Bull. Natl. Mus. Nat. Sci., Ser. B, 36(2), pp. 81–89, May 22, 2010

Which Genus to Study? In Search of Plant Genera Underrepresented or
Overrepresented in the Research from the Flora of Japan
Yudai Okuyama
Department of Botany, National Museum of Nature and Science,
Amakubo 4–1–1, Tsukuba, 305–0005 Japan
E-mail: yokuyama@kahaku.go.jp(Received 16 February 2010; accepted 24 March 2010)

Abstract One good criterion for determining certain plant groups as a research target would be
to choose those much less or much more studied than the average. Here I conducted a brief survey
on research effort already made for each of the 84 angiosperm genera, in which 10 or more species
are recorded as native to Japan. For each of the genera, approximate amount of the research effort
was measured by counting the number of literature titles and the number of nucleotide sequences
available online. I found a clear tendency that the amount of research effort strongly correlateswith the generic size (the number of species in the world for a given genus). Judging from thedeviation from this tendency, I found that four genera were exceptionally well studied and 14 genera were relatively less studied despite their generic size. I propose the statistics presented here
would be one of the good criteria for starting new research projects on the flora of Japan, which isfacing serious loss of diversity largely because of human activities.
Key words : endemic species, flora of Japan, genus, research effort, species richness.

Introduction
The Japanese Archipelago harbors remarkably
rich and unique flora in its relatively small landarea (Iwatsuki, 1995) and thus has been serving
as a valuable field for plant biology including
community-level studies on pollination (Katoet al., 1990, 1993 and 2003; Kato, 2000), seeddispersal (Noma and Yumoto, 1997), phytogeography (Fujii et al., 2002; Fujii and Senni, 2006;
Aoki et al., 2004; Ikeda et al., 2006; Ikeda andSetoguchi, 2006, 2007), and developmental
anatomy (Takahashi, 1994; Ota et al., 2001;
Tobe, 2008) and molecular systematics (Nakazawa et al., 1997; Okuyama et al., 2005, 2008;
Yamaji et al., 2007) using endemic species. Despite the considerable number of studies conducted, however, much of the natural history of theplants native to Japan remains yet to be studied.
Meanwhile, comprehensive field collection ofany data on plants native to Japan is becoming

more and more difficult, with more than a quarterof species now being considered endangered ofextinction largely because of human activities(Environment Agency of Japan, 2000) and increasing deer browsing (Kato and Okuyama,2004). Therefore, some guidelines for establishment of efficient strategies on researches, which
utilize the vast diversity of plants native to Japan,
are needed. To this end, the overall picture on
how our knowledge of natural history in the floraof Japan is distributed is crucial, although it has
not been clearly presented yet.
In this study, I aimed to reveal the general patterns on the research effort made for each of theangiosperm genera native to Japan. I expect thegenus with more constituent species is likely tohave more topics to be studied. If this is true,
there should be a tendency that larger genera
have more research efforts made. In turn, plant
genera that have relatively fewer publications
despite their size might have more important

82

Yudai Okuyama

findings to be revealed, while those with more
publications would serve as model systems forstudies on plant diversity in Japan.
Here, I surveyed the publication records
regarding the 84 genera of Japan, which have 10
or more native species. Specifically, I addressed
the following questions: (1) First, which genus isespecially species rich in Japan compared toother regions? (2) Second, among the plant genera, is there a correlation between the number of
constituent species and research effort made? (3)Third, if the correlation is present, which genera
are overly represented and which are underrepresented in literature in proportion to their species
richness? (4) And finally, which genera should
we prioritize to work on?
Materials and Methods
Data collection
With the aid of the Wild Flora of Japan(Satake et al., 1981, 1989), I selected 84 flowering plant genera in which the number of species
native to Japan exceeds 10. Hereafter I refer tothese 84 genera as “species-rich angiosperm genera of Japan”. Note that this number of genera
might be slightly an underestimate, as the Wild
Flora of Japan does not include herbaceous
plants in Ryukyu Islands. Next, I coded the number of species native to Japan and the number ofendemic species in Japan based on the number of
species listed in the Wild Flora of Japan (Satake
et al., 1981, 1989), and supplemented the information with Flora of Japan (Iwatsuki et al., 1993;
1995, 1999, 2001 and 2006) where possible. In
addition, the worldwide number of species foreach of the genera was also coded based on The
Plant-Book (Mabberley, 1997).
To measure the amount of research effort
made for each genus, two measures were used,
i.e, number of literature titles and the number ofnucleotide sequences each available online. The
approximate number of literature titles regarding
each of the 84 genera was retrieved using Google
Scholar (http://scholar.google.co.jp/) by entering
the two words “genus ‘name’” with quotation

symbols into the form (e.g., for genus Acer,“genus Acer” were used as a key) on December
2, 2009. This should result in the underestimateof the number of literature titles retrieved, as
genus names are not always coupled with theword “genus”, but apparently could prevent theerroneous inflation of the number due to occasional, multiple meanings of the genus name.
Likewise, the number of nucleotide sequences
deposited online were count using the query
form of the nucleotide database of National Center for Biotechnology Information (NCBI) website (http://www.ncbi.nlm.nih.gov/). The full taxonomy path was used as a query to enter into theform to minimize the erroneous hit (e.g., forgenus Acer, “Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core
eudicotyledons; rosids; eurosids II; Sapindales;
Sapindaceae; Acer” was used as a query.)
Data analysis
The relative species richness and the relative
endemicity in Japan were calculated by dividing
the number of native/endemic species in Japanby the number of species in the world for each of
the 84 genera. These values are expected to behigh for genera having Japan as their center ofdiversity, making them suitable for screening
candidate plant lineage for pursuing research inJapan as a valuable research field.
The presence of significant correlation between the overall number of species and the number of literature titles available online, and between the overall number of species and the number of nucleotide sequences deposited online, foreach of the 84 genera, was tested using Spearman’s rank correlation test. Furthermore, linear
regression of the number of literature titles or thenumber of nucleotide sequences deposited online
using the overall number of species for the genus
as an explanatory variable was also conducted,
and 50% and 95% expectation interval was also
arbitrary set and calculated based on the regression in order to find out “outlier” genera in termsof research effort. All statistical analyses in thisResearch Effort in the Flora of Japan83

Fig. 1. The relationship between the number of species and the number of literature titles available online for 84
species-rich angiosperm genera of Japan. The solid line indicates the regression line best goodness-of-fit
according to the Spearman’s rank-correlation test (y0.5428x192.6). 50% and 95% confidence intervalfrom the regression are also shown with broken lines.

study were made using the statistical program
R ver. 2.9.1(R Development Core Team, 2009).

Results
All the measures surveyed in the present study
are listed in Table1. Both the relative species
richness and the relative endemic richness inJapan were found to be highest in the following
five genera, i.e., Hosta (Agavaceae), Tricyrtis(Ruscaceae), Asarum (Aristolochiaceae), Hydrangea (Hydrangeaceae), and Mitella (Saxifragaceae) (Table 1, shown in bold), indicating thatthese genera have their center of diversity inJapan.
Figure 1 shows the scatter plot between thenumber of species in the world and the numberof literature titles available online for the 84
species-rich angiosperm genera of Japan. As
expected, the number of literature titles was positively correlated with the number of species in
the world (Spearman’s rank correlation,P5.0107, r 0.53), indicating the research
effort for each genus is somewhat proportional toits size. The outlier genera in terms of research

effort proportional to the generic size were only
found as those with the number of literature titles
exceeding the 95% credibility threshold as expected from the regression (y0.5428x192.6).
These outlier genera found were Ranunculus(Ranunculaceae), Quercus (Fagaceae), Prunus(Rosaceae), and Rosa (Rosaceae). By placing
50% threshold, more genera were found as theoutliers, in which the number of literature titles
either exceed or fall below the number expectedfrom the regression. Under this criterion, 14 genera, i.e., Calanthe (Orchidaceae), Fimbristylis(Cyperaceae), Eriocaulon (Eriocaulaceae), Stellaria (Caryophyllaceae), Euonymus (Celastraceae), Calamagrostis (Poaceae), Saussurea(Asteraceae), Symplocos (Symplocaceae), Corydalis (Fumariaceae), Thalictrum (Ranunculaceae),
Pedicularis (Orobanchaceae), Saxifraga (Saxifragaceae), Senecio (Asteraceae), and Euphorbia(Euphorbiaceae), were found to have especiallyfewer publications online than expected from theregression.
As shown in Fig. 2, the number of nucleotide
sequences deposited online for each genus also
positively correlated with its number of species

84

Yudai Okuyama

Fig. 2. The relationship between the number of species and the number of nucleotide sequences deposited in
GenBank for 84 species-rich angiosperm genera of Japan. The regression lines are also shown as in Fig. 1(y1.172x371.4).

in the world, but the tendency was weaker(Spearman’s rank correlation, P5.0104,
r 0.40). Again, the outlier genera found were
only those exceeding the number expected fromthe regression (y1.172x371.4) if I put 95%
threshold. These were Prunus (Rosaceae), Cardamine (Brassicaceae), and Primula (Primulaceae). Like in the number of literature titles,
more genera were found as the outliers, forwhich the number of nucleotide sequences areeither exceeding or below the number expectedfrom the regression by placing 50% threshold.

Discussion
Before determining certain plant groups tostudy, it would be good to know which is relatively less studied, and which is relatively more
so. I presented here a first attempt for quantifying
the amount of research effort already made forindividual genera. Although one can start a
research project on plant natural history in various points of view, including that focuses on
populations, species or higher taxa, or communities, it is good to keep in mind that one of themost remarkable methodological progresses onplant biology in the last decades is the wide-

spread and routine use of molecular phylogenetics (Savolainen and Chase, 2003). In light ofphylogenetic information, regardless of that of
populations or species, one can conduct comparative studies on any traits of interest, especiallyin association with the other factors (Martins andHansen, 1997). This will result in a deeper understanding of the origins and adaptive functionsof diverse characteristics of the focal plants. To
this end, it would be a good research strategy tofocus on certain lineages of plants such as genera, especially those having many, say 10 or
more, species native to Japan. Therefore, in thisstudy, I only included the angiosperm generawith 10 or more species native to Japan in theanalyses.
As a result, I revealed that there is a general,
clear trend that more effort tends to be paid togenera with more species. Although this finding
itself might not be so surprising, one can see if acertain genus has a deviation from this generaltrend. To quantify this deviation, here I propose
literature collection index (LCI) and nucleotide
collection index (NCI), where each of the measure is calculated from the number of literature
titles/nucleotide sequences deposited online for acertain genus divided by that expected from the

CARYOPHYLLACEAERANUNCULACEAEFAGACEAEURTICACEAE
MORACEAEPOLYGONACEAESALICACEAEBETULACEAE

ORCHIDACEAE

ARACEAE
CYPERACEAEERIOCAULACEAE
POACEAE

DIOSCOREACEAE
JUNCACEAEPOTAMOGETACEAEAGAVACEAE
LILIACEAE
RUSCACEAE

FamilyPotamogeton
Hosta
LiliumPolygonatum
Tricyrtis
Dioscorea
JuncusLuzulaEriocaulon
Calamagrostis
Poa
Arisaema
Carex
Cyperus
EleocharisFimbristylis
ScirpusCalantheCymbidium
LiparisPlatanthera
Salix
Alnus
BetulaQuercusBoehmeria
Ficus
Polygonum s. l.
Rumex
Stellaria
Aconitum
AnemoneClematis
Ranunculus
Thalictrum

Genus

90
25
100
55
20
850
300
115
400
230
200
150
2000
300
120
250
200
150
44
350
40
400
25
35
400
80
750
200
200
200
300
144
295
600
330

No. ofspecies in
the world
14
12
13
12
11
11
27
11
35
17
17
25
252
26
15
18
24
15
10
10
17
29
11
11
15
18
16
39
10
18
24
13
25
25
17

No. ofnativespecies in
Japan
0
11
7
4
10
5
3
1
25
10
8
21
93
2
1
2
5
7
5
1
7
8
6
7
2
8
3
0
1
3
17
3
12
6
5

No. ofendemic
species in
Japan
1035
54
994
68
56
678
350
268
35
96
706
250
4373
144
237
126
105
35
214
102
50
694
239
1154
1596
174
2181
1036
716
175
283
384
279
377
121

Nucleotide
sequenceson web
307
163
707
100
30
574
159
140
43
77
431
127
1120
220
184
33
215
23
125
290
72
992
426
478
1580
42
953
451
297
60
515
160
263
1904
149

Literature
titles on
web
15.6
48.0
13.0
21.8
55.0
1.3
9.0
9.6
8.8
7.4
8.5
16.7
12.6
8.7
12.5
7.2
12.0
10.0
22.7
2.9
42.5
7.3
44.0
31.4
3.8
22.5
2.1
19.5
5.0
9.0
8.0
9.0
8.5
4.2
5.2

Relative
speciesrichness inJapan (%)
0.0
44.0
7.0
7.3
50.0
0.6
1.0
0.9
6.3
4.3
4.0
14.0
4.7
0.7
0.8
0.8
2.5
4.7
11.4
0.3
17.5
2.0
24.0
20.0
0.5
10.0
0.4
0.0
0.5
1.5
5.7
2.1
4.1
1.0
1.5

Relative
endemic
richness inJapan (%)

Table 1. A summary of species richness, endemism, and research effort made for 84 species-rich angiosperm genera of Japan

1.27
0.79
2.86
0.45
0.15
0.88
0.45
0.55
0.10
0.24
1.43
0.46
0.88
0.62
0.71
0.10
0.71
0.08
0.58
0.76
0.34
2.42
2.07
2.26
3.86
0.18
1.59
1.50
0.99
0.20
1.45
0.59
0.75
3.67
0.40

LCIa

2.17
0.13
2.03
0.16
0.14
0.50
0.48
0.53
0.04
0.15
1.17
0.46
1.61
0.20
0.46
0.19
0.17
0.06
0.51
0.13
0.12
0.83
0.60
2.80
1.90
0.37
1.74
1.71
1.18
0.29
0.39
0.71
0.39
0.35
0.16

NCIb

Research Effort in the Flora of Japan
85

GENTIANACEAE
APOCYNACEAE
RUBIACEAEVERBENACEAECAPRIFOLIACEAESYMPLOCACEAEPRIMULACEAEGERANIACEAEEUPHORBIACEAE
SAPINDACEAEAQUIFOLIACEAECELASTRACEAEELAEAGNACEAE
VIOLACEAEONAGRACEAEAPIACEAEERICACEAE

FABACEAEROSACEAE

ARISTOLOCHIACEAE
CLUCIACEAEPAPAVERACEAE
BRASSICACEAECRASSULACEAEHYDRANGEACEAESAXIFRAGACEAE

FamilyAsarumHypericum
Corydalis
Cardamine
Sedum
Hydrangea
Chrysosplenium
MitellaSaxifraga
Potentilla
PrunusRosa
Rubus
Spiraea
Vicia
Lespedeza
Geranium
Euphorbia
Acer
Ilex
EuonymusElaeagnus
Viola
Epilobium
Angelica
Rhododendron
Vaccinium
Symplocos
Lysimachia
PrimulaGentiana
Cynanchum
GaliumCallicarpa
Lonicera
Viburnum

Genus

70
370
400
200
280
23
60
20
440
500
200
150
250
100
140
40
300
2000
111
400
177
40
400
165
110
850
450
250
150
425
361
100
300
140
180
150

No. ofspecies in
the world
50
35
15
15
17
12
18
11
16
23
15
12
38
13
13
13
12
13
26
23
18
15
55
12
23
51
19
23
15
14
15
22
18
10
21
16

No. ofnativespecies in
Japan
47
29
3
4
9
8
11
10
6
2
4
5
11
3
1
4
2
6
23
7
5
11
13
0
16
42
7
11
4
10
6
12
4
5
11
5

533
244
90
2634
402
202
62
978
415
1076
5412
1944
774
97
1244
45
557
1250
1948
1221
85
58
1136
348
281
2132
614
693
239
2511
1005
462
87
124
656
463

Nucleotide
sequenceson web(Continued)

No. ofendemic
species inJapan

Table 1.

78
720
141
125
242
119
39
33
189
274
1080
996
875
77
689
135
211
953
638
290
63
39
723
196
135
866
572
110
97
409
397
97
169
65
145
194

Literature
titles on
web
71.4
9.5
3.8
7.5
6.1
52.2
30.0
55.0
3.6
4.6
7.5
8.0
15.2
13.0
9.3
32.5
4.0
0.7
24.3
5.8
10.2
37.5
13.8
7.3
20.9
6.0
4.2
9.2
10.0
3.3
4.2
22.0
6.0
7.1
11.7
10.7

Relative
speciesrichness inJapan (%)
67.1
7.8
0.8
2.0
3.2
34.8
18.3
50.0
1.4
0.4
2.0
3.3
4.4
3.0
0.7
10.0
0.7
0.3
20.7
1.8
2.8
27.5
3.3
0.0
14.5
4.9
1.6
4.4
2.7
2.4
1.7
12.0
1.3
3.6
6.1
3.3

Relative
endemic
richness inJapan (%)
0.34
1.83
0.34
0.42
0.70
0.58
0.17
0.16
0.44
0.59
3.59
3.63
2.67
0.31
2.57
0.63
0.59
0.75
2.52
0.71
0.22
0.18
1.76
0.69
0.54
1.32
1.31
0.34
0.35
0.97
1.02
0.39
0.48
0.24
0.50
0.71

LCIa

1.18
0.30
0.11
4.35
0.57
0.51
0.14
2.48
0.47
1.12
8.93
3.55
1.16
0.20
2.32
0.11
0.77
0.46
3.88
1.45
0.15
0.14
1.35
0.62
0.56
1.56
0.68
1.04
0.44
2.89
1.26
0.95
0.12
0.23
1.13
0.85

NCIb

86
Yudai Okuyama

The five genera with the highest relative species/endemic richness in Japan are shown in bold. a Literature collection index. b Nucleotide collection index.

0.07
1.62
0.73
0.42
0.18
1.21
0.32
2.29
0.48
0.26
0.89
0.82
2.01
0.35
0.73
0.41
0.92
0.12
2.34
0.98
0.98
0.51
0.19
0.26
0.68
1.53
16.0
2.8
2.3
0.6
12.5
2.0
5.2
25.0
20.0
20.0
5.7
0.3
15.0
26.0
7.2
4.3
6.1
27.5
8.6
8.4
35.0
20.8
23.3
8.3
1.0
18.3
76
213
157
266
25
896
323
210
166
42
93
591
344
30
945
568
246
75
948
212
958
321
117
645
1513
889
8
5
8
1
5
7
13
10
50
12
17
4
9
13
13
15
11
11
30
21
14
52
14
25
12
11
50
180
350
180
40
350
250
40
250
60
300
1250
60
Ajuga
Veronica
Pedicularis
Utricularia
Adenophora
Artemisia
Aster
Chrysanthemum
Cirsium
Parasenecio
Saussurea
Senecio
Taraxacum

Genus
FamilyLAMIACEAEVERONICACEAE
OROBANCHACEAE
LENTIBULARIACEAECAMPANULACEAE
ASTERACEAE

Nucleotide
sequenceson webNo. ofendemic
species inJapan
No. ofnativespecies inJapan
No. ofspecies in
the world

Table 1.

(Continued)

Literature
titles onweb

Relative
speciesrichness inJapan (%)

Relative
endemic
richness inJapan (%)

LCIa

NCIb

Research Effort in the Flora of Japan87

species number of the genus. For example, forgenus Calanthe, which has 150 spp. worldwide,
the numbers of literature titles and nucleotide sequences deposited online are 23 and 35, so LCI
and NCI can be calculated as 0.0823/(0.5428
150192.6) and 0.0635/(1.172150371.4),
respectively. LCI and NCI for each of thespecies-rich angiosperm genera of Japan are listed in Table 1. Note that LCI and NCI are not
fixed values and will change through time so one
should update them before using it as the criteria
for finding the plant genera under-/over-represented in research ad hoc.
In facing serious loss of plant diversity inJapan, it would be an important practice to quantitatively recognize the plant genera that are especially species-rich in Japan. It is also noteworthy
that, in the perspective of comparative studies,
species-rich genera are especially useful to draw
robust conclusions, as more species enable morecomparisons. In this study, five genera, Hosta(Agavaceae), Tricyrtis (Ruscaceae), Asarum(Aristolochiaceae), Hydrangea (Hydrangeaceae),
and Mitella (Saxifragaceae), were found to havetheir center of diversity in Japan. The five genera
tend to be underrepresented in the literature(LCI: 0.15–0.79; Table 1), although the numberof nucleotide sequences varies among them
(NCI: 0.13–2.48; Table 1), probably because theresearchers outside Japan would have difficultyin access to most of the species. Because large
information on ecological traits, including pollination systems, seed dispersal, habitat preferences, etc. is only available in the wild, the accumulation of natural history information andintensive field researches for these genera would
be urgently needed.
In this study, I used two measures, i.e., numberof literature titles and nucleotide sequences andproposed LCI and NCI as the corresponding
criteria for quantifying the research effort for theplant genera. I would suggest LCI is the morereliable criterion, as the number of literature
titles will not abruptly increase with a small
research effort. In contrast, the number ofnucleotide sequences deposited online can quick-

88

Yudai Okuyama

ly increase with only a small research effort suchas a single molecular phylogenetic study.
In conclusion, the present quantification ofresearch effort for 84 species-rich angiosperm
genera of Japan highlighted its nonuniformity
despite the presence of general tendency that is
proportional to generic size. I hope the present
brief survey serves as a good starting point torecognize the pattern of how information on natural history of the flora of Japan is distributed,
and to establish efficient research strategies
thereafter.
Acknowledgements
The author thanks Atsushi Kawakita for his
critical and helpful comments on the draft version of the manuscript.
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