Factors predicting incidence of butt rot and trunk rot in individual stems of main tree species in a cool-temperate natural mixed forest in Japan

References

• Baddeley A, Rubak E, Turner R. 2015. Spatial point patterns: methodology and applications with R. Boca Raton: CRC Press.
   Google Scholar
• Boddy L. 2001. Fungal community ecology and wood decomposition processes in angiosperms: from standing tree to complete decay of coarse woody debris. Ecol Bull. 49:43–56.
   Google Scholar
• Breiman L. 2001. Random Forests. Mach Learn. 45:5–32.
   Web of Science ®Google Scholar
• Cushman SA, Macdonald EA, Landguth EL, Malhi Y, Macdonald DW. 2017. Multiple-scale prediction of forest loss risk across Borneo. Landsc Ecol. 32:1581–1598.
   Web of Science ®Google Scholar
• Cutler DR, Edwards TC, Beard JKH, Cutler A, Hess KT, Gibson J, Lawler JJ. 2007. Random forests for classification in ecology. Ecology. 88:2783–2792.
   PubMed Web of Science ®Google Scholar
• Deflorio G, Johnson C, Fink S, Schwarze FWMR. 2008. Decay development in living sapwood of coniferous and deciduous trees inoculated with six wood decay fungi. For Ecol Manage. 255:2373–2383.
   Web of Science ®Google Scholar
• Edworthy A, Martin K. 2014. Long-term dynamics of the characteristics of tree cavities used for nesting by vertebrates. For Ecol Manage. 334:122–128.
   Web of Science ®Google Scholar
• Fox EW, Hill RA, Leibowitz SG, Olsen AR, Thornbrugh DJ, Weber MH. 2017. Assessing the accuracy and stability of variable selection methods for random forest modeling in ecology. Environ Monit Assess. 189:316.
   PubMed Web of Science ®Google Scholar
• Gibbons P, Lindenmayer DB, Barry SC, Tanton MT. 2002. Hollow selection by vertebrate fauna in forests of southeastern Australia and implications for forest management. Biol Conserv. 103:1–12.
   Web of Science ®Google Scholar
• Good HM, Basham JT, Kadzielawa SD. 1968. Respiratory activity of fungal associations in zones of heart rot and stain in sugar maple. Can J Bot. 46:27–36.
   Google Scholar
• Holloway GL, Caspersen JP, Vanderwel MC, Naylor BJ. 2007. Cavity tree occurrence in hardwood forests of central Ontario. For Ecol Manage. 239:191–199.
   Web of Science ®Google Scholar
• Hunter ML Jr. 1999. Maintaining biodiversity in forest ecosystems. Cambridge: Cambridge University Press.
   Google Scholar
• Jackson JA, Jackson BJS. 2004. Ecological relationships between fungi and woodpecker cavity sites. Condor. 106:37–49.
   Web of Science ®Google Scholar
• Jönsson MT, Fraver S, Jonsson BG, Dynesius M, Rydgård M, Esseen P-A. 2007. Eighteen years of tree mortality and structural change in an experimentally fragmented Norway spruce forest. For Ecol Manage. 242:306–313.
   Web of Science ®Google Scholar
• Jusino MA, Lindner DL, Banik MT, Walters JR. 2015. Heart rot hotel: fungal communities in red-cockaded woodpecker excavations. Fungal Ecol. 14:33–43.
   Web of Science ®Google Scholar
• Kikuchi K, Akasaka T, Yamaura Y, Nakamura F. 2013. Abundance and use of cavity trees at the tree- and stand-levels in natural and plantation forests in Hokkaido, Japan. J For Res. 18:389–397.
   Google Scholar
• Koch AJ, Munks SA, Driscoll D, Kirkpatrick JB. 2008. Does hollow occurrence vary with forest type? A case study in wet and dry Eucalyptus obliqua forest. For Ecol Manage. 255:3938–3951.
   Web of Science ®Google Scholar
• Kohm KA, Franklin JF. 1997. Creating a forestry for the 21st century: the science of ecosystem management. Washington D.C.: Island Press.
   Google Scholar
• Koiwa T. 2002. Invasion sites of butt rot fungi in Japanese larch. J Jpn For Soc. 84:9–15. (in Japanese).
   Google Scholar
• Liaw A, Wiener M. 2002. Classification and regression by randomForest. R News. 2:18–22.
   Google Scholar
• Lindenmayer DB, Cunningham RB, Pope ML, Gibbons P, Donnelly CF. 2000. Cavity sizes and types in Australian eucalypts from wet and dry forest types -a simple of rule of thumb for estimating size and number of cavities. For Ecol Manage. 137:139–150.
   Web of Science ®Google Scholar
• Lindenmayer DB, Franklin JF, Fischer J. 2006. General management principles and a checklist of strategies to guide forest biodiversity conservation. Biol Conserv. 31:433–445.
   Google Scholar
• Lonsdale D, Pautasso M, Holdenrieder O. 2008. Wood-decaying fungi in the forest: conservation needs and management options. Eur J For Res. 127:1–22.
   Web of Science ®Google Scholar
• Lotwick HW, Silverman BW. 1982. Methods for analyzing spatial processes of several types of points. J Royal Stat Soc. 44:406–413.
   Google Scholar
• Mattila U, Nuutinen T. 2007. Assessing the incidence of butt rot in Norway spruce in southern Finland. Silva Fenn. 41:29–43.
   Web of Science ®Google Scholar
• Messier C, Puettmann KJ, Coates KD. 2013. Managing forests as complex adaptive systems: building resilience to the challenge of global change. Oxford: Routledge.
   Google Scholar
• Ministry of Agriculture, Forestry and Fisheries. 2007. Japan agricultural standards for logs. Tokyo: Ministry of Agriculture, Forestry and Fisheries. (in Japanese).
   Google Scholar
• Ohsawa M, Kuroda Y, Katsuya K. 1994. Heart-rot in old-aged larch forests (I) State of damage caused by butt-rot and stand conditions of Japanese larch forests at the foot of Mt. Fuji. J Jpn For Soc. 76:24–29.
   Google Scholar
• Onodera K, Tokuda S, Abe T, Nagasaka A. 2013. Occurrence probabilities of tree cavities classified by entrance width and internal dimensions in hardwood forests in Hokkaido, Japan. J For Res. 18:101–110.
   Google Scholar
• Prasad AM, Iverson LR, Liaw A. 2006. Newer classification and regression tree techniques: bagging and random forests for ecological prediction. Ecosystems. 9:181–199.
   Web of Science ®Google Scholar
• R Core Team. 2016. R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna. https://www.R-project.org/ ;[accessed 2016 Dec 15].
   Google Scholar
• Ranius T, Niklasson M, Berg N. 2009. Development of tree hollows in pedunculate oak (Quercus robur). For Ecol Manage. 257:303–310.
   Web of Science ®Google Scholar
• Remm J, Lõhmus A. 2011. Tree cavities in forests – the broad distribution pattern of a keystone structure for biodiversity. For Ecol Manage. 262:579–585.
   Web of Science ®Google Scholar
• Ripley BD. 1976. The second-order analysis of stationary point processes. J Appl Probab. 13:255–266.
   Web of Science ®Google Scholar
• Sato T, Yamazaki H, Yoshida T. 2017. Extending effect of a wind disturbance: mortality of Abies sachalinensis following a strong typhoon in a natural mixed forest. J For Res. 22:336–342.
   Google Scholar
• Seymour RS, Kenefic LS. 2002. Influence of age on growth efficiency of Tsuga canadensis and Picea rubens trees in mixed-species, multiaged northern conifer stands. Can J For Res. 32:2032–2042.
   Web of Science ®Google Scholar
• Stockland JN, Siitonen J, Jonsson BG. 2012. Biodiversity in dead wood. Cambridge: Cambridge University Press.
   Google Scholar
• Thor M, Ståhl G, Stenlid J. 2005. Modelling root rot incidence in Sweden using tree, site and stand variables. Scand J For Res. 20:165–176.
   Web of Science ®Google Scholar
• Tokuda S, Ota Y, Hattori T, Shoda-Kagaya E, Sotome K. 2011. The distribution of closely related large genets of Heterobasidion parviporum in a Todo fir (Abies sachalinensis) stand in Hokkaido, Japan. For Pathol. 41:482–492.
   Web of Science ®Google Scholar
• Wilhelmsson L, Arlinger J, Spångberg K, Lundqvist SO, Grahn T, Hedenberg Ö, Olsson L. 2002. Models for predicting wood properties in stems of Picea abies and Pinus sylvestris in Sweden. Scand J For Res. 17:330–350.
   Google Scholar
• Witt C. 2010. Characteristics of aspen infected with heartrot: implications for cavity-nesting birds. For Ecol Manage. 260:1010–1016.
   Web of Science ®Google Scholar
• Worrall JJ, Lee TD, Harrington TC. 2005. Forest dynamics and agents that initiate and expand canopy gaps in Picea–abies forests of Crawford Notch, New Hampshire, USA. J Ecol. 93:178–190.
   Web of Science ®Google Scholar
• Yamada T. 2001. Defense mechanisms in the sapwood of living trees against microbial infection. J For Res. 6:127–137.
   Google Scholar
• Yamane G, Usui G, Kitagawa Y. 1990. Decay damage to stemwoods on afforested Larix leptolepis GORDON in Hokkaido. Bull Hokkaido For Res Inst. 28:64–74. (in Japanese).
   Google Scholar
• Yasuda A, Yoshida T, Miya H, Harvey B. 2013. An alternative management regime of selection cutting for sustaining stand structure of mixed forests of northern Japan - a simulation study. J For Res. 18:398–406.
   Google Scholar
• Yoshida T, Noguchi M, Akibayashi Y, Noda M, Kadomatsu M, Sasa K. 2006. Twenty years of community dynamics in a mixed conifer – broad-leaved forest under a selection system in northern Japan. Can J For Res. 36:1363–1375.
   Google Scholar
• Yoshida T, Noguchi M, Uemura S, Yanaba S, Miya H, Hiura T. 2011. Tree mortality in a natural mixed forest affected by stand fragmentation and by a strong typhoon in northern Japan. J For Res. 16:215–222.
   Google Scholar
• Zahner V, Sikora L, Pasinelli G. 2012. Heart rot as a key factor for cavity tree selection in the black woodpecker. For Ecol Manage. 271:98–103.
   Web of Science ®Google Scholar
• Žemaitis P, Stakenas V. 2016. Ecological factors influencing frequency of Norway spruce butt rot in mature stands in Lithuania. Russ J Ecol. 47:355–363.
   Web of Science ®Google Scholar
• Zheng Z, Zhang SB, Baskin C, Baskin J, Schaefer D, Yang XD, Yang LY. 2016. Hollows in living trees develop slowly but considerably influence the estimate of forest biomass. Funct Ecol. 30:830–838.
   Web of Science ®Google Scholar
• Zinko U, Seibert J, Dynesius M, Nilsson C. 2005. Plant species numbers predicted by a topography-based groundwater flow index. Ecosystems. 8:430–441.
   Web of Science ®Google Scholar