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A new species of the Genus Pelodiscus Fitzinger, 1835 (Testudines: Trionychidae) from Huangshan, Anhui, China

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A new species of the soft-shelled turtle genus Pelodiscus is described based on seven specimens from Huangshan, southern Anhui Province, China. The new species, Pelodiscus huangshanensis sp. nov., is distinguished from other species in the genus Pelodiscus by the following characteristics: (1) Small size (maximum carapace length of 101.16 mm and maximum body length of 190 mm); (2) keel high; (3) tiny yellowish-white spots on the throat; (4) no black pinstripes around the eyes; (5) white longitudinal bands on both sides of the neck in juveniles, absent in adults; (6) plastron yellowish-white, and only a dark patch on each side of the armpit; (7) many tubercles on the dorsal surface, but indistinct in the center; and (8) entoplastron “⌒” shaped. The phylogenetic relationships of the species in Pelodiscus were reconstructed using the sequences of cytochrome b (cyt b) and NADH dehydrogenase subunit 4 (ND4) genes. The new species formed a monophyletic clade with strong support. The uncorrected pairwise distances between the new species and other representatives of Pelodiscus ranged from 5.4% to 9.2% for cyt b and 4.1% to 7.6% for ND4. The new species brings the number of species of the genus Pelodiscus to six; five species are distributed in China, with three species endemic to China.
Dorsal and ventral aspects of the holotype of Pelodiscus huangshanensis sp. nov. (ANU20210001, adult male) Ecological notes. On June 20, 2017, a female individual (raised in Xiuning Institute of Rare Aquatic Animals) laid five eggs with a postpartum weight of 134 g. The eggs are white, nearly spherical; average length 15.95 ± 0.11 (15.79-16.01) mm; average short diameter 15.6 ± 0.16 (15.56-15.89) mm; and average weight 2.12 ± 0.23 (1.84-2.4) g. Hatching occurs at natural temperatures after 60-65 days. The average weight of neonates was 1.30 ± 0.08 (1.20-1.40) g. Three months old horse-hoof soft-shelled turtles are shown in Fig. 5. Etymology. The specific name refers to the type locality of this species, Huangshan City, Anhui Province. We suggest the following common names: horse-hoof soft-shelled turtle in English and "Huáng Shān Mǎ tí Biē (黄山马蹄鳖)" in Chinese. The native people of Huangshan have called it "Mǎ tí Biē (马蹄鳖)" for more than a thousand years. Distribution. This species is currently known only from the type locality, Xiuning County, Huangshan City, Anhui Province, China. Comparisons. Pelodiscus huangshanensis sp. nov. can be distinguished from P. axenaria by the following morphological characters: (1) Many tubercles on the dorsal surface, but indistinct in the center (vs. smooth carapace, no tubercles); (2) plastron yellowish-white, and only a dark patch on each side of the armpit (vs. a single dark-gray central figure enclosed by the hypoplastra and xiphiplastra); and (3) white longitudinal bands on both sides of the neck in juveniles, absent in adults (vs. absence of spots on the neck).
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ZOOTAXA
ISSN 1175-5326 (print edition)
ISSN 1175-5334 (online edition)
Accepted by U. Fritz: 6 Oct. 2021; published: 28 Oct. 2021 137
Zootaxa 5060 (1): 137–145
https://www.mapress.com/j/zt/
Copyright © 2021 Magnolia Press Article
https://doi.org/10.11646/zootaxa.5060.1.7
http://zoobank.org/urn:lsid:zoobank.org:pub:B7FD8234-A78D-47AC-93D5-8D6DF80356E8
A new species of the Genus Pelodiscus Fitzinger, 1835 (Testudines: Trionychidae)
from Huangshan, Anhui, China
YAN-AN GONG1,2,5,6, LI-FANG PENG1,2,5,7, SONG HUANG1,2,8*, YAN-FENG LIN3,9, RU-YI HUANG1,2,10,
YU-HAO XU4,11, DIAN-CHENG YANG1,2,12 & LIU-WANG NIE1,13 *
1Anhui Province Key Laboratory of the Conservation and Exploitation of Biological Resource, College of Life Sciences, Anhui Normal
University, Wuhu, 241000, China
2Huangshan Noah Biodiversity Institute, Huangshan 245000, China
3Fishery bureau of Xiuning County, Huangshan 245400, China
4School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
5Both authors contributed equally to this work.
6
yan_an_gong@sinoophis.com; https://orcid.org/0000-0002-8155-7024
7
lifang_peng@ahnu.edu.cn; https://orcid.org/0000-0001-8668-6397
8
snakeman@ahnu.edu.cn; https://orcid.org/0000-0001-6786-8523
9
linyf@yeah.net; https://orcid.org/0000-0001-9044-5238
10
christina_huang@sinoophis.com; https://orcid.org/0000-0002-1004-3835
11
yuhao_xu@sinoophis.com; https://orcid.org/0000-0001-6094-6680
12
snakeboy@sinoophis.com; https://orcid.org/0000-0001-6390-5251
13
lwnie@ahnu.edu.cn; https://orcid.org/0000-0003-2660-5799
*Corresponding authors.
snakeman@ahnu.edu.cn (S. Huang) and
lwnie@ahnu.edu.cn (L. W. Nie)
Abstract
A new species of the soft-shelled turtle genus Pelodiscus is described based on seven specimens from Huangshan,
southern Anhui Province, China. The new species, Pelodiscus huangshanensis sp. nov., is distinguished from other
species in the genus Pelodiscus by the following characteristics: (1) Small size (maximum carapace length of 101.16
mm and maximum body length of 190 mm); (2) keel high; (3) tiny yellowish-white spots on the throat; (4) no black
pinstripes around the eyes; (5) white longitudinal bands on both sides of the neck in juveniles, absent in adults; (6)
plastron yellowish-white, and only a dark patch on each side of the armpit; (7) many tubercles on the dorsal surface, but
indistinct in the center; and (8) entoplastron “” shaped. The phylogenetic relationships of the species in Pelodiscus were
reconstructed using the sequences of cytochrome b (cyt b) and NADH dehydrogenase subunit 4 (ND4) genes. The new
species formed a monophyletic clade with strong support. The uncorrected pairwise distances between the new species
and other representatives of Pelodiscus ranged from 5.4% to 9.2% for cyt b and 4.1% to 7.6% for ND4. The new species
brings the number of species of the genus Pelodiscus to six; five species are distributed in China, with three species
endemic to China.
Key words: soft-shelled turtle, Pelodiscus huangshanensis sp. nov., phylogeny, taxonomy, morphology
Introduction
Soft-shelled turtles (genus Pelodiscus Fitzinger, 1835) are widely distributed in East Asia, ranging from the Amur
and Ussuri Rivers in Russia through the Korean Peninsula, Japan, and China to southern Vietnam (Fritz et al. 2010;
Praschag et al. 2011; TTWG 2017; Gong et al. 2018). Soft-shelled turtles have been introduced to the Philippines
(Diesmos 2008), West Malaysia, USA (Hawaii), and Thailand (Uetz et al. 2020).
As early as 1834, the typical species P. sinensis had already been described by Wiegmann. The second species
P. maackii was described in 1857 by Brandt. Due to the relatively conservative morphology of the genus Pelodis-
cus, the remaining species were not described until more than 130 years later. In the 1990s, two new species of the
genus Pelodiscus (P. axenaria and P. parviformis) from China were described (Zhou et al. 1991; Tang 1997). The
validity of the latter three species has been repeatedly questioned due to their conservative external morphology
(Chkhikvadze 1987; Yang et al. 2011).
GONG ET AL.
138 · Zootaxa 5060 (1) © 2021 Magnolia Press
Stuckas and Fritz (2011) designated a lectotype for P. sinensis and succeeded in sequencing approximately
1500 base pairs of mtDNA (cytochrome b cyt b; NADH dehydrogenase subunit 4 ND4) of this 180-year-old
type specimen. They subsequently conducted molecular phylogenetic analyses of the genus Pelodiscus. The results
allowed the conclusive recognition of four genetically distinct species: P. axenaria, P. maackii, P. parviformis, and
P. sinensis. Yang et al. (2011) reached the same conclusion concerning the validity of P. parviformis after evaluating
molecular and morphological data. Gong et al. (2018) examined the species diversity of the genus Pelodiscus using
three mtDNA (12S, cyt b, ND4) and five nuclear loci (P26S4, C-mos, Rag2, R35, TB01) and found that diversity
was still underestimated at the species level. Farkas et al. (2019) described a new species from Vietnam and Hainan,
China, P. variegatus, based on morphological characteristics and molecular analyses.
Academics concluded that only P. sinensis was found in Anhui Province (Li & Wu 2019). However, in folk tales
from 1, 000 years ago, the local people in Huangshan (in southern Anhui Province) recognized another kind of soft-
shelled turtle called the “horse-hoof soft-shelled turtle”. This animal once appeared in a poem by the ancient poet
Sheng-yu Mei (1002–1061): “My hometown is far away, it has good tastes, horse-hoof soft-shelled turtle in sand,
oxtail civet in snow” (Cheng, 1491). (Author’s note: The oxtail civet is Paguma larvata). A Huangshan folk song
describes it thus: “the water is clear, the sand lying on the bottom is visible; the abdomen is white without spots; the
flesh is thick; the back is uplifted, and the size is like a horse’s hoof”.
In May to June 2017, seven horse-hoof soft-shelled turtles were sampled in Huangshan, southern Anhui, China.
Based on morphological and molecular comparisons, they should be considered as a new species.
Materials and methods
Sampling. Seven individuals of soft-shelled turtles (one male, two females, and four juveniles) were collected from
Xikou Town, Xiuning County, Huangshan City, Anhui Province, China in May and June 2017. The collected speci-
mens were fixed in approximately 95% ethanol and subsequently transferred to 75% ethanol for permanent storage.
Liver tissue samples were preserved separately in 95% ethanol. The specimens examined in the present study were
preserved and deposited at Anhui Normal University Museum (ANU), Herpetological Museum of Chengdu Insti-
tute of Biology, Chinese Academy of Sciences (CIB), and Shanghai Nature History Museum (SNHM).
Morphological examination. According to the literature (Zhou et al. 1991; Tang 1997; Farkas et al. 2019), we
measured and recorded the following morphological characters: tubercles on the carapace skin; head length (HL,
from snout tip to posterior margin of parietal); head width (HW, the widest part of temporal region); snout length
(SL); eye diameter (ED); the distance between the eyes (DEL, minimum distance between the eyes); carapace
length (CL); carapace width (CW); plastron length (PL); body length (BL, from snout tip to tail end); color of the
carapace and plastron skin; and dark spot(s) present or absent on the plastron. All measurements were made with
electronic calipers and were made to the nearest 0.1 mm.
Molecular phylogeny. Total genomic DNA was extracted from ethanol-preserved liver or muscle tissue using
Tissue DNA Kits (Takara Biotechnology (Dalian) Co., Ltd., Dalian, China). We amplified the fragments of cyt b
(primer Cytb-G, mt-f-na, mt-C2, mt-C2; Spinks et al. 2004; Fritz et al. 2006) and ND4 (ND4-672, H-Leu; Engstrom
et al. 2004; Stuart & Parham 2004) using the Polymerase Chain Reaction (PCR). The PCR products were sequenced
at Shanghai Map Biotech Co., Ltd. The raw sequences were stitched using Seqman in the DNAstar software pack-
age (Burland 2000). The newly generated sequences of cyt b and ND4 genes of seven specimens shared one and
two haplotypes, respectively. The sequences were submitted to GenBank (accession numbers: MK867841 for cyt b;
MK867842 and MW755352 for ND4).
The homologous sequences of all species of the genus Pelodiscus and five outgroup species (Palea stein-
dachneri, Apalone spinfera, A. mutica, Rafetus swinhoei, and R. euphraticus) were downloaded from GenBank
(Engstrom et al. 2004; Jung et al. 2006; Fritz et al. 2010; Stuckas & Fritz 2011; Yang et al. 2011; Ihlow et al. 2013;
Ihlow et al. 2014; Suzuki & Hikida 2014; Dong et al. 2016; Gong et al. 2018) and aligned with the newly gener-
ated sequences using the software MEGA X (Kumar et al. 2018). The downloaded sequences of FR851459 (cyt b)
and FR851460 (ND 4) were sequenced from the lectotype of P. sinensis (Stuckas & Fritz 2011), and the mtDNA
complete sequence of MK867844 (considered as P. axenaria, Yu et al. 2019) should be assigned to Pelodiscus
huangshanensis sp. nov.
A maximum likelihood (ML) tree was reconstructed using RaxML v7.2.6 (Stamatakis et al. 2006) using the
A NEW PELODISCUS FROM CHINA Zootaxa 5060 (1) © 2021 Magnolia Press · 139
GTRGAMMA model with 1000 ultrafast (Minh et al. 2013) bootstrap (BS) replicates. We also calculated the pair-
wise distances (p-distances) among ingroup taxa using the neighbor-joining method (Tamura et al. 2004) in MEGA
X (Kumar et al. 2018).
FIGURE 1. The maximum likelihood (ML) phylogenetic relationship trees based on concatenated cyt b and ND4 fragments.
Numbers near each node indicate the bootstrap support.
Results
The seven horse-hoof soft-shelled turtles formed a monophyletic clade with high support (Fig. 1) and appeared to be
a sister group to the cryptic species Pelodiscus sp. (from Jiangxi Provence), clustering with P. axenaria. The rela-
tionships of the Pelodiscus species were similar to those described by Fritz et al. 2010, Praschag et al. 2011; Stuckas
& Fritz 2011, Yang et al. 2011, and Gong et al. 2018, i.e. ((P. axenaria + (Pelodiscus sp., Pelodiscus huangshanen-
sis sp. nov.)) + (P. maackii + (P. parviformis + (P. sinensis, P. variegatus.))). The p-distances based on fragments
GONG ET AL.
140 · Zootaxa 5060 (1) © 2021 Magnolia Press
of cyt b between the new species and other species of the genus Pelodiscus varied from 5.4% (Pelodiscus sp.) to
9.2% (P. maackii) (Table 1), and those of ND4 varied from 4.1% (Pelodiscus sp.) to 7.6% (P. maackii) (Table 2).
Combined with morphological data, the specimens from Xiuning, Huangshan, Anhui, China are considered to be a
new species.
TABLE 1. uncorrected p-distance (%) based on fragment of cyt b among the genus Pelodiscus.
1 2 3 4 5 6 7
1. P. huangshanensis sp. nov. (n=7) 0.1
2. P. maackii (n=4) 8.1–9.2 0.1–1.2
3. P. parviformis (n=5) 7.9–8.2 2.3–3.0 0.1–0.3
4. P. axenaria (n=5) 6.7–7.1 8.9–9.7 8.0–8.4 1.4–2.4
5. P. sinensis (n=11) 7.7–8.5 2.5–3.5 2.0–2.7 8.3–9.2 0.1–1.7
6. Pelodiscus sp. (n=1) 5.4–5.5 7.7–8.1 7.3–7.5 6.7–7.4 7.0–7.8
7. P. variegatus (n=2) 8.5–8.6 3.2–3.9 3.1–3.3 9.1–9.4 1.4–2.0 8.0 0.1
TABLE 2. uncorrected p-distance (%) based on fragment of ND4 among the genus Pelodiscus.
1 2 3 4 5 6 7
1. P. huangshanensis sp. nov. (n=7) 0.1
2. P. maackii (n=4) 7.0–7.6 0.2–0.4
3. P. parviformis (n=5) 6.4–7.2 2.3–2.8 0.0–0.7
4. P. axenaria (n=5) 5.0–6.3 6.2–7.6 6.0–7.5 1.2–1.8
5. P. sinensis (n=11) 6.7–7.4 2.3–3.3 1.9–2.8 5.9–8.3 0.0–1.3
6. Pelodiscus sp. (n=1) 4.1–4.3 6.9–7.2 5.9–6.4 5.2–6.4 6.1–6.7 –
7. P. variegatus (n=3) 7.1–7.4 2.5–2.9 2.4–2.8 6.5–7.7 0.6–1.3 6.4–6.5 0.1
Pelodiscus huangshanensis sp. nov. Gong, Peng, Huang & Nie, 2021
(Figs. 2–5)
Suggested English name: Huangshan soft-shelled turtle
Suggested Chinese name: 黄山马蹄鳖 (Huáng Shān Mǎ tí Biē)
Holotype. ANU20210001, an adult male (Fig. 2), was found in a stream from Xikou Town, Xiuning County,
Huangshan City, Anhui Province, China (118.02°N, 29.69°E, and 170 m A. S. L.). The coordinates are given only
with a precision of 0.01 degrees to avoid private or commercial sampling. The specimen was collected on 10 June
2017 and deposited at Anhui Normal University Museum (voucher: ANU20210001).
Paratypes. ANU20210002, adult female (Fig 3); ANU20210003, adult female; ANU20210004, juvenile;
ANU20210005, juvenile; CIB116368, juvenile; SNHM5414, juvenile. They were sampled from May to June, 2017
around the site of holotype.
Diagnosis. Pelodiscus huangshanensis sp. nov. differs from the five known congeners by a combination of
the following characters: (1) Small size; maximum carapace length of 84.0 mm and maximum body length of 190
mm; (2) keel high; (3) tiny yellowish-white spots on the throat; (4) no black pinstripes around the eyes; (5) white
longitudinal bands on both sides of the neck in juveniles, absent in adults (Fig. 4); (6) plastron yellowish-white, and
only a dark patch on each side of the armpit; (7) many tubercles on the dorsal surface, but indistinct in the center;
and (8) entoplastron “” shaped.
Description of holotype and Variation. Where they differ from the holotype, features of the paratypes are list-
ed in parentheses (ANU20210002–5, CIB116368, SNHM5414). Holotype of an adult male (the first two are adult
females and the last four are juveniles); carapace length 82.5 mm (adult females 73.4–84.0 mm, juvenile 40.5–55.9
mm); plastron length 79.3 mm (adult females 75.7–86.1 mm, juvenile 39.9–55.8 mm); body length 190.0 mm (adult
females 144.9–160.0 mm, juvenile 88.2–114.7 mm) (Table 3). Back and side of head have many fine dark brown to
black spots; no black pinstripes around the eyes. The neck shows no white longitudinal striae bilaterally (there are
A NEW PELODISCUS FROM CHINA Zootaxa 5060 (1) © 2021 Magnolia Press · 141
white longitudinal bands on both sides of the neck in juveniles). The throat has many tiny yellowish-white spots.
The carapace slightly oval with a high keel. The carapace is olive brown to dark brown. The dorsal surface has many
tubercles, but it is indistinct in the center. The plastron yellowish-white, and only a dark patch on each side of the
armpit. Entoplastron “” shaped.
TABLE 3. Measurements of Pelodiscus huangshanensis sp. nov. (mm), for abbreviations, see the Materials and Methods.
Sex HL HW SL ED DEL CL CW PL BL
ANU20210001 male 51.7 25.8 5.9 5.3 7.0 90.69 80.1 79.3 190.0
ANU20210002 female 38.5 20.8 6.6 5.4 5.2 101.16 84.3 86.1 160.0
ANU20210003 female 41.5 21.4 4.4 4.8 4.8 93.6 73.5 75.7 144.9
ANU20210004 juvenile 27.8 14.2 2.8 2.5 4.3 46.1 44.7 39.9 91.6
ANU20210005 juvenile 28.4 13.2 3.0 2.6 4.1 46.8 42.1 42.5 88.2
CIB116368 juvenile 34.1 17.3 5.0 4.0 5.2 63.2 57.4 55.8 114.7
SNHM5414 juvenile 32.2 16.7 4.3 3.6 4.9 60.6 57.3 52.7 113.0
FIGURE 2. Dorsal and ventral aspects of the holotype of Pelodiscus huangshanensis sp. nov. (ANU20210001, adult male)
Ecological notes. On June 20, 2017, a female individual (raised in Xiuning Institute of Rare Aquatic Animals)
laid five eggs with a postpartum weight of 134 g. The eggs are white, nearly spherical; average length 15.95 ±
0.11 (15.79–16.01) mm; average short diameter 15.6 ± 0.16 (15.56–15.89) mm; and average weight 2.12 ± 0.23
(1.84–2.4) g. Hatching occurs at natural temperatures after 60–65 days. The average weight of neonates was 1.30 ±
0.08 (1.20–1.40) g. Three months old horse-hoof soft-shelled turtles are shown in Fig. 5.
Etymology. The specific name refers to the type locality of this species, Huangshan City, Anhui Province. We sug-
gest the following common names: horse-hoof soft-shelled turtle in English and “Huáng Shān Mǎ tí Biē (黄山马蹄鳖)”
in Chinese. The native people of Huangshan have called it “Mǎ tí Biē (马蹄鳖)” for more than a thousand years.
Distribution. This species is currently known only from the type locality, Xiuning County, Huangshan City,
Anhui Province, China.
Comparisons. Pelodiscus huangshanensis sp. nov. can be distinguished from P. axenaria by the following
morphological characters: (1) Many tubercles on the dorsal surface, but indistinct in the center (vs. smooth carapace,
no tubercles); (2) plastron yellowish-white, and only a dark patch on each side of the armpit (vs. a single dark-gray
central figure enclosed by the hypoplastra and xiphiplastra); and (3) white longitudinal bands on both sides of the
neck in juveniles, absent in adults (vs. absence of spots on the neck).
GONG ET AL.
142 · Zootaxa 5060 (1) © 2021 Magnolia Press
FIGURE 3. Dorsal and ventral aspects of the paratypes of Pelodiscus huangshanensis sp. nov. (ANU20210002, adult female)
FIGURE 4. Head and neck of Pelodiscus huangshanensis sp. nov.; A, B ANU20210001, male; C, D ANU20210004, juvenile.
A NEW PELODISCUS FROM CHINA Zootaxa 5060 (1) © 2021 Magnolia Press · 143
FIGURE 5. The three months old Huangshan soft-shelled turtles.
Pelodiscus huangshanensis sp. nov. can be further distinguished from P. sinensis by the following morphologi-
cal characters: (1) Small size; maximum carapace length 115.6 mm (vs. medium size; maximum carapace length
230 mm); (2) plastron yellowish-white, and only a dark patch on each side of the armpit (vs. plastron yellowish-
white with many dark spots); (3) keel high (vs. keel low); (4) no black pinstripes around the eyes (vs. black pin-
stripes around the eyes); (5) the throat has many tiny yellowish-white spots (vs. large yellowish-white spots with
dark edges); and (6) entoplastron “” shaped (vs. entoplastron “˄” shaped).
Pelodiscus huangshanensis sp. nov. can be further distinguished from P. maackii by the following morphologi-
cal characters: (1) Small size; maximum carapace length of 115.6 mm (vs. larger size; maximum carapace length
more than 350 mm); (2) plastron yellowish-white, and only a dark patch on each side of the armpit (vs. plastron
yellowish-white with no markings or relatively small, faint round to oval dark markings); (3) the throat has many
tiny yellowish-white spots (vs. large yellowish-white spots with dark edges); (4) keel high (vs. keel low); and (5) no
black stripes around the eyes (vs. black pinstripes around the eyes).
Pelodiscus huangshanensis sp. nov. can be further distinguished from P. parviformis by the following mor-
phological characters: (1) Plastron yellowish-white, and only a dark patch on each side of the armpit (vs. plastron
yellowish-white with no markings); (2) many tubercles on the dorsal surface, but indistinct in the center (vs. dorsal
tubercles in longitudinal series more or less discrete; central tubercle in front of marginal ridge of carapace small);
and (3) entoplastron “” shaped (vs. entoplastron “˄” shaped).
Pelodiscus huangshanensis sp. nov. can be further distinguished from P. variegatus by the following morpho-
logical characters: (1) Many tubercles on the dorsal surface, but indistinct in the center (vs. dorsal surface roughened
by longitudinal ridging and smaller protuberances spread over the leathery margin); (2) plastron yellowish-white,
and only a dark patch on each side of the armpit (vs. plastron pinkish white to pale reddish orange distinct, large
dark blotches, underside of leathery margin of carapace pigmented); (3) no black pinstripes around the eyes (vs.
black pinstripes around the eyes); and (4) the throat has many tiny yellowish-white spots (vs. large yellowish-white
spots with dark edges).
Discussion
In the present study, a new species Pelodiscus huangshanensis sp. nov. is described. The number of species of
the genus Pelodiscus is now six, namely P. sinensis (Wiegmann 1834), P. maackii (Brandt 1857), P. axenaria
(Zhou, Zhang & Fang 1991), P. parviformis Tang 1997, P. variegatus Farkas, Ziegler, Pham, Ong & Fritz 2019,
and Pelodiscus huangshanensis sp. nov. Gong, Peng, Huang & Nie. All presently recognized species of the genus
Pelodiscus have been recorded from China, with three species (P. parviformis, P. axenaria, P. huangshanensis sp.
nov.) endemic to China.
Gong et al. (2018) sequenced the fragments of cyt b (LT992688) and ND4 (LT992784) of a specimen from Yic-
GONG ET AL.
144 · Zootaxa 5060 (1) © 2021 Magnolia Press
hun City, Jiangxi Province. In the present study, the uncorrected pairwise distances of cyt b between this specimen
and other species of the genus Pelodiscus ranged from 5.4% to 8.1%, and those of ND4 were from 4.1% to 7.2%.
This should be considered a cryptic species. However, due to the lack of specimens and morphological data, it is
tentatively defined as Pelodiscus sp. (Gong et al. 2018).
Pelodiscus sinensis is the most widely distributed species in the genus. In the phylogenetic tree, the clade of
species group of P. sinensis is divided into several subclades, which may represent possible cryptic species. For
example, P. variegatus had been separated from P. sinensis based on morphological and molecular comparative
studies (Farkas et al. 2019). In the future, more specimens and more genetic markers are needed to determine the
taxonomic status of these subclades.
There are two species of soft-shelled turtle (P. huangshanensis sp. nov. and P. sinensis) distributed in Huang-
shan. P. sinensis is adapted to various natural aquatic habitats. P. huangshanensis sp. nov. has a narrow ecological
niche, being found only in clear rivers with fine sand located in the source area of the Xin’anjiang River (known as
the Qiantangjiang River in Hangzhou, Zhejiang Province, China). The wild population of P. huangshanensis sp.
nov. is greatly reduced due to habitat destruction and over-hunting. Therefore, it is necessary to (1) conduct an in-
depth study of the ecology and population size of this new species; (2) implement the protection of habitat and wild
resources; and (3) carry out captive breeding to increase the population size (in Huangshan, the wild individuals
have been successfully propagated under artificial conditions).
Acknowledgments
This research was funded by the Postdoctoral Research Program of Department of Human Resources and So-
cial Security of Anhui Province (2020B422), Doctoral Research Starting Foundation of Anhui Normal University
(752017), National Natural Science Foundation of China (31471968). We thank Dr. BALÁZS FARKAS for his
suggestions on specimen measurement and manuscript modification, Mr. QI-NENG WU (Xiuning Institute of Rare
Aquatic Animals, Huangshan, Anhui, China) for providing a reproductive female, eggs and neonates for us to take
photos and measure. We thank LetPub (www.letpub.com) for its linguistic assistance during the preparation of this
manuscript.
References
Brandt, J.F. (1857) Observationes quaedam ad generis Trionychum species duas novas spectantes auctore J. F. Brandt. Bulletin de la
Classe physico-mathématique de l’Académie impériale des Sciences de Saint Pétersbourg, 16, 110–111.
Burland, T.G. (2000) DNASTAR’s Lasergene sequence analysis software. Methods Molecular Biology, 132, 71–91.
https://doi.org/10.1385/1-59259-192-2:71
Cheng, M.Z. (1491) Xiuning Zhi. Vol 1. Material production. MingKoji four years (1491) Block-Printed Edition. s.n., s.n. [unknown
publishing and pagination info, in Chinese]
Dong, C.M., Engstrom, T.N. & Thomson, R.C. (2016) Origins of softshell turtles in hawaii with implications for conservation. Con-
servation Genetics, 17 (1), 1–14.
https://doi.org/10.1007/s10592-015-0772-7
Diesmos, A.C., Brown, R.M., Alcala, A.C. & Sison, R.V. (2008) Status and distribution of nonmarine turtles of the philippines. Chelo-
nian Conservation & Biology, 7 (December 2008), 157–177.
https://doi.org/10.2744/CCB-0672.1
Engstrom, T.N., Shaffer, H.B. & McCord, W.P. (2004) Multiple data sets, high homoplasy, and the phylogeny of softshell turtles (Tes-
tudines: Trionychidae). Systematic Biology, 53 (5), 693–710.
https://doi.org/10.1080/10635150490503053
Farkas, B., Ziegler, T., Pham, C.T., Ong, A.V. & Fritz, U. (2019) A new species of Pelodiscus from northeastern Indochina (Testudines,
Trionychidae). ZooKeys, 824 (1), 71–86.
https://doi.org/10.3897/zookeys.824.31376
Fritz, U., Auer, M., Bertolero, A., Cheylan, M., Fattizzo, T., Hundsdörfer, A.K., Sampayo, M.M., Pretus, J.L., ŠIrokÝ, P. & Wink, M.
(2006) A rangewide phylogeography of Hermann’s tortoise, Testudo hermanni (Reptilia: Testudines: Testudinidae): implications
for taxonomy. Zoologica Scripta, 35 (5), 531–543.
https://doi.org/10.1111/j.1463-6409.2006.00242.x
Fritz, U., Gong, S.P., Auer, M., Kuchling, G., Schneeweiss, N. & Hundsdörfer, A.K. (2010) The world’s economically most important
chelonians represent a diverse species complex (Testudines:Trionychidae: Pelodiscus). Organisms Diversity & Evolution, 10 (3),
A NEW PELODISCUS FROM CHINA Zootaxa 5060 (1) © 2021 Magnolia Press · 145
227–242.
https://doi.org/10.1007/s13127-010-0007-1
Gong, S.P., Vamberger, M., Auer, M., Praschag, P. & Fritz, U. (2018) Millennium-old farm breeding of Chinese softshell turtles (Pelo-
discus spp.) results in massive erosion of biodiversity. The Science of Nature, 105 (5–6), 34.
https://doi.org/10.1007/s00114-018-1558-9
Ihlow, F., Ahmadzadeh, F., Ghaffari, H., Hartmann, T. & Rdder, D. (2013) Where to move? Assessment of habitat suitability and ef-
fectiveness of reserves for future conservation planning of Rafetus euphraticus. 49th Annual Meeting of the German Society for
Herpetology and Herpetoculture (DGHT), Bonn, Germany, 2013, 1.
Ihlow, F., Ahmadzadeh, F., Ghaffari, H., Ertan Taşkavak, Hartmann, T., Etzbauer, C. & Rödder, D. (2014) Assessment of genetic struc-
ture, habitat suitability and effectiveness of reserves for future conservation planning of the euphrates soft-shelled turtlerafetus
euphraticus(daudin, 1802). Aquatic Conservation: Marine and Freshwater Ecosystems, 26 (4), 831–840.
https://doi.org/10.1002/aqc.2454
Jung, S.O., Lee, Y.M., Kartavtsev, Y., Park, I.S. & Lee, J.S. (2006) The complete mitochondrial genome of the korean soft-shelled turtle
pelodiscus sinensis (testudines, trionychidae). Mitochondrial DNA, 17 (6), 471–483.
https://doi.org/10.1080/10425170600760091
Kumar, S., Stecher G., Li, M., Knyaz, C. & Tamura, K. (2018) MEGA X: Molecular Evolutionary Genetics Analysis across computing
platforms. Molecular Biology and Evolution, 35, 1547–1549.
https://doi.org/10.1093/molbev/msy096
Li, Y.M. & Wu, X.B. (2019) A revised species list of amphibians and reptiles in the Anhui Province. Biodiversity Science, 27 (9),
1002–1011. [in Chinese with English abstract]
https://doi.org/10.17520/biods.2019036
Minh, B.Q, Nguyen, M.A.T. & von Haeseler, A. (2013) Ultrafast approximation for phylogenetic bootstrap. Molecular Biology and
Evolution, 30 (5), 1188–1195.
https://doi.org/10.1093/molbev/mst024
Praschag, P., Stuckas, H., Päckert, M., Maran, J. & Fritz, U. (2011) Mitochondrial DNA sequences suggest a revised taxonomy of Asian
flapshell turtles (Lissemys Smith, 1931) and the validity of previously unrecognized taxa (Testudines: Trionychidae). Vertebrate
Zoology, 61 (1), 147–160.
Spinks, P.Q., Shaffer, H.B., Iverson, J.B. & McCord, W.P. (2004) Phylogenetic hypotheses for the turtle family Geoemydidae. Molecu-
lar Phylogenetics and Evolution, 32 (1), 164–182.
https://doi.org/10.1016/j.ympev.2003.12.015
Stamatakis, A. (2006) RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models.
Bioinformatics, 22, 2688–2690.
https://doi.org/10.1093/bioinformatics/btl446
Stuart, B.L. & Parham, J.F. (2004) Molecular phylogeny of the critically endangered Indochinese box turtle (Cuora galbinifrons). Mo-
lecular Phylogenetics and Evolution, 31 (1), 164–177.
https://doi.org/10.1016/S1055-7903(03)00258-6
Stuckas, H. & Fritz, U. (2011) Identity of pelodiscus sinensis revealed by DNA sequences of an approximately 180-year-old type
specimen and a taxonomic reappraisal of pelodiscus species (testudines: trionychidae). Journal of Zoological Systematics and
Evolutionary Research, 49 (4), 335–339.
https://doi.org/10.1111/j.1439-0469.2011.00632.x
Suzuki, D. & Hikida, T. (2014) Taxonomic status of the soft-shell turtle populations in japan: a molecular approach. Current Herpetol-
ogy, 33 (2), 171–179.
https://doi.org/10.5358/hsj.33.171
Tang, Y.Z. (1997) Research on a new species of Pelodiscus, Trionychidae in China. Zoological Research, Kunming Institute of Zoology,
18, 13–17. [in Chinese, with English abstract].
Tamura, K., Nei, M. & Kumar, S. (2004) Prospects for inferring very large phylogenies by using the neighbor-joining method. Proceed-
ings of the National Academy of Sciences, 101 (30), 11030–11035.
https://doi.org/10.1073/pnas.0404206101
TTWG [Turtle Taxonomy Working Group] (2017) Turtles of the world. Annotated checklist and atlas of taxonomy, synonymy, distribu-
tion, and conservation status. 8th Edition. Chelonian Research Foundationand Turtle Conservancy. Chelonian Research Mono-
graphs 7. Independent Publisher, Lunenburg, Massachusetts, 292 pp.
Uetz, P., Freed, P. & Hošek, J. (Eds.) (2020) The Reptile Database. Available from: http://www.reptile-database.org, accessed (accessed
24 May 2021)
Yu, X.M., Lin, Y.F., Peng, L.F., Zhang, Y. & Huang, S. (2019) The complete mitochondrial genome of pelodiscus axenaria (testudines:
trionychidae). Mitochondrial DNA Part B, 4 (2), 2154–2155.
https://doi.org/10.1080/23802359.2019.1623132
Yang, P., Tang, Y.Z., Ding L, Guo, X.G. & Wang, Y.Z. (2011) Validity of Pelodiscus parviformis (Testudines: Trionychidae) inferred
from molecular and morphological analyses. Asian Herpetological Research, 2 (1), 21–29.
https://doi.org/10.3724/SP.J.1245.2011.00021
Zhou, G.J, Zhang, X.J. & Fang, Z.G. (1991) Bulletin of a new species Trionyx. Acta Scientiarum Naturalium Universitatis Normalis
Hunanensis, 14, 379–382. [in Chinese with English abstract]
... Two recent studies employing nuclear and mitochondrial DNA sequences revealed that P. axenaria belongs to a species complex comprising three morphologically challenging lineages (Gong et al. 2018(Gong et al. , 2021. One of these lineages was recently described as Pelodiscus huangshanensis Gong, Peng, Huang, Lin, Huang, Xu, Yang & Nie, 2021, whereas another lineage discovered by Gong et al. (2018) still needs to be formally named. ...
... Two recent studies employing nuclear and mitochondrial DNA sequences revealed that P. axenaria belongs to a species complex comprising three morphologically challenging lineages (Gong et al. 2018(Gong et al. , 2021. One of these lineages was recently described as Pelodiscus huangshanensis Gong, Peng, Huang, Lin, Huang, Xu, Yang & Nie, 2021, whereas another lineage discovered by Gong et al. (2018) still needs to be formally named. This 'lineage I' differs both in nuclear and mitochondrial DNA sequences from all other Pelodiscus species and is, according to current understanding, the sister species of P. huangshanensis (Gong et al. 2018(Gong et al. , 2021. ...
... One of these lineages was recently described as Pelodiscus huangshanensis Gong, Peng, Huang, Lin, Huang, Xu, Yang & Nie, 2021, whereas another lineage discovered by Gong et al. (2018) still needs to be formally named. This 'lineage I' differs both in nuclear and mitochondrial DNA sequences from all other Pelodiscus species and is, according to current understanding, the sister species of P. huangshanensis (Gong et al. 2018(Gong et al. , 2021. However, the identity of P. axenaria is obscure, rendering the present classification preliminary. ...
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We describe a new species from the Pelodiscus axenaria complex from Hunan and Jiangxi Provinces, China. Also, the application of the name P. axenaria (Zhou, Zhang & Fang, 1991) is clarified by designating a neotype for this species. Besides its genetic divergence, the new species differs from all other Pelodiscus species, including the two other taxa constituting the complex (P. axenaria, P. huangshanensis), in the following combination of morphological traits: (1) small adult size, <15 cm carapace length; (2) carapace distinctly keeled, more or less strongly tuberculated, usually olive clay-coloured and adorned with greenish black marbling; (3) plastron yellowish white, typically immaculate except for a blurred-edged blotch behind each axilla that does not extend to the entoplastron and some slight black suffusion along its anterior border; (4) underside of the leathery margin of the carapace with varying amounts of dark pigmentation; (5) head olive clay-coloured with numerous black splotches; (6) chin grey brown with pale stipples, throat dark grey, finely spotted with black; (7) neck with a wide yellow lateral band stretching from the tympanum posteriorly, which tends to fade with age; (8) entoplastron boomerang-shaped, the amount of bending of the transverse bar between the two posteriolaterally directed rami >90°.
... Softshell turtles range in size from less than 10-15 cm bony disc length (BDL) (e.g. 'Trionyx' gobiensis Danilov, Hirayama, Sukhanov, Suzuki, Watabe & Vitek, 2014 from the Late Cretaceous of Mongolia; extant Pelodiscus huangshanensis Y. A. Gong, Peng, Huang, Lin, Huang, Xu, Yang & Nie, 2021; extant Pelodiscus shipian S. Gong, Fritz, Vamberger, Gao & Farkas, 2022 from China) to a BDL of 97 cm (completely preserved carapace of an indeterminate taxon described by Gaffney [1979] from the Eocene Bridger Formation of North America), or even larger (estimated based on a fragmentary specimen described by Head et al. [1999] from the middle Eocene of Pakistan). The largest extant trionychids are slightly smaller than this and have a maximum BDL of 74.5 cm (Pritchard, 2001). ...
... cies (e.g. Nilssonia leithi [Gray, 1872], Nilssonia gangetica [Cuvier, 1825], Amyda cartilaginea [Boddaert, 1770]), with a BDL between 38 and 60 cm. In contrast to this, Dogania subplana (Geoffroy Saint-Hilaire, 1809) and Palea steindachneri (Siebenrock, 1906) have a roughly similar size, with 21.7 and 30 cm BDL, respectively (S. Gong et al., 2022;Y. A. Gong et al., 2021;Pritchard, 2001). The overall carapace morphology in different taxa of Pan-Trionychinae is very similar, but one notable difference is the presence or absence of multiple anteroposteriorly extending ridges across the carapace. Such ridges are prominent in S. baba (see above). In extant eastern Asian taxa, similar but weaker ridges are of ...
... For example, for the softshell turtle genus Pelodiscus, three new species (P. variegatus, P. huangshanensis, and P. shipian) and one distinct lineage have been discovered in recent years, highlighting the underestimated diversity of Pelodiscus (Farkas et al., 2019;Gong et al., 2021Gong et al., , 2022. ...
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Nonparametric bootstrap has been a widely used tool in phylogenetic analysis to assess the clade support of phylogenetic trees. However, with the rapidly growing amount of data, this task remains a computational bottleneck. Recently, approximation methods such as the RAxML rapid bootstrap (RBS) and the Shimodaira–Hasegawa-like approximate likelihood ratio test have been introduced to speed up the bootstrap. Here, we suggest an ultrafast bootstrap approximation approach (UFBoot) to compute the support of phylogenetic groups in maximum likelihood (ML) based trees. To achieve this, we combine the resampling estimated log-likelihood method with a simple but effective collection scheme of candidate trees. We also propose a stopping rule that assesses the convergence of branch support values to automatically determine when to stop collecting candidate trees. UFBoot achieves a median speed up of 3.1 (range: 0.66–33.3) to 10.2 (range: 1.32–41.4) compared with RAxML RBS for real DNA and amino acid alignments, respectively. Moreover, our extensive simulations show that UFBoot is robust against moderate model violations and the support values obtained appear to be relatively unbiased compared with the conservative standard bootstrap. This provides a more direct interpretation of the bootstrap support. We offer an efficient and easy-to-use software (available at http://www.cibiv.at/software/iqtree) to perform the UFBoot analysis with ML tree inference.
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In order to clarify whether the populations of Pelodiscus from the main islands of Japan are indigenous or artificially introduced, we constructed a mitochondrial phylogeny among samples from Japan and adjacent regions. The results strongly suggested the presence in Japan of various mitochondrial haplotypes that largely formed two divergent groups, one supposedly corre-sponding to P. sinensis (Wiegmann, 1834) sensu stricto and the other to P. maackii (Brandt, 1857). Haplotypes putatively associated with P maackii were unique to, and broadly prevailing in Japan. This may reflect indigenous nature of P. maackii in Japan, which would be more appropriately referred to as P. japonicus (Temminck and Schlegel, 1835). The others, putatively associated with P. sinensis, were fewer in Japan, and included those shared with individuals sold in a fish market of the continental China, suggesting the current Japanese P. sinensis to be exotic.