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A New Species of Scutiger (Anura: Megophryidae) from the Gaoligongshan Mountain Range, China
Abstract
During recent surveys in Gaoligongshan Mountain Range, Yunnan Province of China, we collected specimens of Scutiger from montane stream area at an elevation of 3000 m. Subsequent study based on morphological, molecular and acoustic data reveals that the newly collected specimens represent an unknown taxon and is described herein: Scutiger tengchongensis sp. nov.. The new species can be distinguished from its congeners by a combination of the following characters: (1) relatively small size (adult males SVL 36.0–40.1 mm, n=8); (2) vomerine teeth absent; (3) dorsum with large prominent, conical-shaped and longitudinal tubercles; (4) large tubercles on dorsum covered by numerous tiny black spines in males in breeding condition; (5) a pair of pectoral glands and a pair of axillary glands present on the chest, and covered by dense tiny black spines in males in breeding condition; (6) pectoral gland about twice the size of axillary gland; (7) inner three fingers with black nuptial spines in males in breeding condition; (8) nuptial spines on first and second fingers larger than those on third finger; (9) black spines on the belly absent; (10) vocal sac absent; and (11) toes webbing rudimentary. The discovery of S. tengchongensis sp. nov. represents the southernmost record of the genus worldwide, and the new species is the smallest known member of the genus in body size.
... The Asian lazy toads Scutiger Theobald, 1868, is a group of amphibians inhabiting southwestern China, northern Myanmar, Nepal, northern India, and northern Pakistan at altitudes ranging from 1000 to 5300 m (Fei et al. 2009;Fei et al. 2012;Jiang et al. 2020;Frost 2023). Currently, there are 27 valid species in the genus, of which 23 species are distributed in China (Fei et al. 2009;Yang and Huang 2019;Jiang et al. 2020;AmphibiaChina 2023;Frost 2023;Zhou et al. 2023). The species in the genus can be classified into five major clades based Scutiger ghunsa Khatiwada, Shu, Subedi, Wang, Ohler, Cannatella, Xie & Jiang, 2019 was weakly supported in the Himalayan clade (Khatiwada et al. 2019) and S. occidentalis Dubois, 1978 has an uncertain phylogenetic position from western Himalaya. ...
... provides additional evidence to support the Paleo-Tibetan origin hypothesis by Hofmann et al. (2017). The unique geomorphic features of the Qinghai-Tibetan Plateau, including rapid uplift and mountainous barrier (Ding et al. 2020;Li et al. 2021;Xu et al. 2021;Miao et al. 2022), may have led to high cryptic species diversity of Scutiger in the region, multiple species were not discovered until about recent ten years Jiang et al. 2016;Yang and Huang 2019;Rao "2020Rao " ", 2022. These specific historical processes and genetic patterns have likely contributed to the diverse and intriguing species patterns observed in Scutiger (Chen et al. 2009;Che et al. 2020;Lin et al. 2023), necessitating further research. ...
... It was synonymized with S. glandulatus (Liu, 1950) by Liu and Hu (1961) for the reason that adults of the former in preservative are difficult to differentiate from those of the latter. However, the name S. glandulatus was adopted by some researchers probably because the pages describing S. brevipes are anterior to those pages describing S. glandulatus (Liu 1950;Ye et al. 1992;Fu et al. 1997;Jiang et al. 2012Jiang et al. , 2016Khatiwada et al. 2019;Yang and Huang 2019;Frost 2023). Fei et al. (2009) discussed that S. brevipes should remain as a junior synonym of S. glandulatus, because "When the precedence between names or nomenclatural acts cannot be objectively determined, the precedence is fixed by the action of the first author citing in a published work those names or acts and selecting from them..." according to article 24. ...
In this study, a new species named Scutiger luozhaensis sp. nov. is described from Luozha, southern Tibet, China. Genetic analysis based on two mitochondrial genes 16S rRNA and COI and the nuclear gene RAG1 revealed that the new species belongs to an independent phylogenetic clade close to S. gongshanensis and S. nyingchiensis and shares no RAG1 haplotype with other species. Morphological comparisons based on examined specimens and literatures indicated that it can be diagnosed from conge-ners by the following combination of characters: (1) body moderate, male body length 47.0-67.2 mm (n = 13), female body length 49.8-66.2 mm (n = 8); (2) maxillary teeth and budding absent; (3) numerous tiny dense nuptial spines present on dorsal surface of fingers I, II and inner surface of finger III of males in breeding condition with similar size; (4) spine patches on belly of males in breeding condition absent; (5) spines on inner surface of forearm and upper arm of males in breeding condition absent; (6) small patches of black spines present near armpit of males in breeding condition absent; (7) adult males without vocal sac; (8) some large warts and tubercles on dorsum gathered into short skin ridges with several spines present on top; (9) space between upper eyelids wider than upper eyelids; (10) spots or irregular cross bands on limbs absent; (11) webbing between toes rudimentary; (12) coloration of dorsal body olive brown to bronze.
... Some voucher specimens are temporarily kept at the herpetology collection of Kadoorie Farm and Botanic Garden, Hong Kong [KFBG] for further studies, and others are deposited at the Museum of Biology, Sun Yatsen University, Guangzhou [SYS]. For the identification of species, references used include Yang (1991), Zhao et al. (1998Zhao et al. ( , 1999, Fei et al. (2005Fei et al. ( , 2009Fei et al. ( , 2012, Zhao (2006), Yang & Rao (2008), Guo & Deng (2009), Fei & Ye (2016, Yang et al. (2016aYang et al. ( , 2016b, Yang & Huang (2019). ...
... In total, we documented the presence of 59 species of amphibians and reptiles in TC-GLGS, including one salamander, 30 batrachians, four lizards and 24 snakes; voucher specimens were collected for all but 12 species (see Appendix 1 for the list of voucher specimens). Leptobrachium tengchongense, Leptolalax tengchongensis, and Scutiger tengchongensis were revealed to be new species described by our team (Yang et al. 2016a,b;Yang & Huang 2019). A further 17 species have not been previously reported in TC-GLGS (Xue 1995;Yang & Rao 2008), and 10 genera were new records for the area. ...
... Subsequent molecular study revealed a sister relationship to Oreolalax jingdongensis in the 16S rRNA gene fragment, but Oreolalax sp. still presents a certain degree of genetic divergence (Jian-Huan Yang, Scutiger tengchongsnsis (Image 3b) This species was described by our team during a previous survey (Yang & Huang 2019). S. tengchongensis is very distinct from local anurans by dorsum having large conical-shaped and longitudinal tubercles covered by numerous tiny black spines; adult males have a pair of pectoral glands and a pair of axillary glands present on the chest, which are covered by dense tiny black spines; adult males have inner three fingers with black nuptial spines (Yang & Huang 2019). ...
... Some voucher specimens are temporarily kept at the herpetology collection of Kadoorie Farm and Botanic Garden, Hong Kong [KFBG] for further studies, and others are deposited at the Museum of Biology, Sun Yatsen University, Guangzhou [SYS]. For the identification of species, references used include Yang (1991), Zhao et al. (1998Zhao et al. ( , 1999, Fei et al. (2005Fei et al. ( , 2009Fei et al. ( , 2012, Zhao (2006), Yang & Rao (2008), Guo & Deng (2009), Fei & Ye (2016, Yang et al. (2016aYang et al. ( , 2016b, Yang & Huang (2019). ...
... In total, we documented the presence of 59 species of amphibians and reptiles in TC-GLGS, including one salamander, 30 batrachians, four lizards and 24 snakes; voucher specimens were collected for all but 12 species (see Appendix 1 for the list of voucher specimens). Leptobrachium tengchongense, Leptolalax tengchongensis, and Scutiger tengchongensis were revealed to be new species described by our team (Yang et al. 2016a,b;Yang & Huang 2019). A further 17 species have not been previously reported in TC-GLGS (Xue 1995;Yang & Rao 2008), and 10 genera were new records for the area. ...
... Subsequent molecular study revealed a sister relationship to Oreolalax jingdongensis in the 16S rRNA gene fragment, but Oreolalax sp. still presents a certain degree of genetic divergence (Jian-Huan Yang, Scutiger tengchongsnsis (Image 3b) This species was described by our team during a previous survey (Yang & Huang 2019). S. tengchongensis is very distinct from local anurans by dorsum having large conical-shaped and longitudinal tubercles covered by numerous tiny black spines; adult males have a pair of pectoral glands and a pair of axillary glands present on the chest, which are covered by dense tiny black spines; adult males have inner three fingers with black nuptial spines (Yang & Huang 2019). ...
We present the results from a series of herpetological surveys conducted in the Tengchong Section of Gaoligongshan National Nature Reserve, Yunnan Province, China between April 2014 and November 2018. A total of 59 species of amphibians and reptiles (one salamander, 30 batrachians, four lizards, and 24 snakes) were recorded during the surveys including three newly described amphibian species and 17 new records for Tengchong, 10 of which also represent new generic records for the area. Natural history notes of some little-known species are presented. Our survey results clearly demonstrate that the herpetofauna diversity of this mountain range is still underestimated and warrants further systematic study.
... Our findings in Tibetan Scutiger, together with evidence from Andean Telmatobius and Sierra Nevada R. sierrae (Amphib-iaWeb, 2021;Brunetti et al., 2017), suggest that underwater acoustic communication may occur in some other highelevation frogs. Anurans predominantly communicate through vocalizations (Vitt & Caldwell, 2014), and airborne calls have been documented for multiple frog species that live in locations with elevations higher than 3000 m (e.g., Blancas S anchez, 1959;Fei, 2020;Navas, 1996a;Yang & Huang, 2019). The anuran vocal sac and tympanic middle ear increase calling efficiency and facilitate aerial hearing but may not be essential for underwater acoustic communication (Rand & Dudley, 1993;Starnberger et al., 2014;Van Bergeijk, 1966;Womack et al., 2017;Zheng, 2019), although at least in Xenopus it appears that a middle ear is advantageous for hearing under water (e.g., Christensen-Dalsgaard & Elepfandt, 1995;Mason et al., 2009;Vedurmudi et al., 2018). ...
... Similarly, within Scutiger, S. glandulatus and Scutiger sp. belong to the same clade, with several species from the remaining clades having documented aerial calls (Che et al., 2020;Chen et al., 2009;Fei, 2020;Hofmann et al., 2017;Yang & Huang, 2019). In a third megophryid genus, Oreolalax, which is closely related to Scutiger and Leptobrachium (Feng et al., 2017;Fu et al., 2007;Pyron, 2014;Zheng et al., 2004), conspicuously loose skin has been determined to be a male nuptial trait in Oreolalax lichuanensis, reported as a male secondary sexual character in Oreolalax pingii, and can be observed in breeding males of Oreolalax popei (Fei et al., 2009(Fei et al., , 2010. ...
Underwater calls of frogs are poorly documented, probably because they are usually weak and difficult to detect out of water because the impedance contrast at the water–air interface limits sound transmission. The tympanic middle ear and vocal sacs, which may not be essential for underwater acoustic communication, are often reduced in high‐elevation anurans. In addition to the Andean Telmatobius and Sierra Nevada Rana sierrae, many other highland frog species may vocalize underwater rather than be mute as previously thought. We report evidence from the eastern Tibetan Plateau supporting this speculation. In two species of the megophryid genus Scutiger, breeding males emitted trill‐like calls in series under submerged rocks at elevations of approximately 3700 m a.s.l. Because the few high‐elevation anurans known to vocalize underwater are all highly aquatic, this strategy is possibly used because the signal receivers usually remain in water during the breeding season. The finding of underwater calling in Scutiger characterized by reduced middle ears was partly guided by co‐occurrence of loose skin and underwater vocalization in some frog species and constitutes another independent case of such co‐occurrence. We suggest that the presence/absence of loose skin folds should be routinely included in the morphological descriptions of anurans, because an increased surface/volume ratio facilitates effective cutaneous respiration that is required for metabolically costly underwater behaviors which are usually cryptic to human observers.
... Morphological comparisons with all known Scutiger congeners were based on data from the original and supplemental descriptions in the literature (Blyth, 1855;Günther, 1896;Bedriaga, 1898;Liu, 1950;Liu and Hu, 1960;Dubois, 1974Dubois, , 1978Dubois, , 1979Fei, 1977;Liu et al., 1978Liu et al., , 1979Yang et al., 1979;Fang, 1985;Huang, 1985;Fei andYe, 1986, 2016;Fei et al., 1995Fei et al., , 2009Fei et al., , 2012Delorme and Dubois, 2001;Ye and Fei, 2007;Jiang et al., 2012Jiang et al., , 2016Khatiwada et al., 2019;Yang and Huang, 2019;Rao, 2022Rao, "2020Shi et al., 2023;Zhou et al., 2023;. ...
... Family Megophryidae is the eighth largest family in the order Anura, with 7 genera and 242 species (AmphibiaWeb, https://amphibiaweb.org/lists/index.shtml). The members of this family exhibit various patterns of sexual dimorphism (Zheng et al., 2008;Hudson et al., 2011;Sung et al., 2014;Rowley et al., 2015;Li et al., 2019;Yang & Huang, 2019). For example, toes of males have rudimentary webbing and wide lateral dermal fringes and those of females only have weak or absent lateral dermal fringes in Leptolalax applebyi Rowley & Cao, 2009(Rowley et al., 2012. ...
... This genus comprises 23 recognized species, most of which distributed in the Hengduan Shan and adjacent regions to the east (Province Sichuan, China). Of these 23 taxa, at least six nominal species are only known from their type localities [2,25]. The Himalayan Scutiger group has been shown to be an excellent model for phylogeographic and evolutionary research due to its high local endemism (associated with many, so far undescribed lineages), the extremely limited distributional ranges and adaptation to high elevations of these species and the occurrence of strictly allopatric speciation [2,26,27]. ...
The Himalayas are one of earth’s hotspots of biodiversity. Among its many cryptic and undiscovered organisms, including vertebrates, this complex high-mountain ecosystem is expected to harbour many species with adaptations to life in high altitudes. However, modern evolutionary genomic studies in Himalayan vertebrates are still at the beginning. Moreover, in organisms, like most amphibians with relatively high DNA content, whole genome sequencing remains bioinformatically challenging and no complete nuclear genomes are available for Himalayan amphibians. Here, we present the first well-annotated multi-tissue transcriptome of a Greater Himalayan species, the lazy toad Scutiger cf. sikimmensis (Anura: Megophryidae). Applying Illumina NextSeq 500 RNAseq to six tissues, we obtained 41.32 Gb of sequences, assembled to ~111,000 unigenes, translating into 54362 known genes as annotated in seven functional databases. We tested 19 genes, known to play roles in anuran and reptile adaptation to high elevations, and potentially detected diversifying selection for two (TGS1, SENP5) in Scutiger. Of a list of 37 genes, we also identify 27 candidate genes for sex determination or sexual development, all of which providing the first such data for this non-model megophryid species. These transcriptomes will serve as a valuable resource for further studies on amphibian evolution in the Greater Himalaya as a biodiversity hotspot.
... Gaoligong, which possibly has harboured S. fusicaudus for more than 11 million years. The stable climatic conditions there make these mountains a "museum" of diverse organisms (e.g., Ai et al., 2018;Chen, Poly, David, & Jiang, 2017a;Fan et al., 2017;Yang & Huang, 2019). Furthermore, the complex topography of the sky-island mountains has facilitated allopatric speciation over long evolutionary time-scales by physical isolation, resulting in the appearance of narrowly distributed endemic species (e.g., Fan et al., 2017;Wan et al., 2018). ...
Aim
The aim of this study was to conduct comprehensive phylogeographic and demographic analyses to examine the degree to which topographic and climatic conditions have affected the patterns of diversification and migration in a strictly montane inhabitant, the montane long‐tailed mole ( Scaptonyx fusicaudus ).
Location
The mountains of south‐western China and adjacent mountains including Mts. Bashan, Dalou and Qinling also known as the sky islands in south‐western China.
Taxon
The long‐tailed mole ( S. fusicaudus ), a semi‐fossorial mammal distributed in the sky islands of south‐western China, is a relict species and the sole representative of the tribe Scaptonychini.
Methods
We sequenced one mitochondrial and six nuclear genes from 113 samples across the species’ range. We estimated phylogenetic relationships and divergence times, conducted genetic structuring and species delimitation using multiple approaches and used Approximate Bayesian Computation to test potential gene flow. We conducted ecological niche modelling to predict the species’ potential distribution in the present, the last glacial maximum and the last interglacial (LIG).
Results
The species comprises a minimum of 17 operational taxonomic units which are isolated in different mountain ranges. The lowlands and large rivers act as barriers to dispersal, and have isolated evolutionary lineages for up to 11 million years. Long‐distance dispersal is evident among a few discrete montane archipelagos. Suitable climatic conditions during the LIG are limited to only a few sites, thus geographically restricting climatic stable areas across geological periods (from the LIG to the present).
Main conclusions
For low‐vagility species, the complex topography of the sky islands has promoted exceptional diversification through a combination of eco‐environmental stability as well as geographic fragmentation. The mountains have acted as a buffer against climate change, and have provided continuously suitable habitats for S. fusicaudus since the early Late Miocene, supporting the hypothesis that the sky islands constitute “museums” of ancient lineages. Lowlands and river valleys have acted as barriers preventing gene flow, while the montane archipelagos could have provided stepping stones to facilitate dispersal.
The torrent frogs of the genus Amolops represent a great anuran diversification in southern China and Southeast Asia. Previous studies have shown that, the diversity of this genus still remains underestimated. During herpetological surveys from 2021 to 2022, several Amolops specimens were collected from the international border regions of southwestern Yunnan Province, China. Herein, we utilized molecular phylogenetic and morphological data to identify these specimens. Our findings indicate the presence of a separate and previously unknown lineage in the A. viridimaculatus group, which we formally describe as a new species. Furthermore, the specimen from Xishuangbanna National Nature Reserve clustered with A. vitreus from the paratype, supporting the morphological diagnosis. Therefore, we describe a new species and a new species record for China. Our study contributes to the species richness of the genus Amolops as well as the diversity of amphibians in China. Notably, our discovery brings the total number of Amolops species to 85 and the total number of torrent frog species known to occur in China to 53. In addition, our study further confirmed that Yunnan and Indochina Peninsula have similar faunal composition, implying that more studies are needed to achieve a complete understanding of the species diversity and distribution pattern.
To date, 10 species of the genus Microhyla have been recorded in China, of which six were distributed in Yunnan Province. Microhyla hmongorum Hoang, Nguyen, Phan, Pham, Ninh, Wang, Jiang, Ziegler, and Nguyen, 2022 was also speculated to be distributed in Xishuangbana, Yunnan Province, China. However, there is no evidence of documentation of M. hmongorum .
We report the first country record of Microhyla hmongorum , based on specimens collected from Yunnan border region. Morphologically, the specimen was consistent with the original descriptions of M. hmongorum . Phylogenetically, the sequences of the specimens from China clustered with the sequence of type specimens of M. hmongorum from Vietnam, with uncorrected pairwise distances of 0.9% at the 16S gene fragment analysed. Therefore, we report M. hmongorum as a new record species in China.
Oligodon hamptoni is a rare species of Kukri Snake known from only two specimens, both collected nearly a century ago in northern Myanmar. Here, we report the third record of this species based on a photograph taken in Mt. Gaoligongshan, Tengchong City, Yunnan Province, China, approximately 235 km northeast of the nearest record in Bhamo District, Kachin State, Myanmar. We also provide a detailed redescription of the holotype, showing that the photo record from Mt. Gaoligongshan can be unambiguously identified to this species. This rediscovery represents the first observation of O. hamptoni in China and is the first report of this species in almost 100 years.
We updated the checklists of extant, native amphibians and reptiles of China based on the previously published checklist of reptiles in 2015, the online checklist of amphibians on the database AmphibiaChina, newly published data as of December 2019, and previously uncollected literature prior to 2015. In total, the amphibian fauna of China consists of 515 species in 62 genera, 13 families, and three orders (Anura: 431 species in 47 genera and nine families; Caudata: 82 species in 14 genera and four families; Gymnophiona: one species in one genus and one family), while the reptilian fauna of China consists of 511 species in 135 genera, 35 families, and three orders (Crocodylia: one species in one genus and one family; Testudines: 34 species in 18 genera and six families; Squamata 466 species in 116 genera and 28 families [Serpentes: 256 species in 73 genera, 18 families; Lacertilia: 211 species in 43 genera and 10 families]). Specifically, for amphibians between 2015 and 2019, one family was recorded from China for the first time, two new genera were described, a genus was resurrected, a genus was recorded from China for the first time, 74 new, valid species were either described or resurrected, 18 recognized species were recorded from China for the first time, and six genera and eight species were considered as junior synonyms. For reptiles between 2015 and 2019, five subfamilies were elevated to the full family status, one new subfamily and a new genus were described, three genera were resurrected, three recognized genera were recorded from China for the first time, 35 new species were described, two species were resurrected from synonyms, six subspecies were elevated to the full species status, 10 recognized species were recorded from China for the first time, four genera and four species were considered as junior synonyms, and distribution records of one genus and four recognized species were removed from China. Furthermore, by reviewing literature before 2015, we make additional changes on the previous reptile checklist, including adding new records of three genera, elevating three subspecies to full species status, adding new records of three recognized species, synonymizing three genera and two species as junior synonyms, and removing the distribution record of a single recognized species from China. Lastly, we revise the Chinese common names of some reptilian groups with recomanda-tions to maintain the stability of the Chinese common names. The number of new species and new national records for amphibians and reptiles between 2015 and 2019 in China accounts for 17.1% and 10.2% of the total number of species in each group, respectively. Because new species are described at considerable speed and given the constant changes in the taxonomy of China’s herpetofuna, it is crucial to update the checklists regularly and discuss the existing taxonomic problems, so that such information reflects the most current state of knowledge and are available for taxonomic researchers and conservation biologists alike.
The various systems proposed to describe concisely, in the form of a formula, the number and arrangement of keratodont rows in the oral disk of anuran tadpoles, are reviewed and classified. A distinction is made between individual and collective keratodont formulae. The different systems are compared and evaluated, and proposals are made to standardize the use of various signs, numerals and letters in keratodont formulae. Nine standardized systems (seven all‐cardinal and two cardinal‐ordinal systems) are finally retained: these should cover all needs according to the kind of use and the level of precision required.
The Himalaya presents an outstanding geologically active orogen and biodiversity hotspot. However, our understanding of the historical biogeography of its fauna is far from comprehensive. Many taxa are commonly assumed to have originated from China-Indochina and dispersed westward along the Himalayan chain. Alternatively, the " Tibetan-origin hypothesis " suggests primary diversification of lineages in Paleo-Tibet, and secondary diversification along the slopes of the later uplifted Greater Himalaya. We test these hypotheses in high-mountain megophryid anurans (Scutiger). Extensive sampling from High Asia, and analyses of mitochondrial (2839 bp) and nuclear DNA (2208 bp), using Bayesian and Maximum likelihood phylogenetics, suggest that the Himalayan species form a distinct clade, possibly older than those from the eastern Himalaya-Tibet orogen. While immigration from China-Indochina cannot be excluded, our data may indicate that Himalayan Scutiger originated to the north of the Himalaya by colonization from Paleo-Tibet and then date back to the Oligocene. High intraspecific diversity of Scutiger implies limited migration across mountains and drainages along the Himalaya. While our study strengthens support for a " Tibetan-origin hypothesis " , current sampling (10/22 species; 1 revalidated: S. occidentalis) remains insufficient to draw final conclusions on Scutiger but urges comparative phylogeographers to test alternative, geologically supported hypotheses for a true future understanding of Himalayan biogeography.
Vocalizations of anuran amphibians have received much attention in studies of behavioral ecology and physiology, but also provide informative characters for identifying and delimiting species. We here review the terminology and variation of frog calls from a perspective of integrative taxonomy, and provide hands-on protocols for recording, analyzing, comparing, interpreting and describing these sounds. Our focus is on advertisement calls, which serve as premating isolation mechanisms and, therefore, convey important taxonomic information. We provide recommendations for terminology of frog vocalizations, with call, note and pulse being the fundamental subunits to be used in descriptions and comparisons. However, due to the complexity and diversity of these signals, an unequivocal application of the terms call and note can be challenging. We therefore provide two coherent concepts that either follow a note-centered approach (defining uninterrupted units of sound as notes, and their entirety as call) or a call-centered approach (defining uninterrupted units as call whenever they are separated by long silent intervals) in terminology. Based on surveys of literature, we show that numerous call traits can be highly variable within and between individuals of one species. Despite idiosyncrasies of species and higher taxa, the duration of calls or notes, pulse rate within notes, and number of pulses per note appear to be more static within individuals and somewhat less affected by temperature. Therefore, these variables might often be preferable as taxonomic characters over call rate or note rate, which are heavily influenced by various factors. Dominant frequency is also comparatively static and only weakly affected by temperature, but depends strongly on body size. As with other taxonomic characters, strong call divergence is typically indicative of species-level differences, whereas call similarities of two populations are no evidence for them being conspecific. Taxonomic conclusions can especially be drawn when the general advertisement call structure of two candidate species is radically different and qualitative call differences are thus observed. On the other hand, quantitative differences in call traits might substantially vary within and among conspecific populations, and require careful evaluation and analysis. We provide guidelines for the taxonomic interpretation of advertisement call differences in sympatric and allopatric situations, and emphasize the need for an integrative use of multiple datasets (bioacoustics, morphology, genetics), particularly for allopatric scenarios. We show that small-sized frogs often emit calls with frequency components in the ultrasound spectrum, although it is unlikely that these high frequencies are of biological relevance for the majority of them, and we illustrate that detection of upper harmonics depends also on recording distance because higher frequencies are attenuated more strongly. Bioacoustics remains a prime approach in integrative taxonomy of anurans if uncertainty due to possible intraspecific variation and technical artifacts is adequately considered and acknowledged.
A new species of Scutiger Theobald, 1868 is described from Medog, southeastern Tibet, China, based on morphological and molecular data. The new species was previously identified as Scutiger nyingchiensis, but it can be differentiated from the latter and all other congeners by the following combination of characters: (1) medium adult body size, SVL 50.5-55.6 mm in males and 53.8-57.2 mm in females; (2) maxillary teeth absent; (3) web rudimentary between toes; (4) prominent, conical-shaped tubercles on dorsal and lateral surfaces of body and limbs; (5) tubercles covered by black spines in both sexes in breeding condition; (6) a pair of pectoral glands and a pair of axillary glands present and covered by black spines in males in breeding condition, width of axillary gland less than 50% of pectoral gland; (7) nuptial spines present on dorsal surface of first and second fingers, and inner side of third finger in males in breeding condition; (8) spines absent on the abdominal region; (9) vocal sac absent. In addition, the distribution and conservation status of the new species are also discussed.
Phylogenies are increasingly used in all fields of medical and biological research. Moreover, because of the next generation sequencing revolution, datasets used for conducting phylogenetic analyses grow at an unprecedented pace. RAxML (Randomized Axelerated Maximum Likelihood) is a popular program for phylogenetic analyses of large datasets under maximum likelihood. Since the last RAxML paper in 2006, it has been continuously maintained and extended to accommodate the increasingly growing input datasets and to serve the needs of the user community.
I present some of the most notable new features and extensions of RAxML, such as, a substantial extension of substitution models and supported data types, the introduction of SSE3, AVX, and AVX2 vector intrinsics, techniques for reducing the memory requirements of the code and a plethora of operations for conducting post-analyses on sets of trees. In addition, an up-to-date, 50 page user manual covering all new RAxML options is available.
The code is available under GNU GPL at https://github.com/stamatak/standard-RAxML.
Alexandros.Stamatakis@h-its.org.
The Gaoligong Shan Mountains (GLGS) of southwestern Yunnan, China, which form the southeastern extent of the Himalaya Mountains, are a narrow range running northsouth, rising over 4,000 m in the north and receding into the lowlands in the south. The range is defined by the Irrawaddy lowlands to the west and by the Nujiang (also known as the Salween River) to the east. We summarize results of five recent ornithological expeditions that surveyed altitudinal transects in the southern and northern GLGS. The GLGS are a designated UNESCO World Heritage Site and are considered a hotspot by multiple conservation organizations. We used bird distributions to examine the hotspot status of the GLGS, and we discuss the value of the local species diversity for conservation. We found that the GLGS have tremendous avian diversity for a temperate region, with at least 486 documented avian taxa in the region. However, there is relatively little endemism in the GLGS per se, and ∼50% of GLGS breeding bird species are near the edge of their range. Our data do not suggest that the GLGS are a major evolutionary center for birds; however, the larger eastern Himalaya region (of which the GLGS are a part), does appear to be a center of endemism and evolution. The GLGS may have been-and are likely to remain-an important and precious refuge for the preservation of Asian montane forest birds. © 2011 by The American Ornithologists' Union. All rights reserved.
A re-analysis of a published data set from Ye et al. (1992) indicates that their phylogeny for the genus Sc~rtiger does not reflect the most parsimonious explanation of the data. The consensus of the resulting trees from the original data set is a "bush" with only three resolved nodes. A re-evaluation of the character states, and their respective polarizations, resulted in alternative phylogenetic hypotheses. However, measures of homoplasy and data consistency for the re-evaluated topologies were relatively low, suggesting that little confidence could be obtained in these relationships. More data are needed to generate a defensible hypothesis of the relationships within the genus Scutiger. absent (0); present (1))di antsst3 state for Oreoiaiax Figure 1. Phylogeny of Oreolalax with the character states of linea musculinae optimized on the tree. The primitive condition of linea musculinae for the phylog-eny of Scutiger is 1.
We announce the release of an advanced version of the Molecular Evolutionary Genetics Analysis (MEGA) software, which currently contains facilities for building sequence alignments, inferring phylogenetic histories, and conducting molecular evolutionary analysis. In version 6.0, MEGA now enables the inference of timetrees, as it implements our RelTime method for estimating divergence times for all branching points in a phylogeny. A new Timetree Wizard in MEGA6 facilitates this timetree inference by providing a graphical user interface (GUI) to specify the phylogeny and calibration constraints step-by-step. This version also contains enhanced algorithms to search for the optimal trees under evolutionary criteria and implements a more advanced memory management that can double the size of sequence data sets to which MEGA can be applied. Both GUI and command-line versions of MEGA6 can be downloaded from www.megasoftware.net free of charge.
The mating calls of six forms belonging to four genera Megophrys , Oreloalax , Scutiger and Leptolalax were recorded in Wawu Mountain National Forest Park , Sichuan Province of China , using cassette tape recorder (Aiwa) and Sony tape with an external microphone . All recordings were analyzed with an IBM PC based¡¡ SIGNAL¡–software anal2 ysis system (Engineering Design , USA) . The range of analyzed frequency was set as 0 -10 kHz. Acoustic analysis shows that the dominant frequency of L 1 oshanensis , M1 minor , M1sp1 , S 1 (S 1) chintingensis , O1 omeimontis , and O1schmidti is 452119 , 345614 , 229318 , 107615 , 107110 and 184914 Hz on average respectively ; the note duration is 4612 , 9018 , 9916 , 7212 , 7818 and 11013 millisecond on average respectively ; the note interval is 14014 , 25310 , 68114 , 151717 , 46113 and 61915 millisecond on average respectively. One2Way ANOVA analysis indicates that there are significant differences among the analyzed six forms on the dominant frequency , the note duration , and the note inter2 val (P < 0101) . Multiple comparisons using Least2Significant Difference (LSD) show that the difference of the dominant frequency between S 1 (S 1) chintingensis and O1 omeimontis is not significant (P = 01917 > 0105) ; on the note dura2 tion , only L 1 oshanensis is significantly different from M1 minor , M1sp1 , O1 omeimontis and O1schmidti (P < 0101) ; on the note interval , L 1 oshanensis is not significantly different from M1 minor , the same with M1sp1versus O1 schmidti and O1 omeimontis versus O1 schmidti (P > 0105) . Correlation analysis indicates that there are no significant correlation among the three acoustic characters of dominant frequency , note duration and note interval , and two environmental factors of the elevation and air temperature (P > 0105) except that the note interval is significantly linear correlated with the ele2 vation (r = 01943 , P = 01005 < 0101) . In the light of above , it is suggested that acoustic characteristics of calls are useful in distinguishing forms ; the change of the note interval with the elevation may be a kind of strategy of reproduction.
Since its introduction in 2001, MrBayes has grown in popularity as a software package for Bayesian phylogenetic inference using Markov chain Monte Carlo (MCMC) methods. With this note, we announce the release of version 3.2, a major upgrade to the latest official release presented in 2003. The new version provides convergence diagnostics and allows multiple analyses to be run in parallel with convergence progress monitored on the fly. The introduction of new proposals and automatic optimization of tuning parameters has improved convergence for many problems. The new version also sports significantly faster likelihood calculations through streaming single-instruction-multiple-data extensions (SSE) and support of the BEAGLE library, allowing likelihood calculations to be delegated to graphics processing units (GPUs) on compatible hardware. Speedup factors range from around 2 with SSE code to more than 50 with BEAGLE for codon problems. Checkpointing across all models allows long runs to be completed even when an analysis is prematurely terminated. New models include relaxed clocks, dating, model averaging across time-reversible substitution models, and support for hard, negative, and partial (backbone) tree constraints. Inference of species trees from gene trees is supported by full incorporation of the Bayesian estimation of species trees (BEST) algorithms. Marginal model likelihoods for Bayes factor tests can be estimated accurately across the entire model space using the stepping stone method. The new version provides more output options than previously, including samples of ancestral states, site rates, site d(N)/d(S) rations, branch rates, and node dates. A wide range of statistics on tree parameters can also be output for visualization in FigTree and compatible software.
DNA barcoding is a proven tool for the rapid and unambiguous identification of species, which is essential for many activities including the vouchering tissue samples in the genome 10K initiative, genealogical reconstructions, forensics and biodiversity surveys, among many other applications. A large-scale effort is underway to barcode all amphibian species using the universally sequenced DNA region, a partial fragment of mitochondrial cytochrome oxidase subunit I COI. This fragment is desirable because it appears to be superior to 16S for barcoding, at least for some groups of salamanders. The barcoding of amphibians is essential in part because many species are now endangered. Unfortunately, existing primers for COI often fail to achieve this goal. Herein, we report two new pairs of primers (➀, ➁) that in combination serve to universally amplify and sequence all three orders of Chinese amphibians as represented by 36 genera. This taxonomic diversity, which includes caecilians, salamanders and frogs, suggests that the new primer pairs will universally amplify COI for the vast majority species of amphibians.
Background
Identifying species of organisms by short sequences of DNA has been in the center of ongoing discussions under the terms DNA barcoding or DNA taxonomy. A C-terminal fragment of the mitochondrial gene for cytochrome oxidase subunit I (COI) has been proposed as universal marker for this purpose among animals.
Results
Herein we present experimental evidence that the mitochondrial 16S rRNA gene fulfills the requirements for a universal DNA barcoding marker in amphibians. In terms of universality of priming sites and identification of major vertebrate clades the studied 16S fragment is superior to COI. Amplification success was 100% for 16S in a subset of fresh and well-preserved samples of Madagascan frogs, while various combination of COI primers had lower success rates.COI priming sites showed high variability among amphibians both at the level of groups and closely related species, whereas 16S priming sites were highly conserved among vertebrates. Interspecific pairwise 16S divergences in a test group of Madagascan frogs were at a level suitable for assignment of larval stages to species (1–17%), with low degrees of pairwise haplotype divergence within populations (0–1%).
Conclusion
We strongly advocate the use of 16S rRNA as standard DNA barcoding marker for vertebrates to complement COI, especially if samples a priori could belong to various phylogenetically distant taxa and false negatives would constitute a major problem.
Evolution, weighting, and phylogenetic utility of mitochondrial gene sequences and a compilation of conserved polymerase chain reaction primers. C SIMON, F FRATI, A BECKENBACH, B CRESPI, H LIU, P
A diversity of hypotheses have been proposed for phylogenetic relationships and taxonomy within the genus Odorrana, and great progress has been made over the past several decades. However, there is still some controversy concerning relationships among Odorrana species. Here, we used many paratypes and topotypes and utilized 1.81 kb of mitochondrial sequence data to generate a phylogeny for approximately 4/5 of Odorrana species, and Odorrana haplotypes form a strongly supported monophyletic group relative to the other genera sampled. The deepest phylogenetic divergences within Odorrana separate three lineages whose interrelationships are not recovered with strong support. These lineages include the ancestral lineage of O. chapaensis, the ancestral lineage of a strongly supported clade comprising many western species, and the ancestral lineage of a strongly supported clade comprising all other Odorrana sampled. Within the latter clade, the first phylogenetic split separates O. ishikawae from a well-supported clade comprising its other species. These divergences likely occurred in the middle Miocene, approximately 12-15 million years ago. Separation of the ancestral lineage of Odorrana from its closest relative, Babina in our study, likely occurred in the early Miocene or possibly late Oligocene. Rates of lineage accumulation remained high from the middle Miocene through the Pleistocene.
A molecular phylogeny of the high-elevation Tibetan megophryid frogs was reconstructed using mitochondrial and nuclear gene sequences. Both parsimony and Bayesian analysis produced similar tree topologies, which identified the genus Leptobrachium as a sister group to Vibrissaphora, and the genera Oreolalax and Scutiger as monophyletic groups. Within the latter two genera, several species groups were also clearly recognized. At least 13 megophryids display reversed sexual size dimorphism (RSSD), where males are equal to or larger than females. According to our phylogenetic hypothesis, RSSD may have independently evolved at least five times or as many as seven times in this group. The multiple origins of RSSD within this group provide an excellent opportunity for studying the relationship between body size sexual dimorphism and other life-history traits and for determining the costs and benefits of RSSD.
We describe MUSCLE, a new computer program for creating multiple alignments of protein sequences. Elements of the algorithm
include fast distance estimation using kmer counting, progressive alignment using a new profile function we call the log‐expectation score, and refinement using tree‐dependent
restricted partitioning. The speed and accuracy of MUSCLE are compared with T‐Coffee, MAFFT and CLUSTALW on four test sets
of reference alignments: BAliBASE, SABmark, SMART and a new benchmark, PREFAB. MUSCLE achieves the highest, or joint highest,
rank in accuracy on each of these sets. Without refinement, MUSCLE achieves average accuracy statistically indistinguishable
from T‐Coffee and MAFFT, and is the fastest of the tested methods for large numbers of sequences, aligning 5000 sequences
of average length 350 in 7 min on a current desktop computer. The MUSCLE program, source code and PREFAB test data are freely
available at http://www.drive5. com/muscle.
Une espèce nouvelle de Scutiger Theobald 1868 de l'Himalaya occidental (Anura: Pelobatidae)
- A Dubois
Dubois, A. 1978. Une espèce nouvelle de Scutiger Theobald
1868 de l'Himalaya occidental (Anura: Pelobatidae). Senckenbergiana Biologica 59:163-171.
- L Fei
- S.-Q Hu
- C.-Y Ye
- Y.-Z Huang
Fei, L., S.-Q. Hu, C.-Y. Ye, and Y.-Z. Huang. 2009. Fauna
Sinica. Amphibia. Vol. 2 Anura. Science Press, Beijing. [In
Chinese]
- L Fei
- C.-Y Ye
Fei, L., and C.-Y. Ye. 2016. Amphibians of China. Vol. 1.
Science Press, Beijing.
An Illustrated Key to Chinese Amphibians
- L Fei
- Y.-Z C.-Y. Ye
- J.-P Huang
- F Jiang
- Xie
Fei, L., C.-Y. Ye, Y.-Z. Huang, J.-P. Jiang, and F. Xie. 2005.
An Illustrated Key to Chinese Amphibians. Sichuan
Publishing House of Science and Technology, Chongqing.
[In Chinese]
Colored Atlas of Chinese Amphibians and Their Distributions
- L Fei
- J.-P C.-Y. Ye
- Jiang
Fei, L., C.-Y. Ye, and J.-P. Jiang. 2012. Colored Atlas of
Chinese Amphibians and Their Distributions. Sichuan
Publishing House of Science and Technology, Chengdu.
[In Chinese]
On the generic classification of Asian high altitude pelobatid toads (Amphibia: Pelobatidae)
- L Fei
- S.-S C.-Y. Ye
- Li
Fei, L., C.-Y. Ye, and S.-S. Li. 1989. On the generic
classification of Asian high altitude pelobatid toads
(Amphibia: Pelobatidae). Acta Zoologica Sinica 35:381-389.
- D R Frost
Frost, D. R. 2017. Amphibian Species of the World: an
Online Reference. Version 6.0 (accessed on 12 July 2017).
- K Jiang
- D.-Q Rao
- S.-Q Yuan
- J.-S Wang
- P.-P Li
- M Hou
- M.-H Chen
- J Che
Jiang, K., D.-Q. Rao, S.-Q. Yuan, J.-S. Wang, P.-P. Li, M.
Hou, M.-H. Chen, and J. Che. 2012. A new species of the
genus Scutiger (Anura: Megophryidae) from southeastern
Tibet, China. Zootaxa 3388:29-40.
Amphibia and Reptilia of Yunnan
- D T Yang
- D Q Rao
Yang, D. T., and D. Q. Rao. 2008. Amphibia and Reptilia of
Yunnan. Kunming, Yunnan Publishing Group.
- J.-H Yang
- Y.-Y. Wang
- B P L Chan
Yang, J.-H., Y.-Y. Wang, and B. P. L. Chan. 2016b. A new
species of the genus Leptobrachium (Anura: Megophryidae)
from the Gaoligongshan Mountain Range, China. Zootaxa
4150:133-148.
- J.-H Yang
- Y.-Y Wang
- G.-L Chen
- D.-Q Rao
Yang, J.-H., Y.-Y. Wang, G.-L. Chen, and D.-Q. Rao. 2016a.
A new species of the genus Leptolalax (Anura: Megophryidae) from Mt. Gaoligongshan of western Yunnan Province,
China. Zootaxa 4088:379-394.