Bull. Natl. Mus. Nat. Sci., Ser. B, 37(2), pp. 63–74, May 22, 2011

RbcL Phylogeny of Japanese Pteridophyte Flora and Implications
on Infrafamilial Systematics
Atsushi Ebihara
Department of Botany, National Museum of Nature and Science,
Amakubo 4–1–1, Tsukuba, 305–0005 Japan
E-mail: ebihara@kahaku.go.jp(Received 15 February 2011; accepted 23 March 2011)

Abstract A molecular phylogenetic analysis of the Japanese pteridophyte flora was performed
using chloroplast rbcL sequences of 93% of Japanese taxa. The obtained tree is provided here andnoteworthy or novel results on the infrafamilal taxonomy of the pteridophytes are documented byfamily.
Key words : infrafamilial taxonomy, lycophyte, monilophyte, pteridophyte, rbcL.

The pteridophyte flora of Japan comprising
733 taxa has been almost covered by a sequence
data-set for DNA barcoding (Ebihara et al.,2010). The barcoding project used two chloroplast DNA regions, rbcL and trnH-psbA, and theformer alone is not enough for solving deep phylogeny at family or higher levels, while the latter
seems unsuitable for phylogenetic analysis due toits frequent indels. Even if the resolution is limited, it is worth while to visualize general phylogenetic relationships in rich floristic sampling. In
monilophytes, family-level phylogeny has almost
been solved using multiple DNA markers(Schuettpelz and Pryer, 2007) and is reflected inrecent classifications (Smith et al., 2006). Infrafamiliar relationships, especially those thathave not yet appeared in previous studies, arediscussed in this paper.
Materials and Methods
Chloroplast rbcL sequences of 1205 bp inlength used for the present analysis are exactly
the same as those used in Ebihara et al. (2010),
but five of 689 sequences examined by Ebihara etal. (2010) were excluded from the present analysis because of their incomplete length. A phylo-

genetic analysis was performed by MrBayes
3.1.2 (Ronquist and Huelsenbeck, 2003); each offour Markov chain Monte Carlo (MCMC) chainsfor two independent runs, 20 million generations,sampled every 1000 generations using the
GTRIG substitution model, using the “constraint” options for the families defined by Smithet al. (2006) except for Woodsiaceae and Dryopteridaceae whose monophyly is not supported
in the analysis by Schuettplez and Pryer (2007).
The first half (10000) trees were discarded as aburn-in period based on the diagnosis of theresult by Tracer 1.5 (Rambaut and Drummond,2007). The obtained consensus tree is rooted
with lycophytes (Lycopodiaceae, Selaginellaceae
and Isoetaceae).
Results and Discussion
The tree reconstructed in this paper (a tree divided into ten parts; Figs. 1–10) show the present
results of Bayesian inference of infrafamiliar
relationships and the family or higher-level relationships by Schuettpeltz and Pryer (2007). Since
two of the Smith et al. (2006)’s families, Dryopteridaceae and Woodsiaceae, are posssibly
non-monophyletic (Schuettpeltz and Pryer,

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Atsushi Ebihara2007), infrafamiliar relationships by Schuettpeltz
and Pryer (2007) are partially adopted for the two
families.
Twenty-nine of the 37 families recognized bySmith et al. (2006) plus three lycophyte families
are distributed in Japan. The following discussion is in sequence of the families adopted bySmith et al. (2006), but families without any
novel knowledge are omitted. The infrafamilial
classifications generally follow Iwatsuki (1995),
but have been modified adopting the results ofrecent study.

Ophioglossaceae(Fig. 2)The paraphyletic placement of Ophioglossumin the present outcome does not match the result
by Hauk et al. (2003) which suggested its monophyly. The most diversified group of Ophioglossaceae in Japan is Botrychium sect. Sceptridium
comprising more than 10 taxa. In the sect. Sceptridium all the three polyploid species [tetraploid
B. formosanum Tagawa (Sahashi, 1981), andhexaploid B. atrovirens (Sahashi) M. Kato (Sahashi, 1979) and B. japonicum (Prantl) Underw.
(Sahashi, 1984)] form a distinct clade.

Lycopodiaceae(Fig. 1)
Both the Huperzia group and the Lycopodiellagroup are supported as monophyletic, but the Lycopodium s.s. group is paraphyletic in the present
tree. The latter result does not match the result of
Wikström and Kenrick (2000) using rbcL andtrnL intron sequences.

Cyatheaceae(Fig. 3)
Cyathea lepifera (J. Sm. ex Hook.) Copel. andC. mertensiana (Hance) C. Chr. et Tardieu belong to the Sphaeropteris group, one of the threemajor groups of the genus (Conant et al., 1996;
Korall et al., 2007), and the remaining six Japanese species belong to the Cyathea s.s. group.
Cyathea tuyamae H. Ohba, an endemic species

Fig. 1. A part of the results of Bayesian inference of infrafamiliar phylogeny including Lycopodiaceae,
Selaginellaceae and Isoetaceae, based on chloroplast rbcL sequences of 684 Japanese pteridophytes. Posterior
probabilities 0.90 are shown. Family delimitations, shown by bars on the right side, follow Schuettpelz andPryer (2008).

RbcL Phylogeny of Japanese Pteridophyte

Fig. 2. A part of the results of Bayesian inference of infrafamiliar phylogeny including Ophioglossaceae,
Psilotaceae, Equisetaceae and Marattiaceae, based on chloroplast rbcL sequences of 684 Japanese pteridophytes, rooted with lycophytes. Posterior probabilities 0.90 are shown. Family delimitations, shown by bars
on the right side, follow Smith et al. (2006).

Fig. 3. A part of the results of Bayesian inference of infrafamiliar phylogeny including Osmundaceae, Hymenophyllaceae, Gleicheniaceae, Dipteridaceae, Lygodiaceae, Schizaeaceae, Marsileaceae and Salviniaceae, basedon chloroplast rbcL sequences of 684 Japanese pteridophytes, rooted with lycophytes. Posterior probabilities
0.90 are shown. Schematic relationships between families follow Smith et al. (2006).

65

66

Atsushi Ebiharaof Minami-iojima Isl. (Volcano Isls.) characterized by branching trunks, is closely related to C.
spinulosa Wall. ex Hook. having non-branchingtrunks.
Lindsaeaceae(Fig. 4)
The genus Lindsaea is apparently polyphyletic; L. odorata Roxb. (sect. Osmolindsaea) is sister to Tapeinidium. Among the other Lindsaea
species, L. orbiculata (Lam.) Mett. ex Kuhn, L.
simulans Ching, L. cambodgensis H. Christ andL. kawabatae Sa. Kurata form an unsolved complex. Lindsaea heterophylla Dryand. is also included in the complex, and this result does notconflict with the hypothesis of its hybrid origin(Kramer, 1971). Further careful study is necessary especially for bipinnate Lindsaea species.
Dennstaedtiaceae(Fig. 4)The current generic classifications are supported by the present phylogeny. Five of the eight
Microlepia taxa share exactly the same rbcL
sequence — this suggests some Japanese Microlepia species are hybrid-origin polyploids, andshare a maternal ancestor.
Pteridaceae(Fig. 5)All of the five robust clades recognized by
Schuettpelz et al. (2007) within Pteridaceae are
distributed in Japan. The PT clade including

Fig. 4. A part of the results of Bayesian inference of infrafamiliar phylogeny including Cyatheales (Plagiogyriaceae, Cibotiaceae and Cyatheaceae), Lindsaeaceae and Dennstaedtiaceae, based on chloroplast rbcL
sequences of 684 Japanese pteridophytes, rooted with lycophytes. Posterior probabilities 0.90 are shown.
Schematic relationships between families follow Smith et al. (2006).

RbcL Phylogeny of Japanese Pteridophyte

67Fig. 5. A part of the results of Bayesian inference of infrafamiliar phylogeny including Pteridaceae based on
chloroplast rbcL sequences of 684 Japanese pteridophytes, rooted with lycophytes. Posterior probabilities
0.90 are shown. Names of the clades are based on Schuettpelz et al. (2007). Schematic relationships
between families follow Smith et al. (2006).

Pteris, Onychium and Pityrogramma (introduced), has the largest number of members. The
other four clades are: AD (Adiantum, Haplopteris [Vittaria] and Antrophyum), CR (Coniogramme and Cryptogramma), CH (Cheilanthes) and CE (Ceratopteris and Acrostichum). In
the PT clade, the position of Pteris vittata L. isunsolved, but the tree clearly suggests at least the
species occupies the most basal position among
Japanese Pteris species. Pteris fauriei Hieron.
and its related species (P. boninensis H. Ohba, P.
kawabatae Sa. Kurata, P. kiuschiuensis Hieron.,P. laurisilvicola Sa. Kurata, P. natiensis Tagawa,P. oshimensis Hieron., P. setulosocotulata Hayata
and P. yakuinsularis Sa. Kurata) form an unsolved complex. Considering the fact that they
are mostly known as apogamously reproducing
taxa (Takamiya, 1996), detailed study on their
origins and relationships is necessary.
Aspleniaceae(Fig. 6)
There is little discordance with previous phylogenetic analysis (Schneider et al., 2004a). Of
nine clades recognized by Schneider et al.
(2004a), members of the seven clades are distributed in Japan. All the Hymenasplenium species

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Atsushi Ebihara

Fig. 6. A part of the results of Bayesian inference of infrafamiliar phylogeny including Aspleniaceae based on
chloroplast rbcL sequences of 684 Japanese pteridophytes, rooted with lycophytes. Posterior probabilities
0.90 are shown. Names of the clades are based on Schneider et al. (2004a) except for Ab, which is an
unnamed clade including Asplenium bullatum. Schematic relationships between families follow Smith etal. (2006).

are included in Clade I [the names of the clades
follow those in Schneider et al. (2004a)]. Asplenium ruta-muraria L. is in Clade III. Asplenium
scolopendrium L. is in Clade IV. Asplenium
antiquum Makino, A. griffithianum Hook., A.
loriceum H. Christ ex C. Chr., A. nidus L., A.
prolongatum Hook., A. setoi N. Murak. et Seriz.,A. tenerum G. Forst. and A. trigonopterum Kunze
are in Clade V. Asplenium ensiforme Wall. ex
Hook. et Grev., A. laserpitiifolium Lam., A.
micantifrons (Tuyama) Tuyama ex H. Ohba, A.
polyodon G. Forst., A. pseudowilfordii Tagawa,A. wilfordii Mett. ex Kuhn and A. yoshinagae
Makino are in Clade VI. Asplenium boreale(Ohwi ex Sa. Kurata) Nakaike, A. capillipes
Makino, A. coenobiale Hance, A. incisum
Thunb., A. normale D. Don, A. oligophlebium

Baker, A. pekinense Hance, A. ruprechtii Sa.
Kurata, A. sarelii Hook., A. shimurae (H. Itô)Nakaike, A. tenuicaule Hayata, A. trichomanes
L., A. tripteropus Nakai and A. viride Huds. are
in Clade VII. Asplenium ritoense Hayata and A.
wrightii D. C. Eaton ex Hook. are in an unnamed
clade with A. bullatum Wall. ex Mett.
Woodsiaceae(Fig. 7)This family sensu Smith et al. (2006) is possibly non-monophyletic according to the succeeding analysis by Schuettpelz and Pryer (2007), andBlechnaceae and Onocleaceae are perhaps ingroups of Woodsiaceae. Most of the Japanesetaxa of this family have already been sampled
by Sano et al. (2000a, 2000b), Adjie et al. (2008)
and Takamiya (2008), and our result does not

Fig. 7. A part of the results of Bayesian inference of infrafamiliar phylogeny including Woodsiaceae, Blechnaceae and Onocleaceae, based on chloroplast rbcL sequences of 684 Japanese pteridophytes, rooted withlycophytes. Posterior probabilities 0.90 are shown. Schematic relationships between families and major
clades of Woodsiaceae follow Schuettpelz and Pryer (2007).

RbcL Phylogeny of Japanese Pteridophyte

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Atsushi Ebihara

show any particular incongruence with them.
Cornopteris is a genus easily recognizable by its
fleshy horn-shaped projections at the base of costules but is clearly nested in Athyrium (Adjie
et al., 2008). The recent separation of the basal
member of Athyrium (A. niponicum (Mett.)
Hance and A. sheareri (Baker) Ching) plus Kuniwatsukia as a redefined genus Anisocampium(Liu et al., 2011) is a practical treatment forkeeping Cornopteris as a genus, though the position of A. distentifolium Tausch ex Opiz is still
unsolved.

era, Thelyptetis and Stegnogramma, in Japanese
Thelypteridaceae, our result shows Stegnogramma is nested in Thelypteris s.l. and related particularly to T. flexilis (H. Christ) Ching and T.
omeiensis (Baker) Ching (Cyclogramma).
Though Smith and Cranfill (2002) have alreadypointed out the 32-generic system by Pichi Sermolli (1977) after Holttum (1971, 1982) is nolonger natural (e.g. Christella is polyphyletic) intheir preliminary study, the system seems usefulfor grouping the Japanese taxa. Molecular analysis employing global sampling and taxonomic
revision is still awaited.

Thelypteridaceae(Fig. 8)
Although Iwatsuki (1995) recognized two gen-Fig. 8. A part of the results of Bayesian inference of infrafamiliar phylogeny including Thelypteridaceae basedon chloroplast rbcL sequences of 684 Japanese pteridophytes, rooted with lycophytes. Posterior probabilities
0.90 are shown. Genera by Pichi Sermolli (1977) are also indicated (Ccg: Cyclogramma, Ccs: Cyclosorus,
Chr: Christella, Glp: Glaphyropteridopsis, Ltr: Lastrea, Mtp: Metathelypteris, Pgp: Phegopteris, Pnm: Pneumatopteis, Prn: Pronephrium, Psc: Pseudocyclosorus, Psp: Pseudophegopteris, Ptp: Parathelypteris, Sps:
Sphaerostephanos, Stg: Stegnogramma and Tlp: Thelypteris s.s.).

Fig. 9. A part of the results of Bayesian inference of infrafamiliar phylogeny including Dryopteridaceae basedon chloroplast rbcL sequences of 684 Japanese pteridophytes, rooted with lycophytes. Posterior probabilities
0.90 are shown. Schematic relationships between major genera follow Schuettpelz and Pryer (2007).

RbcL Phylogeny of Japanese Pteridophyte

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Atsushi Ebihara

Onocleaceae(Fig. 7)
As molecular data suggested that the genus
Onoclea is paraphyletic against Matteuccia,
Gastony and Ungere (1997) proposed to transfer
Onoclea orientalis (Hook.) Hook. and O. intermedia (C. Chr.) M. Kato, T. Suzuki et N. Nakato
to the genus Pentarhizidium. The generic combination Pentarhizidium orientale (Hook.) Hayata
is accepted here.
Dryopteridaceae(Fig. 9)
Dryopteris
Acrophorus nodosus C. Presl is nested in Dry-

opteris and sister to D. hendersonii (Bedd.) C.
Chr.D. shikokiana (Makino) C. Chr., both often
separated as Nothoperanema. Ctenitis maximowicziana (Miq.) Ching is not included in the cladeof Ctenitis, but in a member of Dryopteris closely related to the above three species. Sections andsubsections by Hirabayashi (1974) after Ito(1939) are roughly supported, but a number of
exceptions are found: e.g., a group of the members of sect. Lophodium, i.e., D. laeta (Kom.) C.
Chr., D. fragrans (L.) Schott, and D. amurensis(Milde) H. ChristD. expansa (C. Presl) FraserJenk. et Jermy, are not closely related to eachFig. 10. A part of the results of Bayesian inference of infrafamiliar phylogeny including Lomaripsidaceae, Tectariaceae, Davalliaceae and Polypodiaceae, based on chloroplast rbcL sequences of 684 Japanese pteridophytes, rooted with lycophytes. Posterior probabilities 0.90 are shown. Numbers of the clades of Polypodiaceae are based on Schneider et al. (2004b). 1: Loxogrammoid clade, 2: Drynarioid-selligueoid clade, 3:
Platycerioid-microsoroid clade and 4: Neotropical clade. Schematic relationships between families follow
Smith et al. (2006).

RbcL Phylogeny of Japanese Pteridophyte

other, at least in the chloroplast DNA marker. As
Japanese Dryopteris is known for its high percentage of apogamous taxa (Takamiya, 1996),
phylogeny using chloroplast DNA needs carefulinterpretation.
Polystichum – Cyrtomium
Lu et al. (2005) suggested the polyphyly ofCyrtomium. Concerning Japanese species, C.
balansae (H. Christ) C. Chr. and C. hookerianum(C. Presl) C. Chr., without terminal pinna, shouldbe transferred to Polystichum. The present result
concerning Polystichum does not contradict thesectional classification by Daigobo (1972), but
relationships within sect. Metapolystichum, themost diversified section in Japan. is still unsolved.
Polypodiaceae(Fig. 10)
As already reviewed by Schneider et al.
(2004b), the present taxonomy of Polypodiaceae
has many problems; e.g., Polypodium andMicrosorum are not monophyletic. Monotypic
genus Drymotaenium is clearly nested in Lepisorus (Wang et al., 2010), so Lepisorus miyoshianus (Makino) Fraser-Jenk. et Subh. Chandra isan appropriate generic combination. Wang et al.
(2010) also proposed a new classification of thetribe
Lepisorae.
Accordingtothem,
Neocheiropteris ensata (Thunb.) Ching andMicrosorum fortunei should be transferred to
Neolepisorus. Microsorum buergerianum (Miq.)
Ching and Neocheiropteris subhastata (Baker)
Tagawa should be transferred to Lepidomicrosorium. Japanese species of Polypodium are separated into the “Neotropical clade” and the“Platycerioid-microsoroid clade” sensu Schneider et al. (2004b), but not to the “Polypodium
clade”. Monotypic Pleurosoriopsis is also in the
Neotropical clade (Schneider et al., 2004b). For
the other tribes, global taxonomic revision reflecting molecular phylogeny has not yet been
published.

73

Acknowledgments
I wish to thank Dr. Toshihide Kato for his help
in phylogenetic analysis, and also thank the following persons for their assistance with collection of plant material: S. Fujimoto, T. Fujita, K.
Fuse, M. Higuchi, Y. Horii, E. Ichikawa, R.
Imaichi, Y. Ishizaka, T. Ishiwatari, T. Iwata, Y.
Kakugawa, F. Kasetani, K. Kawahara, Y. Kimura,
K. Kokubo, G. Kokubugata, T. Kuramata, S.
Matsumoto, T. Minamitani, M. Mishima, H.
Miyazaki, K. Mizunashi, A. Murata, T. Nakamura, M. Nakazawa, A. Narita, K. Ohora, Ta. Oka,
To. Oka, O. Okegawa, Y. Okuyama, N. Sahashi,
S. Serizawa, Y. Sugisaki, M. Suzuki, T. Suzuki,
S. Tagane, M. Takamiya, T. Takara, K. Takayama, Y. Tsujita, C. Tsutsumi, A. Uchida, K. Ueno,
M. Uzawa, K. Yamaoka, H. Yamashita, Y.
Yamashita, K. Yasuda and M. Yokota.
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