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Description of a New Species of the Rhinolophus trifoliatus-Group (Chiroptera: Rhinolophidae) from Southeast Asia


Abstract and Figures

A new species of woolly horseshoe bat in the Rhinolophus trifoliatus species group is described from Sabah in Malaysian Borneo. Two specimens from Central and West Kalimantan, Indonesia are referred to this species. A fourth specimen from western Thailand is referable to this species but on the basis of ~10% genetic divergence at the cytochrome oxidase-I gene is described as a separate subspecies. Morphologically and acoustically the two subspecies are similar. With a forearm length of 52.90–54.70 mm, a skull length of 24.27–26.57 mm and a call frequency of 49.2–50.0 kHz, the new species overlaps in size and call frequency with the sympatric R. trifoliatus. However, it differs significantly in having a dark noseleaf and a uniformly dark brown pelage, resembling, but being intermediate in size between R. sedulus and R. luctus, which have a skull length of 18.99–20.17 and 26.35–32.07 mm, respectively. It also differs from R. trifoliatus in the shape and size of the rostral inflation. It can be distinguished from R. beddomei (forearm length 55.00–63.44 mm) and R. formosae (forearm length 53.85–62.40 mm), which are endemic to the Indian Subcontinent and Taiwan, respectively, by its relatively smaller body size. Acoustic and genetic data are included in the comparison between the species. Both character states support the conclusions based on morphology. Further surveys in intact evergreen forest together with a re-examination of museum specimens may reveal that this species is widespread in Southeast Asia.
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Description of a new species of the Rhinolophus trifoliatus-group
(Chiroptera: Rhinolophidae) from Southeast Asia
1, 12
Princess Maha Chakri Sirindhorn Natural History Museum, Prince of Songkla University, Hat Yai, Songkhla,
90112, Thailand
Durrell Institute of Conservation and Ecology, School of Anthropology and Conservation, University of Kent,
Canterbury, CT2 7NR, United Kingdom
Fauna and Flora International Indonesia Programme, Jakarta, Indonesia
Institute for Tropical Biology and Conservation, Universiti Malaysia Sabah, Kota Kinabalu, Malaysia
Museum Zoologicum Bogoriense, Research Center for Biology-Indonesian Institute of Sciences (LIPI), Jl. Raya Jakarta
Cibinong Km. 46, Cibinong 16911 Bogor, Indonesia
Center for General Education, National Taipei University, New Taipei City 23741, Taiwan
School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS, United Kingdom
No.68, Flat No.M2, IBIS Galleria, 2nd cross, Near M.R. Garden, KEB Layout, Sanjay Nagar, Bangalore 560094,
Karnataka, India
Harrison Institute, Bowerwood House, St. Botolph’s Road, Sevenoaks, Kent, TN13 3AQ, United Kingdom
Imaging and Analysis Centre, Natural History Museum, Cromwell Road, London, SW7 5BD, United Kingdom
Mammal Section, Vertebrate Division, Life Science Department, Natural History Museum, Cromwell Road, London, SW7 5BD,
United Kingdom
Corresponding author: E-mail:
A new species of woolly horseshoe bat in the Rhinolophus trifoliatus species group is described from Sabah in Malaysian Borneo.
Two specimens from Central and West Kalimantan, Indonesia are referred to this species. A fourth specimen from western Thailand
is referable to this species but on the basis of ~10% genetic divergence at the cytochrome oxidase-I gene is described as a separate
subspecies. Morphologically and acoustically the two subspecies are similar. With a forearm length of 52.90–54.70 mm, a skull
length of 24.27–26.57 mm and a call frequency of 49.2–50.0 kHz, the new species overlaps in size and call frequency with the
sympatric R. trifoliatus. However, it differs significantly in having a dark noseleaf and a uniformly dark brown pelage, resembling,
but being intermediate in size between R. sedulus and R. luctus, which have a skull length of 18.99–20.17 and 26.35–32.07 mm,
respectively. It also differs from R. trifoliatus in the shape and size of the rostral inflation. It can be distinguished from R. beddomei
(forearm length 55.00–63.44 mm) and R. formosae (forearm length 53.85–62.40 mm), which are endemic to the Indian Subcontinent
and Taiwan, respectively, by its relatively smaller body size. Acoustic and genetic data are included in the comparison between the
species. Both character states support the conclusions based on morphology. Further surveys in intact evergreen forest together with
a re-examination of museum specimens may reveal that this species is widespread in Southeast Asia.
Key words: Borneo, evergreen forest, Malaysia, Indonesia, new species, Rhinolophus, trifoliatus-group, Southeast Asia, Thailand
Rhinolophus is the single extant genus in the
family Rhinolophidae. With at least 87 species cur-
rently recognised, it is also one of the most diverse
among bat genera and is widely distributed through-
out much of the Old World (Simmons, 2005; Yoshi -
yuki and Lim, 2005; Soisook et al., 2008; Wu et al.,
2008, 2009; Wu and Thong, 2009; Zhou et al., 2009;
Taylor et al., 2012). Within the genus, the species
have been arranged into several groups based
mainly on morphological characters (e.g., shape of
the sella, noseleaf and cranial features). This has led
to differences of opinion regarding the systematics
(e.g., Guillén et al., 2003). None theless, the most
widely accepted and most comprehensive review
of the Rhinolophidae can be found in Csorba et al.
Acta Chiropterologica, 17(1): 21–36, 2015
PL ISSN 1508-1109 © Museum and Institute of Zoology PAS
doi: 10.3161/15081109ACC2015.17.1.002
For echolocation, all species of Rhinolophus, and
the sister genus Hipposideros, use a high duty cycle,
long and narrow band, constant frequency (CF)
com ponent, which is adapted for the detection of
fluttering insects (Kalko and Schnitzler, 1998).
Recent studies of the echolocation characters of
the ‘CF bats’ strongly suggest that acoustic cha-
racters are useful for species identification (Fran-
cis and Haber setzer, 1998; Francis et al., 1999;
Kingston et al., 2001; Thabah et al., 2006; Soisook
et al., 2008; Hughes et al., 2010; Ith et al., 2011;
Taylor et al., 2012; Thong et al., 2012). Moreover,
acoustic divergence within species, which may re-
sult from the isolation of populations and adaptation
due to local environment, can result in genetic drift
and in some cases has led to speciation (Kingston
and Rossiter, 2004; Chen et al., 2009; Taylor et al.,
Species in the ‘trifoliatus-group’ are character -
ised by the presence of a lateral lappet on each side
of the base of the sella of the noseleaf. Currently, the
group is widely distributed from the Indian subcon-
tinent, eastwards to Southeast and eastern Asia, and
is represented by five species (Csorba et al., 2003;
Simmons, 2005). Until this study, three species of
this group were known to occur in Southeast Asia,
namely R. luctus, R. trifoliatus and R. sedulus (Fran -
cis, 2008) whilst two species, R. beddomei and
R. formosae, were thought to be geographically
more restricted, recorded from the Indian Subconti -
nent and Taiwan, respectively (Csorba et al., 2003;
Simmons, 2005).
In 2010, R. beddomei was reported for the first
time from Southeast Asia based on the morphologi-
cal characters of a single specimen collected from
evergreen forest in western Thailand (Soisook et al.,
2010). However, the authors acknowledged that the
smaller size of the Thai specimen and the disjunct
distribution suggested that additional specimens
could confirm this as a different species (Soisook et
al., 2010). Fortunately, recent field surveys by a net-
work of researchers in Southeast Asian countries
using harp traps in forest habitats has provided addi-
tional material. This, combined with a re-examina-
tion of a specimen collected from Sabah in 1983 by
Charles M. Francis and housed in the Natural His -
tory Museum, London makes a more thorough com-
parative study possible. Francis’s specimen was pro-
visionally identified and labelled R. trifoliatus (see
also Payne et al., 1985).
With a larger sample size and with acoustic and
genetic data available to compare with other con-
generic species, these specimens have proved to be
distinct from other taxa within the group and are
described here as a new species.
Studied Specimens
Specimens are preserved in ethanol or as dry skins. Where
possible, the skulls and bacula have been extracted and
cleaned. Voucher specimens examined for this publication are
deposited in the following institutions: the zoological collec-
tion of the Princess Maha Chakri Sirindhorn Natural History
Museum (PSUZC), Prince of Songkla University (PSU),
Hat Yai, Thai land; the Harrison Institute (HZM), Sevenoaks,
UK; Museum Zoologicum Bogoriense (MZB), Research
Center for Biology-Indonesian Institute of Sciences (LIPI),
Bogor, Indonesia; Na tion al Museum of Natural Science
(NMNS), Taiwan; and the Natural History Museum (BMNH),
London, UK.
The list of examined specimens is as follows; R. beddomei
India: ♂BMNH. (holotype of beddomei), Wynaad,
Madras; ♀BMNH., Konkan, Maharashtra; ♂ BMNH., Sirsi, Karnataka; ♂HZM.2.36212, Kannadimazhli -
gai, Courtallum Hills, Tirunelveli District, Tamil Nadu;
♂BMNH., Rojampela Range; Sri Lanka: ♀BMNH. (holotype of sobrinus), Kala Oya, North Western
Province; ♂HZM.1.27643, Mapalagama, Talgaswela, Southern
Province; R. formosae — Taiwan: ♀NMNS.006665; ♂002272;
♀004066; ♂006392; ♂006663; ♀006670; ♀003229; ♀005449;
R. trifoliatus — Myanmar: (sex unknown) BMNH.,
(sex unknown) BMNH85.8.1.111, Mergui, Tenasserim; (sex un-
known) BMNH., Bankachon, S. Tenasserim;
Thailand: ♀BMNH.78.2311, ♀BMNH78.2312, Ban Bang Non,
Muang Ranong; ♀PSUZC-MM2006.167, Khao Kor Hong, Hat
Yai, Songkhla Province; ♀PSUZC-MM2005.160, Namom,
Songkhla Province; ♀PSUZC-MM2006.140, ♂PSUZC-
MM2006.141, Wildlife Education Centre, Hat Yai, Songkhla
Province; Malaysia: ♀BMNH.65.4164, Long Ba Padang
Batu, Ulu Sabai, Sarawak; (sex unknown) BMNH. 51.124,
Long Lama Caves, Baram River, Sarawak; ♂BMNH.,
♂BMNH.65.337, Gunung Tahera, Pahang; Singapore:
♀BMNH. (holotype of edax); R. luctus — Myanmar:
♀BMNH.50.396, ♀BMNH.50.397, Nam Tamai; ♂BMNH., Sokleik; ♀BMNH., Chin Hills; ♀BMNH., Bankachon, S. Tenas se rim; Vietnam: ♀HZM.1.31766,
Pu Mat Reserve; ♀HZM.2. 32212, ♂HZM.2. 32213, Phong
Nha-Ke Bang Prop. NP; T129 (I.E.B.R); Bach Ma NP;
Cambodia: ♂HZM.4.32764, Mt. Samkos Wildlife Sanctua-
ry, Cardamom Mountains; ♀HZM. 6.36475, Tatai Lieu;
♀HZM.5.36141, no exact locality; Thailand: ♂BMNH.78.
2310, Amphoe Samung, Chiang Mai; ♂PP070915.27, Nam Nao
cave, Petchabun; ♀BMNH.70.1463, KM 79, Highway 23,
Nakhon Ratchasima Province; ♀BMNH. 78.2309, Pak Thong
Chai, Sakaerat, Nakhon Ratchasima Province; ♀PSUZC-
MM2005.36, Khao Ang Runai Wildlife Sanctuary, Chacher -
ngsao Province; ♂PP071108.1, Krung Ching, Nakhon Si
Thammarat; Malaysia: ♀BMNH., Semangko, Selangor;
♂BMNH.56.127, Taiping, Perak; (sex unknown) BMNH.89.
1.8.4 (holotype of foetidus), Sarawak; R. sedulus — Malaysia:
♂BMNH.65.334, Jenka, Temerloh, Pahang; ♀BMNH7.1.1.292
(holotype of R. sedulus), Sarawak; (sex unknown) BMNH., Paitan, Sabah.
22 P. Soisook, M. J. Struebig, S. Noerfahmy, H. Bernard, I. Maryanto, et al.
In Sabah, Malaysia, a female specimen of the trifoliatus-
group was collected at around 1,600 m a.s.l. on Gunung
(Mount) Trus Madi (approx. 5º34’N, 116º29’E) by Charles M.
Francis in 1983 (Sheldon and Francis, 1985). This specimen
was subsequently transferred to the BMNH and described as
a ‘melanistic R. trifoliatus (Payne et al., 1985). Only one
subsequent record of this taxon has been reported from Sabah.
It was found in undisturbed lowland forest in Maliau Basin con-
servation area (4º45’N, 116º58’E), together with R. sedulus and
R. trifoliatus in 2011, but was released (Struebig et al., 2013).
In Central Kalimantan, Indonesian Borneo, bats were cap-
tured in a harp trap set across established trails in the intact
undisturbed forest of Tanjung Puting National Park (2º60’S,
112º00’E) in June 2004 (Struebig et al., 2006). This area is char-
acterised by wetlands, mangroves and swamp forests with
a small area of dry, undisturbed forest in the north of the na-
tional park where the individual was captured. Two specimens
(male and female) provisionally identified as ‘R. luctus?’
were collected. The male specimen (MS02506-1) is deposited in
the HZM (see below) and the female specimen (MS040711.1)
is stored in the University of Palang karaya, Indonesia. R. sedu-
lus and R. trifoliatus, as well as 20 other bat species were also
recorded from the area (Struebig et al., 2006). In West Kali -
mantan, an individual with the same size and external ap pear -
ance as the new species was recorded in a logging concession in
Nanga Tayap sub-district (approximately 1º30’S, 110º42’E;
Noer fahmy, un publ ished data), and was subsequently released.
Again, both R. sedulus and R. trifoliatus were also recorded.
The taxon has not yet been found elsewhere on Borneo despite
extensive surveys (Stru ebig et al., 2010, 2012).
In Thailand, a single specimen was collected from Mae
Nam Pha Chi Wildlife Sanctuary, Ra tchaburi Province, western
Thailand (13º15’N, 99º21’E) at an elevation of 431 m a.s.l. on
20 April 2008. The area is characterised by steeply rugged
mount ains which are mostly covered by dry evergreen forest
(see Soisook et al., 2010 for more information of the area). The
bat was captured in a harp trap set across a seasonal streamlet
surrounded by primary evergreen forest.
External and craniodental measurements were taken with
a digital caliper to the nearest 0.01 mm. The definitions of meas-
urements follow Bates and Harrison (1997) and Csorba et al.
(2003) unless otherwise stated. They include: FA: forearm
length, from the extremity of the elbow to the extremity of the
carpus with the wings folded; E: ear length, from the lower bor-
der of the external auditory meatus to the tip of the pinna; T: tail
length, from the tip of the tail to its base adjacent to the anus;
TIB: length of tibia, from the knee joint to the ankle; HF: foot
length, from the extremity of the heel behind the os calcis to the
extremity of the longest digit, not including the claws; 5MET:
fifth metacarpal, from the extremity of the carpus to the distal
extremity of the metacarpal; 4MET, 3MET: as above but for the
fourth and third metacarpals respectively; 3D1PH: first phalanx
of the third digit, taken from the proximal to the distal extrem-
ity of the phalanx; 3D2PH: second phalanx of the third digit,
taken from the proximal to the distal extremity of the phalanx;
NL: noseleaf width, taken across the outer borders of the
horseshoe; SL: skull length, taken from the occiput to the ante-
rior part of the canine; CCL: condylo-canine length, from an
exoccipital condyle to the anterior part of a canine; ZB: zygo-
matic breadth, the greatest width of the skull across the zygo-
matic arches; BB: breadth of braincase, taken at the posterior
roots of the zygomatic arches; MW: mastoid width, the greatest
distance across the mastoid region; PC: post orbital constriction,
taken at the narrowest point; PL: palatal length, taken along the
palate, not including the posterior spike; C–M
: maxillary
toothrow length, from the most anterior part of the upper canine
to the back of the crown of the third upper molar; M
: pos-
terior palatal width, taken across the outer borders of the poste-
rior upper molar; C
: anterior palatal width, taken across the
outer border of the upper canine; C–M
: mandibular toothrow
length, from the most anterior part of the lower canine to the
back of the crown of the third lower molar; M: mandible length,
from the most posterior part of the condyle to the most anterior
part of the first lower incisors; AMSW: anterior median swell -
ing width, taken across the anterior median chambers, in dorsal
view; ALSW: anterior lateral swelling width, taken across the
anterior lateral chambers, in dorsal view. BL: baculum length,
taken from the most posterior to the most anterior margin of the
baculum, measured with a graticule in the eyepiece of a micro-
scope; Body mass (MASS, in grams) was recorded using a 10 g
Pesola scale to the nearest 1.0 g.
For the fluid specimen BMNH.84.1970, the images of the
skull as well as the craniodental measurements were taken with
a computed tomography (CT) scan to avoid potential damage to
the specimen. The specimen was imaged using a Nikon Metrol -
ogy HMX ST 225. The sample was scanned using a tungsten re-
flection target, at an accelerating voltage of 180 kV and current
of 150 µA using a 500 ms exposure time. A 0.5 mm copper fil-
ter was used and 6,284 projections were taken over a 360° rota-
tion. The voxel size of the resulting dataset was 16µm. The 3D
volumes were reconstructed using CT Pro (Nikon Metro logy,
Tring, UK) and TIFF stacks exported using VG Studio Max
(Volume Graphics GmbH, Heidelberg, Germany). Drishti (Li -
ma ye, 2012) was used to generate a 3D rendering and take
measurements of the specimen.
A Principal Component Analysis (PCA) using a correlation
matrix was undertaken to compare the skull measurements of
each species. The analysis was performed in R 3.0.2 (R Found -
ation for Statistical Computing, Vienna).
Echolocation Calls Recording and Analysis
The echolocation calls of the hand-held specimens of bats in
the ‘trifoliatus-group’ from India, Taiwan, Thailand and Indo -
nesian Borneo were recorded with a Pettersson D-240X bat de-
tector, set in 10× time expansion mode, and connected to a dig-
ital sound recorder. Calls were analysed in BatSound Pro 4.14
(Pettersson Electronics and Acoustic AB). The frequency of
maximum energy (fmaxe) was measured in the power spectrum,
whereas the call duration (d) and inter-pulse interval (ipi) were
measured in the oscillogram. The spectrogram was produced
using an automatic sample Fast Fourier Transform (FFT) with
Hanning window.
Genetic Analysis
Tissue samples were collected from the wing membrane or
liver of newly sacrificed bats or wet specimens and stored in ab-
solute ethanol (see Appendix for the list of specimens). DNA
extraction, amplification and sequencing followed the protocols
for mammalian DNA barcodes analyses as outlined in Ivanova
New Rhinolophus from Southeast Asia 23
et al. (2012). A 657 bp fragment of the cytochrome oxidase-I
(COI) gene was analysed and the sequence deposited at the
Barcode of Life Data Systems (BOLD). Public data of other
species in the trifoliatus-group, as well as some other represen-
tatives of the Southeast Asian philippinensis-group (R. mar-
shalli, R. macrotis, R. paradoxolophus and R. philippinensis),
megaphyllus-group (R. borneensis, R. robinsoni), pearsoni-
group (R. pearsoni) and pusillus-group (R. acuminatus), which
are published in Francis et al. (2010) and are available in BOLD,
are also included in the analysis (see Appendix). The phyloge-
netic tree was constructed using Maximum likelihood (ML),
with a Kimura-2-parameter (K2P) substitution model. Bootstrap
support based on 500 replicates was estimated. All analyses
were performed in MEGA 6 (Tamura et al., 2013).
Rhinolophus francisi
Soisook, Struebig, Bates and Miguez, sp. nov.
(Figs. 1–6, Tables 1–2)
BMNH.84.1970 (field number CMF830703.1),
adult female, body in alcohol, skull intact (original
skull images taken with computed tomography),
collected by Charles M. Francis on 3 July 1983.
The measurements (in mm) of the holotype are as
follow; FA: 53.12; E: 25.72; T: 29.86; TIB: 27.78;
HF: 15.20; 3MET: 35.94; 4MET: 41.85; 5MET:
42.85; 3D1P: 18.61; 3D2P: 26.30; SL: 26.57;
CCL: 23.85; ZB: 13.51; BB: 12.06; MW: 12.09;
PC: 3.00; PL: 3.85; CM
: 9.78; M
: 9.94;
: 7.16; C–M
: 10.88; M: 18.32; AMSW: 5.18;
ALSW: 7.35.
Type locality
Gunung Trus Madi, Sabah, Malaysia (approx.
5º34’N, 116º29’E), at an elevation of about 1,600 m
HZM.3.36543 (field number MS020506-1),
adult male, dry skin, skull extracted, collected by
Matthew Struebig on 25 June 2004, from Tan-
jung Puting National Park, Central Kalimantan,
Indo ne sia (2º60’S, 112º00’E); MZB.20723 (field
number AJG.331), adult female, body in alcohol,
skull extracted, from Gunung Palung National
Park in West Kalimantan, Indonesia (1º11’S,
24 P. Soisook, M. J. Struebig, S. Noerfahmy, H. Bernard, I. Maryanto, et al.
IG. 1. Face, noseleaf and ventral pelage (a, b), sella (c) and dorsal pelage (d) of R. francisi sp. nov., ♂PSUZC-MM.2008.51
(holotype of thailandicus subsp. nov.) from Thailand. Not to scale
New Rhinolophus from Southeast Asia 25
Referred specimens
A specimen from Thailand (PSUZC-MM.
2008.51) is included under the description of the
R. francisi subsp. nov. (see below).
The species is named in honour of Charles M.
Francis, who, for many years, has contributed great -
ly to the taxonomic study of Southeast Asian bats.
He also collected the holotype of this species from
Sabah, Malaysian Borneo in 1983. The proposed
English name is ‘Francis’s Woolly Horseshoe Bat’.
This is a medium-large Rhinolophus with a FA of
52.90–54.70 mm (Table 1) and SL of 24.27–26.57
mm (Table 2). The noseleaf is dark brown with well-
developed lateral lappets (Fig. 1). The dorsal and
ventral pelage is uniformly whitish-brown basally
and greyish-brown at the tips. In the skull, the ante-
rior median swelling is well inflated and relatively
large, with an AMSW of 4.76–5.18 mm. The supra-
orbital depression is deep and each supraorbital
ridge is very well defined (Figs. 2a, 2c and 3a). The
sagittal crest is well developed. The upper canine
) exceeds the second upper premolar (P
) in
height (Figs. 2b and 3a) but is about equal to it in
crown area (Figs. 2d and 4a). The first upper premo-
lar (P
) is very small and with a distinct cusp (Figs.
2b, 2d and 4a). It is situated within the toothrow and
in contact with the C
and P
. The palatal length
(PL) is about one-third (34.5–35.4%) of the maxil-
lary toothrow length (C–M
). The lower incisors
) are tricuspidate. The lower canine (C
) ex-
ceeds the height of the third lower premolar (P
which is about equal in height to the first lower
molar (M
). The second or middle lower premolar
) is very small and extruded from the toothrow,
so that the first and the third lower premolars (P
) are in contact or nearly so (Figs. 2d and 4a).
This is a medium-large Rhinolophus with
a FA of 52.90–54.70 mm and a MASS of 16.0–
18.0 g (Table 1). The ear is relatively large with
a pointed tip (Fig. 1); the height of the ear (E) is
23.81–27.00 mm. The noseleaf is dark brown. The
anterior noseleaf is rounded and relatively large,
with a greatest width (NL) of 12.21–12.36 mm; it
does not cover the lower lip. The connecting process
is long and projects anteriorly. There are well-devel-
oped lateral lappets. The sella is broader at the base
and connects to the lateral lappets on both sides; it is
abruptly concave in the middle; the upper part is
parallel sided and continues to the tip, which is
rounded off. The lancet is high; slightly concave in
the middle and with a pointed tip. The lower lip has
one mental groove. The dorsal and ventral pelage is
uniformly whitish-brown basally and greyish-brown
at the tips. In the wing, the third metacarpal (3MET)
is the shortest, 35.94–37.47 mm; the fourth (4MET)
is subequal to the fifth metacarpal (5MET), 41.22–
42.47 mm and 42.85–43.99 mm, respective ly. The
plagiopatagium and uropatagium are dark brown
and without hairs.
In the skull, the SL and CCL are 24.27–26.57
mm and 21.72–23.85 mm, respectively (Table 2).
The anterior median swelling is well inflated
and bulbous (Figs. 2a, 2c and 3a), with an AMSW of
4.76–5.18 mm. The anterior lateral swelling width
(ALSW) is 6.53–7.35 mm. The posterior swelling is
small and uninflated. The supraorbital depression is
deep and the supraorbital ridges are very well de-
fined (Figs. 2c and 3a). The sagittal crest is very
well developed and connected to the supraorbital
ridge (Figs. 2a, 2c and 3a). The zygomatic breadth
(ZB) exceeds that of the mastoid width (MW),
12.16–13.51 mm and 11.31–12.09 mm, respectively.
Each zygoma is strong with a distinct triangular-
shaped dorsal arch in the midpart (Figs. 2a and 3a).
The upper canine (C
) exceeds the second upper
premolar (P
) in height (Figs. 2b and 3a) and is about
equal in crown area (Figs. 2d and 4a). The first upper
premolar (P
) is very small and with a distinct cusp
(Figs. 2b and 4a). It is situated within the toothrow
and is in contact with the C
and P
. The maxillary
toothrow length (C–M
) is 9.30–9.83 mm. It is
slightly convergent anteriorly; the width of C
(6.07–7.16 mm) is 68.51–72.03% that of M
(8.86–9.94 mm). The palatal length (PL) is moder-
ate, 3.21–3.85 mm or 34.52–38.05% of the C–M
In the mandible, the lower incisors (I
) are tri-
cuspidate (Figs. 2d and 4a). The lower canine (C
exceeds the height of the third lower premolar (P
is about equal in height to the first lower molar
); P
is about half the height of P
. The second or
middle lower premolar (P
) is very small and almost
fully extruded from the toothrow (Figs. 2d and 4a),
so that the first and the third lower premolars (P
) are in contact or nearly so.
Rhinolophus francisi emits a typical long nar-
row band FM/CF/FM signal. Based on hand-held
specimens from Kalimantan and Thailand (n = 2),
the most energy is in the second harmonic with an
26 P. Soisook, M. J. Struebig, S. Noerfahmy, H. Bernard, I. Maryanto, et al.
R. f. francisi
R. f. thailandicus R. beddomei R. formosae R. trifoliatus R. luctus
XHolotype n = 3
YHolotype n = 7 n = 42 n = 19 n = 22
MASS 18.0 [1] 16.00 20.0 ± 2.9 14.8 ± 1.8 56.2
(11.9–25.3) (12.5–17.0) [4] [1]
FA 53.12 53.53 ± 1.01 52.97 59.83 ± 3.94 57.58 ± 1.85 52.15 ± 1.90 70.33 ± 4.44
52.90–54.70 (55.00–63.44) [5] (53.85–62.40) (48.92–54.11) [10] (61.80–77.30) [17]
E 25.72 25.70, 27.00 [2] 23.81 27.50, 27.60 [2] 29.32 ± 2.52 25.78 ± 0.38 36.11 ± 2.91
(24.45–31.30) [6] (25.35–26.20) [4] (31.48–39.60) [10]
T 29.86 33.00, 38.00 [2] 30.91 37.00, 38.50 [2] 33.53 ± 2.65 34.29 ± 1.71 50.99 ± 6.39
(29.40–36.50) [5] (32.31–36.43) [4] (41.00–64.30) [13]
TIB 27.78 29.50, 29.60 [2] 28.33 30.21 ± 1.34 31.16 ± 1.38 26.02 ± 1.19 36.60 ± 2.07
28.90–31.91 [5] (28.15–33.70) [36] (24.55–28.29) [10] (33.73–40.23) [11]
HF 15.20 13.50, 15.50 [2] 14.08 12.10, 13.50 [2] 12.03 ± 0.49 16.25 ± 2.13
(11.40–12.44) [4] (12.00–18.71) [12]
NL 12.36 12.21 11.00 [1] 11.23 ± 0.21 15.25 ± 2.02
(11.00–11.43) [4] (11.70–17.15) [7]
5MET 42.85 43.36 [1] 43.99 45.28, 46.28 [2] 43.33 ± 0.80 58.81 ± 3.08
(42.27–44.06) [4] (55.17–62.40) [4]
4MET 41.85 41.22 [1] 42.47 44.08, 44.12 [2] 41.39 ± 0.96 57.05 ± 2.73
(40.22–42.39) [4] (54.14–60.09) [4]
3MET 35.94 36.15 [1] 37.47 37.77, 37.78 [2] 36.49 ± 1.08 50.03 ± 2.57
(35.51–38.00) [4] (47.72–53.38) [4]
3D1P 18.61 19.71 [1] 18.52 19.52, 21.55 [2] 21.06 ± 0.84 28.28 ± 1.02
(20.34–22.10) [4] (27.21–29.54) [4]
3D2P 26.30 26.31 [1] 27.75 27.75, 28.38 [2] 29.20 ± 1.61 38.99 ± 1.03
(27.74–30.93) [4] (37.96–40.32) [4]
ABLE 1. Body mass (in grams) and external measurements (mm) of R. francisi sp. nov., R. beddomei, R. formosae, R. trifoliatus, and R. luctus. Mean ± SD, minimum and maximum values
are given. Sample sizes where differing from those given under n are included in brackets. Definitions of measurements are included in the Materials and Methods section
New Rhinolophus from Southeast Asia 27
R. f. francisi
R. f. thailandicus R. beddomei R. formosae R. trifoliatus R. luctus R. sedulus
XHolotype n = 2
YHolotype n = 6 n = 8 n = 14 n = 20 n = 3
SL 26.57 24.27, 25.36 24.37 26.06 ± 0.96 25.55 ± 0.42 22.21 ± 0.83 30.52 ± 1.51 19.55 ± 0.59
(25.01–27.16) (24.71–26.18) (21.64–24.31) [12] (26.35–32.07) [16] (18.99–20.17)
CCL 23.85 22.23, 22.75 21.72 23.41 ± 0.81 24.03 ± 0.62 20.31 ± 0.96 27.41 ± 1.01 17.42, 18.28 [2]
(22.35–24.49) [5] (23.34–24.82) [5] (19.48–22.39) [11] (25.13–28.64) [16]
ZB 13.51 13.00, 13.39 12.16 13.64 ± 0.75 12.67 ± 0.42 11.70 ± 0.45 15.40 ± 0.67 9.90 ± 0.39
(12.51–14.52) (11.99–13.42) (10.92–12.50) [13] (14.46–16.45) (9.67–10.35)
BB 12.06 10.00, 10.51 9.93 10.82 ± 0.65 11.62 ± 0.12 9.54 ± 0.42 12.22 ± 0.42 8.25 ± 0.24
(9.80–11.54) (11.45–11.78) (8.80–10.09) [13] (11.62–13.13) (8.05–8.52)
MW 12.09 11.44, 11.44 11.31 11.77 ± 0.52 10.78 ± 0.34 10.55 ± 0.30 13.34 ± 0.47 9.02, 9.63 [2]
(10.97–12.25) (10.39–11.36) (10.05–10.93) [12] (12.50–13.89) [17]
PC 3.00 2.28, 2.99 2.44 2.50 ± 0.33 2.47 ± 0.20 2.19 ± 0.23 3.12 ± 0.43 2.22 ± 0.14
(2.11–2.97) (2.25–2.84) (1.89–2.69) [13] (2.37–3.93) (2.11–2.38)
PL 3.85 3.74 [1] 3.21 3.80 ± 0.32 3.89 ± 0.18 2.94 ± 0.26 4.55 ± 0.39 2.23 ± 0.24
(3.34–4.16) (3.68–4.19) (2.48–3.41) (3.96–5.34) (2.05–2.51)
9.78 9.73, 9.83 9.30 9.84 ± 0.48 9.88 ± 0.19 8.60 ± 0.35 11.88 ± 0.52 7.21 ± 0.24
(9.33–10.52) (9.63–10.17) (8.07–9.42) (10.62–12.81) (6.63–7.57)
7.16 6.65, 6.91 6.07 6.71 ± 0.43 6.98 ± 0.20 8.37 ± 0.30 7.72 ± 0.43 4.63 ± 0.08
(6.09–7.24) (6.70–7.22) (7.92–8.99) (6.60–8.52) (4.55–4.70)
9.94 9.24, 9.68 8.86 9.64 ± 0.48 9.21 ± 0.32 8.37 ± 0.30 11.02 ± 0.68 7.26 ± 0.22
(9.16–10.24) (8.78–9.55) (7.92–8.99) (9.98–12.86) (7.07–7.50)
10.88 10.13, 10.34 10.01 10.51 ± 0.51 10.42 ± 0.14 9.10 ± 0.39 12.59 ± 0.62 7.72 ± 0.53
(9.92–11.11) (10.30–10.64) (8.38–10.03) (11.19–13.84) (7.12–8.12)
M 18.32 17.82, 18.11 17.15 18.34 ± 0.66 17.92 ± 0.48 15.65 ± 0.66 22.04 ± 1.10 13.41 [1]
(17.46–19.13) (17.20–18.71) (14.70–16.79) [12] (19.80–23.67)
AMSW 5.18 5.18, 5.18 4.76 4.86 ± 0.31 4.72 ± 0.28 4.13 ± 0.14 5.90 ± 0.31 3.98 ± 0.06
(4.46–5.18) (4.30–5.07) (3.85–4.29) (5.43–6.73) [19] (3.93–4.05)
ALSW 7.35 7.02, 7.02 6.53 6.79 ± 0.40 6.77 ± 0.24 5.99 ± 0.12 8.51 ± 0.46 5.31 ± 0.16
(6.18–7.24) (6.43–7.19) (5.73–6.14) (7.32–9.06) (5.13–5.45)
ABLE 2. Craniodental measurements of R. francisi sp. nov., R. beddomei, R. formosae, R. trifoliatus, R. luctus and R. sedulus. Mean ± SD, minimum and maximum values are given. Sample
sizes where differing from those given under n are included in brackets. Definitions of measurements are included in the Materials and Methods section
28 P. Soisook, M. J. Struebig, S. Noerfahmy, H. Bernard, I. Maryanto, et al.
FIG. 2. Lateral view (a, b), dorsal view (c), and occlusal view (d) of the upper (left) and lower toothrow (right) of R. francisi sp. nov.,
♀BMNH.84.1970 (holotype) from Sabah, Malaysia. Scale = 10 mm
fmaxe of the CF segment of 49.2–50.0 kHz. The call
duration (d) is 20.2–39.9 ms. The inter-pulse inter-
val (ipi) varies between 30.7 and 126.0 ms.
Comparison with other species
Rhinolophus francisi differs significantly in size
from the larger R. luctus and smaller R. sedulus
(Table 1). It is closely similar to other medium-sized
woolly horseshoe bat species, namely R. trifol iatus,
R. beddomei and R. formosae, the latter two of
which have a slightly longer FA (Table 1) and are
known to be restricted to the Indian Subcontinent
and Taiwan, respectively. Although similar in size, it
differs from R. trifoliatus in having brown hairs and
a dark brown noseleaf and ear membranes, whereas
the hairs are yellowish brown and noseleaf and the
ears are yellow in R. trifoliatus.
In the skull, R. francisi overlaps in size (e.g., SL
and CCL) with R. beddomei and R. formosae and
is slightly larger than R. trifoliatus (Table 2, Fig. 3).
It is distinctly smaller than R. luctus and larger than
R. sedulus (Table 2, Fig. 3). The PCA based on 13
craniodental measurements also clearly indicates
the similarity of the skull size between R. francisi,
R. beddomei and R. formosae and the distinction
from R. luctus and R. sedulus (Fig. 5). The sagittal
crest of R. francisi, although well defined, is much
less developed anteriorly than in R. beddomei and
R. trifoliatus (Fig. 3). The Taiwanese R. formosae is
essentially similar in the size and shape of the skull
to that of R. francisi but has distinctly shorter upper
canines (Fig. 3) and the anterior median swelling is
slightly more inflated (Fig. 3). The first upper pre-
molar (P
) of R. formosae is partially extruded so
that the upper canine (C
) and the second upper pre-
molar (P
) are nearly in contact (Fig. 4c). In R. fran-
cisi, at least in specimens examined, the P
is situ-
ated in the middle of the toothrow (Fig. 4a). In the
lower toothrow, the canine (C
) of R. francisi is
larger than that of R. formosae in crown area (Fig.
4a versus 4c). In R. beddomei, the teeth are more
massive than in R. francisi (Fig. 4a versus 4b).
In the acoustic characters, the call frequency of
R. francisi, which has an fmaxe of 49.2–50.0 kHz,
is closely similar but slightly lower than that of the
sympatric and similar sized species R. trifoliatus,
which has an fmaxe of 50.0–53.5 kHz in Thailand
(Soisook et al., 2010) and 50–54 kHz in peninsular
Malaysia and Sabah (Francis, 2008). Two individu-
als of R. beddomei recorded from Shendu runey,
New Rhinolophus from Southeast Asia 29
IG. 3. Lateral (left of each row) and dorsal view (right of each row) of skulls of: a — R. francisi sp. nov., ♂PSUZC-MM.2008.51
(holotype of thailandicus subsp. nov.) from Thailand; b — R. beddomei ♂BMNH. (holotype) from India; c — R. formosae
♀NMNS006665 from Taiwan; d — R. trifoliatus ♀BMNH. (holotype of edax) from Singapore; e — R. luctus BMNH.
(holotype of foetidus) from Sarawak, Malaysia; f — R. sedulus ♀BMNH. (holotype) from Sarawak, Malaysia. Scale = 10 mm
30 P. Soisook, M. J. Struebig, S. Noerfahmy, H. Bernard, I. Maryanto, et al.
FIG. 4. Occlusal view of left upper toothrow (left of each row) and right lower toothrow (right of each row) of: a — R. francisi sp. nov.,
♂PSUZC-MM.2008.51 (holotype of thailandicus subsp. nov.) from Thailand; b — R. beddomei ♂BMNH. (holotype)
from India; c — R. formosae ♀NMNS006665 from Taiwan; d — R. trifoliatus ♀BMNH. (holotype of edax) from Singapore;
e — R. luctus BMNH. (holotype of foetidus) from Sarawak, Malaysia; f — R. sedulus ♀BMNH. (holotype) from
Sarawak, Malaysia. Scale = 10 mm
Agasthyamalai Hills, Kerala (southern West ern
Ghats), India, emitted an fmaxe of 43.0–45.5 kHz
with d of 56.0–72.0 ms (K. Desh pande, unpublished
data). Wordley et al. (2014) reported an fmaxe of
R. beddomei as 41.7–43.3 kHz from the Anamalai
Hills (southern Western Ghats), India. In Taiwan, in-
dividuals of R. formosae, which were captured and
subsequently released had an fmaxe of 44.4–44.6
kHz and a d of 36.0–63.0 ms (n = 3) (S.-F. Chen, un-
published data). The fmaxe of the larger species,
R. luctus, is 32.0 kHz in Thailand (Soisook et al.,
2010) and 40–42 kHz in Sabah and peninsular Ma -
lay sia (Francis, 2008). The smaller species, R. sedu-
lus, has an fmaxe of 67 kHz in peninsular Malaysia
and 62–76 kHz in Sabah (Francis, 2008).
Genetic analyses
An analysis of the cytochrome oxidase-I (COI)
partial gene sequence shows that Rhinolophus
francisi differs genetically by 14.67% from the sim-
ilar sized R. trifoliatus, and by 11.79% and 14.87%
from the two slightly larger species, R. beddomei
and R. formosae, respectively. It also differs by
14.91% from the smallest species of the group,
R. sedulus, and by 12.32% from the largest species
R. luctus (Table 4).
A maximum-likelihood phylogenetic reconstruc-
tion based on these sequence data showed only mod-
erate bootstrap support (62%) for a monophyletic
New Rhinolophus from Southeast Asia 31
IG. 5. Principal component analysis (PC1 and PC2) based on 13 craniodental characters of 41 specimens of R. francisi sp. nov. (black
diamonds), R. beddomei (squares), R. formosae (circles), R. trifoliatus (triangles), R. luctus (crosses) and R. sedulus
(asterisks). Loading scores are in Table 3
grouping of R. francisi with R. beddomei, R. for-
mosae, R. luctus, R. sedulus and R. trifoliatus, but is
in line with our morphology-based designation of
this taxon to the trifoliatus-group (Fig. 6). Nonethe -
less, specimens of R. francisi from Kalimantan and
Thailand showed sequence divergence of 10.03%
from each other (Table 4), a relatively large dif-
ference when it is considered that some species
within the trifoliatus-group (e.g., R. luctus versus
Character PC1 PC2 PC3
SL -0.287 0.016 0.166
CCL -0.287 0.098 0.188
ZB -0.284 0.003 -0.034
BB -0.276 0.172 0.179
MW -0.282 -0.094 0.018
PC -0.239 -0.774 -0.315
-0.288 0.001 0.125
PL -0.273 0.259 0.267
-0.255 0.405 -0.835
-0.279 0.224 -0.064
-0.288 -0.012 0.104
AMSW -0.276 -0.229 -0.004
ALSW -0.287 -0.138 0.078
Eigenvalues 11.772 0.447 0.225
% of total variance explained 90.550 3.440 1.730
ABLE 3. Factor loading scores of the characters used in PCA
and variance explained by the first three components.
Definitions of measurement are included in the Materials and
Methods section
32 P. Soisook, M. J. Struebig, S. Noerfahmy, H. Bernard, I. Maryanto, et al.
R. beddomei) can show as little as 2.84% sequence
divergence at the same marker. On the other hand,
we note that the sequence divergence between R. tri-
foliatus and R. formosae was as large as 16.19%
(Table 4). Currently, because the single specimen of
R. francisi known from Thailand shows no discrete
morphological or echolocation differences from the
Kalimantan specimen, we consider that the Thai
bat is likely to represent a different subspecies of
R. francisi, as described below. Nevertheless, more
specimens from future surveys using harp traps in
evergreen forest in Thailand may reveal that the two
disjunct populations are actually distinct at species
The three specimens, ROM MAM 111303, 111309
and 111321, from south-central Vietnam reported as
Rhinolophus JLE sp. B’ in Francis et al. (2010)
were all genetically very similar to each other (boot-
strap support = 98%). These bats formed a well-sup-
ported monophyletic clade (bootstrap support =
85%) with R. francisi (Fig. 6), interestingly showing
a well-supported sister relationship (bootstrap sup-
port = 81%) with the specimen from Borneo (aver-
age sequence divergence 6.62%) to the exclusion
of the geographically closer bat from Thailand (av-
erage sequence divergence 7.98%) (Table 4).
Although none of the three specimens from Vietnam
was examined, the picture of the skull of ROM
MAM 111303 on BOLD website (www. boldsys- looks very similar to R. francisi. In sum-
mary, these phylogenetic analyses, while prelimi-
nary, suggest that Rhinolophus JLE sp. B also
belongs to R. francisi, probably as a separate sub -
species, however, we cannot rule out the possibility
that multiple species are present. Further detailed
examination of the morphology, measurements, and
echolocation data, if available, is re com mended to
confirm the taxonomic status of these specimens.
Ecology and conservation notes
In Borneo, the type specimen from Gunung Trus
Madi in Sabah was caught in a mist net set in forest
on a mountain ridge (C. M. Francis, personal com-
munication). It was found along with seven other bat
species during the expedition in 1983 (Sheldon and
Francis, 1985). A second individual was captured in
undisturbed evergreen forest of Maliau Basin and
subsequently released. The specimens from Kali -
man tan were collected in undisturbed (Tanjung Pu -
ting National Park; Gunung Palung National Park),
and logged evergreen forest (Nanga Tayap —
specimens subsequently released), at sites where
both R. sedulus and R. trifoliatus were also present
Species 1 2 3 456789101112131415
1. R. francisi 10.03/1.42 1.46 1.82 1.54 1.50 1.73 0.88 1.72 1.67 1.70 1.76 1.77 1.95 1.66 1.74
2. R. trifoliatus 14.67 0.80/0.17 1.45 1.74 1.23 1.63 1.59 1.89 1.64 1.94 2.02 2.01 1.89 1.87 1.79
3. R. beddomei 11.79 8.15 NA 1.74 0.80 1.60 1.80 2.20 1.82 2.06 1.92 2.06 2.18 2.01 2.09
4. R. formosae 14.87 16.19 11.41 0.00/0.00 1.61 2.00 1.69 1.95 1.74 1.82 1.77 1.78 2.02 1.88 1.80
5. R. luctus 12.32 9.14 2.84 12.67 1.09/0.20 1.45 1.52 2.13 1.69 1.89 1.93 1.94 1.96 1.90 1.88
6. R. sedulus 14.91 13.52 10.45 16.04 10.62 4.02/0.81 1.72 2.22 2.04 2.35 2.33 2.23 2.12 2.19 2.33
7. R. JLE sp. B 7.30 13.88 10.48 14.90 11.22 13.49 0.31/0.17 1.93 1.83 1.86 1.95 1.97 1.91 1.76 1.82
8. R. acuminatus 18.73 18.40 17.32 18.59 20.12 20.61 19.53 NA 1.77 1.69 1.72 1.69 1.75 2.10 1.80
9. R. borneensis 16.83 15.97 13.56 16.49 15.68 18.96 16.48 17.27 NA 1.62 1.54 1.59 2.02 1.10 1.47
10. R. macrotis 18.06 19.93 16.42 17.63 18.22 21.65 17.70 15.98 13.67 NA 0.86 0.89 1.97 1.83 1.50
11. R. marshalli 16.97 18.58 14.47 15.72 16.66 20.65 16.97 14.54 11.50 4.08 0.53/0.26 0.74 1.99 1.87 1.46
12. R. paradoxolophus 17.81 19.64 15.46 16.78 17.78 20.02 17.46 15.52 12.82 4.86 3.20 NA 1.91 1.81 1.52
13. R. pearsoni 19.92 18.34 18.48 20.12 18.50 19.91 19.04 15.57 19.26 17.91 16.80 17.39 5.59/0.86 1.92 1.76
14. R. philippinensis 16.16 17.48 16.09 17.45 16.90 18.94 15.70 19.63 6.48 15.61 14.59 14.46 0.18 0.00/0.00 1.58
15. R. robinsoni 16.43 17.71 15.72 16.81 16.74 20.43 16.56 17.32 11.89 12.72 10.62 12.66 17.01 12.32 NA
ABLE 4. Matrix showing pairwise sequence divergence (%) at the cytochrome oxidase-I gene among species included in the genetic analysis (bottom left corner) together with standard
error (SE; %) (upper right corner). The average divergence within species and SE are shown in bold
(Struebig et al., 2006). In Thailand, a single speci-
men from Mae Nam Pha Chi was captured in a harp
trap set over a seasonal streamlet surround ed by
dense primary evergreen forest at an elevation of
431 m a.s.l. It was found at dawn in the same trap as
Nycteris tragata, R. microglobosus, Myotis murico -
la, Kerivoula papillosa and Pho nis cus jagorii (Soi -
sook et al., 2010). The collection sites of Trus Madi,
Tanjung Puting and, Mae Nam Pha Chi are legally
protected forests, as are survey sites Maliau Basin
and Gunung Palung. However, the hunting of mam-
mals may still be a problem across this region, and
is considered as major threat to wildlife.
Rhinolophus francisi is currently known from
only six records; with two records in Sabah,
Malay sian Borneo; three in Indonesian Borneo
(Kaliman tan) and a single record in Thailand (see
below). The species may be distributed more widely
in these regions, but has been rarely captured despite
extensive surveys. Genetic da ta also suggest that
this species is likely to occur in Vietnam, although
this needs to be confirmed.
Rhinolophus francisi thailandicus
Soisook and Bates subsp. nov.
(Figs. 1, 3–6; Tables 1–2)
PSUZC-MM.2008.51 (field number PS080420.6),
adult male, body in alcohol, skull and baculum
ex tracted, collected by Pipat Soisook, Tuanjit
Sri thong chuay, Piyawan Niyomwan and Priwan
Sri som, on 20 April, 2008.
Type locality
Pu Nam Ron Stream, Mae Nam Pha Chi WS.,
Ratchaburi Province, Western Thailand (13º15’N,
99º2’E, 431 m a.s.l.).
This subspecies is very similar to the nominate
subspecies from Borneo with a FA of 52.97 mm and
a SL of 24.37 mm. The rostral swelling is relatively
narrower than in the specimens from Borneo, with
an AMSW and ALSW of 4.76 and 6.53 mm, respec-
tively. The 3D1P is relatively short; it is 66.74% of
the length of the 3D2P. The sagittal crest is less
New Rhinolophus from Southeast Asia 33
FIG. 6. Maximum likelihood tree based on DNA barcodes of the six currently known species in the trifoliatus-group and other species
of Southeast Asian Rhinolophus. The genetic distance within and between species are in Table 3. Specimens included in this analysis
are listed in the Appendix
developed than in the nominate subspecies. Genet i -
cally, it differs from the nominate subspecies by
10.03% at a section of the cytochrome oxidase-I
The subspecific name, thailandicus, means ‘of or
from Thailand’ indicating where this subspecies is
found. The proposed English name of the subspecies
is ‘Thailand Woolly Horseshoe Bat’.
Description and taxonomic notes
As in the nominate subspecies from Borneo, the
Thai subspecies, R. f. thailandicus is a medium-
large Rhinolophus. The general appearance is
similar to francisi from Borneo and overlaps in size,
with a FA of 52.97 mm (Table 1). The body mass
(MASS) is 16.0 g. The height of the ear is of 23.81
mm. The noseleaf width (NL) is 12.21 mm (Table
1). The wing measurements are larger than those of
R. f. francisi; the third metacarpal (3MET) is 37.47
mm; the fourth (4MET) is 42.47 mm and the fifth
metacarpal (5MET) is 43.99 mm (Table 1).
In the skull, the SL and CCL are 24.37 mm
and 21.72 mm, respectively (Table 2). The AMSW
and ALSW are of 4.76 mm and 6.53 mm, respec-
tively. The supraorbital ridge is very well defined
and connected to a well-developed sagittal crest
(Fig. 3a). The zygomatic breadth (ZB) is 12.16 mm
which exceeds the mastoid width (MW), 11.31 mm
(Fig. 3a; Table 2). Each zygoma has a distinct trian-
gular-shaped dorsal arch (Fig. 3a). Both the upper
and lower dentition are as in R. f. francisi but are
slightly smaller in size; C–M
is 9.30 mm; C
6.07 mm; M
8.86 mm. The palatal length (PL)
is 3.21 mm (Table 2).
The morphological comparison with other
spe cies is as in the nominate form of R. francisi.
The size of Thai specimen is the smallest of the
species. It is intermediate in size between the
slightly larger R. beddomei and the slightly smaller
R. trifoliatus (Tables 1–2; Fig. 5). As noted above,
a future study with more specimens from Thailand
may prove that the subspecies from Thailand is
specifically distinct.
In Thailand, we are grateful to Mattana Srikrachang, Piya -
wan Niyomwan, as well as the director and staff of the Wildlife
Research Division, DNP for their support. We thank all staff
at the Mae Nam Pha Chi WS for their assistance in the field.
At PSU, we thank Chutamas Satasook, Sara Bumrungsri, Saw -
walak Billasoi, Jirapan Yimkaew, Uraiporn Pimsai, Boun savane
34 P. Soisook, M. J. Struebig, S. Noerfahmy, H. Bernard, I. Maryanto, et al.
Douangboubpha and Tuanjit Srithongchuay for their support
and help in specimen preparation and measurements. We are
also grateful to the Indonesian Ministry of Forestry for research
permissions in Kalimantan, as well as PT. Suka Jaya Makmur
for access to their logging concession in Nanga Tayap. In
Malaysia, we thank the Economic Planning Unit, Sabah Bio -
diversity Council and Maliau Basin Management Com mittee
for access to research sites in Sabah. In the UK, we are ex-
tremely grateful to the late David Harrison as well as Malcolm
Pearch, Nikky Thomas and Beatrix Lanzinger at the Harrison
Institute, for their help during PS’s stay in the UK. At the
Natural History Museum, London, we thank Paula Jenkins for
her support, Rebecca Summerfield for her help in imaging with
CT scanner, and all those who curate and manage the mammal
collection, which was an essential resource for this paper. We
also thank Yen-Jean Chen of the National Museum of Natural
Science, Taiwan for access to the collections. Thanks also go to
Alex Borisenko of the University of Guelph who helped with
coordinating the DNA Barcodes. We are indebted the Darwin
Initiative, DEFRA, UK (Project No; 18002) for financial sup-
port in building taxonomic capacity in Southeast Asian coun-
tries, and Bat Conser va tion International, British American To -
bac co, The Leverhulme Trust and Mohamed Bin Zayed Species
Conservation Fund for supporting field studies of MJS, HB and
SN on Borneo. Thanks also go to Mahesh Sankaran at the
National Centre for Bio log ical Sciences and the Kerala For est
Department (India), and the Rufford Small Grants Found ation
(UK) for support to KD. The bat research of PS was partially
supported by the Higher Edu cation Research Promotion and
National Research University Project of Thailand (NRU), Of -
fice of the Higher Education Com mission. Finally, we would
like to thank Tigga Kingston and the Southeast Asian Bat Con -
servation Research Unit ( for promoting
networking amongst bat researchers in Southeast Asia.
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New Rhinolophus from Southeast Asia 35
Received 08 December 2014, accepted 14 March 2015
Species Catalog number State/Province Country BOLD Process ID
R. f. francisi TP040205 Central Kalimantan Indonesia ABBID008-08
R. f. thailandicus PSUZC-MM.2008.51 Ratchaburi Thailand MSSEA060-10
R. beddomei HZM 1.27943 Sri Lanka ABBM439-05
R. formosae EU166918 Taiwan GBMA2071-09
R. formosae NC_011304 Taiwan GBMA1977-09
R. trifoliatus CMF920703-01 Pahang Malaysia BM506-04
R. trifoliatus ROM MAM 113012 Johor Malaysia ABRSS308-06
R. trifoliatus ROM MAM 113018 Johor Malaysia ABRSS310-06
R. trifoliatus ROM MAM 113041 Johor Malaysia ABRSS324-06
R. trifoliatus ROM MAM 113120 Johor Malaysia ABRSS380-06
R. trifoliatus ROM MAM 113042 Johor Malaysia ABRSS325-06
R. trifoliatus ROM MAM 113101 Johor Malaysia ABRSS365-06
R. trifoliatus ROM MAM 113019 Johor Malaysia ABRSS311-06
R. trifoliatus ROM MAM 113043 Johor Malaysia ABRSS326-06
R. trifoliatus ROM MAM 113112 Johor Malaysia ABRSS372-06
R. trifoliatus SMF 83405 Sabah Malaysia BM508-04
R. trifoliatus SMF 83719 Sabah Malaysia BM137-03
R. trifoliatus SMF 83717 Sabah Malaysia BM154-03
R. trifoliatus ROM MAM 102116 East Kalimantan Indonesia ABRSS160-06
R. trifoliatus ROM MAM 102000 East Kalimantan Indonesia ABRSS063-06
R. trifoliatus ROM MAM 101999 East Kalimantan Indonesia BM262-03
R. trifoliatus D03_bs48 Central Kalimantan Indonesia ABBID050-09
R. trifoliatus PP060504.1 Ratchaburi Thailand MSSEA061-10
R. trifoliatus SB060514-09 Songkhla Thailand ABBTH048-07
R. luctus ROM MAM 114936 Hunan China ABCMA356-06
R. luctus ROM MAM 114948 Hunan China BM386-04
R. luctus EBD 25678 Houaphan Laos ABBM271-05
R. luctus AGS980430-30 Louang Namtha Laos ABBM353-05
R. luctus CMF970516-42 Attapu Laos ABBM174-05
R. luctus ROM MAM 118019 Khammouan Laos BM045-03
R. luctus ZMMU S-175170 Vietnam BM627-04
R. luctus ROM MAM 111387 Quang Nam Vietnam BM374-04
R. luctus HZM 6.36475 Kaoh Kong Cambodia ABBSI040-04
R. luctus PP070915.27 Ratchaburi Thailand MSSEA060-10
R. luctus AGS970412-02 Krabi Thailand ABBM063-05
R. sedulus ROM MAM 113050 Johor Malaysia BM431-04
R. sedulus ROM MAM 117877 Negeri Sembilan Malaysia BM141-03
R. sedulus B06_bs31 Central Kalimantan Indonesia ABBID029-09
R. JLE sp. B ROM MAM 111309 Quang Nam Vietnam ABRVN492-06
R. JLE sp. B ROM MAM 111321 Quang Nam Vietnam ABRVN503-06
R. JLE sp. B ROM MAM 111303 Quang Nam Vietnam BM367-04
R. pearsoni ROM MAM 112450 Vietnam ABRVN666-06
R. pearsoni SB060520-13 Loei Thailand ABBTH105-07
R. pearsoni SB060518-02 Loei Thailand ABBTH064-07
R. pearsoni SB060518-01 Loei Thailand ABBTH063-07
R. marshalli HZM 4.35974 Myanmar ABBM466-05
R. marshalli EBD 24975 Houaphan Laos ABBM326-05
R. marshalli INECOL M0155 Vientiane Laos ABBM369-05
R. marshalli EBD 23915 Vientiane Laos ABBM240-05
R. paradoxolophus ROM MAM 107629 Tuyen Quang Vietnam ABRVN113-06
R. macrotis ABBTH021-07 Satun Thailand SB060512-01
R. acuminatus BM MS091003.1 Brunei MSSEA094-10
R. robinsoni SB060512-12 Satun Thailand ABBTH032-07
R. borneensis MZB MS100806 Sumatra Indonesia MSSEA079-10
R. philippinensis SMF 83403 Sabah Malaysia BM503-04
R. philippinensis SMF 83709 Sabah Malaysia BM166-03
R. philippinensis SMF83710 Sabah Malaysia BM147-03
R. philippinensis EBD 23567 Sabah Malaysia ABBM023-05
R. philippinensis EBD 23568 Sabah Malaysia ABBM022-05
List of specimens included in the genetic analyses
36 P. Soisook, M. J. Struebig, S. Noerfahmy, H. Bernard, I. Maryanto, et al.
... Our analysis showed the diversification of Rhinolophidae in the region began around late Oligocene till early Miocene. R. JLEsp (undescribed species [69]; the acronym from [70] denoting Judith L. The majority of potential cryptic species or incipient species within rhinolophids species complexes diverged in mid-Pliocene within the last 2 Ma indicates rapid radiation in Plio-Pleistocene, with the exception of the R. pearsonii complex that diverged during mid-Miocene 7.38 Ma (HPD = 5.2-9 Ma) indicated a support to split R. pearsonii into multiple different species. The time divergence construction using secondary calibration at multiple nodes in BEAST supported the evolutionary distinction between the clades within species complexes and the incipient species might further be considered as distinct species. ...
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Background Family Rhinolophidae (horseshoe bats), Hipposideridae (leaf-nosed bats) and Rhinonycteridae (trident bats) are exclusively distributed in the Old-World, and their biogeography reflects the complex historic geological events throughout the Cenozoic. Here we investigated the origin of these families and unravel the conflicting family origin theories using a high resolution tree covering taxa from each zoogeographic realm from Africa to Australia. Ancestral range estimations were performed using a probabilistic approach implemented in BioGeoBEARS with subset analysis per biogeographic range [Old-World as whole, Australia–Oriental–Oceania (AOO) and Afrotropical–Madagascar–Palearctic (AMP)]. Result Our result supports an Oriental origin for Rhinolophidae, whereas Hipposideridae originated from the Oriental and African regions in concordance with fossil evidence of both families. The fossil evidence indicates that Hipposideridae has diversified across Eurasia and the Afro-Arabian region since the Middle Eocene. Meanwhile, Rhinonycteridae (the sister family of Hipposideridae) appears to have originated from the Africa region splitting from the common ancestor with Hipposideridae in Africa. Indomalaya is the center of origin of Rhinolophidae AOO lineages, and Indomalayan + Philippines appears to be center of origin of Hipposideridae AOO lineage indicating allopatric speciation and may have involved jump-dispersal (founder-event) speciation within AOO lineage. Wallacea and the Philippines may have been used as stepping stones for dispersal towards Oceania and Australia from the Oriental region. Multiple colonization events via different routes may have occurred in the Philippines (i.e., Palawan and Wallacea) since the Late Miocene. The colonization of Rhinolophidae towards Africa from Asia coincided with the estimated time of Tethys Ocean closure around the Oligocene to Miocene (around 27 Ma), allowing species to disperse via the Arabian Peninsula. Additionally, the number of potential cryptic species in Rhinolophidae in Southeast Asia may have increased since Plio-Pleistocene and late Miocene. Conclusion Overall, we conclude an Oriental origin for Rhinolophidae, and Oriental + African for Hipposideridae. The result demonstrates that complex historical events, in addition to species specific ecomorphology and specialization of ecological niches may shape current distributions.
... These are either very rare or have a patchy distribution, and thus are rarely captured. R. francisi was only described in 2015, and is reported from five localities in Borneo (Soisook et al., 2015), producing overlapping frequencies with the common species R. trifoliatus, Hipposideros doriae and Coelops robinsoni, are also similarly rare and patchily distributed, and produce very high frequency broadband calls with a very abbreviated, or absent, CF component (Kingston, 2016). On the other hand the CF calls of R. pusillus and H. larvatus should be relatively simple to discriminate by the classifier but so far there are no available recordings for these species since they are highly localised to karst outcrops (Phillipps & Phillipps, 2016). ...
Bats comprise a quarter of all mammal species, provide key ecosystem services and serve as effective bioindicators. Automated methods for classifying echolocation calls of free-flying bats are useful for monitoring but are not widely used in the tropics. This is particularly problematic in Southeast Asia, which supports more than 388 bat species. Here, sparse reference call databases and significant overlap among species call characteristics makes the development of automated processing methods complex. To address this, we outline a semi-automated framework for classifying bat calls in Southeast Asia and demonstrate how this can reliably speed up manual data processing. We implemented the framework to develop a classifier for the bats of Borneo and tested this at a landscape in Sabah. Borneo has a relatively well-described bat fauna, including reference calls for 52% of all 81 known echolocating species on the island. We applied machine learning to classify calls into one of four call types that serve as indicators of dominant ecological ensembles: frequency-modulated (FM; forest-specialists), constant frequency (CF; forest-specialists and edge/gap foragers), quasi-constant frequency (QCF; edge/gap foragers), and frequency-modulated quasi constant frequency (FMqCF; edge/gap and open-space foragers) calls. Where possible, we further identified calls to species/sonotype. Each classification is provided with a confidence value and a recommended threshold for manual verification. Of the 245,991 calls recorded in our test landscape, 85% were correctly identified to call type and only 10% needed manual verification for three of the call types. The classifier was most successful at classifying CF calls, reducing the volume of calls to be manually verified by over 95% for three common species. The most difficult bats to classify were those with FMqCF calls, with only a 52% reduction in files. Our framework allows users to rapidly filter acoustic files for common species and isolate files of interest, cutting the total volume of data to be processed by 86%. This provides an alternative method where species-specific classifiers are not yet feasible and enables researchers to expand non-invasive monitoring of bat species. Notably, this approach incorporates aerial insectivorous ensembles that are regularly absent from field datasets despite being important components of the bat community, thus improving our capacity to monitor bats remotely in tropical landscapes.
... The Family Rhinolophidae is represented globally by a single genus, Rhinolophus with 87 species in 15 species groups based on close morphological relationships (Csorba et al. 2003, Soisook et al. 2015. Rhinolophus luctus is listed under the trifoliatus group with 4 other species-R. ...
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Bangladeshi chiropteran fauna is poorly studied and there is a lack of complete inventories. A total of 39 species of bats have been reported to occur in the country. Great Woolly Horseshoe Bat Rhinolophus luctus, (Temmick 1834) has been expected to occur in northeast Bangladesh based on its presence in north-eastern India and adjoining areas. However, there had been no published report on the occurrence to date. We first report the occurrence of R. luctus in a northeastern forest of Bangladesh. A pair of R. luctus were spotted opportunistically and photographed on September 4, 2019 along the shoreline of a rocky stream in Patharia Hill Reserve Forest while surveying non-human primates. This forest is an important reservoir for several globally threatened species in northeast Bangladesh though the characterization of its biodiversity is yet incomplete. Further study into the regions faunal diversity may reveal additional species, particularly the bats. So, complete assessments of the conservation status of Bangladeshi bat fauna is urgently needed to implement effective conservation measures.
Insularity provides ample opportunities for species diversification. Sri Lanka is home to a large diversity of species, many of which are endemic but morphologically similar to species found in southern India, due to recent speciation events, suggesting a complex evolutionary history. However, in some taxa although morphological diversity has been noted, the genetic level variations are minimal. Among the wide-ranging horseshoe bats such a phenomenon is noted. In this study, we used bioacoustics, morphometric and molecular data to evaluate the relationships between the taxa of lesser woolly horseshoe bats in the India and Sri Lanka. Our study reveals that the two taxa—Rhinolophus beddomei Andersen, 1905 and here we have validated the existing subspecies from peninsular India and R. sobrinus Andersen, 1918 from Sri Lanka are genetically very close to R. perniger Hodgson, 1843. Currently the taxa—beddomei and sobrinus are recognized as subspecies of Rhinolophus beddomei Andersen, 1905. We provide a detailed description of the taxa beddomei and sobrinus as the original descriptions are limited in nature.
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Imbak Canyon Conservation Area (ICCA) is one of the conservation areas managed by the Sabah Foundation, which comprise of mixed vegetation forest landscape. A bat survey was conducted at ICCA from August 16th to 26th, 2017. A total of 141 individuals of bats representing 17 species were recorded from the eight nights of mist netting and harp trapping at various sites within the conservation area. Echolocation calls from 120 individuals of insectivorous bats representing 13 species were recorded, with 90% accuracy in relative amount. The captured bats were screened for ectoparasites from Order Diptera (91%), Mesostigmata (5%) and Ixodida (1%), and indicate that there is 66.7% prevalence. The results from the survey are paramount in enhancing information and knowledge on Bornean bats and their obligate ectoparasites.
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Systematics and taxonomy are the backbone of all components of biology and ecology, yet cryptic species present a major challenge for accurate species identification. This is especially problematic as they represent a substantial portion of undiscovered biodiversity, and have implications for not only species conservation, but even assaying potential risk of zoonotic spillover. Here, we use integrative approaches to delineate potential cryptic species in horseshoe bats (Rhinolophidae), evaluate the phenotypic disparities between cryptic species, and identify key traits for their identification. We tested the use of multispecies coalescent models (MSC) using Bayesian Phylogenetic and Phylogeography (BPP) and found that BPP was useful in delineating potential cryptic species, and consistent with acoustic traits. Our results show that around 40% of Asian rhinolophid species are potentially cryptic and have not been formally described. In order to avoid potential misidentification and allow species to be accurately identified, we identified quantitative noseleaf sella and acoustic characters as the most informative traits in delineating between potential cryptic species in Rhinolophidae. This highlights the physical differences between cryptic species that are apparent in noseleaf traits which often only qualitatively described but rarely measured. Each part of the noseleaf including the sella, lateral lappets, and lancet furrows, play roles in focusing acoustic beams and thus, provide useful characteristics to identify cryptic Rhinolophus species. Finally, species delimitation for cryptic species cannot rely on genetic data alone, but such data should be complemented by other evidence, including phenotypic, acoustic data, and geographic distributions to ensure accurate species identification and delineation.
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Classical and molecular cytogenetic methods were applied to study the karyotypes of one species of Hipposideridae and three taxa of the Rhinolophidae subgenus Aquias from Malaysian Borneo. Except for four chromosomal pairs with autapomorphic arm combinations, the karyotype of Coelops robinsoni was found to be similar to the closely related Aselliscus stoliczkanus. From the three Rhinolophus taxa studied, only R. trifoliatus was found to share the karyotype with conspecifics from Peninsular Malaysia. In contrast, the karyotype of R. luctus foetidus from Sarawak, Borneo differed in the composition of the Y-autosomal translocation products from the closely related R. morio from Peninsular Malaysia, formerly also a subspecies of R. luctus. Therefore, elevation to specific rank is suggested for R. l. foetidus. Examination of the chromosomal set of male R. sedulus specimens from Borneo with 2n = 45 and a Neo-X1X2Y sex chromosome system revealed extreme differences to the karyotype of specimens from Peninsular Malaysia with 2n = 28, to date also classified as R. sedulus. Therefore, with Sarawak, Borneo, as the type locality for R. sedulus, the taxon from Peninsular Malaysia is here described as a new species. Key words: sex-autosome translocations, cytotaxonomy, fluorescence in-situ hybridization
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Discus on several mammals species in Java island
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Buku ini berisi 52 spesies mamalia terpilih di Pulau Jawa dengan kriteria endemik, status konservasi, peran alamiah penting dan keunikannya; dilengkapi dengan nama ilmiah, nama lokal, gambar dan peta sebaran. Ditulis secara rinci dengan gaya bahasa yang sederhana dan lugas sehingga mudah dipahami berbagai kalangan. Detail informasi yang disajikan dalam buku ini meliputi klasifikasi, deskripsi, ekologi, habitat, ancaman, dan status konservasinya sesuai dengan Permen LHK No. 106 Tahun 2018 serta status populasinya menurut IUCN dan CITES. Buku ini diharapkan dapat membantu para pengambil kebijakan dan masyarakat dalam mengenal lebih jauh mamalia yang ada di Pulau Jawa dan membantu dalam upaya konservasinya. Selain itu juga untuk melengkapi khazanah ilmu pengetahuan di Indonesia.
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Field surveys in the Song Thanh and Saola Quang Nam Nature Reserves (Quang Nam Province , central Vietnam) were conducted in 2018 and 2019. In total, 197 individuals of small mammals were captured and studied in the field or collected as voucher specimens. Based on these data, an updated checklist of small mammals of Quang Nam Province is provided. A total of 78 species in 15 families and 6 orders is recorded from both reserves: viz., 57 species in the Song Thanh Nature Reserve and 39 species in the Saola Quang Nam Nature Reserve. Records of 20 species are new to the mammal checklist of Quang Nam Province.
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Among several rendering techniques for volumetric data, direct volume rendering is a powerful visualization tool for a wide variety of applications. This paper describes the major features of hardware based volume exploration and presentation tool - Drishti. The word, Drishti, stands for vision or insight in Sanskrit, an ancient Indian language. Drishti is a cross-platform open-source volume rendering system that delivers high quality, state of the art renderings. The features in Drishti include, though not limited to, production quality rendering, volume sculpting, multi-resolution zooming, transfer function blending, profile generation, measurement tools, mesh generation, stereo/anaglyph/crosseye renderings. Ultimately, Drishti provides an intuitive and powerful interface for choreographing animations.
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Bats play crucial roles in ecosystems, are increasingly used as bio-indicators and are an important component of tropical diversity. Ecological studies and conservation-oriented monitoring of bats in the tropics benefit from published libraries of echolocation calls, which are not readily available for many tropical ecosystems. Here, we present the echolocation calls of 15 species from the Valparai plateau in the Anamalai Hills, southern Western Ghats of India: three rhinolophids (Rhinolophus beddomei, R. rouxii (indorouxii), R. lepidus), one hipposiderid (Hipposideros pomona), nine vespertilionids (Barbastella leucomelas darjelingensis, Hesperoptenus tickelli, Miniopterus fuliginosus, M. pusillus, Myotis horsfieldii, M. montivagus, Pipistrellus ceylonicus, Scotophilus heathii, S. kuhlii), one pteropodid (Rousettus leschenaultii) and one megadermatid (Megaderma spasma). Discriminant function analyses using leave-one-out cross validation classified bats producing calls with a strong constant frequency (CF) component with 100% success and bats producing frequency modulated (FM) calls with 90% success. For five species, we report their echolocation calls for the first time, and we present call frequencies for some species that differ from those published from other parts of the species' ranges. This exemplifies the need for more local call libraries from tropical regions to be collected and published in order to record endemic species and accurately identify species whose calls vary biogeographically.
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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 free of charge.
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Borneo’s rainforests are renowned for their high levels of biodiversity, yet information on the distribution and structure of this diversity is lacking, particularly for less charismatic taxonomic groups. We quantified bat diversity across ten sites within a contiguous tract of largely undisturbed rainforest in the Heart of Borneo (HoB) transboundary conservation area. Using comparative analyses of 1,362 bat captures from six sites in Brunei Darussalam, together with data from four additional sites in neighbouring territories, we show that the main differences in bat assemblage composition between sites were driven by the abundances of a few cave-roosting species. Beta diversity (distance decay) was notably low and non-significant. Bat assemblage structure in these undisturbed palaeotropical forests is therefore relatively homogenous in the absence of environmental gradients. By adding 15 bat species to the Brunei national inventory, we confirm the area of north Borneo to be species-diverse and therefore a priority for conservation efforts. However, we also highlight that coastal forest to be included in a recent extension to the HoB hosts bat assemblages with the fewest species and lowest densities. We maintain that extending the HoB in Brunei to include a more diverse portfolio of habitat types is still warranted on the grounds of maximising botanical diversity and habitat area, as long as it does not detract attention from interior forests that support higher vertebrate diversity.
There is substantial variation in the reported effects of logging on tropical forest fauna. In addition to inherent variation in disturbance sensitivity among taxa, another contributing factor is that most studies use comparative analyses of unlogged versus logged forests, which cannot fully account for heterogeneity in disturbance as well as underlying environmental gradients. To better understand how logging affects biodiversity, we examined changes in bat assemblages across a disturbance gradient ranging from old growth to forest logged several times. In one of the first evaluations of repeatedly logged forest, we use both comparative and gradient analyses to reveal substantial signals in assemblage change in response to habitat alteration. Despite multiple rounds of extraction in the most degraded forest, neither approach revealed a definitive effect of logging on site-based richness. However, each approach generated insight into assemblage compositional responses to forest degradation. Structural differences were evident between old-growth and repeatedly logged forest, and depauperate assemblages characterised degraded sites with low, open canopy. Ordinations identified species that best contributed to the signal of assemblage change, and also key associated forest-structure variables. Models of trap-based abundance confirmed not only the importance of forest height in determining assemblage change but also the role of tree-cavity availability in supporting forest specialists, indicating that efforts to supplement this resource could aid restoration. While highlighting the ecological importance of unlogged stands, we show that heavily degraded forests—even those that have been repeatedly logged—still hold some potential value for tropical biota and could have a role in conservation.