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Biochemical Systematics and Ecology 48 (2013) 136143

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Biochemical Systematics and Ecology


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Phylogenetic analyses and improved resolution of the family


Bovidae based on complete mitochondrial genomes
Chengzhong Yang a, Changkui Xiang b, Wenhua Qi a, c, Shan Xia a, d, Feiyun Tu a,
Xiuyue Zhang a, Timothy Moermond a, Bisong Yue a, e, *
a

Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University,
Chengdu 610064, PR China
b
School of Industry Manufacturing, Chengdu University, Chengdu 610106, PR China
c
School of Life Sciences and Engineering, Chongqing Three Gorges University, Chongqing 404100, PR China
d
Department of Science Education, Chengdu Normal University, Chengdu 611130, PR China
e
Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University,
Chengdu 610064, PR China

a r t i c l e i n f o

a b s t r a c t

Article history:
Received 2 July 2012
Accepted 15 December 2012
Available online 20 January 2013

Efforts have been made to investigate the phylogeny of the family Bovidae; however, the
relationships within this group still remain controversial. To further our understanding of
the relationships, we sequenced the mitochondrial genome of the Himalayan goral, Naemorhedus goral, an IUCN Redlist near threatened conservation dependent species. Then we
conducted molecular phylogenetic relationships of the Bovidae based on Bayesian and
Maximum Likelihood methods. The results indicate that the basal divergence within the
Bovidae is between the Bovinae and a strongly supported clade of the remaining Bovidae
species. The two Neotragus species (the suni and pygmy antelope) clustered with the
impala, Aepyceros melampus (Aepycerotinae), and together they formed the most basal of
the non-Bovinae. All the genera of the Antilopinae clustered together except Neotragus,
which suggested that the Antilopinae was a paraphyletic subfamily. The present study
conrmed a close relationship between the genera Capricornis and Naemorhedus while
supporting their designation as separate genera and suggested that the Capricornis-Naemorhedus-Ovibos clade (serows, gorals, and the muskox) should be placed in the Caprinae.
Bison, Bos, and Tragelaphus (bison & cattle and kudus and nyalas) were paraphyletic. The
very close relationship between Bison and Bos suggested that Bos and Bison should be
integrated into a single Bos genus. Saiga and Pantholops (the Chiru or Tibetan Antelope),
unique genera which have sometimes been lumped together, were placed in different
groups: Saiga within the Antilopinae and Pantholops at the base of the Caprinae. Our results also supported a new taxonomy which places the three species of Hemitragus into
three monospecic genera: the genus Hemitragus is restricted to the Himalayan tahr, and
two new genera are created: Arabitragus for the Arabian tahr and Nilgiritragus for the
Nilgiri tahr.
2012 Elsevier Ltd. All rights reserved.

Keywords:
Naemorhedus goral
Mitochondrial genome
Molecular phylogeny
Bovidae

* Corresponding author. Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University,
Chengdu 610064, PR China. Tel.: 86 28 85412488; fax: 86 28 85414886.
E-mail address: bsyue@yahoo.com (B. Yue).
0305-1978/$ see front matter 2012 Elsevier Ltd. All rights reserved.
http://dx.doi.org/10.1016/j.bse.2012.12.005

C. Yang et al. / Biochemical Systematics and Ecology 48 (2013) 136143

137

1. Introduction
The phylogenetic status of the conservation dependent gorals, Naemorhedus species, and the related species of Capricornis,
the serows, remains uncertain and needs to be claried (Corbet and Hill, 1992; Groves and Grubb, 1985; Mead, 1989). Due to
limitations of collecting samples from threatened Naemorhedus and Capricornis species, it is difcult to perform molecular
phylogenetic analysis to nd out their precise classication scheme. Fortunately, more molecular data samples from these
species have become available, and we here contribute a complete genetic analysis from Naemorhedus goral, the last species of
this genus to be sampled. The Himalayan goral, N. goral, a small, elusive high mountain goat antelope of the family Bovidae,
has a narrow distribution zone in China occurring only along the southern border of Tibet. Owing to excessive hunting, and
habitat loss, its wild populations have been declining for decades. Consequently, the Himalayan goral is protected in China
under the Wild Animal Protection Law as a Category II key species (Li et al., 2000) and listed by IUCN as near threatened. N.
goral along with the other three goral species may be considered as conservation dependent species and all four are listed in
Appendix I of CITES (Duckworth and MacKinnon, 2008). In order to domesticate, genetically improve, and systematically
conserve the Himalayan goral, it is necessary to dene the genetic characteristics of this species and its relationship to other
species within the family Bovidae.
The bovids (oxen, sheep, goats, antelopes and allies) include 137 living and more than 300 fossil species (Savage and
Russell, 1983). They are found in Africa, Europe, Asia and North America, with the great majority being in Africa. The Bovidae includes more species than any other extant family of large mammals, but their phylogenetic relationships remain largely
unresolved, showing that Simpsons (1945) view that Bovidae is one of the most troublesome groups of mammals to classify
still applies today.
The origin, development, and relationships within the Bovidae are poorly understood and opinions on these topics differ
widely. Thus, the classication of the bovids, particularly with respect to the recognition of the subfamilies and tribes, is
noteworthy for its lack of consensus. Numerous versions of bovid taxonomy exist (e.g., Simpson, 1945; Haltenorth, 1963;
Gentry, 1992; Grubb, 2001), and controversy persists over which version most accurately reects phyletic relationships. There
is considerable disagreement in the allocation of genera to tribes and subfamilies, from the ve subfamilies and 13 tribes of
Simpson (1945) to the 10 subfamilies and 28 tribes of Haltenorth (1963). The most recent version of bovid taxonomy (Grubb,
2001) proposes 9 subfamilies and 17 tribes for the extant bovid species.
Intertribal relationships also have resulted in considerable difference of opinion. Although monophyly of the majority of
the subfamilies and tribes is supported by morphological and molecular data, the evolutionary relationships among most of
them are still surrounded by controversy. Therefore, the identity of sister taxa among these subfamilies or tribes, and interrelationships among genera and species within them remain uncertain. This is reected in the growing literature, which
encompasses paleontological, morphological, and molecular data, all of which attempt to clarify various aspects of bovid
evolution among tribes and subfamilies (e.g., Georgiadis et al., 1990; Gentry, 1992) and within them (e.g., Janecek et al., 1996).
The phylogenetic relationships within Bovidae have been investigated using both mitochondrial and nuclear sequences
(Hassanin and Douzery, 1999, 2003; Gatesy and Arctander, 2000a,b). However, these studies did not resolve conclusively the
phylogenetic relationships within Bovidae. Phylogenetic reconstruction based on a single gene or a short DNA segment may
sometimes compromise phylogenetic accuracy (Hernandez-Fernandez and Vrba, 2005) and may be responsible for discrepancies between different studies. Complete mitochondrial genomes have been commonly applied to phylogenetic
analysis at different levels: Hassanin et al. (2012) reconstructed the phylogenetic tree of Cetartiodactyla including the
Bovidae. However, the phylogenetic position of phylogenetic relationships within Bovidae may be affected when more
species are sampled (Zwick and Hillis, 2002). Here, after sequencing the complete mitochondrial genome of N. goral, we
conducted the phylogenetic analyses within the Bovidae based on complete mitochondrial genomes, which will improve our
understanding of evolutionary biology of this animal group.
2. Materials and methods
2.1. DNA sample
Muscle of the wild N. goral was obtained from the Mount Qomolangma (Everest) Nature Reserve in Tibet Province. Total
DNA was extracted following the method of Sambrook and Russell (2001).
2.2. PCR amplication and sequencing
The N. goral mitochondrial genome was amplied in twenty-three overlapping fragments using the long and accurate
polymerase chain reaction (LA-PCR) technique according to the manufacturers instructions (TaKaRa, Beijing, China). A set of
primers described by Hassanin et al. (2009) were used in the amplication. PCR cycling was carried out on a PTC-100 thermal
cycler (BioRad, Hercules, CA, USA). The amplication was carried out in 25 ml reaction volumes with 2.5 ml of 10  ExTaq buffer
(Mg2 Free), 1.03.0 ml dNTP (2.5 mM each), 2.0 ml MgCl2 (25 mM), 1 ml of each primer (10 uM), 0.2 ml ExTaq polymerase (5 U/
ml), and approximately 200 ng total genomic DNA as the template. PCR conditions were an initial pre-denaturation for 5 min
at 95  C, followed by 35 cycles of 30 s denaturations at 94  C, 45 s annealing at 5061  C, 13 min extensions at 72  C, and
a nal extension at 72  C for 10 min. The PCR products were puried using the DNA Agarose Gel Extraction Kit (Omega Bio-

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C. Yang et al. / Biochemical Systematics and Ecology 48 (2013) 136143

Tek, Norcross, GA, USA). The puried DNA was then sequenced on an ABI 3730 DNA Analyzer using a BigDye chemistry kit
(Applied Biosystems, Inc., Carlsbad, CA, USA), in which the same PCR primers were used.
2.3. Sequence analysis
DNA sequences were analyzed using the software MEGA 4.0 program (Tamura et al., 2007). The locations of protein-coding
and rRNA genes were determined by comparison with corresponding known sequences from three other species: Naemorhedus baileyi, Naemorhedus caudatus and Naemorhedus griseus. The tRNA genes were identied with tRNAscan-SE v.1.21
(Lowe and Eddy, 1997). Two tRNA genes, which were not found with tRNAscan-SE, were identied by comparison with
homologues from N. caudatus.
2.4. Phylogenetic analysis
To further address the phylogenetic relationships within the Bovidae, the 12 heavy-strand encoded protein-coding genes
were aligned according to Nikaido et al. (2001). After removal of gaps and ambiguous sites adjacent to gaps, 10,713 nucleotides were obtained. Multiple alignments of the 12 of the concatenated protein-coding genes from N. goral and 90 other
species (Table 1) were performed using Clustal X (Tompson et al., 1997) with the default setting. Two species of Tragulidae (a

Table 1
The sequences GenBank accession numbers for the 91 species used for phylogenetic analysis.
Species

GenBank no.

Species

GenBank no.

Addax nasomaculatus
Aepyceros melampus
Alcelaphus buselaphus
Ammotragus lervia
Antilope cervicapra
Antidorcas marsupialis
Bison bison
Bison bonasus
Bos grunniens
Bos indicus
Bos javanicus
Bos primigenius
Boselaphus tragocamelus
Bubalus bubalis
Bubalus depressicornis
Budorcas taxicolor
Capra caucasica
Capra falconeri
Capra ibex
Capra nubiana
Capricornis crispus
Capricornis sumatraensis
Capricornis swinhoei
Cephalophus adersi
Cephalophus callipygus
Cephalophus dorsalis
Cephalophus jentinki
Connochaetes gnou
Connochaetes taurinus
Damaliscus pygargus
Dorcatragus megalotis
Eudorcas rufrons
Gazella bennettii
Gazella cuvieri
Gazella dorcas
Gazella gazella
Hemitragus jayakari
Hemitragus jemlahicus
Hippotragus equinus
Hippotragus niger
Hyemoschus aquaticus (Out Group)
Kobus ellipsiprymnus
Kobus leche
Litocranius walleri
Madoqua kirkii
Madoqua saltiana

JN632591
JN632592
JN632594
NC_009510
NC_012098
JN632596
JN632601
NC_014044
NC_006380
NC_005971
JN632605
NC_013996
EF536350
NC_006295
EF536351
NC_013069
JN632609
FJ207525
FJ207526
FJ207527
NC_012096
FJ207534
NC_010640
JN632611
JN632614
JN632615
JN632616
JN632626
JN632627
FJ207530
JN632631
JN632633
JN632635
JN632636
JN632637
JN632640
FJ207523
FJ207531
JN632647
JN632648
JN632650
JN632651
JN632652
JN632653
JN632654
JN632655

Naemorhedus baileyi
Naemorhedus caudatus
Naemorhedus goral (This study)
Naemorhedus griseus
Nanger dama
Nanger granti
Nanger soemmerringii
Neotragus batesi
Neotragus moschatus
Oreamnos americanus
Oreotragus oreotragus
Oryx beisa
Oryx dammah
Oryx gazella
Oryx leucoryx
Ourebia ourebi
Ovis ammon
Ovis aries
Ovis canadensis
Ovis vignei
Ovibos moschatus
Pantholops hodgsonii
Pelea capreolus
Philantomba maxwellii
Philantomba monticola
Procapra gutturosa
Procapra przewalskii
Pseudois nayaur
Pseudois schaeferi
Pseudoryx nghetinhensis
Raphicerus campestris
Redunca arundinum
Redunca fulvorufula
Rupicapra pyrenaica
Rupicapra rupicapra
Saiga tatarica
Sylvicapra grimmia
Syncerus caffer
Taurotragus derbianus
Tetracerus quadricornis
Tragelaphus angasii
Tragelaphus eurycerus
Tragelaphus imberbis
Tragelaphus oryx
Tragulus kanchil (Out Group)

JN632663
NC_013751
JX188255
JN632664
JN632665
JN632666
JN632667
JN632668
JN632669
FJ207535
JN632675
JN632676
NC_016421
NC_016422
JN632679
JN632680
HM236188
NC_001941
NC_015889
HM236186
FJ207536
NC_007441
JN632684
JN632685
JN632687
JN632689
NC_014875
FJ207537
NC_016689
EF536352
JN632693
JN632694
JN632695
FJ207538
FJ207539
JN632700
JN632701
EF536353
EF536354
EF536355
JN632702
JN632703
EF536356
JN632704
JN632709

C. Yang et al. / Biochemical Systematics and Ecology 48 (2013) 136143

139

mouse-deer, Tragulus [javanicus] kanchil, and a chevrotain, Hyemoschus aquaticus) were used as an out group to root the tree
of Bovidae (Table 1). Bayesian phylogenetic analyses were conducted using MrBayes 3.1.2 (Ronquist and Huelsenbeck, 2003).
The best tting model (TIM3I G) of sequence evolution for Bayesian analyses were obtained by Modeltest 3.7 (Posada and
Crandall, 1998) under the Akaike Information Criterion (AIC). Four independent Markov chains Monte Carlo (MCMC) ran
simultaneously for ten million generations, sampling one tree per 200 generations, and the rst 25% of the samples were
discarded as the burn-in. At program termination, the average standard deviation of split frequencies was 0.003260. Tracer
v1.3 (Rambaut and Drummond, 2005) was used to check chain convergence and parameter mixing. Maximum likelihood
(ML) analyses were performed in RAxML Web-Servers (Stamatakis et al., 2008) using default parameters with 1000 bootstrap
replicates.
3. Results
3.1. Some characteristics of the mitochondrial genome
The whole sequence of the Himalayan goral, N. goral, mitochondrial genome and its genomic structure was determined
and deposited in GenBank with the accession number JX188255. The total length of the sequence was 16,555 bp. As presented
in Table 2, the N. goral was found to consist of 13 protein-coding genes, two rRNA genes (12S rRNA and 16S rRNA), 22 tRNA
genes, and a control region. These components were the same as for other mammalian mitochondrial genomes. Most of these
genes were encoded on the H strand, except for the ND6 gene and eight tRNA genes (tRNA-Gln, tRNA-Ala, tRNA-Asn, tRNACys, tRNA-Tyr, Trna-Ser, tRNA-Pro, tRNA-Glu), which were encoded on the L strand. The base composition of the H strand was:
Table 2
Mitochondrial genome organization of the Himalayan goral, Naemorhedus goral.
Genea

tRNA-Phe
12S rRNA
tRNA-Val
16S rRNA
tRNA-Leu(UUR)
ND1
tRNA-Ile
tRNA-Gln
tRNA-Met
ND2
tRNA-Trp
tRNA-Ala
tRNA-Asn
OL
tRNA-Cys
tRNA-Tyr
COI
tRNA-Ser(UCN)
tRNA-Asp
COII
tRNA-Lys
ATP8
ATP6
COIII
tRNA-Gly
ND3
tRNA-Arg
ND4L
ND4
tRNA-His
tRNA-Ser(AGY)
tRNA-Leu(CUN)
ND5
ND6
tRNA-Glu
Cytb
tRNA-Thr
tRNA-Pro
D-loop
a
b
c

Position

Length (bp)

From

To

1
69
1026
1093
2660
2737
3693
3759
3833
3902
4944
5012
5082
5155
5187
5255
5324
6866
6942
7011
7698
7767
7928
8608
9392
9461
9808
9877
10167
11545
11614
11675
11744
13548
14076
14149
15292
15362
15428

68
1025
1092
2659
2734
3692
3761
3830
3901
4945
5010
5080
5154
5189
5254
5322
6868
6934
7009
7694
7765
7967
8608
9388
9460
9807
9876
10173
11544
11613
11673
11743
13564
14075
14144
15288
15361
15427
16555

Codon
Start

68
957
67
1657
75
956
69
72
69
1044
67
69
73
35
68
68
1545
69
68
684
68
201
681
781
69
347
69
297
1378
69
60
69
1821
528
69
1140
70
66
1128

Strandc

0
0
0
0
0
2
0
3
2
0
2
1
1
0
3
0
1
3
7
1
3
1
40
1
3
0
0
0
7
0
0
1
0
17
0
4
3
0
0

H
H
H
H
H
H
H
L
H
H
H
L
L
L
L
L
H
L
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
L
L
H
H
L
H

Stop

ATG

TA

ATA

TAG

ATG

TAA

ATG

TAA

ATG
ATG
ATG

TAA
TAA
T

ATA

TA

ATG
ATG

TAA
T

ATT
ATG

TAA
TAA

ATG

AGA

tRNA abbreviations follow the IU-PAC-IUB three-letter code.


Negative numbers indicate that adjacent genes overlap.
H and L indicate genes transcribed on the heavy and light strand, respectively.

Intergenic nucleotideb

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C. Yang et al. / Biochemical Systematics and Ecology 48 (2013) 136143

A, 33.6%; G, 13.2%; T, 27.2%; C, 26.0%, which reected the typical AT-rich pattern commonly seen in the vertebrate mitochondrial genomes.
3.2. Phylogenetic analysis
Phylogenetic trees of the Bovidae constructed using BI and ML methods showed a similar topology (Fig. 1). The basal
divergence within Bovidae was between the Bovinae and a strongly supported clade of the remaining non-bovinine species
(PP 1.00, BS 78) (Fig. 1). Within the Bovinae, the trees indicated that Bison & Bos (bison and cattle), and Tragelaphus (kudus
and nyalas) were paraphyletic. The non-Bovinae clade included the Cephalophinae, Antilopinae, Reduncinae, Peleinae,
Alcelaphinae, Hippotraginae, Caprinae, Aepycerotinae and Clade A (which consisted of two species of Neotragusdthe suni and
the pygmy antelope). Clade A clustered with the impala, Aepyceros melampus (Aepycerotinae), both of which formed a most
basal clade in non-Bovinae (PP 1.00, BS 73) (Fig. 1). Within the Cephalophinae (duikers), all genera clustered together and
no polyphyletic phenomenon appeared. The Cephalophinae was associated with the Antilopinae. Within the Antilopinae, all

Fig. 1. Molecular phylogenetic tree derived from complete DNA sequence of 12 mitochondrial protein-coding genes using Bayesian inference and ML analysis.
The numbers beside the nodes are Bayesian posterior probabilities (PP) and bootstrap support (BS). Tragulus (javanicus) kanchil and Hyemoschus aquaticus were
set as out-groups.

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the genera clustered together except Neotragus (Clade A), which clustered with the Aepycerotinae. The saiga, Saiga tatarica,
was placed in the Antilopinae (PP 1.00, BS 79). The subfamily Peleinae, which is composed of only one species, the Grey
Rhebok (Pelea capreolus), nested within the Reduncinae (reedbucks, Redunca, waterbucks and kobs, Kobus), which indicated
the Reduncinae is non-monophyletic. The Hippotraginae (the sable and roan antelopes) sistered to the Alcelaphinae
(hartebeests and wildebeests), and the Oryx species appeared polyphyletic.
Within the Caprinae (goats and sheep), the consensus tree (1) placed Pantholops hodgsonii (the chiru or Tibetan antelope)
at the basal position of the Caprinae with strong support values (PP 1.0, BS 100); (2) conrmed that Capricornis and
Naemorhedus (serows and gorals) have a very close relationship (PP 1.00, BS 100); and (3) indicated that Hemitragus (the
tahrs) was very likely a polyphyletic genus with the two species showing different afliations.
4. Discussion
In the past few decades, extensive efforts have been made to investigate the Bovidae phylogeny; however, relationships
within this group remain unclear. One possibility is that the DNA sequences from different markers are highly divergent in
their evolutionary rates and that the substitution rate for each marker varies among lineages examined; therefore, phylogenetic reconstruction based upon a single gene or a short DNA segment is highly likely to produce an incorrect tree topology
(Nikaido et al., 1999). The complete mitochondrial genome provides a higher level of support than those based on individual
or partial mitochondrial genes (Krzywinski et al., 2006). Mitochondrial DNAs, especially those encoding protein, have been
frequently utilized as a powerful tool for evolutionary studies of animals (Boore and Brown, 1998). The present study
demonstrated that the phylogenetic analyses based on complete mitochondrial genomes served well to resolve relationships
within the Bovidae.
Two main clades have been consistently retrieved within the Bovidae, a basal group comprising the Bovinae and a large,
more derived assemblage, which includes all the other subfamilies (Allard et al., 1992; Hassanin and Douzery, 1999). The
result of this study strongly supported the division of the Bovidae into those two clades with full posterior probability and
bootstrap value (PP 1.00, BS 100). This nding appeared solid and rejected the subdivision into Aegodontia and Boodontia
previously suggested by Schlosser (1904).
Antilopinae is, from a phylogenetic standpoint, probably the least understood subfamily of the Bovidae (Rebholz and
Harley, 1999). The taxonomy of this subfamily has presented formidable confusion ever since the early attempts at classication by Sclater and Thomas (1897). The present study revealed that Neotragus (the suni and the pygmy antelope) clustered
with the Aepycerotinae (the impala), and together they formed the most basal clade of the non-Bovinae, which also suggested
that the Antilopinae was a paraphyletic subfamily. Paraphyletic phenomena may be among the possible reasons for the
difcult taxonomy of the Antilopinae.
The Cephalophinae (the duikers) is one group whose taxonomic placement is very difcult because its species present
a complex assemblage of primitive characters. It has been placed as a sister group of various other subfamilies: for example,
the Bovinae (Gentry, 1992), Reduncinae (reedbucks, Redunca, waterbucks and kobs, Kobus) (Gatesy and Arctander, 2000a),
Antilopinae (Matthee and Davis, 2001), Neotragini (Kingdon, 1982a,b), a clade composed of the Caprinae (goats & sheep),
Alcelaphinae (hartebeest and wildebeest) and Hippotraginae (the sable and roan antelopes) (Castresana, 2001), a clade
containing the Reduncinae, Alcelaphinae and Hippotraginae (Gatesy and Arctander, 2000b) and, nally, all the other nonbovine groups (Georgiadis et al., 1990). However, the molecular evidence from the present study revealed a sister relationship between the Cephalophinae and the Antilopinae, which was strongly supported by a Bayesian tree with full posterior
probability (PP 1.00). The relationship was also supported by an ML tree, but the bootstrap value was not high (BS 58).
Pantholops and Saiga were originally considered close relatives and placed in their own tribe within the Caprinae
(Simpson, 1945). Over the past century, these problematic genera have bounced back and forth between the Antilopinae and
the Caprinae (Schaller, 1977; Gentry, 1992). The result of our present study strongly supported the hypothesis that Saiga be
placed within the Antilopinae and that Pantholops (the Chiru or Tibetan Antelope) be placed within the Caprinae (Hassanin
et al., 2012).
Based on Hassanins classication revision (Hassanin and Douzery, 1999), the long-tailed goral (N. caudatus) was placed in
an enlarged tribe, called Caprini sensu lato, within the subfamily Antilopinae (Bovidae). The genera Capricornis and Naemorhedus were classied into three and four species, respectively (Corbet and Hill, 1992; Groves and Grubb, 1985; Mead, 1989);
however, the phylogenetic relationships of these genera and species have remained under question. The present study conrmed a close relationship between Capricornis and Naemorhedus (PP 1.00, BS 100) while supporting their designation as
separate genera. And the results suggested that the Capricornis-Naemorhedus-Ovibos clade (serows, gorals, and the muskox)
should be placed in the Caprinae, which is consistent with the previous studies (Hernandez-Fernandez and Vrba, 2005;
Ropiquet and Hassanin, 2005). A previous study (Ropiquet and Hassanin, 2004) indicated that Naemorhedus, Ovibos, Oreamnos
(the mountain goat), and Rupicapra (the chamois) clustered together based on three markers (cytochrome b,12S rRNA and exon
4 of the K-casein gene). However, the present study as well as a recent report (Hassanin et al., 2012) based on mtDNA genomes
consistently placed Ovibos (the muskox) with Naemorhedus-Capricornis, and Oreamnos (the mountain goat) with Budorcas (the
takin), and, while both clades fell clearly in the Caprinae, the two clades were distinct and distant from each other (Fig. 1).
Our consensus tree showed a very close relationship between Bison and Bos (the bison and cattle) under the subfamily
Bovinae. Due to their close phylogenetic relationship, it has been suggested that Bos and Bison should be integrated into
a single Bos genus (Hernandez-Fernandez and Vrba, 2005). Bubalus bubalis (the water buffalo) was observed more distantly

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related from the Bos-Bison group as previously reported (Hassanin and Douzery, 1999). The close relationship of Bison and Bos
compared to a more distant relationship to Bubalus was also supported from morphological, paleontological, and reproductive data (Miyamoto et al., 1989). Molecular data of the Bovini suggested two lineages: buffalo (Bubalus [water buffalos &
anoas] and Synceros [the African cape buffalo]) versus cattle (Bos, Bison) (Lenstra and Bradley, 1999; Simpson, 1945).
The phylogenetic trees from the present study in general conrmed the monophyly of the Bovinae and the Caprinae;
however the Antilopinae appeared to be polyphyletic, which is consistent with a previous study (Hernandez-Fernandez and
Vrba, 2005).
Most of the previous phylogenetic studies based on DNA indicated a close relationship between Hemitragus (tahrs) with
Capra (goats) (Gatesy et al., 1997; Hassanin and Douzery, 1999). Indeed, in the present study, the close relation of Hemitragus
jemlahicus (the Himalayan tahr) with Capra conrmed the relationship. However, our result revealed that Hemitragus jayakari
(the Arabian tahr) clustered with Ammotragus (the Barbary sheep). Thus, we suggest Hemitragus is polyphyletic. A previous
study (Ropiquet and Hassanin, 2005) also indicated that Hemitragus jemlahicus was associated with Capra, but that Hemitragus jayakari was allied with Ammotragus lervia (as conrmed in our study), and that Hemitragus hylocrius (the Nilgiri tahr)
was a sister-group of Ovis (sheep). Combining with the morphological, cytogenetic and biogeographic information
(Lundrigan, 1996; Schaller, 1977; Benirschke and Kumamoto, 1982, 1980), we support a new taxonomy which places the three
species of Hemitragus into three monospecic genera: the genus Hemitragus is then restricted to the Himalayan tahr, and two
new genera are created: Arabitragus for the Arabian tahr and Nilgiritragus for the Nilgiri tahr (Ropiquet and Hassanin, 2005).
In the present study, the trees generated from mtDNA genomes provided reasonable phylogenetic relationships within the
Bovidae. However, the mitogenomic dataset of the Bovidae still lacks representatives of some key taxa such as the Hunters
hartebeest (Beatragus hunteri) and the extinct Balearian mouse-goat (Myotragus balearicus), which are crucial for establishing the Bovidae mitogenomic tree and may affect the relationships in a phylogenetic analysis (Lalueza-Fox et al., 2005).
Although using mitogenomic datasets to restructure the phylogenetic tree of Bovidae acquired high support values, they can
also be systematically biased, just like the effect of a single gene or a short DNA segment (Nikaido et al., 1999). The family
Bovidae is difcult to classify in part because it appears to represent a rapid early radiation into many forms without clear
connections among them. Furthermore, certain morphological traits have evolved several times within the family to create
convergence that obscures true phylogenetic relationships (Gentry, 1992). Therefore, a more complete mitochondrial genome
set, including more key species as well as multiple nuclear markers, is needed to achieve an unambiguous resolution of the
phylogeny of the Bovidae.

Acknowledgments
This research was funded by National Science and Technology Support Project of China (2012BAC01B06). We would like to
thank Guo Cai for his help in sample collection.

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