Bull. Natl. Mus. Nat. Sci., Ser. B, 37(2), pp. 79–86, May 22, 2011

The Phylogenetic Positions of Four Endangered Vaccinium
Species in Japan
Chie Tsutsumi
Department of Botany, National Museum of Nature and Science,
Amakubo 4–1–1, Tsukuba, 305–0005 Japan
E-mail: tsutsumi@kahaku.go.jp(Received 15 February 2011; accepted 23 March 2011)

Abstract In total, 19 species and several varieties of Vaccinium are recognized in Japan. Five ofthem are evaluated to be endangered. In this study, molecular phylogenetic analyses for four of thefive endangered species were performed using nuclear ITS and chloroplast matK regions in orderto clarify whether they are recent derivatives, as suggested by morphological comparison. The
result showed that V. amamianum, V. boninense, V. sieboldii, and V. yakushimense have the same orsimilar sequences to V. emarginatum, V. wrightii, V. ciliatum, and V. hirtum and relatives, respectively. Small genetic divergences between the endangered species and their respective relatives
infer that the endangered species are likely neo-endemic.
Key words : endangered species, ITS, matK, molecular phylogeny, Vaccinium.

Introduction
Vaccinium L. (Ericaceae) consists of about 500
species distributed in worldwide except Australia(Vander Kloet and Dickinson, 2009). It is a morphologically diverse genus including terrestrial
or epiphytic shrubs and lianas (Vander Kloet,1990). It is divided into more than 30 sections(e.g., Sleumer, 1941; Vander Kloet and Dickinson, 2009), although the systematics is controversial (e.g., Sleumer, 1941; Stevens, 1969; Vander
Kloet, 1996; Vander Kloet and Dickinson, 1992,
1999, 2009). Molecular phylogenetic studies of
Vaccinium and Vaccinieae showed that Vaccinieae is monophyletic while Vaccinium is polyphyletic (Kron et al., 1999, 2002; Powell andKron, 2002). Kron et al. (2002) and Powell andKron (2002) clarified several monophyletic sections in Vaccinium, although the other taxa within Vaccinieae remain unresolved.
Nineteen species and seven varieties of Vaccinium are recognized in Japan (Yamazaki,1993). Among them, five species, i.e., V. amamianum Hatus. [treated as V. emarginatum Hayata

in Yamazaki (1993)], V. boninense Nakai, V.
microcarpum (Turcz. ex Rupr.) Schmalh., V.
sieboldii Miq. and V. yakushimense Makino areendangered in the Red List of Japanese vascularplants (Environment Agency of Japan, 2000;
Ministry of the Environment, Japan, 2007).
Vaccinium amamianum is an evergreen epiphytic shrub in evergreen forests and criticallyendangered (CR) according to modified IUCN
conservation ratings. It occurs only on AmamiOshima in Japan and is quite rare (Hotta, 2004).
Vaccinium amamianum was considered to beclose to, but distinct from V. emarginatum in Taiwan by the pubescent branches, small leaves andterminal racemose inflorescences (Hatusima,
1962, 2002). Yamazaki (1989, 1993), however,treated it as a synonym of V. emarginatum basedon their morphological similarities.
Vaccinium boninense is an evergreen shrub
and is vulnerable species (VU). It is distributed
only on the Bonin Islands (Nakai, 1926; Toyoda,
1981; Yamazaki, 1993). It is morphologicallysimilar to V. wrightii A. Gray distributed in the
Ryukyu Islands and Taiwan, but distinct from it

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Chie Tsutsumi

by the hairs on calyx and corolla, the narrow
sepal, the short pedicel, and the short awn ofanther (Yamazaki, 1993). Vaccinium boninense,
along with V. wrightii and V. bracteatum Thunb.,
are included in sect. Bracteata (Sleumer, 1941;
Stevens, 1969; Yamazaki, 1993), while Vander
Kloet and Dickinson (2009) assigned V. wrightii
and relatives to sect. Eococcus.
Vaccinium microcarpum (VU) is an evergreen
dwarf shrub distributed in Hokkaido and highmountains in Honshu, Japan, and also widely incool regions of the northern hemisphere (Yamazaki, 1993). It is quite similar to V. oxycoccus
L. Vander Kloet (1983b) treated V. microcarpum
as conspecific with V. oxycoccus by the morphological similarities, while Yamazaki (1993) treated them as distinct species by the leaf size andpresence/absence of hairs on the pedicel.
Vaccinium sieboldii (CR) is a deciduous erect
shrub and distributed in very limited, 65 km widein western Shizuoka and Aichi Prefecture, central
Japan (Yamazaki, 1993; Takahashi, 2001; Hirai
et al., 2010). Morphologically it is quite similar
to, but different from V. ciliatum Thunb. in thelong pedicel and sparse hairs on the leaf beneathand pedicel (Yamazaki, 1993). It is assigned tosect. Ciliata including V. ciliatum, V. oldhamii
Miq. and relatives (Sleumer, 1941; Yamazaki,1993). A study on their genetic diversities andphylogenetic relationships also revealed that V.
sieboldii is quite close to V. ciliatum (Hirai et al.,2010).
Vaccinium yakushimense (VU) is one of endemic species in Yakushima Island (Yahara et al.,1987). It is usually epiphytic at high elevations(500 m alt.) (Yamazaki, 1993; Kawahara, 1995;
Takahashi, 2001). Morphologically it is close toV. smallii s.l., and V. hirtum s.l. (Vander Kloet andDickinson, 1992; Yamazaki, 1993). They had
been placed in sect. Cyanococcus (Sleumer,1941) and later they were transferred to sect.
Hemimyrtillus including several European
species (Stevens, 1969; Vander Kloet, 1983a;
Vander Kloet and Dickinson, 1992). Molecularphylogeny, however, showed that V. smallii and V.
hirtum in northeast Asia are neither closely relat-

ed to sect. Cyanococcus nor sect. Hemimyrtillus,
but are close to sections Macropelma, Myrtillus,
Oxycoccoides and Praestantia (Powell and Kron,
2002).
As described above, the morphological similarities between the Japanese endangered Vaccinium species and the respective relatives arewell recognized. However, their taxonomic treatments and systematics remain unclear. To determine the molecular phylogenetic positions of thespecies and recognize the most closely related
species to them, I conducted molecular phylogenetic analyses for the endangered species andtheir morphological relatives, and measured molecular differences between the endangered
species and its relatives. Furthermore, the endemism of the species is also discussed.
Materials and Methods
Leaf samples of 11 Vaccinium species fromJapan and one species from Taiwan were collected in the field or from cultivated plants (Table 1).
One of the five endangered species, V. microcarpum, was not analyzed in this study becausematerial was not available. DNA was extracted
from fresh or silica-gel-dried materials using a
QUIAGEN DNeasy Mini Kit (QUIAGEN,
Valencia, CA) following the manufacturer’s instruction.
The internal transcribed spacer regions of 18S–
26S nuclear ribosomal DNA (ITS), and matK (amaturase-encoding gene) were analyzed. Primers
for amplification are 17SE (Sun et al., 1994) and‘26SE’ (Topik et al., 2005, modified 26SE in Sun
et al., 1994) in the ITS region, and trnK-3914F
and trnK-2R (Johnson and Soltis, 1994) in matKwith internal primers MK-F1 and MK-F2 (Koi etal., 2008). PCR was performed using a DNA
thermal cycler (Perkin-Elmer 9700, Applied
Biosystems, Foster, CA) with Ex Taq DNA polymerase (TaKaRa Bio, Tokyo, Japan) and Ampdirect Plus (Shimadzu, Kyoto, Japan) in 35 denaturation, annealing, and elongation cycles (30 sec
at 94°C, 30 sec at 50–55°C and 90 sec at 72°C)
with a final elongation step (7 min at 72°C). The

Phylogenetic Positions of Endangered Vaccinium

81

Table 1. Species used in molecular phylogenetic analysis, sources and GenBank accession no. of ITS and matKregions
GenBank accession No.
ITS
matK

Species

SourceV. amamianum Hatus.
V. boninense Nakai
V. bracteatum Thunb.

Cultivated in Koishikawa Botanical Garden; Tsutsumi s. n.
Cultivated in Koishikawa Botanical Garden; Tsutsumi s. n.
Yakushima, Kagoshima, Japan; S. Tagane & Y. Tsujita(TNS763429)
Cultivated in Tsukuba Botanical Garden; Tsutsumi ARA1
Kaohsiung Co., Taiwan; Tsutsumi et al.(TNS736868)
Kaohsiung Co., Taiwan; Tsutsumi et al. (TNS736871)
Shinshiro, Aichi, Japan; Tsutsumi Ho2-20100514
Fukushima, Japan; Tsutsumi Fuku172-20100509
Hamamatsu, Shizuoka, Japan; Tsutsumi 175-19-N-1
Hamamatsu, Shizuoka, Japan; Tsutsumi M20o-20100513
Hamamatsu, Shizuoka, Japan Tsutsumi 175ws-20100513
Hamamatsu, Shizuoka, Japan; Tsutsumi M20s-20100513
Hamamatsu, Shizuoka, Japan; Tsutsumi 175sm-20100513

V. ciliatum Thunb.
V. emarginatum Hayata
V. hirtum Thunb.
V. oldhamii Miq.
V. sieboldii Miq.
V. smallii A. Gray var.
glabrum Koidz.
V. wrightii A. Gray
V. yakushimense
Makino

A
B
A
F
K
M
K
M

AB623180 AB623166
AB623184 AB623168—
AB623177
AB623188
AB623181
AB623182
AB623187
AB623185
AB623189
AB623189
AB623191
AB623190
AB623186

AB623172
AB623166
AB623166
AB623171
AB623169
AB623174
AB623173
AB623175
AB623176
AB623170

Amami-Oshima, Kagoshima, Japan; Ebihara et al. (TNS764246) AB623192 AB623178
Yakushima, Kagoshima, Japan; S. Tagane & Y. Tsujita
AB623183 AB623167(TNS763260)

PCR
products
werepurifiedwith
ExoSAP-IT (USB corporation, Cleveland, OH)following the manufacturer’s instruction. Sequencing was conducted using an ABI PRISM
3130xl Genetic Analyzer (Applied Biosystems).
The sequences obtained were assembled using
Seqman II (Dnastar, Madison, WI). The assembled sequences were aligned by Clustal X program (Thompson et al., 1997) and then aligned
manually. In addition to the sequences analyzed,
registered sequences in GenBank used in Powell
and Kron (2002) were added for phylogenetic
analyses.
Phylogenetic analyses were performed by MrBayes 3.1.2 (Huelsenbeck and Ronquist, 2001;
Ronquist and Huelsenbeck, 2003). The bases that
could not been identified were treated as unknown (N). Gaps were treated as missing data.
MrModeltest 2.0 (Nylander, 2004) was used todetermine the nucleotide substitution model for
Bayesian analysis. Bayesian searches were conducted by mcmc with four chains over four million and two million generations for the ITS
dataset and the matK dataset, respectively, sampling every 100 generations. Trees obtained
before stationary generations were discarded as

Table 2. Differences of sequences in ITS and matKregions between four endangered species andtheir closely related species

V. amamianum–V. emarginatum
V. boninense–V. wrightii
V. boninense–V. bracteatum
V. sieboldii–V. ciliatum
V. sieboldii–V. oldhamii
V. yakushimense–V. smallii
V. yakushimense–V. hirtum (F)

ITS

matK

0–1
1
—
0–3
0–3
3
2

0
1
12
0–1
5–7
3
1

burn-in trees and the rest of trees were used to
calculate posterior probabilities. Leucothoe
fontanesiana (Steudel) Sleumer, Andromeda
polifolia L., and Zenobia pulverulenta (Bartramex Willd.) Pollard were used as outgroups basedon the results of Powell and Kron (2002).
Results
Differences of sequences in nuclear ITS (ca.
650 bp) and chloroplast matK (ca. 1520 bp) between the four endangered species and their closely related species are shown in Table 2. Vaccinium amamianum had no or one substitution dis-82

Chie Tsutsumi

tinguishable from V. emarginatum samples from
Taiwan in the ITS and matK regions. Vaccinium
boninense was close to V. wrightii and differedfrom it in only 1 substitution in each of the ITS

and matK regions. In contrast, V. boninense differed from V. bracteatum in 12 substitutions in
matK, although the ITS region of V. bracteatum
could not be analyzed well in this study. Vaccini-

Fig. 1. Consensus tree by Bayesian analysis based on the nuclear ITS sequence dataset. Figures above branches
indicate posterior probabilities (p0.6) calculated by Bayesian analysis. Names shown by bold indicate samples analyzed in this study.

Phylogenetic Positions of Endangered Vaccinium

um sieboldii had no or a few substitutions distinguishable from V. ciliatum, and differed from V.
oldhamii in 0–3 substitutions in ITS and 5 to 7
substitutions in matK. Vaccinium yakushimense
differed from V. smallii or V. hirtum by a few substitutions in both the nuclear ITS and the chloroplast matK regions.
The molecular phylogenetic trees deduced
from each of the nuclear ITS region and thematK sequences showed that all samples were
nested in the clade Vaccinieae (Figs. 1 and 2).
Vaccinium amamianum, along with V. emarginatum, formed a monophyletic clade with V. caudatifolium Hayata and V. filiforme (J.J. Smith)Sleumer and the clade was nested in the
Agapetes clade shown in Powell and Kron
(2002). Vaccinium boninense formed a cladewith V. wrightii with high supports in both the
ITS and matK trees. The clade was sister to V.
cereum (L.f.) Forster, and then they were close toV. fragile Franch. in the ITS tree, while the clade
formed a monophyletic clade with V. bracteatum,
V. sieboldii, V. ciliatum and V. oldhamii in thematK tree with high posterior probabilities. Vaccinium sieboldii, V. ciliatum and V. oldhamii
formed a monophyletic clade both in the ITS tree
and the matK tree, although the phylogenetic position remained unclear in the ITS tree becauseof low supports of the clade. Vaccinium yakushimense merged in the clade with V. smallii and V.
hirtum. The clade then was sister to the group of
V. japonicum Miq. and V. praestans Lamb. in thematK tree, while the phylogenetic position of V.
yakushimense, V. hirtum and V. smallii remained
unsolved in the ITS tree.
Discussion
The present results revealed the phylogenetic
positions of the four endangered species in Vaccinium, and suggested their closely related
species, which were the same as the candidates
morphologically estimated. The results also
showed genetic divergences between the endangered species and their relatives.
Similarities in both the ITS and the matK83

sequences between V. amamianum and V. emarginatum supported the taxonomic treatment that
V. amamianum is synonymous to V. emarginatum(Yamazaki, 1993), a common species in Taiwan(Li et al., 1998). To clarify the taxonomic treatment and the genetic diversity of V. amamianum
and V. emarginatum, further molecular and morphological analyses are needed using more samples. Vaccinium amamianum and V. emarginatum
are not found in the Okinawa Prefecture, locatedbetween Taiwan and Amami-Oshima Island(Yamazaki, 1993). They were sister to Taiwanese
V. caudatifolium Hayata and Bornean V. filiforme(J.J. Smith) Sleumer. The phylogenetic relationships and patterns of their distributions suggestthat V. amamianum was likely derived fromsoutheastern Asia and it survives only in AmamiOshima Island in Japan. Thus, the endangered V.
amamianum occurs at the isolated northern endof the species group and hardly differentiatedfrom the neighboring V. emarginatum.
About 70% of the species on the Bonin Islands
are related to Southeast Asian species, and considered to be recently derived (Toyoda, 1981;
Shimizu, 2010). Vaccinium boninense is also
morphologically and phylogenetically close to V.
wrightii, a common species in Ryukyus and Taiwan. Vaccinium cereum, close to V. boninense
and V. wrightii in the ITS tree and far from themin the matK tree (Figs. 1 and 2), is suspected tohave a hybrid origin (Powell and Kron, 2002).
The conflict of the phylogenetic position of theclade of V. boninense and V. wrightii between the
ITS tree and the matK tree seems also likely to
be caused by the introgression in the group.
Few difference was observed in the ITS andmatK regions between V. sieboldii and V. ciliatum, while a detail analysis using SSR markers
suggested their differentiation (Hirai et al.,2010). Hirai et al. (2010) also showed a clear distinction between V. sieboldii and V. oldhamii in
SSR markers. Vaccinium sieboldii occurs in quite
restricted area in central Japan and is separate
from V. ciliatum distributed fragmentally in western Japan. Thus, V. sieboldii and V. ciliatum
differentiated recently in fragmental areas, and84

Chie Tsutsumi

Fig. 2. Consensus tree by Bayesian analysis based on the chloroplast matK sequence dataset. Figures above
branches indicate posterior probabilities (p0.6) calculated by Bayesian analysis. Names shown by bold indicate samples analyzed in this study.

Phylogenetic Positions of Endangered Vaccinium

the former is threatened. In contrast, V. oldhamii
is widely distributed in Japan, Korea and China,
overlapping with V. sieboldii and V. ciliatum(Yamazaki, 1993; Hirai et al., 2010).
Vaccinium yakushimense differed from V.
smallii and V. hirtum in a few substitutions, although they are morphologically similar. Vaccinium yakushimense is distinct from those of V.
smallii and V. hirtum in the distribution (Vander
Kloet and Dickinson, 1992; Yamazaki, 1993); V.
yakushimense occurs only at high altitudes ofYakushima Island, southern Kyusyu. Vaccinium
smallii s.l. is distributed in the Kurile islands and
Sakhalin, Russia, North and South Korea, andHonshu and Shikoku, Japan. Vaccinium hirtum
s.l. is distributed in Hokkaido to northern
Kyushu, Japan, and South Korea. Thus, Vaccinium yakushimense evolved as an epiphyte in theisolated southern end of the predominantly terrestrial group.
The four endangered species, V. amamianum,
V. boninense, V. sieboldii and V. yakushimense,are endemic species to quite restricted distributions areas, disjunct from the most closely related
species. Although the samples analyzed are insufficient, the small genetic divergences between
the endangered species and their relatives inferthat the endangered species are neo-endemic andthreatened partly due to limited distribution
areas, or a local variant in the periphery of the
distribution region. Further comparison between
the endangered plants and relatives is necessary
to clarify the taxonomic status and diversificationof endemic or local species that are apt to bethreatened.
Acknowledgments
I thank K. Ando, A. Ebihara, Y. Hirayama, C.I Huang, M. Kato, G. Kokubugata, T. Muramatsu, A. Okuda, C.-I Peng, S. Tagane, Y. Tsujita, H.
Yamashita, C.-K. Yang, and Koishikawa Botanical Garden, The University of Tokyo, for providing the materials and/or help during the field
trips. I also gratefully thank Y. Hirayama, N.
Katayama, and A. Uehara for technical assistance85

and M. Kato for useful comments to the manuscript. This study was supported by Grants-inAid for Scientific Research from the Japan Society for the Promotion of Science and Showa
Seitoku Memorial Foundation.
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