Title

Forest stand structure, composition, and dynamics in 34 sites over Japan

AUTHORS

Masae I. Ishihara^{1, a}, Satoshi N. Suzuki^{1, *}, Masahiro Nakamura^{1, b}, Tsutomu Enoki^{2, h}, Akio Fujiwara^{3, c}, Tsutom Hiura⁴, Kosuke Homma⁵, Daisuke Hoshino⁶, Kazuhiko Hoshizaki⁷, Hideyuki Ida⁸, Ken Ishida⁹, Akira Itoh¹⁰, Takayuki Kaneko¹¹, Kaname Kubota¹², Koichiro Kuraji¹³, Shigeo Kuramoto^{14, d}, Akifumi Makita⁷, Takashi Masaki¹⁵, Kanji Namikawa¹⁶, Kaoru Niiyama^{15, e}, Mahoko Noguchi¹⁴, Haruto Nomiya¹⁷, Tatsuhiro Ohkubo¹⁸, Satoshi Saito¹⁵, Takeshi Sakai^{14, f}, Michinori Sakimoto¹⁹, Hitoshi Sakio⁵, Hirofumi Shibano^{13, g}, Hisashi Sugita^{6, f}, Mitsuo Suzuki²⁰, Atsushi Takashima²¹, Nobuyuki Tanaka¹⁵, Naoaki Tashiro²², Naoko Tokuchi¹⁹, Yakushima Forest Environment Conservation Center²³, Toshiya Yoshida²⁴, Yumiko Yoshida³

¹ Network Center of the Forest and Grassland Survey of the Monitoring Sites 1000 Project, Japan Wildlife Research Center, Tomakomai, Japan

² Kasuya Research Forest, Kyushu University, Sasaguri, Japan

³ The University of Tokyo Chichibu Forest, Graduate School of Agricultural and Life Sciences, Chichibu, Japan

⁴ Tomakomai Research Station, Field Science Center for Northern Biosphere, Hokkaido University, Tomakomai, Japan

⁵ Field Center for Sustainable Agriculture and Forestry, Faculty of Agriculture, Niigata University, Sado, Japan

⁶ Tohoku Research Center, Forestry and Forest Products Research Institute, Morioka, Japan

⁷ Faculty of Bioresource Sciences, Akita Prefectural University, Akita, Japan

⁸ Institute of Nature Education in Shiga Heights, Faculty of Education, Shinshu University, Yamanouchi, Japan

⁹ Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan

¹⁰ Graduate School of Science, Osaka City University, Osaka, Japan

¹¹ Graduate School of Agriculture, Kyoto University, Kyoto, Japan

¹² Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan

¹³ Ecohydrology Research Institute, the Tokyo University Forests, Graduate School of Agricultural and Life Sciences, Seto, Japan

¹⁴ Shikoku Research Center, Forestry and Forest Products Research Institute, Kochi, Japan

¹⁵ Forestry and Forest Products Research Institute, Tsukuba, Japan

¹⁶ Biological Laboratory, Sapporo Campus, Hokkaido University of Education, Sapporo, Japan

¹⁷ Kyushu Research Center, Forestry and Forest Products Research Institute, Kumamoto, Japan

¹⁸ Department of Forest Science, Faculty of Agriculture, Utsunomiya University, Utsunomiya, Japan

¹⁹ Field Science Education and Research Center, Kyoto University, Kyoto, Japan

²⁰ Botanical Gardens, Tohoku University, Sendai, Japan

²¹ Yona Field, Subtropical Field Science Center, Faculty of Agriculture, University of the Ryukyus, Kunigami, Japan

²² Ashoro Research Forest, Kyushu University, Ashoro, Japan

²³ Yakushima Forest Environment Conservation center, Yakushima District Forest Office, Kyushu Regional Forest Office, Forestry Agency, Yakushima, Japan

²⁴ Uryu Experimental Forest, Field Science Center for Northern Biosphere, Hokkaido University, Horokanai, Japan

Present addresses:

^a Field Science Center for Northern Biosphere, Hokkaido University, Hokkaido, Japan

^b Nakagawa Experimental Forest, Field Science Center for Northern Biosphere, Hokkaido University, Horokanai, Japan

^c Forest Therapy Research Institute, The University of Tokyo, Graduate School of Agricultural and Life Sciences, Yamanakako, Japan

^d Hokkaido Research Center, Forestry and Forest Products Research Institute, Sapporo, Japan

^e Tohoku Research Center, Forestry and Forest Products Research Institute, Morioka, Japan

^f Forestry and Forest Products Research Institute, Tsukuba Japan

^g University Forest in Hokkaido, The University of Tokyo, Furano, Japan

^h Shiiba Research Forest, Kyushu University, Shiiba, Japan

^*Author for correspondence: Satoshi N. Suzuki

Network Center of Forest and Grassland Survey, Monitoring Sites 1000 Project, Japan Wildlife Research Center

Email: moni1000f_networkcenter@fsc.hokudai.ac.jp

Telephone number: +81-144-33-2171, Fax number: +81-144-33-2173

Address: c/o Tomakomai Experimental Forest, Hokkaido University,

Takaoka, Tomakomai, Hokkaido 053-0035, Japan

ABSTRACT

This data paper reports tree census data collected in a network of 34 forest sites in Japan. This is the largest forest data set freely available in Japan to date. The network is a part of the Monitoring Sites 1000 Project launched by the Ministry of the Environment, Japan. It covers subarctic to subtropical climate zones and the four major forest types in Japan. Forty two permanent plots usually 1 ha in size were established in old-growth or secondary natural forests. Censuses of woody species > 15 cm girth at breast height were conducted every year or once during 2004 to 2009. The data provide species abundance, survivorship and stem girth growth of 52534 individuals of 334 tree and liana species. The censuses adopted common census protocol, which provide good opportunities for meta-analyses and comparative studies among forests. The data have been used for ecological studies as well as for the biodiversity reports published by the Ministry of the Environment.

KEYWORDS

Plot network, forest, tree species abundance, stem diameter, tree demography, Japan, the Monitoring Sites 1000 Project

INTRODUCTION

Japan has high endemism of plant species (Contreras-Medina et al. 2001; Kier et al. 2009) and qualified as one of 36 terrestrial biodiversity hotspots (Mittermeier et al. 2004). Forests cover 67% of the terrestrial area of Japanese Archipelago. However, natural forests comprise only 27% of forested area and the remains are secondary forests or artificial plantations (Anonymous 2010). Because of wide latitudinal range (22-46°N) and mountainous landscape, various types of natural forests developed under various climates ranging from the subarctic to subtropical.

There are more than 162 forest permanent plots in Japan (Kanzaki 2006). However, few raw data are available at databases such as PlotNet (http://eco1.ees.hokudai.ac.jp/plotnet/home) and Forest Dynamics Database (http://fddb.ffpri-108.affrc.go.jp/). As a result, meta-analysis of different forests was rarely conducted in Japan (but see Hiura 1995; Masaki et al. 1999; Takyu et al. 2005; Ogawa et al. 2010). Especially access of latest data is highly limited in Japan. To conserve the biodiversity, latest data should be freely available.

This data paper reports tree census data collected in a network of 34 natural forest sites, largest forest data set ever published in Japan. The network is part of the Forest and Grassland Survey of the Monitoring Sites 1000 Project launched by the Ministry of the Environment, Japan (Ishihara et al. 2007; Ishihara et al. 2010). Some sites participate in the Japan Long-Term Ecological Research Network (JaLTER), a member of the International Long-Term Ecological Research Network (ILTER). These data were acquired under the common census protocol, which enable comparative studies among forests. Furthermore, the data were collected in recent years from 2004 to 2009.

The network ranges from the subarctic to subtropical climate zones, and covers four major forest types in the Japan (evergreen conifer forest, broadleaf and conifer mixed forest, deciduous broadleaf forest, and evergreen broadleaf forest). Forty two permanent plots usually 1 ha in size were established in old-growth or secondary natural forests. Censuses of woody species ≥15 cm girth at breast height were conducted every year or once during 2004 to 2009. The data provide species abundance, survivorship and stem girth growth of 52534 individuals of 334 tree and liana species. Additional information on stand height, climatic variables and disturbance history are provided.

These data have been used for ecological studies at each site as well as for the biodiversity reports published by the Ministry of the Environment, Japan. The data can be used for meta-analysis testing hypotheses of community ecology and ecosystem functions. Furthermore, it provides the information about the distribution of tree species.

METADATA

1. Title

Tree census data in 34 sites over Japan

2. Identifier

ERDP-2011-01

3. Contributor

A. Data Set Owner

Both the Ministry of the Environment, Japan and the following individuals have the ownership of the data.

B. Data Set Creators

Masae I. Ishihara. Field Science Center for Northern Biosphere, Hokkaido University, Hokkaido, Japan

Satoshi N. Suzuki. Network Center of the Forest and Grassland Survey of the Monitoring Sites 1000 Project, Japan Wildlife Research Center

Masahiro Nakamura. Nakagawa Experimental Forest, Field Science Center for Northern Biosphere, Hokkaido University

4. Project

A. Title:

The Monitoring Sites 1000 Project

B. Personal:

Organization: Biodiversity Center of Japan, Ministry of the Environment, Japan
Address: 5597-1, Kenmarubi, Kamiyoshida, Fujiyoshida City, Yamanashi Prefecture 403-0005 Japan
Phone: +81-555-72-6031 (voice)
Phone: +81-555-72-6035 (fax)
Web Address: http://www.biodic.go.jp/

C. Funding:

Biodiversity Center of Japan, Ministry of the Environment, Japan

D. Objectives:

"The goal of the Monitoring Sites 1000 Project is to detect signs of ecosystem change by long-term monitoring surveys that accumulate and analyze quantitative data on various types of ecosystems throughout Japan. The results of this monitoring can contribute to the development of appropriate measures for conservation of the natural environment. The project surveys about 1,000 sites throughout Japan and to continue monitoring them over the long term. This project was initiated in 2003 in accordance with the National Biodiversity Strategy of Japan (as revised in 2002). In the first phase (2003-2007), the design of survey methods for each ecosystem, locating the 1,000 monitoring sites, and building up the operational frameworks were completed and preliminary surveys were carried out. In 2008, the project entered its second phase in which full surveys were initiated. The monitoring project targets various types of representative ecosystems in Japan, including terrestrial ecosystems (alpine zones, forests/grasslands, and satoyama), inland water ecosystems (lakes and mires/marshes), and marine ecosystems (sandy beaches and rocky shores, tidal flats, seagrass beds, algal beds, coral reefs, and small islets). By developing a collaborative operational network with scientists, local experts, NPOs, and other relevant entities, the project will continue monitoring those ecosystems over a long-term period." (Ministry of the Environment 2009, revised by the Ministry of the Environment in May 2011)

5. Geographic coverage

A. Geographic Description:

Japan

B. Bounding Coordinates:

West: 128.23
East: 143.51
North: 44.37
South: 26.68

Geographic coodinate system is WGS84

6. Temporal coverage

A. Begin:

2004

B. End:

2009

7. Taxonomic coverage

The data include 78 families, 155 genus and 334 species of woody plants (see SpList.csv for detail).

8. Methods

A. Study sites and sampling design

The data were obtained at 42 forest permanent plots in 34 sites. These plots cover major climate zones and biogeographic regions in Japan (Ministry of the Environment 2001, http://www.env.go.jp/press/file_view.php?serial=2872&hou_id=2908) (Table 1, Fig. 1). Furthermore, these plots cover major four forest types found in Japan; evergreen conifer forest, broadleaf and conifer mixed forest, deciduous broadleaf forest, and evergreen broadleaf forest. We classified each plot into one of the four forest types by the dominance of evergreen broadleaf, deciduous broadleaf and conifer tree species as follows:

Evergreen conifer forest (EC): A >0.6
Broadleaf and conifer mixed forest (BC): 0.6 >A >0.4
Deciduous broadleaf forest (DB): A <0.4 & B >0.6
Evergreen broadleaf forest (EB): A <0.4 & B <0.6
, where
A = basal area of conifer tree species / total basal area
B = basal area of deciduous broadleaf tree species / basal area of deciduous and evergreen broadleaf tree species

Most of these forests are old-growth or old secondary forests but some are secondary forests that are younger than 100 years (see SiteList.csv). We classified forests into one of three age category: old-growth (OG), old secondary (OS), and secondary (S).

OG: old-growth forest which was assumed to be >150 years old,

OS: old secondary forest which was assumed to be >100 years old,

S: secondary forest which was assumed to be <100 years old.

Mean annual temperature, mean annual precipitation, and mean maximum snow depth during 1971 to 2000 were extracted from the database Mesh Climate Data 2000, distributed by the Japan Meteorological Agency (2002). The database provides climate variables estimated at the spatial resolution of 1-km. Mean annual temperature was corrected for altitudinal difference between the plot and the 1-km grid mean by the lapse rate of 0.6°C∙100m⁻¹. Snow depth from the database might underestimate or overestimate the snow depth of the plots because snow depth is highly spatially heterogeneous. Therefore, we provide snow depth reported in other publications or according to personal observations in Appendix.pdf.

Table 1. Major climate zones and biogeographic regions of 34 sites.

*Sites located between the cool and warm temperate zones.

Fig. 1. 34 sites over Japan.

B. Field method

B-1. Permanent plots

One to four permanent plots were established in each site. The sizes of the plots are usually 1 ha (100×100 m) raging from 0.1 to 1.2 ha. The shapes of the plots are normally squares or rectangle but some plots have different shapes because we avoided edges of the forest that face artificial forest, roads, or buildings (see Appendix.pdf).

Plots were subdivided into 10×10-m grid cells (Fig. 2). Exceptions were HY-EC1 which was subdivided into 10×10 or 10×5-m gird cells (see Appendix.pdf), and CC-DB1 which was subdivided into sixteen 25×25-m grid cells.

Fig. 2. Layout of 1-ha permanent forest plot divided into 100 grid cells.

B-2. Data collection

Measurements were conducted every year for 20 plots and once for 22 plots. At each plot, we measured mostly at the same season in every census years, normally autumn or winter when the stem growth has ceased. The exceptions were GR and OW (see Appendix.pdf).

Within each grid cell, all live trees with girth at breast height (gbh) >15 cm were tagged with stem identification code, botanically identified, and measured for their gbh to nearest millimeter. For some plots, trees with gbh <15 cm were also measured. Exception is TM-DB2 where only trees with gbh >30 cm were measured. Measurement height on each tree stem was marked by coloring paint for repeated measurements. The position of each tree was recorded to nearest 10 cm as coordinates of the stem within each grid cell for the most of the plots. Exceptions were KM-DB1 where it was measured to nearest 1 m, TM-DB1 and OS-EC1 to nearest 1cm, and CC-DB1, CC-DB2, CC-DB3, OG-DB1, OY-DB1, SD-EB1, TM-DB4 where stem locations were not measured. In some cases, trees which were adjacent to the plot were measured. Such trees can be identified from the X and Y coordinates of the grid cell where the trees were located and those of the stem grid cell position of the trees. For multiple stem trees, all stems with gbh >15 cm were measured, tagged with different stem identification codes, and assigned a common individual identification code. When multiple stems were adhered to each other and each stem was unable to measure, multiple stems were measured as one stem. The gbh of each stem was obtained by dividing the measured gbh of multiple stems by the number of stems.

C. Data verification procedures

Data were manually digitized and checked for typos by the investigators. Furthermore, data were checked for typos by staffs of the Network Center (M. I. Ishihara, S. N. Suzuki and M. Nakamura). Special attentions were paid for:

1) Consistence of individual identification code and tree species or stem location

2) Gbh growth anomalies

3) Recruitments.

When the multiple stems of the same individual (identical individual identification code) were recorded as different species or located apart, we corrected for the typos.

When the stem grew >6.3 cm∙yr⁻¹ in gbh (i.e. >2 cm∙yr⁻¹ in dbh) or shrunk <−3.1 cm∙yr⁻¹ (i.e. < 1 cm∙yr⁻¹ in dbh), we checked for typos and regarded such cases as anomalies. The criteria is based on the fact that 99% of girth growth record between 2004 to 2008 ranged between −1.4 to 3.6 cm∙yr⁻¹, and only 0.14% (104 records) were >6.3 cm∙yr⁻¹ and 0.15% (106 records) were <−3.1 cm∙yr⁻¹. Such anomalies may result from truly anomalous growth, measurement error, measurement at different height, or when the gbh was measured with inclusion of attached vines at the previous census but measured excluding the vines at this census or vice versa.

Although we tried to measure trees with gbh >15 cm to detect accurately the timing of recruitment when the gbh was >15.7 cm (i.e. dbh >5.0 cm), some stems were recorded for the first time when their gbh was >15.7 cm. These trees were treated as newly recruited when the gbh at the first recorded census was <22.0 cm. When the gbh was >22.0 cm, such tree was treated as already recruited by the last census and gbh of the last census was treated as missing values. This is because if the tree was pre-recruitment state at the last census with gbh >15.6 cm and recruited by this census, the gbh at this census should be <21.9 cm (15.6 cm + 6.3 cm∙yr⁻¹).

If any suspicious value remained, the value was recorded as an error (see 11. D.).

D. Taxonomy and Systematics

Most botanical identifications were made in the field and recorded in Japanese common names. Scientific names followed Satake et al. (1989a, b). Both Japanese common names and scientific names are retained in the data (see 11. D). Synonyms in Japanese common names are assigned single scientific name. Nomenclature at family level followed APG III (APG 2009). A large majority of plants were identified to species-level including subspecies and varieties. For some species, the minimum identification level varied between sites. For example, Acer mono was identified to variety-level (e.g. Acer mono var. marmoratum f. dissectum, Acer mono var. glabrum) in Ashoro (AS-DB1, AS-DB2, AS-DB3), Nopporo (NP-DB1), Nibuna-mizusawa (NB-EC1), Otakizawa (OZ-DB1), Kanumazawa (KM-DB1), Ogawa (OG-DB1), Aobayama (AO-EC1), Kanamegawa (KK-DB1), Chichibu (CC-DB1, CC-DB2, CC-DB3), but to species level only in other sites. Eighteen trees (0.03% of all trees) were identified to genus-level only (Salix sp. and Phyllostachys sp.). One hundred thirty nine trees (0.27% of all trees, most of them were in Nibuna-mizusawa (NB-EC1) and Mt. Tsukuba (TB-DB1)) could not be identified (recorded as "NA"). In the original data of Aya (AY-EB1) and Ichinomata (IC-BC1), Castanopsis sieboldii ("sudazii") and Castanopsis cuspidata ("tuburazii") were not distinguished and recorded as "Castanopsis sp." because two species create hybrid (Tanouchi and Yamamoto 1995). In the data of this data paper, "Castanopsis sp." was treated as Castanopsis sieboldii ("sudazii") according to Saito and Sato (2007) for AY-EB1 and to the morphology of seeds and stem (Kuramoto S. unpublished data) and Ishikawa (2009) for Ichinomata.

9. Data status

A. Latest Update: 14 February 2011

The data span the period 2004-2009. Data will be collected continuously after 2009 and the database will be updated as collected and verified.

B. Latest Archive date: 4 March 2011

C. Metadata status: Metadata are complete for this period and stored with the data

10. Accessibility

A. License and Usage Rights:

1) Acceptable use. The dataset should not be used for illegal purpose or to violate the rights of the others. Use of the dataset will be restricted to academic, research, educational, government, recreational, or other not-for-profit professional purposes.

2) Citation. Data users should properly cite this Data Paper in any publications or in the metadata of any derived data products that were produced using the dataset. As the metadata and the dataset can be updated at any time, the date of update should be shown in bibliography.

3) Acknowledgement. Data users should acknowledge as follows in any publications where the dataset contributed to its content: "Data for XXX was provided by the Ministry of the Environment, Monitoring Sites 1000 Project".

4) Notification. Data users will notify the Data Set Contact when any derivative work or publication based on or derived from the Data Set is distributed. The data users will provide the Data Set Contact with two reprints or a PDF file of any publications resulting from use of the data set.

5) Collaboration. Data users are strongly encouraged to consider consultation, collaboration and/or co-authorship with the data owners.

6) Disclaimer. In no event shall the authors, data owners, or the Ministry of the Environment, Japan be liable to for loss of profits, or for any indirect, incidental or consequential damages arising from the use or interpretation of the data.

B. Contact:

Data Set Contact

Satoshi N. Suzuki

Network Center of the Forest and Grassland Survey of the Monitoring Sites 1000 Project, Japan Wildlife Research Center, c/o Tomakomai Experimental Forest, Hokkaido University, Takaoka, Tomakomai, Hokkaido 053-0035, Japan

Telephone: +81-144-33-2171

Email: moni1000f_networkcenter@fsc.hokudai.ac.jp

Contact for details of each site

For details of each site, contact the data contact (3. A).

C. Storage location:

http://db.cger.nies.go.jp/JaLTER/metacat/metacat/ERDP_2011_01.10.2/default

The Biodiversity Center of Japan, Ministry of the Environment and the data owners store the original data (in Japanese).

11. Data Structure

A. Data tables:

B. Format type:

The data files are in ASCII text, comma delimited (csv).

C. Header information:

Headers corresponding to variable names (see 11.D.) are included as first row in the data files.

D. Variable definitions:

The variables are listed in the order they appear in each data file. Variable names are headers included as first row in the data files. "NA" is the code for errors and missing values for all variables.

12. Supplementary Information

A. Notes in Japanese:

Although a number of notes/comments were recorded in the original data in Japanese, they were removed from the data of this Data Paper. If you need the notes/comments, consult the Network Center (10. B).

B. Related data:

Dataset of this data paper are also available in Japanese from web site of the Biodiversity Center of Japan, Ministry of the Environment, Japan (http://www.biodic.go.jp/moni1000/findings/data/index.html), which includes some data that are not included in this data paper due to some reasons.

Trees in some sites have been measured since before the project was launched and/or in a plot of larger area (>1 ha). If you are interested in these extra data, consult the Data Set Contact (10.B) or the data owners (3. A). Some of these data are available from JaLTER Database (http://db.cger.nies.go.jp/JaLTER/metacat/style/skins/jalter-en/index.jsp) or the Forest Dynamics Database (http://fddb.ffpri-108.affrc.go.jp/en/index.html, see also Ogawa et al. 2010) (see Appendix.pdf).

The Forest and Grassland Survey of the Monitoring Sites 1000 Project is also monitoring litter and seed fall by litter traps, ground beetles by pitfall traps and birds by spot-censuses. If you are interested in these data, consult the Data Set Contact (10. B).

13. Acknowledgements

We thank Shigeru Niwa for valuable comments. The data was collected as Monitoring Sites 1000 Project of Ministry of the Environment, Japan.

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