Time series data of a broadleaved secondary forest in Japan as affected by deer and mass mortality of oak trees

Abstract Background Abandonment of broadleaved secondary forests that have been used for various purposes may cause the loss of biodiversity. Some of these forests suffer from diseases such as Japanese oak wilt. An increasing number of deer also impact some of them. Monitoring and recording the status of such forests is important for their proper management. New information This data set provides a concrete example of temporal changes in a temperate broadleaved secondary forest. The forest has been damaged by mass mortality of oak trees caused by Japanese oak wilt disease. In addition, the forest has been under foraging pressure by sika deer (Cervus nippon Temminck). The data set can provide information on how such a forest has changed in species composition of the canopy and sub-canopy layers and in species occurrence in the understory layer.


Introduction
The progress of succession due to underuse or abandonment of secondary forests that have been used for various purposes, such as sources of firewood and charcoal wood, may cause loss of biodiversity in Japan (Washitani 2001, Takeuchi 2010 as well as Europe (Rackham 2008, Müllerová et al. 2015. For example, the loss of mosaic land use maintained by human activity can cause habitat loss for various species which depend on the mosaic (Washitani 2001). Some of these forests suffer from diseases. In Japan, the mass mortality of oak trees caused by Japanese oak wilt disease severely affected oakdominant secondary forests (Kuroda et al. 2012, Nakajima andIshida 2014). The pathogen is a fungus, Raffaelea quercivora Kubono & Shin.Ito, which is carried by a specific beetle, Platypus quercivorus Murayama (Kubono andIto 2002, Kinuura andKobayashi 2006). Though the pathogen and the vector are both native to Japan, abandonment of the secondary forest in recent decades may be related to the epidemic (Nakajima and Ishida 2014).
In addition, deer impact also affects broadleaved forests in Japan (Takatsuki 2009) and other regions of the world (Côté et al. 2004, Gerhardt et al. 2013. In Japan, an increased number of sika deer (Cervus nippon Temminck) has impacted many plantations and natural forests (Takatsuki 2009). Their foraging can suppress regeneration of trees except for deer-unpalatable species (Itô 2015, Itô 2016.
It is important to monitor and record the changes in such forests to manage them properly. This data set provides information on how succession has proceeded in a broadleaf secondary forest in Japan and how the combined effects of the mass mortality of oak trees and deer impacts altered the forest. The data set consists of changes in species composition, stem density and stem diameter at breast height in the canopy and subcanopy layer from 1993 to 2014, and changes in occurrence of woody species in the understory layer from 1992 to 2014.

General description
Purpose: This study was initiated in 1992 to monitor the dynamics of broadleaved secondary forests adjacent to urban areas. Although the study site also contained a conifer plantation, regeneration of broadleaved species within the plantation was also monitored. After periodic surveys (1993, 1996, 1999, 2002 and 2005) were completed (Itô 2007), mass mortality of oak trees affected the forest, alongside deer impacts. To evaluate the compound effect of both types of damage, the study site was surveyed again in 2014 (Itô 2015, Itô 2016).

Sampling methods
Study extent: This study was conducted in the Ginkakuzi-san (also spelled Ginkakuji-san) National Forest, Kyôto City, Japan. This area is located in the warm-temperate zone. The dominant vegetation of the area had been evergreen oak forest approximately 7000 to 1000 years ago, but secondary forests composed of pines and deciduous oaks increased after that (Takahara 2015). In the late 19th century, the forest around the study site was estimated to be covered with small pines, Pinus densiflora Siebold & Zucc., due to human impact (Ogura 2015). After nationalization (in the 1870s), the forest has been protected from felling as a rule. In the 1930s, a mixed forest of pines and deciduous tree species such as Quercus serrata Murray covered the site (Osaka Regional Forest Office 1936). However, the forest has not been completely free from felling; e.g., trees were cut for fuel wood during World War II, and part of the forest was converted to conifer (Cryptomeria japonica (L.f) D.Don and Chamaecyparis obtusa (Siebold & Zucc.) Endl.) plantations in the 1970s. Recently, broadleaved evergreen trees, such as Symplocos prunifolia Siebold & Zucc. and Ilex pedunculosa Miq., were thinned in some parts of the forest, probably to improve light penetration into the forest. Forest diseases also affected the forest. After the 1960s, pine wilt disease strongly affected the national forest and numerous P. densiflora trees died. The responsible pathogen is the nematode Bursaphelenchus xylophilus (Steiner & Buhrer) Nickle, which is thought to have been brought from North America (Mamiya 1988). In the last decade, mass mortality of oak trees affected the forest, as described above. In addition, increased numbers of sika deer have affected the forest (Itô 2015, Itô 2016). Though the population density of the deer in the forest is unknown, camera trap data showed that they inhabited the forest in all seasons (Itô 2015).
Sampling description: A 1.05 ha (210 m × 50 m) study site was established in 1992 ( Fig.  1). The site was divided into 420 quadrats of 5 × 5 m. The study site mainly consisted of broadleaved secondary forest stands, and the rest was a conifer plantation. The plantation was thinned in 1996, and some of the evergreen broadleaved trees were thinned in the eastern part of the site in 2005. After mass mortality, dead stems of Q. serrata were felled, and some stems surrounding the dead stems were also felled. The felled trunks were cut into about 1 m lengths and piled on the floor. The infected wood was covered with plastic sheets and disinfected. The cut stems are denoted in the measurement data file.
Two classes of forest layers were defined: the canopy and sub-canopy layer and the understory layer. Stems in the canopy and sub-canopy layer were defined as having a diameter at breast height (dbh) at least 3.0 cm, and stems in the understory layer were defined as those with a dbh smaller than 3.0 cm or a height shorter than 1.3 m (not including those seedlings and shoots sprouted in the current year). During the period from December 1993 to February 1994, all stems in the canopy and sub-canopy layer were marked, identified by species name, and their dbh measured using a measuring tape with 1 mm precision. After that, dbh was measured in 1996,1999,2002,2005 and 2014 during the non-growing season (October to January of the following year) in the same way. Measurement values in 1999 are missing in the most eastern half of the study site because slope collapse prevention works were conducted near the area.
In 1992, the species of woody plants found in the understory layer were recorded for each quadrat to obtain the understory species composition of the forest in autumn (September to November). The same survey was conducted again in 2014 (July to November). The dynamics of the half of the study site that solely consisted of broadleaved forest was reported in Itô (2015) and Itô (2016), but this is the first report of the whole study site.

Taxonomic coverage
Description: The six surveys from 1993 to 2014 found 61 species in the canopy and subcanopy layer. Table 1 shows their stem density (stems/ha) and basal area (m /ha) in 1993 and 2014. Clerodendrum trichotomum Thunb. was not included in Table 1, because it had only one stem, which was first found in 2002 but had disappeared in 2005. Outline of the study site. A) Contour map. B) Stand type. B: broadleaved, BT: broadleaved (thinned), C: conifer plantation, G: gap (not related to mass mortality of oak trees), GM: gap created or affected by mass mortality of oak trees. A GM in the conifer plantation was generated by a dead oak stem that remained in the plantation.  Fig. 2).
In the understory layer, 88 woody species were found over the two surveys in 1992 and 2014 excluding unidentified species. Table 2 shows the species and the number of quadrats where they were found. Quercus glauca was the most frequent species in both 1992 and 2014. Symplocos prunifolia increased in the number of quadrats from 75 to 274. This may related to gap formation by oak tree deaths and thinning of upper trees as well as the deer-unpalatable trait of the species.  Figure 2.
Changes in dominance of major species. A: stem density, and B: basal area. Table 2.
Changes in number of quadrats where each species was found (out of 420 quadrats) in the understory layer.
Time series data of a broadleaved secondary forest in Japan as affected ...

Type2014
Stand type of the quadrat (B: broadleaved forest, C: conifer plantation, G: gap (not related to mass mortality of oak trees), GM: gap created or affected by the mass mortality of oak trees). Y Position of the northwest corner of the quadrat where the stem was located along the Y axis (m).

X1
Position of the stem along the X axis (m; precision: 0.1 m).

Y1
Position of the stem along the X axis (m; precision: 0.1 m).

Species
Species of the stem.

Start
Year when the stem was first marked.

End
Year when the stem was last found alive (NA denotes that the stem was still alive in 2014). The name (or acronym) in use by the institution having custody of the object(s) or information referred to in the record.

Data set name: Stem measurement data
collectionCode The name, acronym, coden, or initialism identifying the collection or data set from which the record was derived.
datasetName The name identifying the data set from which the record was derived.
basisOfRecord The specific nature of the data record.
catalogNumber An identifier (preferably unique) for the record within the data set or collection.
year The four-digit year in which the Event occurred, according to the Common Era Calendar. country The name of the country or major administrative unit in which the Location occurs.
countryCode The standard code for the country in which the Location occurs. verbatimLocality The original textual description of the place. decimalLatitude The geographic latitude (in decimal degrees, using the spatial reference system given in geodeticDatum) of the geographic center of a Location. decimalLongitude The geographic longitude (in decimal degrees, using the spatial reference system given in geodeticDatum) of the geographic center of a Location.
coordinateUncertaintyInMeters The horizontal distance (in meters) from the given decimalLatitude and decimalLongitude describing the smallest circle containing the whole of the Location. scientificName The full scientific name, with authorship and date information if known. kingdom The full scientific name of the kingdom in which the taxon is classified. phylum The full scientific name of the phylum or division in which the taxon is classified. family The full scientific name of the family in which the taxon is classified. genus The full scientific name of the genus in which the taxon is classified. specificEpithe The name of the first or species epithet of the scientificName. infraspecificEpithet The name of the lowest or terminal infraspecific epithet of the scientificName, excluding any rank designation.