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Mitochondrial DNA hypervariable region-1 sequence variation and phylogeny of the concolor gibbons Nomascus.

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American Journal of Primatology 69:1285–1306 (2007)
RESEARCH ARTICLE
Mitochondrial DNA Hypervariable Region-1 Sequence
Variation and Phylogeny of the Concolor
Gibbons, Nomascus
KERI MONDA1,2, RACHEL E. SIMMONS1,3, PHILIPP KRESSIRER1,4, BING SU1,5,
1
AND DAVID S. WOODRUFF
1
Ecology, Behavior & Evolution Section, Division of Biological Sciences, University of
California, San Diego, La Jolla, California
2
Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill,
North Carolina
3
Genomic Variation Laboratory, Department of Animal Science, University of California,
Davis, Davis, California
4
Medical Center of the Ludwig-Maximilians-University, Munich, Germany
5
Key Laboratory of Cellular and Molecular Evolution, Kunming Institute of Zoology,
Chinese Academy of Sciences, Kunming, Yunnan, China
The still little known concolor gibbons are represented by 14 taxa (five
species, nine subspecies) distributed parapatrically in China, Myanmar,
Vietnam, Laos and Cambodia. To set the stage for a phylogeographic
study of the genus we examined DNA sequences from the highly variable
mitochondrial hypervariable region-1 (HVR-1 or control region) in 51
animals, mostly of unknown geographic provenance. We developed
gibbon-specific primers to amplify mtDNA noninvasively and obtained
4477 bp sequences from 38 gibbons in North American and European
zoos and 4159 bp sequences from ten Chinese museum skins.
In hindsight, we believe these animals represent eight of the nine
nominal subspecies and four of the five nominal species. Bayesian,
maximum likelihood and maximum parsimony haplotype network
analyses gave concordant results and show Nomascus to be monophyletic.
Significant intraspecific variation within N. leucogenys (17 haplotypes) is
comparable with that reported earlier in Hylobates lar and less than half
the known interspecific pairwise distances in gibbons. Sequence data
support the recognition of five species (concolor, leucogenys, nasutus,
gabriellae and probably hainanus) and suggest that nasutus is the
oldest and leucogenys, the youngest taxon. In contrast, the subspecies
N. c. furvogaster, N. c. jingdongensis, and N. leucogenys siki, are not
recognizable at this otherwise informative genetic locus. These results
show that HVR-1 sequence is variable enough to define evolutionarily
significant units in Nomascus and, if coupled with multilocus microsatellite or SNP genotyping, more than adequate to characterize their
phylogeographic history. There is an urgent need to obtain DNA from
Correspondence to: Dr. David Woodruff, Ecology, Behavior & Evolution Section, Division of
Biological Sciences, University of California, San Diego, UCSD, La Jolla, CA 92093-0116.
E-mail: [email protected]
Received 23 August 2006; revised 10 January 2007; revision accepted 12 March 2007
DOI 10.1002/ajp.20439
Published online 23 April 2007 in Wiley InterScience (www.interscience.wiley.com).
r 2007 Wiley-Liss, Inc.
1286 / Monda et al.
gibbons of known geographic provenance before they are extirpated to
facilitate the conservation genetic management of the surviving animals.
Am. J. Primatol. 69:1285–1306, 2007. c 2007 Wiley-Liss, Inc.
Key words: Hylobatidae; control region; noninvasive genotyping;
species; molecular evolution; taxonomy
INTRODUCTION
Until recently, war and habitat inaccessibility frustrated scientific study of
the Indochinese concolor gibbons of the genus Nomascus. They are variously
referred to as the black or crested gibbons but these names are problematic;
although adult males are black, adult females are primarily buff-colored, and the
crest varies from prominent to indistinct, even within a species. The various
species and subspecies are poorly defined and, not surprisingly, their taxonomic
and phylogenetic relationships are still controversial [Bartlett, 2005]. To put our
ignorance of these neglected apes in perspective consider the following report: ‘On
the morning of 24 October 1999, the survey team recorded the songs of three
gibbon pairs in Nang Lu foresty the first scientifically confirmed direct evidence
of living N. c. concolor in Vietnam for about 30 years’ [Geissmann et al., 2000:63].
Since then another two species, N. nasustus and N. hainanus, with the distinction
of being among the most critically endangered primate species in the world, have
also been recognized in northeastern Vietnam and Hainan Island, China
[Geissmann, 2005a,b, 2006b; Geissmann et al., 2003; Groves, 2004; Roos, in
prep.]. Here, we present genetic evidence clarifying the relationships of four of the
five species and nine nominal subspecies (Fig. 1, Appendix 1).
For most of its taxonomic history the genus Nomascus has been treated as a
subgenus of Hylobates and thought to contain only one species, Hylobates
(Nomascus) concolor [Groves, 1972; Marshall & Sugardjito, 1986; and references
therein] with six subspecies: concolor, lu, hainanus, leucogenys, siki and
gabriellae. Ma and Wang [1986] proposed two new Chinese subspecies
jingdongensis and furvogaster, and, following Dao [1983] divided the former
subgenus into two species: the southern Hylobates leucogenys, characterized by
white or yellow cheek-whiskers in black (male) individuals, and the northern
H. concolor, characterized by the lack of contrasting cheek-whiskers in males.
Groves and Wang [1990] supported this species distinction and elevated the
southern yellow-cheeked gibbon H. gabriellae as a third species. Geissmann
[1993] also recognized three species, H. concolor, H. leucogenys, and H. gabriellae,
and subsequently recognized a fourth species, Hylobates (Nomascus) sp. cf.
nasutus [Geissmann, 1995; Geissmann et al., 2000]. Although Zehr [1999]
still considered the concolor group as a single species, most researchers have
favored dividing the subgenus into four or five species and eight or nine
subspecies. Furthermore, with the growing realization of the molecular genetic
distances and antiquity of the four gibbon subgenera relative to the age of other
hominoid genera most recent workers have elevated Nomascus from subgeneric
to generic status [Bartlett, 2005; Brandon-Jones et al., 2004; Geissmann, 1995;
Groves, 2001, 2004; Hall et al., 1998; Mootnick & Groves, 2005; Nadler &
Streicher, 2004; Roos & Geissmann, 2001]. We support this as our own
genetic research confirms the monophyly of the concolor group and its relatively
deep divergence from the other three clades [Simmons, 2005, Simmons et al.,
in prep].
Am. J. Primatol. DOI 10.1002/ajp
Nomascus gibbon phylogeny / 1287
Fig. 1. Outline map showing the historical distribution of Nomascus species and subspecies [from
Konrad & Geissmann, 2006, modified]. Ranges are shown as they are thought to have occurred 50
years ago; current populations are reduced in extent and highly fragmented. Taxa are N. concolor
(con) and its subspecies N. c. lu (lu), N. nasutus (nas), N. hainanus (hai), N. leucogenys (leu) and its
subspecies N. l. siki (siki), and N. gabriellae (gab). The three ?-marks indicate uncertainties
surrounding the identities and current northern ranges of Chinese gibbons surviving east of the
Red River; the identity of gibbons now extirpated from a large area of southwestern Yunnan; and
the identity of gibbons found between the ranges of N. l. siki and N. gabriellae. The map is deceptive
as it does not show either the former 1,000 km northern extension of concolor gibbons into China or
the fact that Hainan Island was broadly connected to both Vietnam and China during Pleistocene
low sea stands. Following tradition, most range limits follow rivers or political boundaries.
Am. J. Primatol. DOI 10.1002/ajp
1288 / Monda et al.
Following the work of Prouty et al. [1983a,b] gibbons of the genus Nomascus
are defined as having 26 pairs of chromosomes (members of the other genera have
2n 5 38, 44 or 50) and their species-level taxonomy has been based on geographic
distribution, pelage and other morphological characters. Unfortunately, historical
range limits of taxa are not well documented and the occurrence of natural
hybridization, which could effect species-level differentiation, remains contentious [Fooden, 1996; Geissmann, 2002, 2006a]. Furthermore, the morphological
criteria are unreliable guides to taxonomy as anatomical and morphological
variation in Nomascus are limited. Although identification of black adult males is
fairly straightforward, it is difficult to determine specific or subspecific status of
females (buff-colored as adults) and immature males [Mootnick, 2006]. Other
morphological traits are even more problematic. For example, species-level
differentiation between N. leucogenys and N. gabriellae was based on differences
in the penis bone [Groves, 1993; Groves & Wang, 1990]. Unfortunately, only one
N. gabriellae baculum had been studied at that time and Geissmann and Lim
[1994] later demonstrated that there was a significant variability in baculum size
and the particular bone examined was incomplete and attributed to the wrong
species [Geissmann, 1995]. So although Corbet and Hill [1992] have tabulated
alleged differences between the various taxa traditionally associated with the
name Hylobates concolor it should be emphasized that, apart from geographic
range, these are minor and of limited utility, and/or ignore population variability.
Groves [1993] was justified in expressing frustration with the mosaic geographic
patterns of character variation in the genus.
Two other approaches to species recognition promise to contribute to the
resolution of the controversies surrounding concolor taxonomy. First, behavior
may provide a more reliable guide to the species-level identification of adults than
morphology. All species of gibbons produce elaborate patterns of vocalization
often referred to as ‘‘songs’’ and many workers have shown how they have
species-specific and sex-specific inherited characteristics [see: Brockelman
& Schilling, 1984; Geissmann, 1993, 2002; Geissmann & Nijman, 2006; Konrad
& Geissmann, 2006; and references therein]. Unfortunately, song variability in
the wild is only now being documented and the songs of captive animals can be
misleading as there is a learned component in their songs. Nevertheless, we can
anticipate a phylogeny that is supported by these species-specific behavioral
attributes [Geissmann, 2002].
Second, several researchers have begun to describe genetic markers that
should serve as unequivocal identifiers of an individual gibbon’s taxonomic
identity and relationships. In this context gibbons have featured significantly in
the development of molecular primatology [Di Fiore & Gagneux, 2006]. In the
first demonstration of noninvasive genotyping involving a non-human primate,
Woodruff [1990, 1993] provided evidence that H. lar was variable at a
microsatellite locus amplified from hair. In a preliminary study of the genetic
differences between gibbon taxa, Garza and Woodruff [1992] sequenced a 252 bp
segment of the cytochrome b (cyt b) gene of the mitochondrial genome from
N. leucogenys, N. gabriellae and an animal identified as siki. The study revealed
genetic evidence of a closer relationship between N. leucogenys and siki than
either taxon to N. gabriellae, and provided evidence against the then prevailing
view of Nomascus as a monospecific clade. Garza and Woodruff [1994]
subsequently showed that taxon-specific cyt b sequence variation could be used
to distinguished individuals of the three concolor taxa then in North American
zoos (N. leucogenys, siki, and gabriellae). However, this data set included only
white-cheeked or buff-cheeked individuals and they were consequently unable to
Am. J. Primatol. DOI 10.1002/ajp
Nomascus gibbon phylogeny / 1289
assess differences that might exist between these taxa and the other black
gibbons. Moreover, the number of informative sites in the cyt b gene was
relatively low (5% within the sample) and thus limited the resolving power of the
locus. To answer questions left unresolved by the cyt b study we therefore
examined the more rapidly evolving mitochondrial hypervariable region (HVR-1,
sometimes called the control region and less accurately termed the d-loop). This
paper combines and updates our results from three unpublished theses and an
untraceable report in Chinese [Kressirer, 1993; Monda, 1995; Simmons, 2005; Su
et al., 1996]. To interpret our data we also review other reports on variation in
gibbon mtDNA [Chatterjee, 2006; Roos, 2004; Whittaker, 2005; Zhang, 1997] and
nuclear loci [Zehr, 1999; Zhang, 1997; Zhang et al., 2004]. The phylogenetic
principles underpinning these analyses are explained by Wagele [2005].
MATERIALS AND METHODS
Our samples representing ten species and subspecies were derived primarily
from gibbons in North American zoos supplemented with specimens of otherwise
unavailable taxa from zoos and museums in Europe and China (Appendix 2). Our
main analysis was based on 476–513 bp sequences of the mtDNA HVR-1 in
33 individuals representing seven taxa. We were also able to incorporate the
results of a 159 bp mtDNA HVR-1 sequence survey for 11 Chinese concolor
gibbons representing five taxa, including the only data for N. c. furvogaster
[Su et al., 1996]. An additional four published hominoid sequences were used as
outgroups in various analyses.
All genotyping was performed non-invasively and non-destructively based on
mtDNA extracted and amplified from 1 to 3 plucked hairs/individual of live
animals or museum skins. We developed a variety of primers to amplify up to
approx. 500 bp of the HVR-1. Most amplifications were performed using
combinations of four oligonucleotides:
L15997 50 -CACCATTAGCACCCAAAGCT-30 [Monda, 1995]
L16205 50 -AACACAACATGCTTACAAGC-30 [Kressirer, 1993]
H16431 50 -GTTGGTGATTTCACGGAGGA-30 [Kressirer, 1993]
H16498 50 -CCTGAAGTAGGAACCAGATG-30 [Monda, 1995]
The primers are identified according to the human nucleotide reference
sequence [Anderson et al., 1981] of the 30 end, and L or H to indicate light or
heavy strand, respectively. Our laboratory protocols are described elsewhere
[Monda, 1995] and are available from DSW. We took several precautions to reduce
the risk of amplifying nuclear sequences of mitochondrial origin (numts)
including re-extracting and verifying key determinations in a second laboratory
without potential contamination from other non-human primate DNA [Simmons,
2005; Simmons et al., in prep.] and comparing our sequences with those reported
for two whole mitochondrial sequences of H. lar and a partial HVR-1 sequence of
H. lar. Verifications typically involved amplification of a 325 bp fragment using
the primers H16431 and L16007 [50 -CCCAAAGCTAAAATTCTAA-30 ; Roos
& Geissmann, 2001].
We aligned the sequences using Clustal X Version 1.81 [Thompson et al.,
1997] and after verification by eye we constructed maximum likelihood,
parsimony, and distance trees using PAUP Version 4.0b [Swofford, 1998] and
Bayesian inference trees with MrBayes Version 3.0b [Huelsenbeck & Ronquist,
2001]. Parsimony analyses used default settings of PAUP and treated gap states
as ‘‘missing data.’’ Distance analyses were performed with default settings of
PAUP to optimize minimum evolution. All trees were then rooted by outgroup.
Am. J. Primatol. DOI 10.1002/ajp
1290 / Monda et al.
Bootstraps of parsimony and distance methods were each composed of 1,000
replicates. The maximum likelihood phylogeny had four steps: a maximum
parsimony tree starting point and then three consecutive heuristic searches using
maximum likelihood criteria. The first search’s likelihood settings employed a
general time reversible model with gamma-distributed rate variation across
sites (GTR1G) and estimated base frequencies, rate matrix, and shape. Nearest
neighbor interchange (NNI) perturbation drove the state changes. Two subsequent heuristic searches used a tree bisection-reconnection (TBR) swapping
and the starting point, rate matrix, base frequencies, and shape of the previous
search. The maximum likelihood tree was then determined from the saved trees
of these three searches. Bayesian trees used the GTR1G model on four MCMC
chains. Generation number and sample frequency were determined by running a
brief preliminary analysis, checking for probability convergence, and estimating
the values necessary for a large set of equally likely trees. After the second
analysis, each Bayesian tree’s probabilities file was examined to verify that the
likelihoods converged around a small value range before determining if an
appropriate burn-in value had been chosen, and the analysis was repeated twice
to ensure that the MCMC chains were long enough and had converged on the
same tree. Ultimately, we used MrBayes to searched for 5,000,000 generations
and with a burn-in value of 100,000.
Network (4.111; www.fluxus-engineering.com) was used to construct
haplotype networks using median joining [Bandelt et al., 1999] and maximum
parsimony [Polzin & Daneschmand, 2003] algorithms. The program TCS
[Clement et al., 2000] was used to construct a statistical parsimony network
joining all haplotypes that connect with a 95% or greater frequency.
RESULTS
The HVR-1 sequences are more informative than the previously published
cyt b sequences. Comparing a subset of ten representative gibbons over 477 bp we
found 123 variable and phylogenetically informative sites, involving 104
transitions and 38 transversions (TS/TV ratio of 2.7:1). Overall, we found a total
of 123 (26%) variable positions and 26 different haplotypes.
Phylogenetic relationships among the eight Nomascus taxa represented by
more than 476 bp of mtDNA HVR-1 sequence are presented in Figures 2 and 3.
All phylogenetic trees show similar patterns of tree topology, with long branch
lengths between outgroup species representing other hominoids (Homo, Pan,
Pongo) (Fig. 2). The concolor gibbons form a monophyletic group (Fig. 2) within
which we see consistent evidence for four clusters of sequences that correspond to
the species-level taxa N. leucogenys, N. concolor, N. gabriellae, and N. nasutus
(Figs. 2 and 3). Bootstrap values (62–91%) show low to moderate support for these
species-level clades (Fig. 2A).
All phylogenetic methods indicate N. nasutus is the most basal group, distinct
from all other clades with highly significant scores for distance bootstrap (87%)
and Bayesian posterior probability (1.00). Depending on which algorithm is used
either N. gabriellae or N. concolor branch off next. N. leucogenys appears as the
youngest clade regardless of method used.
Our two N. nasutus sequences are very similar differing by only 2.6%. Such
differences are relatively small compared with the divergence seen among the
leucogenys and comparable to those found within gabriellae and concolor.
Although we initially treated one of our specimens as N. hainanus, on the advice
of Christian Roos we have concluded that the animal was misidentified (Appendix 2).
Am. J. Primatol. DOI 10.1002/ajp
Nomascus gibbon phylogeny / 1291
Fig. 2. Phylogenetic relations of representative Nomascus gibbons based on variation in the mtDNA
hypervariable region-1. A: distance bootstrap tree; B: Bayesian tree; C: maximum likelihood tree.
Gibbon taxa are described in Appendix 1.
Am. J. Primatol. DOI 10.1002/ajp
1292 / Monda et al.
Fig. 3. Maximum parsimony haplotype network showing phylogenetic relations of representative
Nomascus gibbons. Gibbons are the same as those described in Fig. 2.
Roos (in litt. to DSW, May 2006; in prep.) has now sequenced hainanus of known
provenance and found them to be much more different from nasutus (cyt b 6.8%,
HVR1 14%). This strongly suggests that our Berlin Museum specimen was
misidentified.
Bayesian (Fig. 2B) and maximum likelihood (Fig. 2C) trees show N. concolor
jingdongensis within the concolor cluster; a distance bootstrap (Fig. 2A) shows it
as a very closely related outgroup (nine mutations) to the three N. c. concolor
gibbons (which vary among themselves by up to 12 mutations).
The 19 gibbons identified as N. leucogenys form a very closely related cluster
that is well separated from the cluster identified as N. gabriellae. N. gabriellae
differs from N. leucogenys by three indels, five transversions and 11 transitions;
sites 243–249 are especially variable and may be taxon-specific. The distinction
between N. leucogenys and the monophyletic cluster of three N. gabriellae is
supported at the 81% level in Bayesian and 62% levels in parsimony and distance.
The gibbon identified as siki is seen as an outgroup to the N. leucogenys rather
than N. gabriellae clade; parsimony, maximum likelihood and distance trees show
siki as a closely related outgroup of the N. leucogenys.
In all tree methods used, 15 N. leucogenys individuals form a monophyletic
cluster with two prominent subclusters of closely related individuals we denote as
clades A and B (as discovered by Monda, 1995 , and shown most clearly in
Fig. 2A). We find approximately 2% divergence within each clade and 4%
divergence between clades. These clades differ by four transitions at sites 288,
294, 307, 348. Two additional subclusters are moderately differentiated from the
others (Fig. 2A shows two individuals of Clade C and one, leuc-16, in Clade D). The
division between these subclusters is supported by high posterior probability scores
(0.81) in the Bayesian (Fig. 2B) and distance bootstrap methods (85%) (Fig. 2A).
There are 26 (5.1%) variable sites within clade A, and 25 (4.9%) within clade B, of
which they share only six. Clade A is weakly supported in Bayesian analysis
(posterior probability, 0.75) and weakly supported in parsimony (not shown) and
distance bootstraps (Fig. 2A) (62 and 58%, respectively). Clade B is supported
strongly in Bayesian analysis (0.98) but weakly in bootstraps (parsimony, 56%,
distance, 75%).
The maximum parsimony haplotype network (Fig. 3) shows the above
patterns more clearly and also reveals N. leucogenys clades A and B, and a small
Am. J. Primatol. DOI 10.1002/ajp
Nomascus gibbon phylogeny / 1293
Fig. 4. Relationships among Chinese Nomascus gibbons. Most parsimonious tree based on 159 bp
sequences of the HVR-1. Redrawn from Su et al. [1996: Fig. 2b] showing branch lengths
proportional to the number of base substitutions.
group clustering with the N. l. siki individual as a closely related outlier. The
median joining network gave a similar result. The TCS generated statistical
parsimony network (not shown) recognized four clusters concordant with seven
leucogenys A (excluding animal leuc 11) and five leucogenys B (excluding leuc 4),
two leucogenys D, and the four concolor1jingdongensis. The remaining ten
individuals (plus outgroups Hoolock hoolock and Symphalangus syndactylus)
were not related at our stringent 95% level.
Su et al. [1996] provide some additional information on sequence variation in
five Chinese Nomascus taxa (Appendix 2). Unfortunately, and despite the use of
the same primers as Kressirer [1993], technical problems experienced in
amplifying mtDNA from the museum skin samples resulted in only 159 bp of
comparable sequence for the six taxa compared. Su et al. found no indels and 39
(25%) of the sites (not including the outgroup Symphalangus) were variable with
8–23 transitions and 1–6 transversions. He used a 6:1 TS/TV ratio. The most
parsimonious tree shown (Fig. 4) is identical to the maximum likelihood tree; tree
length 5 78, CI 5 0.73. In agreement with our more comprehensive 477 bp
analyses N. nasutus [misidentified in Su et al. as N. n. hainanus] is seen as the
outgroup. The previously unknown N. c. furvogaster and N. c. jingdongensis are
seen as clustering with N. c. concolor (0–2 TV; 0–17 TS). The two N. leucogenys
from the town of Hekou on the Vietnamese border in southern Yunnan differ
from one another at one transversion and eight transitions.
DISCUSSION
The results reported here were based primarily on DNA extracted from
freshly plucked hair. Although shed hair is no longer regarded as a reliable source
of high quality DNA [Morin & Goldberg, 2003; Thalmann et al., 2004; Woodruff,
2003] noninvasive genotyping has made it possible to study these apes which are
otherwise very difficult to sample. We are confident the sequences presented here
Am. J. Primatol. DOI 10.1002/ajp
1294 / Monda et al.
are verified mtDNA sequences and not confounded by mitochondrial pseudogenes
(numts) or other hominoid contaminants [Bensasson et al., 2001; Simmons et al.,
in preparation; Thalmann et al., 2004].
Our results and their interpretation are critically dependent on the
identification of the individuals studied. The specimen data presented in
Appendix 2 will facilitate their replication and revision when necessary.
The mtDNA relationships seen are supportive of, but less ambiguous than,
the morphology based taxonomy. As this is the first report in which multiple
individuals of each species have been considered, questions presupposing
the availability of information on typical intraspecific genetic variation can now
be addressed. In particular, the large sample of N. leucogenys (19 haplotypes:
the average pairwise distance is 0.03570.014 with a 29.8% percent sequence
difference) can now be compared to the recently published data on comparable
variation in 46 Hylobates lar (0.02470.014 with a 17.9% sequence difference)
[Woodruff et al., 2005]. These percent sequence differences are comparable to our
estimates for taxa represented by smaller sample sizes: N. concolor (N 5 3;
0.049670.0145), N. gabriellae (N 5 3; 0.024770.0214), and N. nasutus (N 5 2;
0.0299). Including the single N. l. siki with the leucogenys changes the average
pairwise distance only slightly: 0.03870.015. Such within taxon variability data
will be invaluable in interpreting the observed between-taxa differences.
At the mtDNA locus studied the concolor gibbons are a monophyletic clade.
Their karyotypic distinction (2N 5 52) and mtDNA genetic distance from the
other three groups of living gibbons supports their recognition as a separate
genus. Divergence between Hylobates and Nomascus is described elsewhere but is
comparable to or greater than that between Nomascus and either Symphalangus
or Hoolock, with highly significant scores for distance bootstrap (100%) and
Bayesian posterior probability (1.00) [Simmons et al., in prep.]. Within the genus
are at least four species or species groups (N. concolor, N. leucogenys, N. nasutus,
and N. gabriellae) that differ at more than the 5% divergence level; a level
comparable to that seen in comparably documented species in Hylobates
[Simmons et al., in prep]. Below that 5% divergence level it is clear that more
genotyping of individuals of known geographic provenance is required to resolve
the issues and that the following discussion of siki, jingdongensis, and furvogaster
must be viewed as preliminary.
Our genetic result showing N. nasutus as the basal group is in agreement
with the findings of Roos [2004] which were based on his survey of cyt b variation.
This conclusion is also supported by a preliminary phylogenetic tree based on
vocal data for all gibbon species, including the four species of crested gibbons
[Konrad & Geissmann, 2006]. Although the relevant bootstrap values in the
behavioral analysis are very low, this tree appears to provide additional support
for Groves [1993] hypothesis that, within Nomascus, northern species are more
basal than the southern species.
Nomascus nasutus is very different from Nomascus concolor, the northern
gibbon with which they have been long confused. The genetic distance between
our two samples is less than the variation between the A and B clades of
N. leucogenys, or between the three N. gabriellae, or between the four
N. c. concolor. This supports our argument that there is only one species
represented in our sample and not two as reported earlier (see Appendix 1).
Christian Roos (in litt. to DSW, April 2006) has recently discovered that Patzi (see
Appendix 2) is genetically closely related to gibbons from the two remaining wild
populations in Vietnam. His results, when published, should resolve the problems
of the relationships between the surviving northeastern populations of gibbons.
Am. J. Primatol. DOI 10.1002/ajp
Nomascus gibbon phylogeny / 1295
In reconstructing the evolutionary relations between N. nasutus and N. hainanus
it is important to realize that today’s isolated island population (Fig. 1) has been
repeatedly connected with those on the mainland whenever sea levels fell 425 m
(Appendix 1); Neogene hypothermal phase paleogeography could also have
brought hainanus and siki into geographic proximity.
Our data permit the first assessment of the genetic merits of the two
subspecies of Chinese N. concolor named by Ma and Wang [1986]. Our 170 bp
analysis involved four representatives of the central subspecies jingdongensis and
they cluster closely with the three N. c. concolor. N. jingdongensis would not
stand out as a distinct taxon if it were a H. lar or N. leucogenys. It is a little
different from the southern N. c. concolor but such differences would be expected
over the geographic distances involved. In the case of the western subspecies,
furvogaster, we have only one museum specimen. Nevertheless, Su et al. [1996]
found this individual’s sequence (Fig. 4) sits even closer to topotypic N. c. concolor
than the four jingdongensis. This suggests that furvogaster has little merit if
mtDNA genetic distances are the metric of subspecific status.
There are two possible explanations for the multiple clades within
N. leucogenys. One is that N. leucogenys contains several distinct haplotypes
that exist in sympatry. This hypothesis can be tested by establishing the
geographic distribution of the various clades, especially clades A and B. It is also
possible that a cryptic taxon has been absorbed into today’s N. leucogenys. The
range of N. leucogenys is large (Fig. 1), but not sufficiently large or geographically
heterogeneous to lead one to expect to find multiple allopatric haplotypes. The
average distance between A and B group individuals (0.036470.0018) is less than
between subspecies in comparable groups, but by a very small margin [macaques
Z0.041; Rosenblum et al., 1997; orangutans Z0.04117.0013; Warren et al.,
2001]. Genotyping N. leucogenys individuals of known geographic provenance will
be crucial to interpret the genetic variation. In either situation (sympatric
variants or allopatric subspecies), it is desirable to maintain the full extent of this
species’ variability in the captive population.
Our mtDNA data do not support the elevation of siki to species status. Three
of the four individuals that cluster with our H. l. siki are identified as
N. leucogenys. Couturier and Lernould [1991] found no reliable morphological
distinction between female siki and N. leucogenys; adult males are of course
indistinguishably black with white cheeks. The pairwise differences between our
sample identified as siki and the leucogenys are within the range of intraspecific
variation seen in N. leucogenys and H. lar. Although Couturier and Lernould
[1991] found their specimens of siki and leucogenys differed by a reciprocal
translocation between chromosomes 1 and 22, no other workers appear to have
karyotyped their samples and the phylogenetic significance of this discovery
remains unexplored.
Some additional data are provided by Zhang [1997] in a little known report
on cytochrome b variation. Zhang compared five new 252 bp sequences for one
H. hoolock of unknown origin, two northern concolor from the Vietnam–China
border, and two N. leucogenys from northern Vietnam to 11 of the 26 sequences
reported by Garza and Woodruff [1992]. His maximum parsimony analysis
showed that Nomascus was a well-defined sister group (bootstrap value 5 98) to
the other three genera (Hoolock and Syndactylus and Hylobates) and, within its
cluster of nine individuals, he found siki as the outgroup to leucogenys, and well
differentiated from both concolor and gabriellae. Although he argued that this
result favored the recognition of siki as a separate species in our opinion the
bootstrap value is too low (86) to warrant such revision.
Am. J. Primatol. DOI 10.1002/ajp
1296 / Monda et al.
Two additional cytochrome b analyses have been reported. Hall et al. [1998]
examined the entire 1,040 bp sequence in six species and all four genera but in
only eight individuals. They confirmed the species-level divergence of leucogenys
and gabriellae but found insufficient variation to resolve the relationships among
the genera. Roos [2003, 2004] provides a more recent analysis of the entire
sequences of 24 Nomascus. In close agreement with our results, he found four
species-level taxa within his samples: nasutus, concolor, leucogenys, gabriellae.
N. nasutus [represented by Patzi] had the deepest root (8% interspecific
divergence). Six N. leucogenys and three N. gabriellae show moderate
intraspecific divergence (4% each) and more than was found among nine
N. concolor. Four siki were examined: two individuals were about 2% different
from gabriellae and two were about 1% different from the leucogenys. In the
absence of specimen and locality data it is not possible to interpret this finding of
paraphyly in siki as it could be due to specimen misidentification and/or
hybridization. Both natural and artificial (captive) hybrids have been identified
[Mootnick, 2006, personal communication, May 2006] and, more generally,
hybridization has to be recognized as a normal process in gibbon evolution
[Arnold & Meyer, 2006].
If the historical taxonomic problems of the gibbons have arisen in part from
the practice of defining taxa based on characters of single individuals we should
be cautious not to further contribute to such malpractice. Although we have tried
to go beyond dependence on a typological approach there are several issues that
still frustrate the elucidation of concolor gibbon phylogeny. First, taxa should not
be defined solely on the basis of maternally transmitted mtDNA patterns.
Comparable genetic studies of nuclear variation (autosomal sequences,
Y-chromosome sequences, and microsatellite allele frequencies) and karyotypes
are essential components of contemporary species characterization. Although
family-wide surveys have not yet been undertaken, an indication of their
resolving power is illustrated by, for example, Chambers et al. [2004], Tanaka
et al. [2004] and Zhang et al. [2004]. Second, vocalization, which may serve as a
partial reproductive isolating mechanism must also be considered [Konrad
& Geissmann, 2006]. Third, it is important to recognize that today’s geographic
ranges for some species are recently contracted and fragmented. Subfossil teeth
and old paintings show that until 1,000–2,000 years ago gibbons ranged 1,600 km
further north in China to the level of the Huang (Yellow) River [Geissmann, 1995;
Groves, 1972; Marshall & Sugardjito, 1986; van Gulik, 1967]; Hoolock and
northern Nomascus have been extirpated over most of their historical ranges.
Finally, there is a need to pursue additional karyological studies of gibbons as
their chromosomes are very unusual among the mammals in exhibiting a ten-fold
higher incidence of chromosomal rearrangements (especially translocations),
most of which appear to be species-specific [Arnold et al., 1996; Couturier et al.,
1992; Bigoni & Stanyon, 2006; Carbone et al., 2006; Hirai et al., 2005; Jauch et al.,
1992; Koehler et al., 1995; Mueller et al., 2003; Nie et al., 2001]. As chromosomal
rearrangements can function as postmating reproductive isolating mechanisms
and contribute to stasipatric speciation [White, 1978; King, 1993] they warrant
close examination in species complexes exhibiting parapatric distribution
patterns like the gibbons. Effort should be made to characterize Nomascus
karyologically before key populations are extirpated. Consideration of the
processes of karyotypic evolution suggested to Mueller et al. [2003] that
Nomascus was the last (youngest) hylobatid genus to diverge [between 10 and
5 Mya according to Groves, 2004]; a conclusion supported by our own work
[Simmons et al., in prep.] and Chatterjee [2006], and at odds with Roos and
Am. J. Primatol. DOI 10.1002/ajp
Nomascus gibbon phylogeny / 1297
Geissmann [2001] who concluded that Nomascus was basal within the family.
This difference of opinion is based on different data to those described here and
with the increased concordance between data-sets it is clear that within a few
years the phylogeny of the surviving gibbons will be fully resolved and stable.
The concolor gibbons are variously listed by regional governments and NGOs
as globally threatened or, in the cases of N. nasutus and N. hainanus, critically
endangered [IUCN, 2006]. Gibbons are hunted for food, the alleged medicinal
value of their parts, and as trophies and pets [Sterling et al., 2006]. In addition,
habitat degradation results in the survivors living in small isolated patches of
forest and their disappearance across much of their historic range [Chivers, 2005;
Konstant et al., 2003; D.S. Woodruff, personal observation in Xishuangbanna,
July 2006]. This is vividly illustrated by the widely separated confirmedoccurrence dots on recent maps of Vietnam [Geissmann et al., 2000; Nadler &
Streicher, 2004]. Time is fast disappearing to document the genetic variability of
the remaining animals and provide a foundation for the sound conservation
management of both captive and free-ranging gibbons. The real promise of
multilocus genetic data is that it will permit a partial reconstruction of the
original phylogeographic patterns. Multilocus genotyping of all available museum
specimens and noninvasive genotyping of the surviving wild individuals will
permit resolution of the taxonomic ambiguities and the estimation of historical
rates of gene flow and natural hybridization.
ACKNOWLEDGMENTS
We thank Kurt Benirschke, Warren Brockelman, Helen Chatterjee, Thomas
Geissmann, Colin Groves, Alan Mootnick and Christian Roos for sharing their
knowledge of gibbons. Ronald Tilson and Cathy Castle facilitated Monda’s
original study of the AZA gibbons. Francine Frasier, Dawn Field, Hopi Hoekstra,
John Huelsenbeck, Pascal Gagneux, Nick Mundy, Sukamol Srikwan and Romel
Hokanson provided advice or technical assistance in the laboratory or with the
phylogenetic analyses. Our studies were supported, in part, by the AZA Gibbon
Taxon Advisory Group, the US National Science Foundation, the Chinese
Academy of Sciences, the University of Munich, and the University of California.
REFERENCES
Anderson S, Bankier AT, Barrell BG, de
Bruijin MHL, Coulson AR, Drouin J, Eperon
IC, Nierlich DP, Roe BA, Sanger F,
Schreier PH, Smith AJH, Staden R, Young
IG. 1981. Sequence and organization of the
human mitochondrial genome. Nature
290:457–465.
Arnold ML, Meyer A. 2006. Natural hybridization in primates: one evolutionary mechanism. Zoology 109:261–276.
Arnold N, Stanyon R, Jauch A, O’Brien P,
Weinberg J. 1996. Identification of complex
chromosome rearrangements in the gibbon
by fluorescent in situ hybridization (FISH)
of a human chromosome 2q specific microlibrary, yeast artificial chromosomes, and
reciprocal chromosome painting. Cytogenet
Cell Genet 74:80–85.
Baker LR, Geissmann T, Nadler T, Long B,
Walston J. 2002. Cambodia: Primate field
guide. Phnom Penh, Cambodia: Fauna &
Flora Cambodia. 8 p.
Bandelt H-J, Forster P, Rohl A. 1999. Medianjoining networks for inferring intraspecific
phylogenies. Mol Biol Evol 16:37–48.
Bartlett TQ. 2005. The hylobatidae. In: Campbell CJ, Fuentes A, MacKinnon KC, Panger
M, Bearder SK, editors. Primates in perspective. New York: Oxford University
Press. p 274–289.
Bensasson D, Zhang D-X, Hartl DL, Hewitt
GM. 2001. Mitochondrial pseudogenes: evolution’s misplaced witnesses. TREE 16:
314–321.
Bigoni F, Stanyon R. 2006. Hylobates concolor.
In: O’Brien SJ, Menninger JC, Nash WG,
editors. Atlas of mammalian chromosomes.
Hoboken, NJ: Wiley. p 160.
Bleisch WV, Jiang X. 2000. Action plan for
conservation of the gibbons of the Wuliang
Am. J. Primatol. DOI 10.1002/ajp
1298 / Monda et al.
Mountains. Sino-Dutch Forest Conservation and Community Development Project,
Kunming, Yunnan, China.
Bleisch W, Zhang Y. 2004. The view across the
border: China and the future of Vietnamese
primates. In: Nadler T, Streicher U, Ha
Thang L, editors. Conservation of primates
in Vietnam. Hanoi: Frankfurt Zool Soc,
Vietnam Primate Conserv Progr, Cuc
Phuong National Park, Endangered Primate Rescue Center. p 107–114.
Brandon-Jones D, Eudey AA, Geissmann T,
Groves CP, Melnick DJ, Morales JC, Shekelle M, Stewart CB. 2004. Asian primate
classification. Int J Primatol 25:97–164.
Brockelman WY, Schilling D. 1984. Inheritance of stereotyped gibbon songs. Nature
312:634–636.
Carbone L, Vessere GM, Hallers BFH, Zhu B,
Osoegawa K, Mootnick M, Kofler A, Wienberg J, Rogers J, Humphray S, Scott C,
Harris RA, Milosavljevic A, de Jong PA.
2006. A high-resolution map of synteny
disruptions in gibbon and human genomes.
PLoS Genet 2:2162–2175.
Chambers KE, Reichard UH, Moller A, Nowak
K, Vigilant L. 2004. Cross-species amplification of human microsatellite markers using
noninvasive samples from white-handed
gibbons (Hylobates lar). Am J Primatol 64:
19–27.
Chan BPL, Fellowes JR, Geissmann T, Zhang
J, editors. 2005. Status survey and conservation action plan for the Hainan gibbon—
version I (last updated November 2005).
Hong Kong: Kadoorie Farm & Botanic
Garden Technical Report 3. p 1–33.
Chatterjee HJ. 2006. Phylogeny and biogeography of gibbons: a dispersal-vicariance
analysis. Int J Primatol 27:699–712.
Chivers DJ. 2005. Gibbons: the small
apes. In: Caldecott J, Miles L, editors. World
atlas of great apes and their conservation.
Berkeley: University of California Press.
p 205–214.
Clement M, Posada D, Crandall KA. 2000.
TCS: a computer program to estimate gene
genealogies. Mol Ecol 9:1657–1659.
Corbet GB, Hill JE. 1992. The mammals of the
Indomalayan Region: a systematic review.
Oxford: British Museum (Natural History)
& Oxford University Press.
Couturier J, Lernould JM. 1991. Karyotypic
study of four gibbon forms provisionally
considered as subspecies of Hylobates
(Nomascus) concolor (Primates, Hylobatidae). Folia Primatol 56:95–104.
Couturier J, Dutrillaux B, Turleau C, DeGrouchy J. 1992. Comparative karyotyping
of four gibbon species or subspecies. Ann
Genet 25:5–10.
Dao VT. 1983. On the north Indochinese
gibbons (Hylobates concolor) (Primates:
Am. J. Primatol. DOI 10.1002/ajp
Hylobatidae) in North Vietnam. J Hum
Evol 12:367–372.
DiFiore A, Gagneux P. 2006. Molecular primatology. In: Campbell CJ, Fuentes A,
MacKinnon KC, Panger M, Bearder SK,
editors. Primates in perspective. New York:
Oxford University Press. p 369–393.
Fooden J. 1996. Zoogeography of Vietnamese
primates. Int J Primatol 67:845–899.
Fooden J, Quan G, Luo Y. 1987. Gibbon
distribution in China. Acta Theriol Sin 7:
161–167.
Garza JC, Woodruff DS. 1992. A phylogenetic
study of the gibbons (Hylobates) using DNA
obtained noninvasively from hair. Mol Phylogen Evol 1:202–210.
Garza JC, Woodruff DS. 1994. Crested gibbon
(Hylobates [Nomascus]) identification using
noninvasively obtained DNA. Zoo Biol 13:
383–387.
Geissmann T. 1989. A female black gibbon,
Hylobates concolor subspecies, from northeastern Vietnam. With appendix: a note on
the Laotian black gibbon, H. concolor lu. Int
J Primatol 10:455–476.
Geissmann T. 1993. Evolution of communication in gibbons (Hylobatidae). Ph.D. dissertation. Zurich University, Switzerland.
Geissmann T. 1995. Gibbon systematics and
species identification. Int Zoo News 42:
65–77.
Geissmann T. 1997. New sounds from the
crested gibbons (Hylobates concolor group):
first results of a systematic revision. In:
Zissler D, editor. Verhandlungen der
Deutschen Zoologischen Gesellschaft: Kurzpublikationen, 90. Jahresversammlung,
Gustav Fischer, Stuttgart. p 170.
Geissmann T. 2002. Taxonomy and evolution
of gibbons. Evol Anthropol 11(Suppl 1):
28–31.
Geissmann T. 2005a. Der Hainan-Schopfgibbon: Der bedrohteste Menschenaffe der
Welt. Gibbon J 1:10–12.
Geissmann T. 2005b. Auf der Suche nach den
letzten Gibbons von Hainan. Gibbon J 1:
18–22.
Geissmann T. 2006a. Gibbon research lab.
Available from: http://www. gibbons.de
Geissmann T. 2006b. Schutz des HainanSchopfgibbons, des seltensten Menschenaffen der Welt: ein Projektbericht. Gibbon J 2:
11–13.
Geissmann T, Lim KKP. 1994. Extraction of
bacula from tanned gibbon skins. Raffles
Bull Zool 42:29–41.
Geissmann T, Nijman V. 2006. Calling in wild
silvery gibbons (Hylobates moloch) in Java
(Indonesia): behavior, phylogeny, and conservation. Am J Primatol 68:1–19.
Geissmann T, Nguyen Xuan D, Lormée N,
Momberg F. 2000. Vietnam primate conservation status review 2000. Part 1:
Nomascus gibbon phylogeny / 1299
Gibbons. Hanoi: Fauna & Flora International, Indochina Programme. 139p.
Geissmann T, La Quang T, Trinh Dinh H, Vu
Dinh T, Dang Ngoc C, Pham Duc T. 2003.
Rarest ape species rediscovered in Vietnam.
Asian Primates 8(3–4):8–9.
Geissmann T, Traber S, von Allmen A. 2006.
Das Nangunhe-Naturreservat, Provinz
Yunnan, China: Ein Projektbericht [Nangunhe Nature Reserve, Yunnan Province,
China: a project report]. Gibbon J 2:14–17.
Groves CP. 1972. Systematics and phylogeny
of gibbons. In: Rumbaugh, DM, editor.
Gibbon and siamang, vol. 1. Basel: Karger.
p 1–89.
Groves CP. 1993. Speciation in living hominoid
primates. In: Kimbel WH, Martin LB,
editors. Species, species concepts, and primate
evolution. New York: Plenum. p 109–121.
Groves CP. 2001. Primate taxonomy. Washington, DC: Smithsonian Institution Press.
Groves CP. 2004. Taxonomy and biogeography
of primates in Vietnam and neighbouring
regions. In: Nadler T, Streicher U, Ha
Thang Long, editors. Conservation of primates in Vietnam. Hanoi: Frankfurt Zool
Soc,
Vietnam Primate Conservation
Programme, Cuc Phuong National Park,
Endangered Primate Rescue Center.
p 15–22.
Groves CP, Wang Y. 1990. The gibbons of the
subgenus Nomascus (Primates, Mammalia).
Zool Res 11:148–154.
Hall LM, Jones D, Wood B. 1998. Evolution of
the gibbon subgenera inferred from cytochrome b DNA sequence data. Mol Phylogen Evol 10:281–286.
Hirai H, Wijayanto H, Tanaka H, Mootnick
AR, Hayano A, Perwitasari-Farajallah D,
Iskandriati D, Sajuthi D. 2005. A whole-arm
translocation (WAT8/9) separating agile
gibbons and its evolutionary features. Chromosome Res 13:123–133.
Huelsenbeck
JP,
Ronquist
F.
2001.
MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17:754–755.
IUCN. 2006. IUCN Red list of threatened species. Available from: http://www.iucnredlist.
org.
Jauch A, Weinberg J, Stanyon R, Arnold N,
Tofanelli S, Ishida T, Cremer T. 1992.
Reconstruction of genomic rearrangements
in great apes and gibbons by chromosome
painting. Proc Natl Acad Sci USA 89:
8611–8615.
Jiang XL, Wang YX. 1999. Population and
distribution of black-crested gibbons (Nomascus concolor jingdongensis) in Wuliang
Nature Reserve, Jingdong, Yunnan. Zool
Res 20:421–425.
King M. 1993. Species evolution: the role of
chromosome change. Cambridge: Cambridge University Press.
Koehler U, Bigoni F, Weinberg J, Stanyon R.
1995. Genomic reorganization in the concolor gibbon (Hylobates concolor) revealed
by chromosome painting. Genomics 30:
287–292.
Konrad R, Geissmann T. 2006. The vocal
diversity and taxonomy of crested gibbons
(genus Nomascus) in Cambodia. Int
J Primatol 27:713–745.
Konstant WR, Mittermeier RA, Rylands AB,
Butynski TM, Eudey AA, Ganzhorn J,
Kormos R. 2003. The world’s top 25 most
endangered primates. Asian Primates 8:
29–34.
Kressirer P. 1993. Eine Molekulare Phylogenie der Gibbons (Hylobatidae). Munchen:
Diplomarbeit der Fakultat fur Biologie der
Ludwig-Maximilians-Universitat.
Ma S, Wang Y. 1986. The taxonomy and
distribution of gibbons in southern China
and its adjacent region, with description
of three new subspecies. Zool Res 7:
393–410.
Ma S, Wang Y, Poirier FE. 1988. Taxonomy,
distribution, and status of gibbons (Hylobates) in southern China and adjacent
areas. Primates 29:277–286.
Marshall J, Sugardjito J. 1986. Gibbon
systematics. In: Swindler DR, Erwin J,
editors. Comparative primate biology,
vol. 1: systematics, evolution and anatomy.
New York: Liss. p 137–185.
Monda K. 1995. A phylogenetic study of the
gibbons (Hylobates) using the control
region of the mitochondrial genome. San
Diego: Master’s thesis, University of
California.
Mootnick AR. 2006. Gibbon (Hylobatidae)
species identification recommended for rescue or breeding centers. Primate Conserv
21:103–138.
Mootnick AR, Groves CP. 2005. A new generic
name for the hoolock gibbon (Hylobatidae).
Int J Primatol 26:971–976.
Morin PA, Goldberg TL. 2003. Determination
of genealogical relationships from genetic
data: a review of methods and applications.
In: Chapais B, Berman CM, editors. Kinship
and behavior in primates. Oxford: Oxford
University Press. p 15–45.
Mueller S, Hollatz M, Weinberg J. 2003.
Chromosomal phylogeny and evolution of
gibbons (Hylobatidae). Hum Genet 113:
493–501.
Nadler T, Streicher U. 2004. The primates of
Vietnam—an overview. In: Nadler T, Streicher U, Ha Thang L, editors. Conservation
of primates in Vietnam. Hanoi: Frankfurt
Zool Soc, Vietnam Primate Conservation
Programme, Cuc Phuong National Park,
Endangered Primate Rescue Center. p 5–11.
Nie W, Rens W, Wang J, Yang F. 2001.
Conserved chromosome segments in
Am. J. Primatol. DOI 10.1002/ajp
1300 / Monda et al.
Hylobates hoolook revealed by human and
H. leucogenys paint probes. Cytogenet Cell
Genet 92:248–253.
Polzin T, Daneschmand SV. 2003. On Steiner
trees and minimum spanning trees in
hypergraphs. Oper Res Lett 31:12–20.
Prouty LA, Buchanan PD, Pollitzer WS,
Mootnick AR. 1983a. Bunopithecus: a
genus-level taxon for the hoolock gibbon
(Hylobates hoolock). Am J Primatol 5:83–87.
Prouty LA, Buchanan PD, Pollitzer WS,
Mootnick AR. 1983b. A presumptive new
hylobatid subgenus with 38 chromosomes.
Cytogen Cell Genet 35:141–142.
Roos C. 2003. Molekulare Phylogenie der
Halbaffen, Schlankaffen und Gibbons. PhD
thesis. Germany: Technical Univ Munich.
Roos C. 2004. Molecular evolution and systematics of Vietnamese primates. In: Nadler
T, Streicher U, Ha Thang L, editors.
Conservation of primates in Vietnam. Hanoi: Frankfurt Zool Soc, Vietnam Primate
Conservation Programme, Endangered Primate Rescue Center, Cuc Phuong National
Park. p 23–28.
Roos C, Geissmann T. 2001. Molecular phylogeny of the major hylobatid divisions. Mol
Phylogen Evol 19:486–494.
Rosenblum LL, Supriatna J, Melnick DJ.
1997. Phylogeographic analysis of pigtail
macaque populations (Macaca nemestrina)
inferred from mitochondrial DNA. Amer J
Phys Anthro 104:35–45.
Sheeran, LK, Zhang Y, Poirier FE, Yang D.
1998. Preliminary report on the behavior of
the Jingdong black gibbon (Hylobates concolor furvogaster). Trop Biodiv 5:113–125.
Simmons RE. 2005. A phylogenetic study of
the gibbons (Hylobatidae). Master’s thesis.
San Diego: University of California.
Simmons RE, Monda K, Woodruff DS. Phylogenetics of gibbons (Hylobatidae): mitochondrial and nuclear DNA sequence data
resolve long-standing questions. in prep.
Sterling EJ, Hurley MM, Minh LD. 2006.
Vietnam: a natural history. New Haven:
Yale University Press.
Su B, Kressirer P, Wang W, Jiang X, Wang YX,
Woodruff DS, Monda K, Zhang YP. 1996.
Molecular phylogeny of Chinese N. c.
concolor gibbons. Sci China (C) 26:414–419.
Swofford DL. 1998. Phylogenetic analysis
using parsimony and other methods
(PAUP Version 4.0b). Sunderland, MA:
Sinauer.
Takacs Z, Morales JC, Geissmann T, Melnick
DJ. 2005. A complete species-level phylogeny of the Hylobatidae based on mitochondrial ND3-ND4 gene sequences. Mol
Phylogen Evol 36:456–467.
Tanaka H, Wijayanto H, Mootnick AR, Iskandriati D, Perwitasari-Farajallah D, Sajuthi
D, Hirai H. 2004. Molecular phylogenetic
Am. J. Primatol. DOI 10.1002/ajp
analyses of subspecific relationships in agile
gibbons (Hylobates agilis) using mitochondrial and TSPY gene sequences. Folia
Primatol 75(Suppl 1):418.
Thalmann O, Hebler J, Poinar HN, Paabo S,
Vigilant L. 2004. Unreliable mtDNA data
due to nuclear insertions: a cautionary tale
from analysis of humans and other great
apes. Mol Ecol 13:321–335.
Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. 1997. The CLUSTAL-X
windows
interface:
Flexible
strategies for multiple sequence alignment
aided by quality analysis tools. Nucleic
Acids Res 25:4876–4882.
Trung LQ, Hoang TD. 2004. Status review of
the Cao Vit black-crested gibbon (Nomascus
nasutus nasutus) in Vietnam. In: Nadler T,
Streicher U, Ha Thang L, editors. Conservation of primates in Vietnam. Hanoi: Frankfurt Zool Soc, Vietnam Primate Conservation
Progr. Cuc Phuong National Park, Endangered Primate Rescue Center. p 90–94.
van Gulik RH. 1967. The gibbon in China. An
essay in Chinese animal lore. Leiden: Brill.
Wagele J-W. 2005. Foundations of phylogenetic systematics. Munich: Pfeil.
Wang Y. 2003. A complete checklist of mammal species and subspecies in China—a
taxonomic and geographic reference.
Beijing: China Forestry Publishing House.
394p.
Warren KS, Verschoor EJ, Langenhuijzen S,
Swan RA, Vigilant L, Heeney JL. 2001.
Speciation and intrasubspecific variation in
Bornean orangutans, Pongo pygmaeus pygmaeus. Mol Biol Evol 18:472–480.
White MJD. 1978. Modes of speciation. San
Francisco: Freeman.
Whittaker DJ. 2005. Evolutionary genetics of
Kloss’s
gibbons
(Hylobates
klossii):
systematics, phylogeography, and conservation. Ph.D. thesis. The City University of
New York. 201p.
Woodruff DS. 1990. Genetics and demography
in the conservation of biodiversity. J Sci Soc
Thailand 16:117–132.
Woodruff DS. 1993. Non-invasive genotyping
of primates. Primates 34:333–346.
Woodruff DS. 2003. Noninvasive genotyping
and field studies of free-ranging nonhuman
primates. In: Chapais B, Berman CM,
editors. Kinship and behavior in primates.
Oxford: Oxford University Press. p 46–68.
Woodruff DS, Monda K, Simmons RE. 2005.
Mitochondrial DNA sequence variation and
subspecific taxonomy in the white-handed
gibbon, Hylobates lar. Nat Hist J Chulalongkorn Univ 1:71–78.
Zehr SM. 1999. A nuclear and mitochondrial
phylogeny of the lesser apes (Primates,
genus Hylobates). Ph.D. thesis. Harvard
University. 221p.
Nomascus gibbon phylogeny / 1301
Zhang Y. 1992. Hainan gibbon (Hylobates concolor
hainanus) threatened. Asian Primates 2:6.
Zhang Y, Sheeran L. 1994. Current status of
the Hainan black gibbon (Hylobates concolor hainanus). Asian Primates 3:3.
Zhang YP. 1997. Mitochondrial DNA sequence
evolution and phylogenetic relationships of
gibbons. Acta Genet Sin 24:231–237.
Zhang YW, Luo HR, Ryder OA, Zhang YP.
2004. Evolution of the tandem repeats in
thymidylate synthase enhancer region
(TSER) in primates. Gene 338:47–54.
Zhou J, Wei F, Li M, Zhang J, Wang D, Pan R.
2005. Hainan black-crested gibbon is
headed for extinction. Int J Primatol 26:
453–465.
APPENDIX 1
Annotated list of currently recognized Nomascus species and subspecies
Nomascus concolor Harlan, 1826. Western black gibbon or black crested
gibbon. The tortuous taxonomic history of N. concolor is discussed by Geissmann
[1989]. Our genetic data are in agreement with the cyt b study by C. Roos
(unpublished) and support the recognition of this taxon as a full species, and do
not support the recognition of three parapatric subspecies—concolor, jingdongensis, furvogaster. Endangered [IUCN, 2006] with less than 2,000 individuals in
China, Vietnam and Laos. Recent reports include Bartlett [2005], Bleisch and
Zhang [2004], Sheeran et al. [1998], Nadler and Streicher [2004].
Nomascus concolor concolor Harlan, 1826. Black gibbon or Tonkin black
crested gibbon. South China (eastern Yunnan) and northwest Vietnam, between
the Black (Song Da) and Red (Song Hong) rivers. Range historically parapatric
with N. c. jingdongensis, N. nasutus, and N. leucogenys [Geissmann et al., 2000;
Nadler & Streicher, 2004], but interactions with those taxa are undocumented
and probably no longer occur.
N. concolor jingdongensis Ma and Wang, 1986. Black gibbon or central
Yunnan black crested gibbon. South China (central Yunnan) between the Mekong
and Black rivers, Wenbu, Jingdong, and Wuliang Mountains [Bleisch & Jiang,
2000; Jiang & Wang, 1999; Sheeran et al., 1998]. Extirpated from most of range
[Geissmann et al., 2000, 2006]. Our genetic data support subjugation within
N. concolor, a view supported by Brandon-Jones et al. [2004], Geissmann et al.
[2000] and C. Roos (unpublished), as the diagnostic features involve only minor
color differences in females.
Nomascus concolor furvogaster Ma and Wang, 1986. Black gibbon or west
Yunnan black crested gibbon. South China (western Yunnan), between the
Mekong and Salween rivers. [Ma & Wang, 1986; Ma et al., 1988]. Genetic
data reported here support subjugation within N. concolor, a view supported
by Geissmann [1995], Geissmann et al. [2000] as the diagnostic features were
based on a subadult female. Geissmann et al. [2006] provide limited recent
observations.
Nomascus concolor lu Delacour, 1951. Loatian black crested gibbon. Bokeo
Province, Laos, westernmost Laos at Ban Nam Khueng and Khao Tham Phra on
the Mekong river and Nam Kan valley at about 201N, where Geissmann recently
confirmed their presence and identity [Geissmann et al., 2000; see also Mootnick,
2006]. This is an isolated allopatric population of a few hundred individuals
separated today from the main population of N. concolor by 250 km occupied by
N. leucogenys. Probably a synonym of N. c. concolor with minor differences
possibly a result of limited hybridization with N. leucogenys [Geissmann, 1989].
Until genetic data are available to test this hypothesis the subspecies should be
recognized; preliminary genetic data support subjugation within N. concolor
[C. Roos, unpublished].
Am. J. Primatol. DOI 10.1002/ajp
1302 / Monda et al.
Nomascus nasutus Kunckel d’Herculais, 1884. Eastern black crested gibbon.
Northeast Vietnam, north and east of the Red River delta and the adjacent coastal
China. Largely extirpated, 20–28 gibbons were re-discovered in Cao Bang and Hoa
Binh Provinces in 2002 [Bleisch & Zhang, 2004; Geissmann et al., 2000; Trung &
Hoang, 2004]. Critically Endangered [IUCN, 2004; Konstant et al., 2003]. This
taxon was referred to awkwardly for many years as Hylobates (Nomascus) sp. cf.
nasutus because of uncertainties over the source of the type specimen (see notes
in Appendix 2) and its relation to N. concolor [see Geissmann, 1989, 2002].
Genetically, we have shown that it is clearly specifically distinct from N. concolor,
a conclusion reached independently by Takacs et al. [2005]. Until recently only
one captive animal (Patzi, see Appendix 2) had been examined and her
relationship to the remaining wild gibbons had not been established. Patzi was
unusual in looking like a concolor gibbon but having a distinctive hainanus-like
vocalization [Geissmann, 1989, 1997] and she may have been a hybrid or an
unrecognized taxon [Geissmann et al., 2002; Groves, 2004]. However, Roos (in
litt. April 2006) has just genotyped apes from both surviving Vietnamese
populations and found them to be very closely related to Patzi at the cyt b
sequence studied. Furthermore, as reported in the Results above, he discovered
the mainland gibbons were significantly different from Hainan Island animals at
this locus and accordingly proposes to elevate nasutus to species rank [Roos, in
prep.]; a decision anticipated by Nadler and Streicher [2004].
N. hainanus Thomas 1892. Hainan black crested gibbon. The population isolated
today on Hainan Island, China, is now restricted to the Bawangling Nature Reserve
[Zhang, 1992; Zhang & Sheeran, 1994]. Dao [1983] thought the island gibbons were
subspecifically distinct from nasutus and several museum specimens in Vietnamese
collections are referred to the subspecies N. n. hainanus. Roos’ (in prep, in litt. to
DSW) cyt b genetic sequence divergence data indicate, however, that although related
to nasutus, hainanus merits full species level status. It is unknown when gibbons first
arrived on the continental island of Hainan but they could have dispersed across
broad (50–70 km wide) dry land connections during one or more Pleistocene
hypothermal phase(s). Today’s population has been physically isolated for less than
10,000 years, since the sea rose above –25 m and flooded the narrow Qiongzhou Strait.
Their genetic divergence from nasutus suggests they have been separated for much
longer and Chatterjee [2006] estimates the species antiquity to be 0.3–1.8 My. The
identity of mainland gibbons referred to this species cannot be accepted without
genetic confirmation. Groves [2001] and Wang [2003] treat hainanus as a full species,
without comment. Now critically endangered, this population fell from an estimated
2,000 animals in the 1950s, to 23 in 1998, and 13 in 2004 [Bleisch & Zhang, 2004;
Chan et al., 2005; Chivers, 2005; Geissmann et al., 2000; Zhou et al., 2005].
N. leucogenys Ogilby, 1840. Northern white-cheeked crested gibbon.
Historical range: China (Mengla county, Xishuangbanna, southern Yunnan),
northern Laos, and northwestern Vietnam [Fooden et al., 1987; Geissmann et al.,
2000]. Corbet and Hill [1992] reported it is sympatric with N. concolor but this
seems unlikely as the historical interactions with other taxa are undocumented.
IUCN [2006]: data deficient. Endangered in Vietnam and o100 individuals in
China [Bleisch & Zhang, 2004; Geissmann et al., 2000; Nadler & Streicher, 2004].
The southern populations are referred to the subspecies N. l. siki.
N. leucogenys siki Delacour, 1951. Southern white-cheeked crested gibbon.
Southern Laos, central Vietnam. During the last 15 years various authors have
included siki as either a subspecies of N. gabriellae [Corbet & Hill, 1992; Groves &
Wang, 1990], or N. leucogenys [Geissmann, 1995], or treated it as a separate
species [Groves, 2001, 2004; Zhang, 1997]. The size and shape of the white cheek
Am. J. Primatol. DOI 10.1002/ajp
Nomascus gibbon phylogeny / 1303
patches of adult males and juveniles are diagnostic features for siki, but adult
females of N. leucogenys and siki are morphologically indistinguishable although
both differ from females of N. gabriellae [Geissmann, 1995; Geissmann et al.,
2000; Mootnick, 2006]. The songs of the three taxa are different [Konrad &
Geissmann, 2006] and siki resembles N. leucogenys more than that of any other
form of crested gibbon including N. gabriellae [Konrad & Geissmann, 2006]. The
boundary between N. leucogenys and siki lies near the lower Ca River south of the
town of Vinh and east of the Annamite Mountains in Nghe An Province, Vietnam.
Further south, N. l. siki is replaced by N. gabriellae, but the southern range limits
of N. l. siki are undocumented. Konrad and Geissmann [2006] have described
vocalizations in northeast Cambodia (Rattanakiri) and provisionally assign those
apes to N. l. siki because of their resemblance to calls of topotypic siki from nearby
Bach Ma, Vietnam. They postulate that a taxon boundary exists somewhere
between Rattanakiri and southern Mondulkiri in eastern Cambodia, and discuss
the roles of the Srepok river and dry dipterocarp forest as possible distribution
barriers. Our mitochondrial DNA sequences suggest that siki is more closely
related to N. leucogenys than to N. gabriellae [Garza & Woodruff, 1992, 1994;
Zhang, 1997; herein] but we recognize that a couple of specimens reported by
others have the opposite affinity; we regard the problem as unresolved until
animals of known geographic provenance are genotyped. Konrad and Geissmann
[2006] discuss the possibility that siki and gabriellae are separated by a broad zone
of intergradation (hybridization) or, alternatively, that a currently unrecognized
taxon occupies a large area of south central Vietnam between their ranges.
N. gabriellae Thomas, 1909. Yellow-cheeked (or buff-cheeked) crested
gibbon. Eastern Cambodia, southern Laos, and southern Vietnam, south of
151300 . Historically thought to be parapatric or hybridize with siki, but their
interactions are poorly documented and the two species are allopatric in
Cambodia today [Baker et al., 2002; Geissmann et al., 2000; Konrad &
Geissmann, 2006]. Endangered.
APPENDIX 2
Specimens examined
North American zoo gibbons used in this study
All taxonomic identifications are those provided by the owners and are the
same as those recorded in the AZA concolor studbook [1990] and ISIS. For each
individual the following data are provided: [the ID number used in Figures in this
paper in square brackets], Studbook number/ISIS number, Sex, House name,
Holding Zoo, Origin, GenBank accession number, and no. of base pairs (bp) of
mtDNA sequenced.
Notes: Studbook number: two individuals had no studbook number (]nsb).
Sex and House name: male or female and name (or not available, na). Holding
Zoo: at the time hair sample was provided, typically 1984–5. Origin: captive born
(cb) or wild born (wb); country or zoo of origin or unknown.
Nomascus leucogenys (24 individuals)
[leuc 1] 11/32055C, F Betsy, National, wb, unknown, EF203867, 497 bp.
[leuc 2] 18/92, F na, Minnesota, wb unknown, EF203868, 530 bp. [leuc 3]
21/1345, F Muneca, Gladys Porter, wb unknown, EF203869, 486 bp. [leuc 4]
24/36233, M Joe, National, wb unknown, EF203870, 510 bp. [leuc 5] 28/36336, F
Am. J. Primatol. DOI 10.1002/ajp
1304 / Monda et al.
Beryl National, wb unknown, EF203871, 497 bp. [leuc 6] 30/92, F China, Gladys
Porter, wb unknown, EF203872, 485 bp. [leuc 7] 31/93, F Goldie, Gladys Porter
Zoo, wb unknown, EF203873, 480 bp. [leuc 8] 42/1318, F Phyllis, Washington
Park, wb unknown, EF203874, 285 bp. [leuc 9] 43/101675, F Mae, National, wb
unknown, EF203875, 521 bp. [leuc 10] 53/101519, M Gilly, Cheyenne, wb
unknown, EF203876, 300 bp. [leuc 11] 55/91, M Archie, Minnesota, wb unknown,
EF203877, 300 bp. [leuc 12] 196/107858, M Mekong, National, cb National,
EF203878, 485 bp. [leuc 13] 213/5926, F Minnesota, cb Minnesota, EF203879,
513 bp. [leuc 14] 229/109732, F Melaka, National, cb National, EF203880, 176 bp.
Comparable sequences were obtained from the following individuals but
are not shown here as they are subsumed within the clusters revealed by
the above animals [Monda, 1995; Woodruff et al., in prep.]. Some are the
descendants of females listed above and were found to have identical mtDNA,
as expected.
1 nsb/110265, M, Beryl’s baby, National, unknown, 474 bp. 2 nsb/91200, ?F,
Hue, Washington Park, cb Washington Park 285 bp. 14/1325, M, Gunther,
Washington Park, wb unknown. 79/100739, M, Bert, National, cb, National,
521 bp. 134/105020, M, Ralph, National, cb National, son of 28 and sib of 1 nsb.
143/107869, F, Siam, National, cb, National, 499 bp. 146/2044, F, Deborah, Gladys
Porter, cb unknown, 536 bp. 207/108291, F, Burma, National, cb National,
daughter of 28 and sib of 1 nsb. 209/88071, M, Tanh Linh, Washington Park, cb
Washington Park, 291 bp. 231/109740, F, Sena, National, cb National, 474 bp.
Nomascus gabriellae (2)
[gabr 1], 122/94241, F Robin, Los Angeles, cb Los Angeles, daughter of 65/
94111, F Bahmetoo, Los Angeles, wb S. Vietnam and 64/94110, M Koo, Los
Angeles, wb S. Vietnam, EF203886, 492 bp. [gabr 2], 180/95141, M Yang
Menggangu, Los Angeles, cb Los Angeles, sib of 122, EF203887, 492 bp.
Symphalangus syndactylus (1)
[Symphalangus], 267/870020, F, Juice, Cheyene Mountain Zoo, cb Cheyene,
EF203866, 385 bp.
Samples studied by Kressirer [1993]
Gibbons were adults unless noted and all identifications were provided by the
owners. For each individual the following data are provided: [the ID number used
in this paper in square brackets], Kressirer [1993] specimen no., Sex, House
name, Holding Zoo or Museum, mtDNA source, GenBank accession number.
N. l. leucogenys
[leuc 15] 4 M juvenile (parents: Jack & Jacqueline), Mulhouse Zoo, tissue
sample 1986, EF203883, 476 bp. [leuc 16] 280 M Claude, Mulhouse Zoo, blood
sample 1986, EF203881, 476 bp. Used by Kressirer [1993] to represent this taxon
and identified as P3leuc in some analyses by him, and subsequently by Monda
[1995] and Simmons [2005]. [leuc 17] 281 M Jack, Mulhouse Zoo, blood sample
1986, EF203882, 476 bp. [leuc 18] 342 M Dodo, Budapest Zoo, arrived from
southeast Asia in 1968, hair sample 1991, EF203884, 476 bp.
N. l. siki
[siki 1] 20 M Charly, Hellabrunn Zoo, Munich, hair sample in 1991,
EF203885, 495 bp. Used by Kressirer [1993] to represent this taxon and identified
Am. J. Primatol. DOI 10.1002/ajp
Nomascus gibbon phylogeny / 1305
as by him as P1siki in some of his analyses, and subsequently by Monda [1995]
and Simmons [2005].
Identical but shorter sequences were obtained from the following individuals
but are not used here: 21 F Charlotte, Hellabrunn Zoo, Munich, hair sample in
1991; 22 F Mimi, Hellabrunn Zoo, Munich, hair sample in 1991.
N. gabriellae
[gabr 3] 340 M Tschico, Budapest Zoo, arrived from Laos in 1987, hair
sample 1991, EF203888, 407 bp. Used by Kressirer [1993] to represent this taxon
and identified as by him as P2gabriellae in some of his analyses, and subsequently
by Monda [1995] and Simmons [2005].
An identical but shorter sequence was obtained from the following individual
but is not used here: 341 F Juschka, Budapest Zoo, transferred from Moscow Zoo
1991, born ca. 1968 in Vietnam, hair sample 1991.
N. nasutus
[nasu 1] 409/410 F Patzi, Humboldt University Museum, ZMB 70036, from
Tierpark Berlin (1962–1986), reported to have been shipped from Hon Gai
(north-eastern Vietnam) but geographic origin unknown, skin sample, EF203889,
446 bp. This individual is discussed in detail by Geissmann [1989] who regards
is as sufficiently different in coloration from the other known northeastern
Vietnamese black gibbons to warrant subspecific status. Used by Kressirer
[1993] to represent this taxon and identified as by him as P4nasutus in some
of his analyses, and subsequently by Monda [1995], Su et al. [1996] and Simmons
[2005]. [nasu 2] Kressirer ]0.2, M, Museum Naturkunde, Berlin, 85357, captive
animal labeled as N. n. hainanus from ‘‘Houchow (?), China’’, EF203890,
519 bp. Our efforts to establish the source locality of this specimen have
failed; there is no Houchou on Hainan Island and there is a reasonable possibility
that this animal was actually from the mainland as an anonymous reviewer of
this manuscript has kindly drawn our attention to a locality named Hou Chau (or
Kou Chau) at 221380 N, 104150 E in Vietnam. Used by Kressirer [1993] to
represent this taxon and identified as by him as P5hainanus in some of his
analyses, and subsequently by Monda [1995], Su et al. [1996] and Simmons
[2005]. We now believe this specimen was misidentified and report it herein
as N. nasutus.
Partial sequences obtained by Su et al. [1996]
For each individual the following data are provided: [ID number in this
paper] specimen identification ] in Su et al. [1996], sex, collection locality, mtDNA
source, collection year, GenBank accession number. Skins are in the Museum of
the Kunming Institute of Zoology unless noted. Comparable sequences were
143 bp, and all shared a 16 bp deletion relative to Symphalangus.
[leuc 19] N. leucogenys-1, M, Hekou, Yunnan, fresh hair sampled, 1994,
EF212884. [leuc 20] N. leucogenys-2, M, Hekou, Yunnan, fresh hair sampled,
1994, EF212885.
[jing 1] N. concolor jingdongensis-1, F, Jingdong, Yunnan, collected 1964,
old skin, EF203891. [jing 2] N. c. jingdongensis-2, M, Jingdong, Yunnan,
collected 1964 old skin, EF212886. [jing 3] N. c. jingdongensis-3, M, Jingdong,
Yunnan, collected 1964 old skin, EF212887. [jing 4] N. c. jingdongensis-4, F,
Jingdong, Yunnan, old skin, details unknown, EF212888.
Am. J. Primatol. DOI 10.1002/ajp
1306 / Monda et al.
[furv 1] N. c. furvogaster, M, Cangyuan, Yunnan, collected 1983, old skin,
EF212889.
[conc 1] N. c. concolor-1, sex unknown, Jianshui, Yunnan, collected 1987 old
skin, EF203893. [conc 2] N. c. concolor-2, F, Luchum, Yunnan, collected 1972, old
skin, EF203894. [conc 3] N. c. concolor-3, F Jianshui, Yunnan, collected 1989, old
skin, EF203892.
[nasu 2] N. nasutus hainanus is Kressirer [1993] P5hainanus: ]0.2, M,
Museum Naturkunde, Berlin, 85357, captive animal from ‘‘Houchow (?), China’’,
and now thought to be N. nasutus from Vietnam (see above).
[Symphalangus] Symphalangus syndactylus is Monda’s ]267/870020, F,
Juice, Cheyene Mountain Zoo, cb Cheyene.
Outgroup sequences from GenBank
An additional four sequences were used as outgroups in some analyses:
[Hoolock], Hoolock (formerly Bunopithecus) hoolock (AF311725)[Roos and
Geissmann]; [numt] a S. syndactylus nuclear insertion (numt) of the HVR-1
(AF035467); [Pongo] Pongo pygmaeus (D38115); [Homo] Homo sapiens
(NC001807).
Am. J. Primatol. DOI 10.1002/ajp
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