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Which Genus to Study? in Search of Plant Genera Underrepresented Or Overrepresented in the Research from the Flora of Japan

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Which Genus to Study? in Search of Plant Genera Underrepresented Or Overrepresented in the Research from the Flora of Japan 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: [email protected] (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 correlates with the generic size (the number of species in the world for a given genus). Judging from the deviation from this tendency, I found that four genera were exceptionally well studied and 14 gen- era 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 is facing serious loss of diversity largely because of human activities. Key words : endemic species, flora of Japan, genus, research effort, species richness. more and more difficult, with more than a quarter Introduction of species now being considered endangered of The Japanese Archipelago harbors remarkably extinction largely because of human activities rich and unique flora in its relatively small land (Environment Agency of Japan, 2000) and in- area (Iwatsuki, 1995) and thus has been serving creasing deer browsing (Kato and Okuyama, as a valuable field for plant biology including 2004). Therefore, some guidelines for establish- community-level studies on pollination (Kato ment of efficient strategies on researches, which et al., 1990, 1993 and 2003; Kato, 2000), seed utilize the vast diversity of plants native to Japan, dispersal (Noma and Yumoto, 1997), phytogeog- are needed. To this end, the overall picture on raphy (Fujii et al., 2002; Fujii and Senni, 2006; how our knowledge of natural history in the flora Aoki et al., 2004; Ikeda et al., 2006; Ikeda and of Japan is distributed is crucial, although it has Setoguchi, 2006, 2007), and developmental not been clearly presented yet. anatomy (Takahashi, 1994; Ota et al., 2001; In this study, I aimed to reveal the general pat- Tobe, 2008) and molecular systematics (Nakaza- terns on the research effort made for each of the wa et al., 1997; Okuyama et al., 2005, 2008; angiosperm genera native to Japan. I expect the Yamaji et al., 2007) using endemic species. De- genus with more constituent species is likely to spite the considerable number of studies conduct- have more topics to be studied. If this is true, ed, however, much of the natural history of the there should be a tendency that larger genera plants native to Japan remains yet to be studied. have more research efforts made. In turn, plant Meanwhile, comprehensive field collection of genera that have relatively fewer publications any data on plants native to Japan is becoming despite their size might have more important 82 Yudai Okuyama findings to be revealed, while those with more symbols into the form (e.g., for genus Acer, publications would serve as model systems for “genus Acer” were used as a key) on December studies on plant diversity in Japan. 2, 2009. This should result in the underestimate Here, I surveyed the publication records of the number of literature titles retrieved, as regarding the 84 genera of Japan, which have 10 genus names are not always coupled with the or more native species. Specifically, I addressed word “genus”, but apparently could prevent the the following questions: (1) First, which genus is erroneous inflation of the number due to occa- especially species rich in Japan compared to sional, multiple meanings of the genus name. other regions? (2) Second, among the plant gen- Likewise, the number of nucleotide sequences era, is there a correlation between the number of deposited online were count using the query constituent species and research effort made? (3) form of the nucleotide database of National Cen- Third, if the correlation is present, which genera ter for Biotechnology Information (NCBI) web- are overly represented and which are underrepre- site (http://www.ncbi.nlm.nih.gov/). The full tax- sented in literature in proportion to their species onomy path was used as a query to enter into the richness? (4) And finally, which genera should form to minimize the erroneous hit (e.g., for we prioritize to work on? genus Acer, “Eukaryota; Viridiplantae; Strepto- phyta; Embryophyta; Tracheophyta; Spermato- phyta; Magnoliophyta; eudicotyledons; core Materials and Methods eudicotyledons; rosids; eurosids II; Sapindales; Data collection Sapindaceae; Acer” was used as a query.) With the aid of the Wild Flora of Japan (Satake et al., 1981, 1989), I selected 84 flower- Data analysis ing plant genera in which the number of species The relative species richness and the relative native to Japan exceeds 10. Hereafter I refer to endemicity in Japan were calculated by dividing these 84 genera as “species-rich angiosperm gen- the number of native/endemic species in Japan era of Japan”. Note that this number of genera by the number of species in the world for each of might be slightly an underestimate, as the Wild the 84 genera. These values are expected to be Flora of Japan does not include herbaceous high for genera having Japan as their center of plants in Ryukyu Islands. Next, I coded the num- diversity, making them suitable for screening ber of species native to Japan and the number of candidate plant lineage for pursuing research in endemic species in Japan based on the number of Japan as a valuable research field. species listed in the Wild Flora of Japan (Satake The presence of significant correlation be- et al., 1981, 1989), and supplemented the infor- tween the overall number of species and the num- mation with Flora of Japan (Iwatsuki et al., 1993; ber of literature titles available online, and be- 1995, 1999, 2001 and 2006) where possible. In tween the overall number of species and the num- addition, the worldwide number of species for ber of nucleotide sequences deposited online, for each of the genera was also coded based on The each of the 84 genera, was tested using Spear- Plant-Book (Mabberley, 1997). man’s rank correlation test. Furthermore, linear To measure the amount of research effort regression of the number of literature titles or the made for each genus, two measures were used, number of nucleotide sequences deposited online i.e, number of literature titles and the number of using the overall number of species for the genus nucleotide sequences each available online. The as an explanatory variable was also conducted, approximate number of literature titles regarding and 50% and 95% expectation interval was also each of the 84 genera was retrieved using Google arbitrary set and calculated based on the regres- Scholar (http://scholar.google.co.jp/) by entering sion in order to find out “outlier” genera in terms the two words “genus ‘name’” with quotation of research effort. All statistical analyses in this Research Effort in the Flora of Japan 83 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 (yϭ0.5428xϩ192.6). 50% and 95% confidence interval from the regression are also shown with broken lines. study were made using the statistical program effort proportional to the generic size were only R ver. 2.9.1(R Development Core Team, 2009). found as those with the number of literature titles exceeding the 95% credibility threshold as ex- pected from the regression (yϭ0.5428xϩ192.6). Results These outlier genera found were Ranunculus All the measures surveyed in the present study (Ranunculaceae), Quercus (Fagaceae), Prunus are listed in Table1. Both the relative species (Rosaceae), and Rosa (Rosaceae). By placing richness and the relative endemic richness in 50% threshold, more genera were found as the Japan were found to be highest in the following outliers, in which the number of literature titles five genera, i.e., Hosta (Agavaceae), Tricyrtis either exceed or fall below the number expected (Ruscaceae), Asarum (Aristolochiaceae), Hy- from the regression. Under this criterion, 14 gen- drangea (Hydrangeaceae), and Mitella (Saxifra- era, i.e., Calanthe (Orchidaceae), Fimbristylis gaceae) (Table 1, shown in bold), indicating that (Cyperaceae), Eriocaulon (Eriocaulaceae), Stel- these genera have their center of diversity in laria (Caryophyllaceae), Euonymus (Celas- Japan. traceae), Calamagrostis (Poaceae), Saussurea Figure 1 shows the scatter plot between the (Asteraceae), Symplocos (Symplocaceae), Cory- number of species in the world and the number dalis (Fumariaceae), Thalictrum (Ranunculaceae), of literature titles available online for the 84 Pedicularis (Orobanchaceae), Saxifraga (Saxifra- species-rich angiosperm genera of Japan. As gaceae), Senecio (Asteraceae), and Euphorbia expected, the number of literature titles was posi- (Euphorbiaceae), were found to have especially tively correlated with the number of species in fewer publications online than expected from the the world (Spearman’s rank correlation, regression. PϽ5.0ϫ10Ϫ7, rϭ0.53), indicating the research As shown in Fig. 2, the number of nucleotide effort for each genus is somewhat proportional to sequences deposited online for each genus also its size.
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