & Li, 1984). Based on Chinese samples, Yan et al. (2016) confirmed that I. borealis forms a monophyletic clade (branching among Dicroglossids) with its Southeast Asian relative Ingerana tenasserimensis (Sclater, 1892), with deep genetic differentiation that clearly supports speciation between these externally resembling taxa (~15% at 12S/16S sequences). In contrast, the placement of Ingerana reticulata has never been assessed, and the species is listed among Ceratobatrachids in many publications, as Liurana reticulata (Fei et al., 2012). ...
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Biodiversity analyses can greatly benefit from coherent species delimitation schemes and up-to-date distribution data. In this article, we have made the daring attempt to delimit and map described and undescribed lineages of anuran amphibians in the Eastern Palaearctic (EP) region in its broad sense. Through a literature review, we have evaluated the species status considering reproductive isolation and genetic divergence, combined with an extensive occurrence dataset (nearly 85k localities). Altogether 274 native species from 46 genera and ten families were retrieved, plus eight additional species introduced from other realms. Independent hotspots of species richness were concentrated in southern Tibet (Medog County), the circum-Sichuan Basin region, Taiwan, the Korean Peninsula and the main Japanese islands. Phylogeographic breaks responsible for recent in situ speciation events were shared around the Sichuan Mountains, across Honshu and between the Ryukyu Island groups, but not across shallow water bodies like the Yellow Sea and the Taiwan Strait. Anuran compositions suggested to restrict the zoogeographical limits of the EP to East Asia. In a rapidly evolving field, our study provides a checkpoint to appreciate patterns of species diversity in the EP under a single, spatially explicit, species delimitation framework that integrates phylogeographic data in taxonomic research.
... The following literatures were consulted for comparative data of all the known congeners of the genus: Hu (1977); Huang and Ye (1997); Fei et al., (1997); Borah et al., (2013), Fei et al., (2012), Yan et al., (2016), Roy et al., (2018) and Jiang et al., 2019. ...
... While reporting L. medogensis from India, Borah et al., (2013) mentioned the diagnostic characters of Liurana genus (then sub-genus of Ingerana) from Ingerana by the presences of grooves, enlarged toe pads, extension of webbings and presence of lingual papilla. However, contradicting Borah et al., (2013), Yan et al., (2016) and Jiang et al., (2019) reported about the absence of grooves on the finger and toe tips and absence of interdigital webbings. The genus Liurana was erected by Dubois (1987) where he had highlighted the following characteristics: (1) fingertips and toe-tips not dilated, without a clearly differentiated circummarginal groove, (2) webbing absent or reduced and (3) lingual papilla present. ...
... The genus Liurana was erected by Dubois (1987) where he had highlighted the following characteristics: (1) fingertips and toe-tips not dilated, without a clearly differentiated circummarginal groove, (2) webbing absent or reduced and (3) lingual papilla present. Given that Dubois was one of the co-authors of Borah et al., (2013), we should not out-rightly agree to the conflicting generic characters mentioned in Yan et al., (2016) and Jiang et al., (2019). In the light of our study on the specimens of Liurana collected from Talley Valley, Aruanchal Pradesh, we have come across that our specimens do have a semblance of groove but without clearly differentiated grooves, agreeing with Dubois (1987). ...
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The moss and leaf litter dwelling small frog group under genus Liurana are represented by only 4 species, all described from China; of which L. medogensis is known to occur in India. In recent years, surveys into Talley Valley Wildlife Sanctuary of Aruanchal Pradesh have revealed the occurrence of L. medogensis along with 3 hitherto unknown species of this genus from the protected area. Herein, we are describing 3 new species of Liurana and have provided a taxonomic key to the species of the genus.
... Many of these candidate species occur in the Himalayas, a region that is regarded as a global biodiversity hotspot, and harbors a rich diversity of highly endemic biota (Myers et al., 2000;Nayar, 1996;Pandit et al., 2000Pandit et al., , 2014. In recent years, a series of new genera, species, and new occurrence records of amphibian families have been reported from the region (Jiang et al., , 2016a(Jiang et al., ,b,c, 2019Khatiwada et al., 2015;Yan et al., 2016). Our results are concordant with this trend in discovering undescribed "hidden" biodiversity in the Himalayas. ...
... Based on the diagnostic characters of the A. monticola group, such as smooth skin, lateral side of head dark with a light-colored upper lip stripe extending to the shoulder, and distinct dorsolateral fold (Stuart et al., 2010;Jiang et al., 2016a), A. chayuensis morphologically falls within this species group (Sun et al., 2013). Conversely, previous analyses of mitochondrial sequence data suggested paraphyly of the A. monticola group due to A. chayuensis not clustering with other members of this group (Jiang et al., 2016;Lyu et al., 2019). Using AHE data, we recovered the A. monticola group to be monophyletic and to contain A. chayuensis (Table S1). ...
The genus Amolops (“torrent frogs”) is one of the most species-rich genera in Ranidae, with 59 recognized species. This genus currently includes six species groups diagnosed mainly by morphology. Several recent molecular studies indicated that the classification of species groups within Amolops remains controversial, and key nodes in the phylogeny have been inadequately resolved. In addition, the diversity of Amolops remains poorly understood, especially for those from incompletely sampled regions. Herein, we investigate species-level diversity within the genus Amolops throughout southern China and Southeast Asia, and infer evolutionary relationships among the species using mtDNA data (16S, COI, and ND2). Molecular analyses indicate nine unnamed species, mostly distributed in the Himalayas. We then utilized anchored hybrid enrichment to generate a dataset representing the major mitochondrial lineages to resolve phylogenetic relationships, biogeography, and pattern of species diversification. Our resulting phylogeny strongly supports the monophyly of four previously identified species groups (the A. ricketti, A. daiyunensis, A. hainanensis, and A. monticola groups), but paraphyly for the A. mantzorum and A. marmoratus groups, as previously defined. We erect one new species group, the A. viridimaculatus group, and recognize Dubois (1992) ‘subgenus’ Amo as the A. larutensis species group. Biogeographic analysis suggests that Amolops originated on the Indo-Burma/Thai-Malay Peninsula at the Eocene/Oligocene boundary, and dispersed outward, exemplifying a common pattern observed for the origin of Asian biodiversity. The early divergence within Amolops coincides with the Himalayas uplift and the lateral extrusion of Indochina at the Oligocene/Miocene boundary. Our results show that paleoclimatic and geomorphological events have profoundly influenced the patterns of lineage diversification within Amolops.
... Amphibians are most vulnerable vertebrate group (Daszak et al., 2003;Stuart et al., 2004) and in contrary, the rate of new and cryptic species discoveries indicates to an underestimation of species richness (Vieites et al., 2009;Yan et al., 2016). ...
... Traditional morphology-based taxonomic methods for species identification requires ample of time which may lead to the extinction of a species before its discovery (Murphy et al., 2011;Spinks et al., 2012). DNA barcoding has eased the demarcation and discovery of amphibians (Vieites et al., 2009;Yan et al., 2016) and could be a principal tool to help efficiently identify species and set their conservation priorities (Murphy et al., 2013;Chambers and Hebert 2016). In Bangladesh, genetic analyses focused mainly on the families Dicroglossidae (Alam et al., 2008;Islam et al., 2008a, b;Howlader et al., 2015aHowlader et al., , 2016 and Microhylidae (Hasan et al., 2012a and2014a;Howlader et al., 2015b), others remained untouched. ...
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Abstract The present review described the research trends and conservation issues on amphibians of Bangladesh based on recent published research works. We found twenty amphibian species (11 dicroglossids, 5 microhylids, 2 ranids, 1 rhacophorid and 1 bufonid) from Bangladesh have morphometric data. These researches involved taxonomy, reproduction biology, cryptic diversity and other natural history gives superficial scenario in amphibian conservation. Most research has been conducted in southeastern and northeastern Bangladesh describe ecological implications and threat due to anthropogenic activities and habitats destructions. Morphological and molecular investigations have resulted in the description of six new species i.e., Minervarya asmati, Microhyla mukhlesuri, Microhyla mymensighensis, Minervarya dhaka, Euphlyctis kalasgramensis, Microhyla nilphamariensis recently. Here genus Zakerana was erected for several South Asian species that previously assigned to Fejervarya, but later into the Minervarya. Bio-acoustic analyses are largely wanting but some cross-breeding experiments exist for Hoplobatrachus spp. A large number of amphibian species have been recognized by some morphometric assessments. Amphibian deformity has been reported from Bangladesh, and this serves as a warning and new challenge for survival in the near future. Relative to other countries, Bangladesh has received little attention on amphibians. Accordingly, many important species may be lost before their discovery. In this paper we proposed the diverse amphibian fauna that occupies habitats ranging from the northern and eastern hills to mangrove Sundarbans forests in the southwest and to the southern Bay of Bengal need proper survey and conservation.
... The algorithm requires a trusted species tree. We used the consensus family tree of amphibians provided by the experts of the AmphibiaWeb, based on a recent literature (Zhang and Wake, 2009;Blackburn and Wake, 2011;Vieites et al., 2011;Kamei et al., 2012;San Mauro et al., 2014;Brown et al., 2015;Peloso et al., 2016;Yan et al., 2016;Feng et al., 2017;Heinicke et al., 2018;Jetz and Pyron, 2018;Streicher et al., 2018;Tu et al., 2018;Yuan et al., 2019; "AmphibiaWeb," 2020), to reconstruct the phylogeny of the species used in our study. First, we reconstructed the species tree using the data provided by the ...
The globin gene repertoire of gnathostome vertebrates is dictated by differential retention and loss of nine paralogous genes: androglobin, neuroglobin, globin X, cytoglobin, globin Y, myoglobin, globin E, and the α- and β-globins. We report the globin gene repertoire of three orders of modern amphibians: Anura, Caudata, and Gymnophiona. Combining phylogenetic and conserved synteny analysis, we show that myoglobin and globin E were lost only in the Batrachia clade, but retained in Gymnophiona. The major amphibian groups also retained different paralogous copies of globin X. None of the amphibian presented αD-globin gene. Nevertheless, two clades of β-globins are present in all amphibians, indicating that the amphibian ancestor possessed two paralogous proto β-globins. We also show that orthologs of the gene coding for the monomeric hemoglobin found in the heart of Rana catesbeiana are present in Neobatrachia and Pelobatoidea species we analyzed. We suggest that these genes might perform myoglobin- and globin E-related functions. We conclude that the repertoire of globin genes in amphibians is dictated by both retention and loss of the paralogous genes cited above and the rise of a new globin gene through co-option of an α-globin, possibly facilitated by a prior event of transposition.
... Hence, its sister relationship with a lineage from Cambodia is seemingly incoherent from a biogeographic standpoint (just as the inclusion of "Amnirana" nicobariensis makes little biogeographic sense, when included in the otherwise African genus Amnirana). However, such disjunct biogeographic patterns have also been reported in other groups of anurans such as the occurrence of the Australasian frog family Ceratobatrachidae in China, Myanmar, and Thailand (Yan et al., 2016); and the Australian-New Guinean subfamily Asterophryinae in Malaysia (Kurabayashi et al., 2011). It is possible that these seemingly anomalous distribution patterns are a result of extinctions or missing/unsampled lineages from the intervening regions, but amphibian oceanic dispersal is becoming more readily accepted as well (da Fonte et al., 2019). ...
Using FrogCap, a recently-developed sequence-capture protocol, we obtained more than 12,000 highly informative exons, introns, and Ultraconserved elements (UCEs), which we used to illustrate variation in evolutionary histories of these classes of markers, and to resolve long-standing systematic problems in Southeast Asian Golden-backed frogs of the genus-complex Hylarana. We also performed a comprehensive suite of analyses to assess the relative performance of different genetic markers, data filtering strategies, tree inference methods, and different measures of branch support. To reduce gene tree estimation errors, we filtered the data using different thresholds of taxon completeness (missing data) and parsimony informative sites (PIS). We then estimated species trees using concatenated datasets and Maximum Likelihood (IQ-TREE) in addition to summary (ASTRAL-III), distance-based (ASTRID), and site-based (SVDQuartets) multispecies coalescent methods. Topological congruence and branch support were examined using traditional bootstrap, local posterior probabilities, gene concordance factors, quartet frequencies, and quartet scores. Our results showed that separate analyses did not yield a single concordant topology. Instead, introns, exons, and UCEs clearly possessed individual categories of phylogenetic signal, resulting in conflicting, yet strongly-supported phylogenetic estimates. However, a combined analysis comprising the most informative introns, exons, and UCEs converged on a similar topology across all analyses, with the exception of SVDQuartets. Bootstrap values were consistently high despite high levels of incongruence and high proportions of gene trees supporting conflicting topologies. Although low bootstrap values did indicate low heuristic support, high bootstrap support did not necessarily reflect congruence or support for the correct topology. This study reiterates findings of some previous studies, which demonstrated that traditional bootstrap values can produce positively misleading measures of support in large phylogenomic datasets. We also showed a remarkably strong positive relationship between branch length and topological congruence across all datasets, implying that very short internodes remain a challenge to resolve, even with orders of magnitude more data than ever before. Overall, our results demonstrate that more data from unfiltered or combined datasets produced demonstrably superior results. Although data filtering reduced gene tree incongruence, decreased amounts of data also biased phylogenetic estimation. A point of diminishing returns was evident, at which higher congruence (from more stringent filtering) at the expense of amount of data led to topological error as assessed by comparison to more complete datasets across different genomic markers. Additionally, we showed that applying a parameter-rich model to a partitioned analysis of concatenated data produces better results compared to unpartitioned, or even partitioned analysis using model selection. Despite some lingering uncertainties, a combined analysis of our genomic data and taxa supplemented from GenBank (on the basis of a few gene regions) sequences revealed highly supported novel systematic arrangements. Based on these new findings, we transfer Amnirana nicobariensis into the genus Indosylvirana; and I. milleti and Hylarana celebensis to the genus Papurana. We also provisionally place H. attigua in the genus Papurana pending verification from positively identified (voucher substantiated) samples.
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Thailand is considered a global biodiversity hotspot that is known to harbour a striking diversity of endemic species. However, several research studies have determined that the level of amphibian diversity in the country has been significantly underestimated. The megophryid genus Leptobrachella Smith, 1925 is currently known to include 89 species that are primarily distributed throughout southern China and Southeast Asia; however, only seven species have been found in Thailand. Based on an integrative approach encompassing genetic and morphological analyses, we have concluded that the population identified from Chiang Rai Province of Thailand is conspecific with Leptobrachella ventripunctata (Fei, Ye, and Li, 1990). Importantly, this is the first confirmation record of this species, based on molecular and morphological evidence in Thailand. The discovery of this species reaffirms that the diversity within the genus has been underestimated with many species yet to be discovered. In addition, the findings of our study further highlight the lack of existing knowledge on amphibian taxonomy and an underestimation of the biodiversity that exists along these national border areas.
The eyes of frogs and toads (Anura) are among their most fascinating features. Although several pupil shapes have been described, the diversity, evolution, and functional role of the pupil in anurans have received little attention. Studying photographs of more than 3200 species, we surveyed pupil diversity, described their morphological variation, tested correlation with adult habits and diel activity, and discussed major evolutionary patterns considering iris anatomy and visual ecology. Our results indicated that the pupil in anurans is a highly plastic structure, with seven main pupil shapes that evolved at least 116 times during the history of the group. We found no significant correlation between pupil shape, adult habits, and diel activity, with the exception of the circular pupil and aquatic habits. The vertical pupil arose at least in the most recent common ancestor of batrachians, and this morphology is present in most early-diverging anuran clades. Subsequently, a horizontal pupil, a very uncommon shape in vertebrates, evolved in most neobatrachian frogs. This shape evolved into most other known pupil shapes, but it persisted in a large number of species with diverse life histories, habits and diel activity patterns, demonstrating a remarkable functional and ecological versatility.
Aim The diversity of brood size across animal species exceeds the diversity of most other life‐history traits. In some environments, reproductive success increases with brood size, whereas in others it increases with smaller broods. The dominant hypothesis explaining such diversity predicts that selection on brood size varies along climatic gradients, creating latitudinal fecundity patterns. Another hypothesis predicts that diversity in fecundity arises among species adapted to different microhabitats within assemblages. A more recent hypothesis concerned with the consequences of these evolutionary processes in the era of anthropogenic environmental change predicts that low‐fecundity species might fail to recover from demographic collapses caused by rapid environmental alterations, making them more susceptible to extinctions. These hypotheses have been addressed predominantly in endotherms and only rarely in other taxa. Here, we address all three hypotheses in amphibians globally. Location Global. Time period Present. Major taxa studied Class Amphibia. Methods Using a dataset spanning 2,045 species from all three amphibian orders, we adopt multiple phylogenetic approaches to investigate the association between brood size and climatic, ecological and phenotypic predictors, and according to species conservation status. Results Brood size increases with latitude. This tendency is much stronger in frogs, where temperature seasonality is the dominant driver, whereas salamander fecundity increases towards regions with more constant rainfall. These relationships vary across continents but confirm seasonality as the key driver of fecundity. Ecologically, nesting sites predict brood size in frogs, but not in salamanders. Finally, we show that extinction risk increases consistently with decreasing fecundity across amphibians, whereas body size is a “by‐product” correlate of extinction, given its relationship with fecundity. Main conclusions Climatic seasonality and microhabitats are primary drivers of fecundity evolution. Our finding that low fecundity increases extinction risk reinforces the need to refocus extinction hypotheses based on a suggested role for body size.
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The critically endangered, insular endemic dicroglossid frog Ingerana charlesdarwini was described from three adult specimens from Mount Harriet National Park, South Andaman (India). The description of this species is here expanded based on fresh collections made from the Andaman archipelago in the Bay of Bengal. Morphometric analysis based on a larger sample size of fourteen specimens including the ones collected during this study revealed that this species is not sexually dimorphic or dichromatic as considered earlier, but is just highly colour polymorphic. Additional notes on its morphology and colouration are provided. Needs for further surveys in the Andaman Islands for documenting the distribution of this species are highlighted.
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A study on the distribution of Ingerana borealis was carried out in Mizoram. Based on morphological comparison with type species of the genera Ingerana, Occidozyga and Phrynoglossus and data on behaviour, Micrixalus borealis is allocated to the genus Ingerana Dubois, 1987. The study also reveals its occurrence up to 1000 m asl, previously unrecorded for this species. The species lives in lotic habitat and is well adapted not only to the slow-moving waters, but also to the fast flowing permanent streams in and near forests. The holophoront of Micrixalus borealis is redescribed and recently collected specimens from Mizoram allocated to this species are described.
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We describe a new-species of high elevation rainforest shrub frog (genus Platymantis) from the Nakanai Mountains of eastern New Britain (Bismarck Archipelago), Papua New Guinea. The distinctive new species possesses a moderate body size (29.5-32.2 mm in four males), widely expanded finger and toe disks, smooth to slightly granular dorsal skin, low but distinctly protuberant supraocular and tarsal tubercles, a conspicuous series of bright yellow flank areolations, a low but distinct intraocular sagittal crest, bronze-brown iris, and a unique advertisement call. We compare the new species with congeneric New Britain taxa and to other phenotypically similar species from the Solomon-Bismarck-Admiralty archipelagos. The new species is phenotypically most similar to P macrosceles Zweifel 1975, and has been collected at only one high elevation site (Tompoi Camp). The available data suggest that the new species, known from 1700 m, is elevationally segregated from P. macroscles (to date, only recorded from 800-900 m in the Nakanai Mountains). New Britain Island has emerged as a major center of endemic ceratobatrachid species diversity. Additional species are anticipated to result from ongoing field work, especially in the western portion of the island, which remains largely unexplored.
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This is the first ever regional colour guide on the amphibians and reptiles of Northeast India. Detailed illustration of 102 species that include 29 species of amphibians, 23 species of lizards, 29 species of snakes, 21 species (all found in Northeast India) of freshwater turtles and tortoises and the single crocodile species- Gharial. A photo gallery of other species (not described in details) of herpetofauna of the region is also included. This section covers 40 species of amphibians and 48 species of reptiles along with their scientific names. A checklist of the Herpetofauna so far known from Northeast India is also incorporated. Useful section of Snakebite and its Management with first aid tips.
Two new taxa of the ceratobatrachid genus Platymantis are described from western New Guinea on the basis of bioacoustic, morphological, ecological and biochemical studies. One of these, described as new species, is known only from in the Fakfak Mountains (Bomberai Peninsula) and the other, described as new subspecies, from Yapen Island. Their nearest relatives appear to be P. batantae Zweifel, 1969, and P. cryptotis Günther, 1999 respectively. Besides data on the new taxa, some morphological, bioacoustic and molecular data are given for P. papuensis Meyer, 1875 from the type locality Biak Island.
— We studied sequence variation in 16S rDNA in 204 individuals from 37 populations of the land snail Candidula unifasciata (Poiret 1801) across the core species range in France, Switzerland, and Germany. Phylogeographic, nested clade, and coalescence analyses were used to elucidate the species evolutionary history. The study revealed the presence of two major evolutionary lineages that evolved in separate refuges in southeast France as result of previous fragmentation during the Pleistocene. Applying a recent extension of the nested clade analysis (Templeton 2001), we inferred that range expansions along river valleys in independent corridors to the north led eventually to a secondary contact zone of the major clades around the Geneva Basin. There is evidence supporting the idea that the formation of the secondary contact zone and the colonization of Germany might be postglacial events. The phylogeographic history inferred for C. unifasciata differs from general biogeographic patterns of postglacial colonization previously identified for other taxa, and it might represent a common model for species with restricted dispersal.