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INTRODUCTION
Pteropus vampyrus (Linnaeus, 1758), also
known as the large flying fox, has the largest
wingspan of any bat species in the world (Andersen,
1912; Corbet and Hill, 1992). It is native to the
Philip pines, western Indonesia, and peninsular
Southeast Asia where it is typically found in coastal
areas living in large colonies comprising thousands
of individuals (Goodwin, 1979; Corbet and Hill,
1992; Jones and Kunz, 2000). Pteropus vampyrus
is an important seed disperser and pollinator of eco-
logically and economically important plants, such as
figs (Ficus spp.) and durian (Durio zibethinus) (Fu -
jita and Tuttle, 1991; Jones and Kunz, 2000; Stier
and Mildenstein, 2005). The efficacy of flying foxes
as seed dispersers requires large, healthy popula-
tions (McConkey and Drake, 2006), which are in-
creasingly rare as in the face of habitat conversion
and intensive hunting (Mickleburgh et al., 1992;
Mohd-Azlan et al., 2001; Struebig et al., 2007).
Pteropus vampyrus is arguably one of the most
well-known Pteropus species in Southeast Asia. Re -
searchers have investigated many aspects of P. vam -
pyrus biology, including ecology (Mohd-Azlan et al.,
2001; Stier, 2003; Gumal, 2004; Mildenstein et al.,
2005; Stier and Mildenstein, 2005) and physiology
(Reeder et al., 2006a, 2006b; Riskin et al., 2010).
Conservation research on P. vampyrus has gained
traction in recent years as the effects of hunting have
Acta Chiropterologica, 20(1): 59–71, 2018
PL ISSN 1508-1109 © Museum and Institute of Zoology PAS
doi: 10.3161/15081109ACC2018.20.1.004
Low levels of population structure among geographically distant populations
of Pteropus vampyrus (Chiroptera: Pteropodidae)
SUSAN M. TSANG1, 2, 3, 5, SIGIT WIANTORO4, MARIA JOSEFA VELUZ3, NANCY B. SIMMONS2,
and DAVID J. LOHMAN1, 3
1Department of Biology, City College and the Graduate Center, The City University of New York, 365 Fifth Avenue,
New York, NY, 10016, USA
2Department of Mammalogy, American Museum of Natural History, Central Park West and 79th Street,
New York, NY, 10024, USA
3Zoology Division, National Museum of the Philippines, Padres Burgos Ave, Ermita, Manila, 1000 Metro Manila, Philippines
4Museum Zoologicum Bogoriense, Indonesian Institute of Sciences, Jl. Raya Jakarta-Bogor, Km. 46, Cibinong, 16911, Indonesia
5Corresponding author: E-mail: stsang@amnh.org
Pteropus vampyrus, the largest bat in the world, has a broad geographic range covering much of Southeast Asia. The wide
distribution of P. vampyrus and its ability to cross oceanic expanses makes management of this threatened species an international
concern. Pteropus vampyrus is an essential seed disperser and pollinator of rain forest trees, many of which are ecologically and
economically important. Understanding population dynamics of P. vampyrus is thus critical to addressing conservation issues and
global health concerns. We used phylogenetic inference and population genetic indices to infer past gene flow between populations
of P. vampyrus throughout most of the species’ range. Population genetic parameters indicate low levels of nucleotide variability
with high haplotype diversity across its range, implying a demographic scenario of recent population expansion after a bottleneck.
Subspecies were not found to be monophyletic from the genetic data, which may reflect some level of genetic variation on even
shallower time scales. The low level of population genetic structure throughout the species range is not necessarily surprising given
its high vagility and seasonal migratory behavior. However, it cannot be entirely excluded that these results may reflect historical
connectivity or lineage sorting issues rather than more recent persistent gene flow. These findings highlight the need for international
cooperation and monitoring to ensure persistence of populations and to create a species management plan that can protect the species
throughout its range. Increased genetic sampling is needed to ascertain P. vampyrus’ commonly used dispersal routes and to assess
the possibility of asymmetric gene flow among populations.
Key words: Southeast Asia, population genetics, Indonesia, flying fox, Philippines, Pteropus vampyrus
been recognized (Struebig et al., 2007; Harrison et
al., 2011; Croes, 2012; Heng, 2012). Additional ly,
there have been more studies in the past decade fo-
cused on screening P. vampyrus for zoonotic path o -
gens and parasites including Nipah virus, Hen dra
virus, and Hepatocystis species (Yob et al., 2001;
Sendow et al., 2006; Olival et al., 2007; Wang et al.,
2008; Epstein et al., 2009; Rahman et al., 2010,
2013; Sohayati et al., 2011; Breed et al., 2013).
Pteropus vampyrus has been an exemplar in
studies of evolutionary relationships among ge-
nera in the family Pteropodidae, as well as phylo-
genetic analyses of the genus Pteropus (Giannini
et al., 2008; Almeida et al., 2014; S.M.T., S.W.,
M.J.V., N. Sugita, N.B.S., and D.J.L., unpublished
data). However, population dynamics within this
or any other Pteropus species have never been in-
vestigated across their range. A previous study of
P. vampyrus population structure was limited in its
taxonomic and genetic sampling, but suggested little
genetic differentiation among Sundaic populations
(Olival, 2008). A clear understanding of this spe-
cies’ genetic diversity is important for conservation
management, managing of gene flow in rainforest
tree species, and modeling disease ecology of zoo -
notic pathogens. Unfortunately, population genetic
data on this or any other Pteropus species are too
sparse to even speculate on these questions. We aim
to remedy this lacuna on the population dynamics
and connectivity of P. vampyrus so that conservation
management needs can be met and questions related
to gene flow and potential routes of pathogen dis-
persal can be addressed. This study will provide
a framework for future research, including targeted
satellite telemetry projects to acquire observational
evidence of the dispersal patterns we infer. We
hypothesize that gene flow between P. vampyrus
populations may be adequately described by an iso-
lation-by-distance model of migration, with popula-
tions becoming increasingly genetically differenti-
ated as geographic distance between them increases.
Lack of genetic differentiation between Sundaic
populations (Olival, 2008) suggests that some de-
gree of gene flow exists among populations, while
past re search on Malaysian P. vampyrus suggests
that dispersal is localized (Epstein et al., 2009).
Infrequent dispersal between distant populations
would result in population structure that increases
with geographic distance. Conversely, frequent gene
flow among P. vam pyrus populations would reduce
the signal of an isolation-by-distance model and
result in little differentiation across the range of the
species.
MATERIALS AND METHODS
We sampled fresh tissues from adult individuals in popula-
tions throughout Indonesia and the Philippines (Appendix). We
took 4 mm2wing biopsy punches from a majority of the bats
represented, and opportunistically collected liver samples from
specimens vouchered for the reference collections of the
Museum Zoologicum Bogoriense or National Museum of the
Philippines, following standard protocols (Corthals et al.,
2015). Bat capture, handling, and sampling methods were ap-
proved by the IACUC committee at City College of New York
— CUNY through protocol No. 896.2 to D. J. Lohman and
S. M. Tsang. Permits for fieldwork were granted from the
Ministry of Foreign Research and Technology and the Ministry
of Forestry and Environment in Indonesia, and the Department
of Environment and Natural Resources and the Biodiversity
Management Bureau in the Philippines. Canopy mist nets were
set up 20 to 30 m above the ground by having a local tree
climber tie the nets to a pole extending above the highest trees
in flyways identified during prior reconnaissance. A single rope
went through both sides of the mist net loops to create a double
pulley system to allow for efficient lowering of the net. We used
either 6 m, 9 m, or 12 m nets depending on the distance between
trees in the flyway. When bats were caught in the mist net, the
pulley was immediately lowered to extract the animal. Bats
were placed into individual cloth holding bags that were misted
with water to keep them cool until the bats could be processed.
Additional tissue samples were obtained from wild-caught bats
from Lubee Bat Conservancy (Gainesville, Florida), Lee Kong
Chian Museum of Natural History (formerly Raffles Museum of
Biodiversity Research, Singapore), and the Royal Ontario Mu -
se um (Toronto, Canada). By combining tissue samples from
bats we collected with material obtained from other institutions,
we were able to sample 39 individuals representing colonies
across the species’ range (Fig. 1): Philippines (n= 11, combined
three sites: Negros Occidental, Leyte, Palawan), Borneo (n= 2),
Sumatra (n= 7), Java (n= 8), Bali (n= 5), Flores/Sumba-
wa (eastern Lesser Sundas, n=3), and peninsular Southeast Asia
(n= 3). We assumed that each colony was a separate population
that did not interbreed with the others, as inferred by recognized
subspecies differences or by large geographic distances (≥ 500
km) separating the colonies. Each of the six recognized P. vam -
pyrus subspecies (Table 1 and Fig. 1 — Corbet and Hill, 1992;
Koopman, 1993, 1994; Simmons, 2005) was represented in at
least one of the populations, with the exception of unsampled
P. v. edulis, which is restricted to Timor, for a total of 39 indi-
viduals. Samples of Acerodon celebensis, Pteropus hypome-
lanus, and P. alecto were included as outgroup taxa to root the
tree. We generated all sequence data used in our analyses.
Tissue samples were extracted using a Qiagen DNEasy
Blood and Tissue Kit. Two mitochondrial loci, five nuclear
exons, and three nuclear introns were amplified: cyt-b(Kocher
et al., 1989), D-loop (Brown et al., 2011), ATP7A, BDNF,
PLCB4 (Eick et al., 2005), RAG-1, RAG-2 (Giannini et al.,
2008), COPS7A-4 (Igea et al., 2010), FGB-7 (Nesi et al., 2011),
and STAT5A (Piaggio and Perkins, 2005) (Table 2). Thermal
cycle profiles were as follows: 35 cycles of initial denaturation
at 95º C for 1 min, annealing at 52º C for 30 s, extension at 72º
C for 2 min; then a final extension at 72º C for 3 min.
Successfully amplified PCR products were cleaned using
ExoSAP or a vacuum manifold. Products were run on an
Applied Biosystems 3730xl automated sequencer using ABI
Big Dye version 3.1. Genes were aligned using Geneious 5.4.3
60 S. M. Tsang, S. Wiantoro, M. J. S. Veluz, N. B. Simmons, and D. J. Lohman
and MAFFT 7.0 (Katoh and Standley, 2013). To infer popula-
tion history, a phylogeny of all P. vampyrus individuals were re-
constructed based on a gene tree using a partitioned Bayesian
analysis of all 10 loci implemented in MrBayes 3.2 (Ronquist
and Huelsenbeck, 2003). Gene substitution models were esti-
mated using jModelTest2 (Darriba et al., 2012) (Table 2). The
analysis was simulated for 10 million generations, with a sam-
pling frequency of 1,000 generations with 25% burn-in. We
evaluated models of demographic history by first mapping the
geographic provenance of each specimen onto the MrBayes
consensus tree. The null hypothesis of no migration between
populations predicts that individuals from the same population
would form a monophyletic clade. If there was prior gene flow
between populations, individuals would not necessarily be most
closely related to others in the same geographically defined
population. An isolation-by-distance model predicts that popu-
lations that are geographically adjacent would be more closely
related to one another than to those that are distant (e.g., the
amount of gene flow is negatively related to geographical dis-
tance). However, long-distance dispersal can facilitate gene
flow between geographically distant individuals, resulting in
colonies comprised of individuals that are not necessarily each
other’s closest relative.
Five commonly used population genetic diversity indices
were calculated for each genetic marker using DnaSP (Rozas et
al., 2003). Nucleotide diversity (π) is the average number of
nucleotide differences per site between two randomly chosen
sequences. Haplotype diversity (h) is a measure of the unique-
ness of a haplotype within a population and calculated as the
probability that two randomly selected haplotypes are not the
same. Both are important for understanding genetic variability
(Nei, 1987). The Watterson parameter theta (θ) estimates the
mutation rate since θ is four times the effective population size
(Ne) times the mutation rate (μ) (θ = 4Neμ). The number of seg-
regating sites (S) aids in calculation of the mutation rate and
Tajima’s D. Under an infinite alleles model, S is equivalent to
the total number of mutations. Tajima’s D compares patterns of
genetic variation to a neutral model which allows for interpreta-
tion of biological scenarios such as selection or population size
changes (Tajima, 1989). Populations were also compared using
the allelic fixation index, FST (Nei, 1973). Other measures of
genetic variation between populations have been recently pre-
sented as an alternative to FST (e.g., G’ST, D), but given the low
variability among Pteropus, FST remains the best measure of
population differentiation (Whitlock, 2011).
RESULTS
All nuclear and mitochondrial genes were ampli-
fied successfully and uploaded to GenBank (Acces -
sion Nos. MG920856–MG921147 — see Appendix).
Population structure of Pteropus vampyrus 61
Current range
Probable range
sumatrensis
vampyrus edulis
lanensis
pluton
natunae
FIG. 1. Range map of P. vampyrus subspecies following to the IUCN species listing (Bates, 2008). Sampling localities for fresh
tissue are marked with black circles, museum loans with black diamonds. Some specimen loans were from the same locality as the
wild-caught specimens, and are marked with only the black circle for clarity
The poorly resolved intraspecific phylogenetic con-
sensus tree inferred by MrBayes for all genes sug-
gests low levels of population structure among most
P. vampyrus populations (Fig. 2A, individual gene
trees in Supplementary Fig. S1). No single sub-
species was recovered as a monophyletic group. The
mitochondrial tree (Fig. 2B) generally agreed with
the nuclear tree in that there were no subspecies re-
covered as a monophyletic clade. Having another in-
dividual from the same colony as the closest relative
on the tree was only estimated in a handful of in-
stances (e.g., the Southern Leyte colony or the Flo -
res colony). The single individual sampled from
peninsular Southeast Asia was more closely related
to specimens from Sumatra and West Java, as pre-
dicted by an isolation-by-distance (IBD) model.
Peninsular Malaysia is approximately 1,000 km from
southern Vietnam (even farther if bats avoid flying
over water), whereas peninsular Malaysia is only
ca. 700 km from sites where we sampled in South
Sumatra and West Java. Satellite telemetry has re -
corded P. vampyrus flying from peninsular Malaysia
to Sumatra over the Strait of Malacca (Epstein et al.,
2009), but direct radio telemetric observations of
long distance dispersal have not been made outside
of peninsular Malaysia. The IBD model of popula-
tion structure on the mainland of Southeast Asia
could be further tested by including populations
from Thailand, Cambodia, and southern Myanmar.
However, many populations, particularly those on
islands of the Indo-Australian Archipelago, include
individuals more closely related to bats on another
island than to others from the same colony or popu-
lation: closest relatives could not be predicted by an
isolation-by-distance model. For example, some
Phil ippine individuals were found to be sister to
Sumatran, Javan, or Lesser Sundaic individuals.
Genetic diversity indices for P. vampyrus were
low for each marker, except for the hypervariable
mitochondrial D-loop (Table 2). Populations of
P. vam pyrus appear to be almost panmictic in all
markers. Most FST values were lower than 0.1, and
Tajima’s D was not significant for most of the genes,
indicating lack of deviation from the null model of
evolution. For genes where results were signifi-
cant, all of the values of Tajima’s D were negative,
suggesting a population expansion after a recent
bottleneck.
62 S. M. Tsang, S. Wiantoro, M. J. S. Veluz, N. B. Simmons, and D. J. Lohman
TABLE 1. List of recognized subspecies of P. vampyrus. Names follow Simmons (2005), with information from Corbet and Hill
(1992) and Koopman (1993, 1994) considered as well
Subspecies Type locality Range Synonyms
edulis Timor (Indonesia) Timor funereus
lanensis Mindanao (Philippines) Philippines
natunae Panjang, Natuna (Indonesia) Natuna Islands, Borneo
pluton Bali (Indonesia) Lesser Sundas kopangi
sumatrensis Sumatra (Indonesia) Sumatra, Peninsular Southeast Asia malaccensis
vampyrus Java (Indonesia) Java celaeno, caninus, javanicus, kalou,
kelaarti, nudus, phaiops, pteronotus
TABLE 2. Genetic substitution models and genetic diversity indices for P. vampyrus in this study. Genetic substitution models were
estimated using jModelTest2. π — nucleotide diversity, h— haplotype diversity, θ — Watterson estimator, S — segregating sites,
FST — fixation index
Gene Model π hθ S Tajima’s D D significance FST
mitochondrial
cyt-bTrN 0.00651 0.992 0.01430 55 -2.0168 < 0.05 0.00469
D-loop HKY+G 0.27709 0.998 0.19520 307 1.6310 ns 0.01092
nuclear
RAG-1 HKY+G 0.00245 0.690 0.00733 17 -2.2505 < 0.01 0.14924
RAG-2 HKY 0.00325 0.892 0.00560 15 -1.3738 ns 0.08514
STAT5A TVM 0.00512 0.776 0.01263 18 -2.0607 < 0.05 0.02837
PLCB4 HKY 0.00173 0.316 0.00558 6 -1.8999 < 0.05 0
BDNF TVM 0.00136 0.280 0.00355 5 -1.6553 ns 0.06474
FGB7 TrN 0.00499 0.917 0.01053 23 -1.7910 ns 0.04418
COPS7A4 HKY+G 0.00310 0.830 0.00417 9 -0.8306 ns 0.08428
ATP7A K81+G 0.00124 0.492 0.00320 7 -1.7662 ns 0.08619
DISCUSSION
The results suggest potentially moderate to high
levels of gene flow in the populations of P. vam -
pyrus. The potential for gene flow between sites
may reflect known aspects of the species natural his-
tory as highly vagile animals with large foraging
ranges (Epstein et al., 2009) and seasonal migration
(e.g., Soegiharto, 2009). The lack of genetic diver-
sity in the nuclear introns used is unusual compared
to previous studies that have utilized the same genes
in bats — for instance, FGB-7 was previously used
to study the phylogeography of three African ptero -
podids and had much higher levels of genetic vari-
ability (Nesi et al., 2011). COP7A-4 was designed
by Igea et al. (2010) specifically to target highly
variable introns, and was recommended from a re-
cent study of rhinolophid bats for studies of recently
diverged taxa (Dool et al., 2016). Additionally, sim-
ilar population patterns have been found in another
island flying fox species, P. niger (Larsen et al.,
2014). While this study cannot completely exclude
the possibility of incomplete lineage sorting and his-
torical connectivity leading to similar tree topolo-
gies, the current patchy resource landscape may be
a contributing factor to migratory behavior. Defor -
estation leading to loss of local food sources for
P. vampyrus, coupled with their ability to disperse, is
likely leading to more connectivity; and therefore,
more gene flow. Additionally, optimal habitats for
roosting are decreasing rapidly, and would lead to
more contact between what may have originally
been two separate populations.
Variation in fruit availability across the Southeast
Asian landscape (Cannon et al., 2007) may explain
some of the high degree of connectivity between the
populations sampled, particularly as forested areas
are now highly fragmented. Many forests in
Southeast Asia are dominated by trees in the
Diptero carpaceae, which typically reproduce syn-
chronously en masse (‘mast fruiting’) at non-regular
intervals and induce trees in other families in the
same area to do the same (Sakai, 2002). Many ani-
mals in the region are capable of long distance dis-
persal to take advantage of the surfeit of temporally
and spatially patchy resources afforded by the mast
flowering (e.g., Apis dorsata, the Asian giant honey-
bee — Itioka et al., 2001) and fruiting (e.g., Sus bar-
batus, Bornean bearded pig — Curran and Leigh -
ton, 2000). Since P. vampyrus is a generalist
fru givore (Stier and Mildenstein, 2005) and is capa-
ble of dispersing over large areas (Epstein et al.,
2009), col onies often move to locales with abundant
food instead of staying at a single roost throughout
the year. For instance, the resident colony in the
Bogor Botanical Garden in West Java, Indonesia,
leaves from June to October, which is the peak of the
dry season on Java (S.M.T., personal observation).
Presumably the same individuals return after each
hiatus, though the reason for leaving — perhaps for-
aging or mating — remains unclear. Individuals
sampled from the sprawling Indonesian archipelago
were sometimes most closely related to Philippine
individuals or specimens from mainland Southeast
Asia — not necessarily other specimens from the
Indonesian archipelago.
This high rate of inferred dispersal has important
consequences for the species’ ecology and conserva-
tion, and suggests that transnational management
plans are essential. International strategies for pro-
tecting P. vampyrus do not exist, nor do initiatives to
monitor populations that cross national boundaries
(e.g., the population studied by Epstein et al. (2009),
which occurs from peninsular Malaysia to Sumatra).
Legislation similar to the Convention on the Conser -
vation of Migratory Species of Wild Animals (CMS:
http://www.cms.int) or the Agreement on the Con -
ser vation of Bats in Europe (EUROBATS) can act as
a model for how Pteropus may be protected region-
ally. The provisions in these agreements require that
signatory parties agree to restrict the capture of bats,
except for scientific research, species recovery pro-
grams, traditional subsistence needs, or extraordi-
nary circumstances. Raising awareness of conserva-
tion issues related to bats, protection of roost and
foraging sites, and promotion of research that can
benefit conservation management are just some of
the activities covered by these legal agreements.
Using these agreements as models may help build
future conservation policies that can help protect
migratory bat species such as P. vampyrus. For
instance, the Philippines is the only Southeast Asian
country that is a signatory party of CMS but it is
possible to create agreements under CMS that in-
clude non-signatory countries.
Clinal variation in P. vampyrus body size has
been noted in the literature, though pelage col-
oration has not been linked to particular subspecies
(Andersen, 1912; Corbet and Hill, 1992). Our analy-
ses suggest that no subspecies are monophyletic;
genome-scale data could establish or refute the
monophyly of subspecies with more evidence. The
authors have previously collected extensive mor-
phologic data from all the subspecies of P. vampyrus
that suggest there are significant differences be-
tween subspecies that uphold the validity of these
Population structure of Pteropus vampyrus 63
64 S. M. Tsang, S. Wiantoro, M. J. S. Veluz, N. B. Simmons, and D. J. Lohman
0.0030
SW132 P. v. sumatrensis South Sumatra
SW010 P. v. pluton Bali
LBC-904529 Pteropus hypomelanus
SW001 P. v. vampyrus West Java
WRS-G1339 P. v. sumatrensis Singapore F1
SW133 P. v. pluton Flores
SW006 P. v. vampyrus West Java
SW012 Pteropus hypomelanus
SW003 P. v. vampyrus West Java
SW007 P. v. pluton Bali
SW008 P. v. pluton Bali
LBC-904502 P. v. vampyrus West Java
WAM-30434 Pteropus alecto
SMT207 Pteropus hypomelanus
SW011 P. v. pluton Bali
SW009 P. v. pluton Bali
LBC-930092 P. v. sumatrensis Sumatra
MJV505 P. v. lanensis Palawan
0.8815
1
1
1
0.5551
1
0.9706
1
0.9982
0.9999
0.5819
1
0.9421
0.5021
0.6549
0.6985
1
0.987
0.5625
0.7787
0.6758
1
0.6027
LBC-930088 P. v. sumatrensis Sumatra
ROM-110948 P. v. sumatrensis Vietnam
ROM-110949 P. v. sumatrensis Vietnam
LBC-904503 P. v. vampyrus West Java
LBC-930091 P. v. sumatrensis Sumatra
LBC-930093 P. v. sumatrensis Sumatra
SW140 P. v. pluton Sumbawa
SW134 P. v. pluton Flores
SW077 P. v. vampyrus East Java
SW078 P. v. vampyrus East Java
MJV435 P. v. lanensis Southern Leyte
MJV436 P. v. lanensis Southern Leyte
MJV420 P. v. lanensis Southern Leyte
MJV419 P. v. lanensis Southern Leyte
SMT213 P. v. lanensis Negros Occidental
SMT212 P. v. lanensis Negros Occidental
SMT210 P. v. lanensis Negros Occidental
SMT211 P. v. lanensis Negros Occidental
SMT208 P. v. lanensis Negros Occidental
LBC-930089 P. v. sumatrensis Sumatra
SW002 P. v. vampyrus West Java
SW131 P. v. sumatrensis South Sumatra
MJV504 P. v. lanensis Palawan
SW127 P. v. natunae West Kalimantan
SW128 P. v. natunae West Kalimantan
a
)
FIG. 2. Intraspecific phylogenetic tree of P. vampyrus based on A) all 10 loci and B) mitochondrial loci only, analyzed with MrBayes 3.2 simulated for 10 million generations, with
a sampling frequency of 1,000 and 25% burn-in. Posterior probabilities are indicated above each node. The topology of the mitochondrial tree does not differ greatly from the nuclear tree,
and both suggest near panmixia throughout the species range
í
í
A
Population structure of Pteropus vampyrus 65
0.05
MJV504 P. v. lanensis Palawan
SW007 P. v. pluton Bali
LBC-904529 Pteropus hypomelanus
LBC-930088 P. v. sumatrensis Sumatra
SW134 P. v. pluton Flores
MJV420 P. v. lanensis Southern Leyte
SW013 Pteropus hypomelanus
SMT210 P. v. pluton Bali
SMT207
LBC-930092 P. v. sumatrensis Sumatra
SW002 P. v. vampyrus West Java
SW078 P. v. vampyrus East Java
SW006 P. v. vampyrus West Java
SW140 P. v. pluton Sumbawa
SMT211 P. v. lanensis Negros Occidental
MJV505 P. v. lanensis Palawan
SW131 P. v. sumatrensis South Sumatra
SW012 Pteropus hypomelanus
SW010 P. v. pluton Bali
WRS-G1339 P. v. sumatrensis Singapore F1
SW011 P. v. pluton Bali
SW128 P. v. natunae West Kalimantan
SW003 P. v. vampyrus West Java
ROM-110949 P. v. sumatrensis Vietnam
MJV419 P. v. lanensis Southern Leyte
SW001 P. v. vampyrus West Java
LBC-930093 P. v. sumatrensis Sumatra
SW132 P. v. sumatrensis South Sumatra
SMT213 P. v. lanensis Negros Occidental
SW009 P. v. pluton Bali
LBC-904503 P. v. vampyrus West Java
MJV436 P. v. lanensis Southern Leyte
SMT212 P. v. lanensis Negros Occ
ROM-110948 P. v. sumatrensis Vietnam
SW014 Pteropus hypomelanus
SW133 P. v. pluton Flores
MJV435 P. v. lanensis Southern Leyte
LBC-904502 P. v. vampyru
SW127 P. v. natunae West Kalimantan
SMT208 P. v. lanensis Negros Occidental
LBC-930089 P. v. sumatrensis Sumatra
SW077 P. v. vampyrus East Java
SW008 P. v. pluton Bali
WAM-30434 Pteropus alecto
LBC-930091 P. v. sumatrensis Sumatra
1
1
0.9803
0.9982
0.9987
1
0.9425
0.9265 0.9998
0.6035
0.861
0.9915
0.8059
0.5832
0.7073
0.9885
0.693
0.8686
0.727
0.9278
0.6279
0.7758
0.7756
0.8869
0.7192
0.5925
0.5231
v. v ampyrus West Java
Negros Occidental
b)
FIG. 2. Continued
B
names (S.W. and S.M.T., unpublished data). These
morphologic subspecies boundaries are incongru-
ous with our genetic results that do not find sub-
species to be monophyletic. This suggests that
there may indeed be some genetic variation, but on
comparatively shallow time scales. However, these
data included primarily historical specimens, and do
not account for recent changes in distribution due to
threats posed by overhunting and habitat loss. To
determine whether there has been a more recent shift
in the validity of the subspecies, measurements from
more recent populations of poorly known sub-
species (e.g., P. v. edulis) are needed. The low level
of genetic variability of P. vampyrus throughout its
species range suggests little possibility for local
adaptation, and may be related to the ability of
P. vampyrus to occupy such a variety of different
habitats. Genomic tests for recent adaptations may
indicate whether there are population-level differ-
ences due to localized environmental differences
(e.g., diet and different microbiomes) or anthropo -
genic exposure (e.g., urbanization has led to selec-
tion for heavy metal tolerance in mouse populations
— Harris et al., 2013).
Colony size is an ecologically important trait in
pteropodid bats, one that has implications for popu-
lation structure and genetic diversity patterns, since
it affects their migration patterns, roosting ecology,
and mating behavior (Wilson and Graham, 1992;
Brooke et al., 2000; Jones et al., 2003; Fahr et al.,
2015). In Pteropus giganteus, a large and closely-re-
lated habitat generalist, colonial species, habitat
fragmentation due to land use change has resulted in
smaller colonies that are more numerous because
fewer trees are available for roosting at any one site
(Hahn et al., 2014). Fragmentation of large colonies
is also likely occurring in P. vampyrus (S.M.T., per-
sonal observation). In the past, large (> 2,000 indi-
viduals) colonies were found in the Philippines and
throughout Indonesia, but colonies of that size are
now limited to a small number of areas with little or
no human disturbance and to large, undisturbed
forests — particularly pristine mangrove forests.
The largest P. vampyrus colony in the world (ca.
20,000 individuals) is in Subic Bay in the Phil -
ippines, which is on the site of a former American
naval base with a large dipterocarp forest and
a buffer zone surrounding it (Mildenstein et al.,
2005). Another large colony (> 5,000 individuals)
found through this study was on a remote island sur-
rounded by mangrove forest in a marine protected
area in Flores, Indonesia (S.M.T., personal observa-
tion). In both of these cases, regular disturbance
at the roosting site is not possible given the re-
stricted accessibility to local people. In highly dis-
turbed islands, such as Java, Sumatra, West Kali -
man tan, and Bali, colonies of P. vampyrus may
number fewer than 1,000 individuals (S.M.T., per-
sonal observation). Further work is needed to de -
termine the impact of smaller colony size on the ge-
netic stability and persistence of the species, but
little is currently known about yearly roosting ecol-
ogy patterns of P. vampyrus colonies in most parts of
their range.
The low level of population structure may mean
that connectivity between populations of P. vam -
pyrus is moderate to high, which has direct conse-
quences for understanding how bat-borne pathogens
may have evolved and may evolve in the future.
Understanding population genetic diversity and fre-
quency of gene flow among host populations can
have a direct effect on studies of pathogen transmis-
sion (e.g., predicting source populations — Wool -
house et al., 2005; Epstein and Field, 2015) and
other aspects of pathogen biology (e.g., infection cy-
cles, rates of transmission, and degree of host dam-
age — Lion and Boots, 2010; Morand and Krasnov,
2010; Carlsson-Granér and Thrall, 2015). Some
studies have challenged these predictions — either
by showing no increase in pathogen aggressiveness
in a contiguous host population (Tack et al., 2014)
or that increased host population connectivity may
also result in higher degrees of host resistance to
patho gens, meaning that diseases are more likely to
appear in isolated populations instead (Carlsson-
Granér and Thrall, 2002; Jousimo et al., 2014). The
role that host biology, particularly population con-
nectivity plays in maintaining pathogen persistence
and prevalence, is then an important factor to con-
sider in studying transmission dynamics and essen-
tial to informing strategies for combating the spread
of zoonotic pathogens in the event of a pandemic.
As anthropogenic pressure increasingly stresses
P. vampyrus populations, the potential for pathogen
transmission and outbreaks increase (Daszak et al.,
2001; Dobson and Foufopoulos, 2001; Plowright et
al., 2008, 2015). Biodiversity loss has been linked to
the increasing pathogen emergence (Daszak et al.,
2001; Patz et al., 2004; Pongsiri et al., 2009), and
safeguarding flying fox populations and natural
spaces may decrease the likelihood of transmission.
Steep declines in P. vampyrus populations across
the range of this species might also result in dire
consequences for forest regeneration, as the fruits of
early successional plant species constitute the bulk
of their preferred diet (Stier and Mildenstein, 2005).
66 S. M. Tsang, S. Wiantoro, M. J. S. Veluz, N. B. Simmons, and D. J. Lohman
Excessive hunting of P. vampyrus in Borneo
threatens the continued persistence of populations
(Strue big et al., 2007; Harrison et al., 2011), and
population modeling in Malaysia suggests that
current levels of hunting are unsustainable (Epstein
et al., 2009). Flying foxes in Sumatra and Java are
occasionally hunted for medicinal purposes (Croes,
2012), though hunters have found it increasingly
difficult to locate populations in recent years
(S.M.T., personal observation). Persistent hunt ing of
P. vampyrus throughout its range leading to popula-
tion crashes should be explored further by including
sampling of historical specimens in future studies.
Pteropus vampyrus is listed under CITES Ap -
pendix II and by IUCN as Near Threatened, but few
national laws exist in Southeast Asia to enforce pro-
tection. Given the ongoing, significant declines
across its range due to overhunting, the species may
soon be categorized as Vulnerable (Bates et al.,
2008). There is little or no local incentive for re-
gional protection of P. vampyrus in Southeast Asia,
and local residents throughout most of this region
lack incentive for biodiversity conservation (e.g.,
Harada, 2003) and access to environmental educa-
tion (Sulistyawati et al., 2006). There is minimal to
no enforcement of quotas or hunting bans on bats,
and seizure activities are rarely initiated by local en-
forcement agencies (Nijman, 2005; Shepherd and
Njiman, 2008). Despite their CITES status, flying
foxes in Indonesia are not listed as a protected spe -
cies (Maryanto et al., 2008). Although the species is
found broadly across Malaysia, hunting bans exist in
only three of 16 Malaysian states and federal territo-
ries (Heng, 2012), and in Thailand and Cambodia
(Epstein et al., 2009). Incidental protection due to
the proximity of Pteropus colonies to religious sites
or government grounds occurs in Thailand (S. Bum -
rungsri, personal communication), Cambodia (Ra -
von et al., 2014), Vietnam (L. Q. Dang, personal
communication), and the Philippines, Bali, and
Myanmar (S.M.T., personal observation), but none
of these sites have legal protection to deter hunting
or persecution of flying foxes. The health of
P. vampyrus populations should be considered both
a conservation and a public health issue to the
Association of Southeast Asian Nations (ASEAN)
member nations, with the exception of Lao PDR,
where P. vampyrus does not occur. Southeast Asia is
one of the most densely populated areas in the world
(United Nations Department of Economic and
Social Af fairs Population Division, 2015) and these
issues should be addressed as a precautionary meas-
ure, not a reactionary one.
SUPPLEMENTARY INFORMATION
Contents: Supplementary Fig. S1. Intraspecific phylo-
genetic tree of P. vampyrus based on each molecular mark er an-
alyzed separately with MrBayes 3.2 simulated for 10 million
generations, with a sampling frequency of 1,000 and 25%
burn-in. Posterior probabilities are indicated above each node.
Sup plementary Information is available exclusively on BioOne.
ACKNOWLEDGEMENTS
We thank the Biodiversity Management Bureau (Phil ip -
pines), the Department of Environment and Natural Resources
(Philippines), the Ministry of Environment and Forestry (Indo -
nesia), the Ministry of Research and Technology (Indonesia)
and local government entities that granted permission to make
fieldwork possible. We thank Judith Eger (Royal Ontario Muse -
um), Burton Lim (Royal Ontario Museum), Kelvin Lim (Lee
Kong Chian Natural History Museum, formerly Raffles Mu se -
um of Biodiversity Research), Brian Pope (Lubee Bat Conser -
vancy), John Sha (Wildlife Reserves Singapore), and Allyson
Walsh (Lubee Bat Conservancy) for sharing tissue samples. We
are indebted to Abdulrahman, Arvin C. Diesmos, Godfrey Jako -
salem, Lisa Paguntalan, the late Edy Toyibi, Sheherazade, Yusep
Synata, Rolly Urriza, and the staff of BKSDA Jawa Barat,
BKSDA Nusa Tenggara Barat, and BKSDA Sumatera Utara for
assistance in the field. We thank Rudolf Meier, who hosted SMT
with funding from an NSF EAPSI Fellowship (OISE-1108298),
and to Kristofer M. Helgen, who provided insight at many
stages of this study. We thank two anonymous reviewers
for helpful comments on an earlier version of this manuscript.
This work was funded by a National Geographic Young
Explorers Grant (9272-13) to SMT, American Philosophical
Society Lewis and Clark Fund for Exploration Award to
SMT, Fulbright Indonesia Research Fellowship to SMT, and
NIH grant R21 AI105050-01 to DJL, NBS, and Vijaykrishna
Dhanasekaran.
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Population structure of Pteropus vampyrus 69
APPENDIX
Sample information for specimens of P. vampyrus used in this study, including subspecies identifications, collection localities,
sample numbers, and GenBank accession info for genetic data derived from each sample. LBC = Lubee Bat Conservancy, FL, USA;
RMBR = Raffles Museum of Biodiversity Research/Lee Kong Chiang Museum of Natural History, Singapore; ROM = Royal Ontario
Museum, Canada. Due to the potential direct threats to colonies, latitude and longitude data for wild-caught specimens were omitted,
but available via correspondence with the authors
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70 S. M. Tsang, S. Wiantoro, M. J. S. Veluz, N. B. Simmons, and D. J. Lohman
Received 31 August 2016, accepted 08 January 2018
Associate Editor: Wiesław Bogdanowicz
î
Population structure of Pteropus vampyrus 71
Subspecies Specimen ID Locality cyt-bD-loop ATP7A BDNF FGB7 PLCB4 RAG-1 RAG-2 STAT5A
P. v. vampyrus LBC-904502 West Java MG921055 MG920997 MG920909 MG920955 MG921121 MG920867 MG921025 MG920928
P. v. vampyrus LBC-904503 West Java MG921085 MG921056 MG921004 MG920898 MG920957 MG921122 MG920871 MG921019
P. v. sumatrensis LBC-930088 Sumatra MG921057 MG920999 MG920901 MG920977 MG921119 MG920862 MG921024 MG920943
P. v. sumatrensis LBC-930089 Sumatra MG921102 MG921058 MG920998 MG920902 MG920972 MG921125 MG920880 MG921023 MG920945
P. v. sumatrensis LBC-930091 Sumatra MG921086 MG921000 MG920888 MG920971 MG921120 MG920863 MG921043
P. v. sumatrensis LBC-930092 Sumatra MG921059 MG921002 MG920913 MG920978 MG921117 MG920870 MG921016
P. v. sumatrensis LBC-930093 Sumatra MG921081 MG921003 MG920954 MG921124 MG920869 MG921046
P. v. vampyrus MZB-36229/SW001 West Java MG921091 MG921065 MG920986 MG920956 MG921113 MG920861 MG921027 MG920942
P. v. vampyrus MZB-36230/SW002 West Java MG921084 MG921066 MG920985 MG920963 MG921118 MG920860 MG921033
P. v. vampyrus MZB-36231/SW003 West Java MG921099 MG921067 MG920904 MG921130 MG920868 MG921031 MG920924
P. v. vampyrus MZB-36248/SW006 West Java MG921097 MG921068 MG921001 MG920890 MG920964 MG921131 MG920887 MG921026
P. v. pluton SW007 Bali MG921103 MG920912 MG921132 MG920858 MG921029 MG920941
P. v. pluton SW008 Bali MG921105 MG920993 MG920958 MG921133 MG920865 MG921015 MG920920
P. v. pluton SW009 Bali MG921109 MG920994 MG920889 MG920969 MG921143 MG921040
P. v. pluton SW010 Bali MG921069 MG921008 MG920905 MG920952 MG921140 MG921034 MG920922
P. v. pluton SW011 Bali MG921108 MG921070 MG921009 MG920914 MG920981 MG921142 MG921041 MG920923
P. v. vampyrus MZB-36947/SW077 East Java MG921100 MG921071 MG920992 MG921138 MG920859 MG921048 MG920930
P. v. vampyrus MZB-36948/SW078 East Java MG921098 MG921072 MG921013 MG920916 MG920951 MG921116 MG920856 MG921047
P. v. natunae MZB-36930/SW127 West Kalimantan MG921088 MG921073 MG921011 MG920900 MG920983 MG921112 MG920864 MG921021 MG920935
P. v. natunae MZB-36931/SW128 West Kalimantan MG921082 MG921074 MG921005 MG920903 MG920974 MG921114 MG920884 MG921022 MG920937
P. v. sumatrensis MZB-36933/SW131 South Sumatra MG921080 MG921075 MG920990 MG920893 MG920973 MG921115 MG920881 MG920944
P. v. sumatrensis SW132 South Sumatra MG921079 MG921076 MG920899 MG920962 MG921129 MG920872 MG921018 MG920936
P. v. pluton MZB-36937/SW133 Flores MG921087 MG921077 MG921010 MG920895 MG920976 MG921127 MG920885 MG921017 MG920946
P. v. pluton MZB-36938/SW134 Flores MG920929
P. v. pluton MZB-36934/SW140 Sumbawa MG921083 MG921078 MG920892 MG920965 MG921128 MG920879 MG921020 MG920947
P. v. sumatrensis ROM-110949 Vietnam MG921094 MG921061 MG920984 MG920908 MG920968 MG921144 MG920931
P. v. sumatrensis ROM-110948 Vietnam EF584230 MG921060 MG920995 MG920918 MG920953 MG921126 MG920933
P. v. lanensis PNM-7427/MJV419 Southern Leyte, Philippines MG920938
P. v. lanensis PNM-7428/MJV420 Southern Leyte, Philippines MG921092 MG921050 MG921012 MG920919 MG920961 MG921147 MG920866 MG921035 MG920927
P. v. lanensis PNM-6911/MJV435 Southern Leyte, Philippines MG921093 MG921051 MG920907 MG920960 MG921146 MG920886 MG921030
P. v. lanensis PNM-7429/MJV436 Southern Leyte, Philippines MG921089 MG921052 MG920988 MG920911 MG920959 MG921111 MG920877 MG921044 MG920925
P. v. lanensis PNM-7430/MJV504 Palawan, Philippines MG921096 MG921053 MG920989 MG920891 MG920967 MG921110 MG920875 MG921045 MG920934
P. v. lanensis PNM-7431/MJV505 Palawan, Philippines MG921090 MG921054 MG920987 MG920897 MG920970 MG921137 MG920873 MG921028 MG920921
P. v. lanensis SMT208 Negros Occidental, Philippines MG921101 MG921006 MG920966 MG921145 MG920857 MG921036 MG920926
P. v. lanensis SMT210 Negros Occidental, Philippines MG921104 MG920906 MG920950 MG921135 MG920883 MG921037
P. v. lanensis SMT211 Negros Occidental, Philippines MG921106 MG921062 MG921014 MG920910 MG920949 MG921134 MG920878 MG921039 MG920940
P. v. lanensis SMT212 Negros Occidental, Philippines MG921063 MG920896 MG920980 MG921136 MG920874 MG921042 MG920932
P. v. lanensis SMT213 Negros Occidental, Philippines MG921107 MG921064 MG921007 MG920917 MG920979 MG921141 MG920876 MG921032 MG920939
P. v. sumatrensis WRS-G1339 Malaysia (Singapore Zoo F1) MG921095 MG921049 MG920996 MG920894 MG920982 MG921123 MG920882 MG921038 MG920948
P. hypomelanus SW012 Madura MG920991 MG920915 MG920975 MG921139
APPENDIX
