Measurement of ungulate palatability to and browsing pressure on the Japanese flora

Measurement of ungulate palatability to and browsing pressure on the Japanese flora | Authorea try { document.documentElement.classList.add('js'); } catch (e) { } var _gaq = _gaq || []; _gaq.push(['_setAccount', 'G-8VDV14Y67G']); _gaq.push(['_trackPageview']); (function() { var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true; ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js'; var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s); })(); Skip to main content Preprints Collections Wiley Open Research IET Open Research Ecological Society of Japan All Collections About About Authorea FAQs Contact Us Quick Search anywhere Search for preprint articles, keywords, etc. Search Search ADVANCED SEARCH SCROLL Ecological Research This is a preprint and has not been peer reviewed. Data may be preliminary. 9 January 2025 V1 Latest version Share on Measurement of ungulate palatability to and browsing pressure on the Japanese flora Authors : Fumito Koike 0000-0002-6588-6485 [email protected] and Masayo Isozaki Authors Info & Affiliations https://doi.org/10.22541/au.173640023.35822462/v1 Published Ecological Research Version of record Peer review timeline 366 views 183 downloads Contents Abstract Supplementary Material Information & Authors Metrics & Citations View Options References Figures Tables Media Share Abstract The modern era has led to ungulates becoming dominant and altering natural ecosystems. They browse or graze unevenly on palatable plants, causing a change in the vegetation of unpalatable species. Ungulated palatability is a primary plant trait in plant community assembly. Browsing pressure at a site is the threshold palatability value between browsed and unbrowsed plants at the site, and it should be used for managing an ungulate population to conserve endangered and culturally important plants and maintaining the regeneration of forests with palatable trees. Thus, estimating palatability and browsing pressure are crucial techniques for ecosystem management. Herein, we compared four methods to estimate palatability based on a browsing scar survey and the palatability of 195 plant species from boreal to warm-temperate zones in Japan. Based on the palatability, a browsing pressure map for planning regional ecosystem management was depicted. The four methods assessed typically yielded similar results, although simple logistic regression caused outliers for extremely palatable and unpalatable plants. The species-to-species comparison matrix method, which is a method involving survey data restriction, accepts broad types, whereas the likelihood-distance method and Bayesian logistic regression methods necessitate a countable number of examined plants. The plants listed in the results can be used as indicator species to determine browsing pressure in field surveys. Thus, these methods for estimating palatability and browsing or grazing pressures will contribute to future progress in plant community studies and ungulate management. Technical note Measurement of ungulate palatability to and browsing pressure on the Japanese flora Fumito Koike, Masayo Isozaki Graduate School of Environment and Information Sciences Yokohama National University 79-7 Tokiwadai, Hodogaya-ku, Yokohama 240-8501, Japan Fumito Koike, [email protected] , Tel: +81-45-339-4356 Masayo Isozaki, [email protected] , [email protected] Corresponding author: Fumito Koike ORCID Fumito Koike 0000-0002-6588-6485 CONFLICT OF INTERESTS The authors declare that they do not have any conflicts of interest. Abstract The modern era has led to ungulates becoming dominant and altering natural ecosystems. They browse or graze unevenly on palatable plants, causing a change in the vegetation of unpalatable species. Ungulated palatability is a primary plant trait in plant community assembly. Browsing pressure at a site is the threshold palatability value between browsed and unbrowsed plants at the site, and it should be used for managing an ungulate population to conserve endangered and culturally important plants and maintaining the regeneration of forests with palatable trees. Thus, estimating palatability and browsing pressure are crucial techniques for ecosystem management. Herein, we compared four methods to estimate palatability based on a browsing scar survey and the palatability of 195 plant species from boreal to warm-temperate zones in Japan. Based on the palatability, a browsing pressure map for planning regional ecosystem management was depicted. The four methods assessed typically yielded similar results, although simple logistic regression caused outliers for extremely palatable and unpalatable plants. The species-to-species comparison matrix method, which is a method involving survey data restriction, accepts broad types, whereas the likelihood-distance method and Bayesian logistic regression methods necessitate a countable number of examined plants. The plants listed in the results can be used as indicator species to determine browsing pressure in field surveys. Thus, these methods for estimating palatability and browsing or grazing pressures will contribute to future progress in plant community studies and ungulate management. KEY WORDS Cervus nippon , Indicator species, Plant trait, Browsing or grazing pressure estimation, Wildlife management 1. INTRODUCTION Large mammals have become dominant, changed natural ecosystems, and caused conflicts with humans following the modern era (Iida et al 2018; Carpio et al. 2021; Liu et al. 2024). Ungulates browse or graze unevenly on palatable plants and prevent natural forest regeneration with palatable species, typically causing unpalatable plant vegetation (Treydte et al. 2013; Arcese et al. 2014; Fensham et al. 2014; Zamora-Nasca et al. 2020; Barrere et al. 2024), although different seasonality and plant growth capacities can cause complicated patterns (Augustine et al. 1998). Ungulate palatability is a critical plant trait that determines vegetation (Lloyd et al. 2010; The Society of Vegetation Science 2011), and immediate ungulate palatability evaluation to Japanese flora is necessary. The browsing pressure at a site, depending on animal density and plant resources, can be defined as the threshold palatability value between browsed and unbrowsed plants at the site (Arcese 2014; Nuttle et al. 2014; Capo et al. 2021). The browsing pressure should be used for managing the ungulate population in natural ecosystems to conserve endangered and culturally important plants, and to maintain palatable tree regeneration (Arcese et al. 2014; Capo et al. 2021). A geographic map of browsing pressure can be utilized for damage control in regional ecosystem management by regulating ungulate activity and population mitigation, determining possible crops in regional agriculture, and identifying possible tree species to be planted in regional forestry (Nuttle et al. 2014). Palatability measurement is a critical technique for studying plant communities affected by ungulate browsing. By presenting two or more choices to animals and assessing the often-taken choices, cafeteria experiments in controlled environments are often used to compare palatability (Lloyd et al. 2010; Engel et al 2014). Although detailed analytical methods have been developed (Engel et al 2014), they are not suitable for natural ecosystems with a large number of plant species. Another approach is to observe browsing scars in the natural ecosystems of different plant species (Owen-smith et al, 1987). Palatability was quantified as (number of individual plants of a species with browsing scars/number of individual plants of the focal species present at the site) (Owen-Smith and COOPER 1987). Using this method, we can compare the palatability to plants growing at the same site; however, it is not possible to compare plants of the whole flora with those growing at several sites under different browsing pressure levels. One method to assess palatability and browsing pressure in a wider range is using a logistic regression model that assumes (number of plants with browsing scars/number of plants of the species present in the site) as the dependent variables and in binomial distribution, and “plant species” representing palatability and “sites” representing browsing pressure as the qualitative independent variables (Shinoda and Akasaka 2017). Another way is using a “species-to-species comparison matrix” (Koike 2011). When species A browses heavier than species B at the same site, the element of the matrix (column A, row B) is considered to be 0 and (column B, row A) as 1. The eigenvector in the table provides quantitative palatability. Instead of 0 or 1, the difference in palatability can be subsequently measured more quantitatively using logit transformation of (number of plants with browsing scars/number of plants of the species present at the site), and the reliability of the difference value (i.e., distance between two plant species) can be assessed as a likelihood distribution. Palatability can be reconstructed using a species-to-species distance matrix (Koike 2011). In these methods, browsing pressure is estimated as the palatability of half-browsed plant species. Despite strong demands on field methods to estimate palatability and browsing pressure, methods have not been compared and discussed. Herein, we compared four methods for estimating palatability based on browsing scar surveys, including two variations of the logistic regression method applied to Japanese flora from warm temperate to boreal climates. The plants listed in the results could be used as indicator species to assess browsing pressure in future field surveys. Finally, as an example, we present a regional browsing pressure map. 2. METHODS 2.1 Survey data Browsing scar surveys were conducted in Hokkaido, the lowland Pacific Ocean side of central Honshu, and on Yakushima Island from 2009 to 2024, excluding plant growing season from May to August (Fig. 1). We did not distinguish browsing scars of the sika deer ( Cervus nippon Temminck 1836), Japanese serow ( Capricornis crispus Temminck 1836), or Reeves’ muntjac ( Muntiacus reevesi Ogilby 1839) because of challenges in identifying reliable browse scar. The browsing scar primarily consisted of the sika deer given that the highest elevation is 1000 m in Yamanashi Prefecture. Surveys of a few plots in the distribution range of Reeves’ muntjac were conducted in 2016 during the range expansion of this species (Asada 2011). We recorded the presence or absence of browsing scars between 20 and 100 cm in height on individual plants. We considered 50 cm × 50 cm as a unit “individual” for the survey for widely spread individuals or large patches of clonal plants. We typically recorded a maximum of five individuals and < 50 m survey line length to study more species and more sites rather than examining the exact browsing ratio for a limited number of species at a few sites. Cliffs and the inside of dense shrubs were not examined because ungulates cannot access them (Perea et al. 2016). We did not consider hierarchical foraging patterns (Miranda et al. 2010) in the ungulate’s decision-making model as selecting the landscape first, vegetation patch, and finally browsing an individual plant, because our survey lines were at the level of the vegetation patch, and ungulates usually had enough time for iterated foraging of individual plants. 2.2 Ungulate palatability to plant We compared four methods for estimating palatability. The first method was the “species-to-species comparison matrix method” (Fig. 2) (Koike 2011). A species-to-species comparison matrix was constructed for each site. Element of the matrix at the s -th site was d sij = 1 if the damage for species i was larger than that for species j and d sij = 0 if the damage for species j was larger than that for species i . Herein, we used browsing rate (number of browsed individuals) / (examined individuals) as the damage indicator. The comparison matrices d sij were obtained for each site. We obtained a more reliable species-to-species palatability comparison matrix D ij by averaging the table for all sites. The element of the eigenvector v i of D ij provides the palatability of the i -th species. The second method included the “likelihood distance method,” whose basic idea is similar to the species-to-species comparison matrix method. However, we considered the magnitude of difference, D ij , in palatability between species i and j to be a stochastic distribution. The numbers of browsed and examined individuals were used to obtain the stochastic distribution of browsing probability using the likelihood of a binomial distribution on the logit-transformed axis (Fig. 3). One-dimensional scaling was implemented (Koike 2011), and the coordinates of the species represented palatability. Details of the distance calculation and likelihood-based directional multidimensional scaling are available on the website (Koike 2011). The third method included “Bayesian logistic regression,” wherein the logit of browsing probability, P si , is assumed as the linear combination of the species and site. This method restricts the stochastic distribution of the palatability of i -th species, species i , and browsing pressure of the s -th site, site s , to normal distributions with zero means to prevent extreme values (Shinoda and Akasaka 2017). Herein, we used the stochastic modeling system STAN (rstan 2.21.3) for the estimation (Supporting Information 1). Logit P si = intercept + species i + site s equation 1 The fourth method includes “simple logistic regression” using basic statistic packages such as GLM on R (version 4.1.2). The equation is the same as that in Equation 1 of the Bayesian logistic regression, except for the lack of restriction by a normal distribution. 2.3 Site browsing pressure We defined “half-browsed palatability” as the palatability value involving half the plant browsed at the site in the “species-to-species comparison matrix” and “likelihood distance” methods. This value is the browsing safety; a large value indicates that only palatable plants are browsed, and a small value indicates high browsing pressure, such that even fewer palatable plants are browsed. In the calculation, the browsing ratio, which is the browsed individuals/examined individuals of species i at site s, Q si , was Logit Q si = a s + a 1 palatability of the i -th species equation 2 To reduce the degrees of freedom, we assumed the slope a 1 to be common to all sites (Fig. 4). We can provide browsing probabilities for individual plants, for example, 0, 0.1, and 0.7, respectively, depending on the survey criteria if we record browsing damage on individual plants semi-qualitatively as no browsing, few browsing scars found, and heavily browsed. However, if we need browsing pressures comparative to those based on numbers of browsed and unbrowsed individuals, the survey criteria should be the binary as 0 (unbrowsed) or >0 (browsed). Half-browsed palatability is half-browsed palatability at the site s = - a s/ a 1 . equation 3 In “simple logistic regression” and “Bayesian logistic regression” methods, the equation is half-browsed palatability at the site s = - intercept - site s equation 4 As the absolute palatability values of the four methods differed, the palatability values were standardized for mean =0 and standard deviation = 1 in this research. 2.4 Browsing pressure map As an application of palatability analysis, we created a browsing pressure map of a 1 km × 1 km rural landscape with arable land and forests in Saroma Town, Hokkaido (Fig. 5). We conducted a plant damage survey in 2005 that was independent of the Japanese flora survey. Survey lines were set in every 200 m × 200 m grid and browsing scars from nine common grassland and forest species were surveyed. Individual plants, with a maximum of 20 individuals per species, were examined in each line. Three browsing levels were recorded for each individual: heavily browsed by > 70% visible plant mass, browsed scars observed but not heavier than the heavily browsed category, and not browsed. Palatability and browsing pressure were calculated using the species-to-species comparison matrix method and by assuming three levels of browsing severity: 85% browsing ratio (center of 70%–100%), 35% browsing ratio (center of 0%–70%), and 0% (no scars) browsing ratio, respectively. The average browsing ratio for each species was calculated in every survey line for species-to-species comparison. The palatability in standardized Japanese flora for the indicator species was estimated by reduced major axis method using common species. Half-browsing palatability at survey lines was determined based on the estimated palatability and number of browsed and not browsed individuals. A geographic information system (GIS) model predicting spatial distribution of half-browsed palatability in a landscape was obtained using linear regression with the half-browsed palatability of the survey line as the objective variables, explanatory variables were local environments within 20 m (areas of forest, arable land, and residents and cattle sheds) and forest area within 200m as core home range of deer. 3. RESULTS 3.1 Palatability to Japanese Flora Supplementary Information 2 provides all the survey data. Appendix 1 presents the palatability values obtained for the Japanese flora. Palatable plants (palatability > 1.4 standard deviation of Japanese flora) included Salix spp. and Ficus erecta Thunb. var. erecta , Acer crataegifolium Siebold et Zucc. f. macrophyllum (H.Hara) Hayashi, Stachyurus praecox Siebold et Zucc. var. ovalifolius (Nakai) Ohba comb. nud., Diplazium donianum (Mett.) Tardieu var. donianum , Stephanandra gracilis Franch. et Sav., Helwingia japonica (Thunb.) F.Dietr., Lasianthus japonicus Miq., Calanthe triplicata (Willemet.) Ames., Chenopodium album L., Prunus incisa Thunb., Lasianthus tashiroi Matsum., Acer japonicum Thunb. var. stenolobum H.Hara, Vitis amurensis Rupr. var. coignetiae (Pulliat ex Planch.) Nakai and Aucuba japonica Thunb. f. brachyphylla (Honda) H.Hara. There were 11 tree or shrub species, one liana, two forest floor herbs, including a fern, and one arable weed. Palatability to Miscanthus kanehirae Honda was −0.95, Carex spp. was −0.65, average of dwarf bamboos ( Sasa and Arundinaria ) was −0.32, and average of weed and pasture grasses ( Setaria and Dactylis ) was −1.07. The studied ungulates strongly preferred woody species and did not prefer grass. Unpalatable species (palatability < −1.8 standard deviation of Japanese flora) were Vernicia fordii (Hemsl.) Airy Shaw, Pachysandra terminalis Siebold et Zucc., Abies firma Siebold et Zucc., Arisaema spp., Alocasia macrorrhizos auct. non (L.) G.Don, Jacobaea cannabifolia (Less.) E.Wiebe, and Stephania japonica (Thunb.) Miers var. macrophylla Yamam. 3.2 Comparison of the palatability estimation methods The species-to-species comparison matrix and distance likelihood methods yielded similar results (r = 0.97) (Fig. 6). The Bayesian logistic regression gave similar results to the previous two methods (r = 0.93 and 0.95), whereas several less palatable plants, Jacobaea cannabifolia and Abies firma , deviated slightly from the previous two methods. Simple logistic regression generally gives similar results to other methods but gives extreme outliers for extremely palatable species and extremely unpalatable plants. 3.3 Browsing pressure map In Saroma Town, the most palatable plant among the indicator species was P. ssiori , followed by C. japonicum and V. coignetiae . The least palatable plant was A. sachalinensis followed by P. robustus and S. virgaurea (Table 1). The correlation coefficient between this survey (Table 1) and Japanese flora (Appendix 1) was r = 0.85 for the six common species. Forest was a negative parameter for half-browsing palatability, and plants distant from the forest were browsed less in the geographical analysis (Table 2). Plants close to arable land and buildings, such as houses and cowsheds, were browsed less. This geographical prediction model was depicted as a browsing pressure map showing safe places for ungulate browsing (Fig. 7). 4. Discussion The strong preference for woody plants over graminoids suggests that the studied ungulates, probably sika deer, are browsers, although they depend on graminoids where palatable plants are unavailable (Campos-Arceiz and Takatsuki 2005). The four methods assessed yielded generally similar results, and they can be used to estimate the angular palatability to plant species. The type of survey data restricts the method, the species-to-species comparison matrix method accepts the broadest survey methods even for a rough-estimated damage degree as “heavily damaged,” “less damaged”, and “nondamaged,” whereas the likelihood-distance and logistic regression methods require a countable number of assessed plants and browsed plants as integer values. If we consider robustness, the simple logistic regression method sometimes gives extreme values for less-browsed species and is not recommended. Thus, if the data are described as a countable number of damaged and undamaged plants, the three methods can be used as a species-to-species comparison matrix method, likelihood distance method (Koike 2011), and Bayesian logistic regression (Shinoda and Akasaka 2017). If the data are uncountable, the species-to-species comparison matrix method is the only solution (Koike 2011). Browsing pressure is one of the key factors in managing natural ecosystems, and was previously obtained using one indicator species (Capo et al. 2021) with narrow range; however, any species in Appendix 1 can be simultaneously used as the indicator species and will provide browsing pressure with a reliable and wider range from extremely low browsing pressure to extremely high pressure. Browsing pressure can be used to regulate the population management of natural plant communities to conserve endangered and culturally important plants with palatability values. Calanthe triplicate is a nationally vulnerable species (https://ikilog.biodic.go.jp/Rdb/booklist) and was highly palatable (1.56). Therefore, maintaining half-browsed palatability at least higher than 1.56 (i.e. quite low browsing pressure) is necessary to conserve this species, suggesting a quite low ungulate population density. The average palatability of Fagaceae trees ( Quercus , Castanopsis , Pasania, and Castanea ) was moderate (0.28), and the half-browsed palatability was maintained at higher than this value for successful regeneration. The alien tree Jacobaea cannabifolia is an unpalatable species in southern Japan that may become dominant in areas under high browsing pressure. The dominant forest in the boreal climate under high browsing pressure may be the native Abies species. A geographic map of browsing pressure can be utilized to control damage in managing regional ecosystems through fencing and hunting. 5. Accessibility Appendix 1 shows the plant palatability from boreal to warm temperate zones in Japan. Supporting Information 1 shows the browsing scar survey data for the above list. All these data are according to CC BY 4.0. 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The palatability by species-to-species comparison matrix in these indicator species and those standardized in Japan (average of three methods in Appendix 1) are shown. *Estimated by common species to Appendix 1 using reduced major axis method. Padus ssiori (F.Schmidt) C.K.Schneid. 0.326 1.196 Cercidiphyllum japonicum Siebold et Zucc. 0.321 2.177 * Vitis coignetiae Pulliat ex Planch. 0.291 1.399 * Impatiens noli-tangere L. 0.287 1.295 * Micromeles alnifolia (Siebold et Zucc.) Koehne 0.279 1.087 * Celastrus orbiculatus Thunb. var. orbiculatus 0.279 1.087 * Ulmus laciniata (Trautv.) Mayr ex Schwapp. 0.270 1.336 Acer japonicum Thunb. 0.268 1.42 Ulmus davidiana Planch. var. japonica (Rehder) Nakai 0.257 1.056 Taxus cuspidata Siebold et Zucc. 0.257 0.517 * Dactylis glomerata L. 0.218 -1.216 Artemisia indica Willd. var. maximowiczii (Nakai) H.Hara 0.213 -0.624 * Solidago virgaurea L. subsp. asiatica (Nakai ex H.Hara) Kitam. ex H.Hara 0.186 -1.325 * Parasenecio robustus (Tolm.) Kadota 0.186 -1.325 * Abies sachalinensis (F.Schmidt) Mast. 0.171 -1.521 Table 2. The model predicts half-browsing palatability, which is a negative indicator of browsing pressure, in a 1 × 1 km area of Saroma Town, Hokkaido. Considered variables were covers of forest, arable land area within 20 m from the survey line, house and cow shed cover within 20 m, and forest area within 200 m representing core hiding place. All variables were standardized before analysis. *P<0.05, +<P<0.1 Intercept 1.16 * Arable land within 20 m 0.316 + House and cow shed within 20 m 0.263 * Forest within 200 m -0.436 * Figure legends Fig. 1 Study area. Fig. 2 The species-to-species comparison matrix method. Fig. 3 Diagram of distance in palatability between plant species. The z ij represents distance between species i and species j , and is obtained from field survey. The horizontal coordinate axis representing palatability is reconstructed from distances between various plant species by a kind of multidimensional scaling. Browsed probability at site s , p s , is assumed as the logistic function of palatability as p s = exp( x - a s ) / (1+ exp( x - a s )). In this diagram z 23 is available at site 3, however no information is available at site 2, because both species 2 and 3 are not browsed. At site 1, sp1 is browsed completely and sp3 is not browsed. The distance between sp1 and sp3 is greater than the value determined by the slope of the logistic function, however the upper-limit of the distance is not clear. Such situation in distance is described using likelihood and used in “likelihood distance method”. Fig. 4 A hypothetical diagram to assess “half-browsed palatability”, which is the palatability when half of the plants are browsed at the site. Logistic lines A-1 to E-5 represent each site, and + is the plant species having a palatability value. Half-browsed palatability is determined by logistic regression. Fig. 5 Survey lines (dark green lines) and land covers (green: forests, red: residents and cattle sheds, and no color: arable land including meadows and pastures) of the studied 1 km × 1 km area in Saroma Town, Hokkaido, Japan. Survey lines (dark green lines in left panel) and land covers (green: forests, red: residents and cattle sheds, no color: arable land including meadows and pastures in right panel) of the studied 1km x 1km area in Saroma Town, Japan. Fig. 6. Comparison of the palatability of Japanese flora obtained by the four methods. Fig. 7 Map of half-browsing palatability, which is a negative indicator of browsing pressure of the 1 km × 1 km area in Saroma Town, Hokkaido, Japan. Supplementary Material File (figs.pdf) Download 394.88 KB Information & Authors Information Version history V1 Version 1 09 January 2025 Peer review timeline Published Ecological Research Version of Record 1 Jan 2026 Published Copyright This work is licensed under a Non Exclusive No Reuse License. Collection Ecological Research Keywords 6: community ecology browsing or grazing pressure estimation cervus nippon indicator species plant and animal plant trait wildlife management Authors Affiliations Fumito Koike 0000-0002-6588-6485 [email protected] Yokohama National University Faculty of Environment and Information Sciences View all articles by this author Masayo Isozaki Yokohama National University Graduate School of Environment and Information Sciences Faculty of Environment and Information Sciences View all articles by this author Metrics & Citations Metrics Article Usage 366 views 183 downloads .FvxKWukQNSOunydq8rnd { width: 100px; } Citations Download citation Fumito Koike, Masayo Isozaki. Measurement of ungulate palatability to and browsing pressure on the Japanese flora. Authorea . 09 January 2025. 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