Cohesive framework for modelling plant cover class data

2019 ◽  
Vol 10 (10) ◽  
pp. 1749-1760 ◽  
Author(s):  
Kathryn M. Irvine ◽  
Wilson J. Wright ◽  
Erin K. Shanahan ◽  
Thomas J. Rodhouse
PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9383
Author(s):  
Hiroki Itô

A lot of vegetation-related data have been collected as an ordered plant cover class that can be determined visually. However, they are difficult to analyze numerically as they are in an ordinal scale and have uncertainty in their classification. Here, I constructed a state-space model to estimate unobserved plant cover proportions (ranging from zero to one) from such cover class data. The model assumed that the data were measured longitudinally, so that the autocorrelations in the time-series could be utilized to estimate the unobserved cover proportion. The model also assumed that the quadrats where the data were collected were arranged sequentially, so that the spatial autocorrelations also could be utilized to estimate the proportion. Assuming a beta distribution as the probability distribution of the cover proportion, the model was implemented with a regularized incomplete beta function, which is the cumulative density function of the beta distribution. A simulated dataset and real datasets, with one-dimensional spatial structure and longitudinal survey, were fit to the model, and the parameters were estimated using the Markov chain Monte Carlo method. Then, the validity was examined using posterior predictive checks. As a result of the fitting, the Markov chain successfully converged to the stationary distribution, and the posterior predictive checks did not show large discrepancies. For the simulated dataset, the estimated values were close to the values used for the data generation. The estimated values for the real datasets also seemed to be reasonable. These results suggest that the proposed state-space model was able to successfully estimate the unobserved cover proportion. The present model is applicable to similar types of plant cover class data, and has the possibility to be expanded, for example, to incorporate a two-dimensional spatial structure and/or zero-inflation.


2014 ◽  
Vol 25 (3-4) ◽  
pp. 53-68
Author(s):  
I. V. Goncharenko ◽  
H. M. Holyk

Cenotic diversity and leading ecological factors of its floristic differentiation were studied on an example of two areas – Kyiv parks "Nivki" and "Teremki". It is shown that in megalopolis the Galeobdoloni-Carpinetum impatientosum parviflorae subassociation is formed under anthropogenic pressure on the typical ecotope of near-Dnieper hornbeam oak forests on fresh gray-forest soils. The degree of anthropogenic transformation of cenofloras can be estimated by the number of species of Robinietea and Galio-Urticetea classes, as well as neophytes and cultivars. Phytoindication for hemeroby index may be also used in calculation. We propose the modified index of biotic dispersion (normalized by alpha-diversity) for the estimation of ecophytocenotic range (beta-diversity) of releves series. We found that alpha-diversity initially increases (due to the invasion of antropophytes) at low level of antropogenic pressure, then it decreases (due to the loss of aboriginal species) secondarily with increasing of human impact. Also we found that beta-diversity (differential diversity) decreases, increasing homogeneity of plant cover, under the influence of anthropogenic factor. Vegetation classification was completed by a new original method of cluster analysis, designated as DRSA («distance-ranked sorting assembling»). The classification quality is suggested to be validated on the "seriation" diagram, which is а distance matrix between objects with gradient filling. Dark diagonal blocks confirm clusters’ density (intracluster compactness), uncolored off-diagonal blocks are evidence in favor of clusters’ isolation (intercluster distinctness). In addition, distinction of clusters (syntaxa) in ordination area suggests their independence. For phytoindication we propose to include only species with more than 10% constancy. Furthermore, for the description of syntaxonomic amplitude we suggest to use 25%-75% interquartile scope instead of mean and standard deviation. It is shown that comparative analysis of syntaxa for each ecofactor is convenient to carry out by using violin (bulb) plots. A new approach to the phytoindication of syntaxa, designated as R-phytoindication, was proposed for our study. In this case, the ecofactor values, calculated for individual releves, are not taken into account, however, the composition of cenoflora with species constancies is used that helps us to minimize for phytoindication the influence of non-typical species. We suggested a syntaxon’s amplitude to be described by more robust statistics: for the optimum of amplitude (central tendency) – by a median (instead of arithmetic mean), and for the range of tolerance – by an interquartile scope (instead of standard deviation). We assesses amplitudes of syntaxa by phytoindication method for moisture (Hd), acidity (Rc), soil nitrogen content (Nt), wetting variability (vHd), light regime (Lc), salt regime (Sl). We revealed no significant differences on these ecofactors among ecotopes of our syntaxa, that proved the variant syntaxonomic rank for all syntaxa. We found that the core of species composition of our phytocenoses consists of plants with moderate requirements for moisture, soil nitrogen, light and salt regime. We prove that the leading factor of syntaxonomic differentiation is hidden anthropogenic, which is not subject to direct measurement. But we detect that hidden factor of "human pressure" was correlated with phytoindication parameters (variables) that can be measured "directly" by species composition of plant communities. The most correlated factors were ecofactors of soil nitrogen, wetting variability, light regime and hemeroby. The last one is the most indicative empirically for the assessment of "human impact". We establish that there is a concept of «hemeroby of phytocenosis» (tolerance to human impact), which can be calculated approximately as the mean or the median of hemeroby scores of individual species which are present in it.


Author(s):  
М. А. Babaeva ◽  
S. V. Osipova

The regularities of changes in the resistance of different groups of fodder plants to adverse conditions were studied. This is due to the physiological properties that allow them to overcome the harmful effects of the environment. As a result of research species - plant groups with great adaptive potential to the harsh continental semi-desert conditions were identified. Monitoring observation and experimental studies showed too thin vegetation cover as a mosaic, consisting of perennial xerophytic herbs and semishrubs, sod grasses, saltwort and wormwood, as well as ephemera and ephemeroids under the same environmental conditions, depending on various climatic and anthropogenic factors. This is due to the inability or instability of plant species to aggressive living environment. It results in horizontal heterogeneity of the grass stand, division into smaller structures, and mosaic in the vegetation cover of the Kochubey biosphere station. The relative resistance to moderate stress was identified in the following species from fodder plants Agropyron cristatum, A. desertorum, Festuca valesiaca, Cynodon dactylon, Avena fatua; as for strong increasing their abundance these are poorly eaten plant species Artemisia taurica, Atriplex tatarica, Falcaria vulgaris, Veronica arvensis, Arabidopsis thaliana and other. On the site with an increasing pressure in the herbage of phytocenoses the number of xerophytes of ruderal species increases and the spatial structure of the vegetation cover is simplified. In plant communities indigenous species are replaced by adventive plant species. The mosaic of the plant cover of phytocenoses arises due to the uneven distribution in the space of environmental formation, i.e. an edificatory: Salsola orientalis, S. dendroides, Avena fatua, Cynodon dactylon, Artemisia taurica, A. lercheanum, Xanthium spinosum, Carex pachystyli, under which the remaining components of the community adapt. Based on the phytocenotic indicators of pasture phytocenoses it can be concluded that the vegetation cover is in the stage of ecological stress and a decrease in the share of fodder crops and an increase in the number of herbs indicates this fact.


2006 ◽  
pp. 43-57 ◽  
Author(s):  
H. N. Lysenko ◽  
I. A. Korotchenko

Changes in the set of syntaxa have been traced for the plant cover of the «Mikhaylovskaya Tselina» meadow-steppe (an isolated part of the Ukrainian Steppe Nature Reserve, Sumy Region, Ukraine) with the help of the Braun-Blanquet approach. The area vegetation syntaxa prodromus includes 2 classes, 2 rders, 3 alliances, 9 associations, and 6 subasso­ciations, 2 of the latter described anew. The plant cover is highly dynamic and undergoes expressed meso­phytization, especially within the area where strict protection has been maintained since 1961. Amplitudes of the principal ecological factors and also peculiarities of their shift under exogenic regulation are determined with the help of the method of synecological phyto­indication (i. e. not single species but total species sets of communities serve as indicators). The essential transformations of the reserve meadow steppes are probably caused by the «insular» character of the reserve, its small size, also by the poorness of the set of natural grazers and hence the inadequacy of regulation by means of mowing.


2003 ◽  
pp. 50-61 ◽  
Author(s):  
V. A. Smagin ◽  
M. G. Napreenko

The paper characterizes the 3 associations comprising plant communities with Sphagnum rubellum in the south-eastern part of the Baltic region. The new syntaxa differ from each other both in their floristic characters and the pronounced affinity to definite regional mire types and particular habitats. The ass. Drosero-Sphagnetum rubelli is typical of the relatively most thorough ranges. It is observed from the Kaliningrad region to the Karelian Isthmus and, according to the published reference, occurs even throughout the whole area around the Baltic Sea. Its most typical habitat is that of margins of mire lakes and pools. The ass. Eriophoro-Sphagnetum rubelli occurs in central plateaus of convex plateau-like bogs, typical of the areas adjacent to the Baltic Sea coast. It occupies extended flat mire ecotopes with the water level 0.2–0.25 m deep. The ass. Empetro-Sphagnetum rubelli is characteristic of the retrogressive complex in the convex bogs of the East-Baltic Province. It is mostly observed along the coast of the Gulf of Finland. Its stands are rather dynamic and unstable in both space and time. The presence of communities comprised by these 3 associations is an important vegetation character of the series of regional mire types. Assuming an association level of the respective syntaxa seems rational for the purposes of adequate reflection of plant cover diversity.


2020 ◽  
pp. 75-99
Author(s):  
O. I. Sumina

One of the thermokarst relief forms is baidzharakh massif — the group of mounds separated by trenches formed as a result of the underground ice-wedge polygonal networks melting (Fig. 1). Study of baidzharakh vegetation took place on the northeast coast of the Taimyr Peninsula (the Pronchishcheva Bay area) and on the New Siberian Islands (the Kotelny Island) in 1973–1974 (Sumina, 1975, 1976, 1977a, b, 1979 et al.). The aim of this paper is to produce the classification of baidzharakh mound and trenches communities according to the Brown-Blanquet approach (Westhoff, Maarel, 1978) and to compare these data with the community types earlier established on domination principle (Sumina, 1975 et al.). The information obtained in the 1970s could be helpful in a comparative assessment of the thermokarst process dynamics over the past 4 decades, as well as for comparing these processes in other regions of the Arctic. Both studied areas are located in the northern part of the arctic tundra subzone. On the Taimyr Peninsula (and in particular in the Pronchishcheva Bay area) the plakor (zonal) communities belong to the ass. Salici polaris–Hylocomietum alaskani Matveyeva 1998. Our relevés of plakor tundra on the Kotelny Island demonstrate similarity with the zonal communities of the northeast coast of the Taimyr Peninsula (Table 2). Relevés of communities of thermokarst mounds were made within their boundaries, the size of ~ 30 m². In trenches sample plots of the same area had rectangular shape according to trench width. Relevés of plakor tundra were made on 5x6 m plots. There were marked: location in relief, moistening, stand physiognomy, nanorelief, the percent of open ground patches and degree of their overgrowing, total plant cover, that of vascular plants, mosses, and lichens (especially — crustose ons), and cover estimates for each species. The shape of thermokarst mounds depends on the stage of thermodenudation processes. Flat polygons about 0.5 m height with vegetation similar to the plakor tundra are formed at the beginning of ice melting (Fig. 3, a), after which the deformation of the mounds (from eroded flat polygon (Fig. 3, b) to eroded conical mound (Fig. 3, c). Such mounds of maximal height up to 5 m are located on the middle part of steep slopes, where thermodenudation is very active. The last stage of mound destruction is slightly convex mound with a lumpy surface and vegetation, typical to snowbed sites at slope foots (Fig. 3, d, and 5). Both on watersheds and on gentle slopes mounds are not completely destroyed; and on such elongated smooth-conical mounds dense meadow-like vegetation is developed (Fig. 6). On the Kotelny Island thermokarst mounds of all described shapes occur, while in the Pronchishcheva Bay area only flat polygons, eroded flat polygons, and elongated smooth-conical mounds are presented. Under the influence of thermodenudation the plakor (zonal) vegetation is being transformed that allows to consider the most of mound and trench communities as the variants of zonal association. On the base of 63 relevés, made in 14 baidzharakh massifs, 2 variants with 7 subvariants of the ass. Salici polaris–Hylocomietum alaskani Matveyeva 1998 were established, as well as 1 variant of the azonal ass. Poo arcticae– Dupontietum fisheri Matveyeva 1994, which combines the vegetation of wet trenches with dense herbmoss cover. A detailed description of each subvariant is done. All these syntaxa are compared with the types of mound and trenh communities established previously by the domination principle (Sumina, 1975, 1976, 1979 et al.) and with Brown-Blanquet’ syntaxa published by other authors. The Brown-Blanquet approach in compare with domination principle, clearly demonstrates the similarity between zonal and baidzharakh massifs vegetation. Diagnostic species of syntaxa of baidzharakh vegetation by other authors (Matveyeva, 1994; Zanokha, 1995; Kholod, 2007, 2014; Telyatnikov et al., 2017) differ from ours. On the one hand, this is due to the fact that all mentioned researchers worked in another areas, and on the other, with different hierarchial levels of syntaxa, which are subassociations (or vicariants) in cited works or variants and subvariants in the our. Communities of mounds as well as of trenches in different regions have unlike species composition, but similar apearance, which depends on the similarity of the life form composition and community pattern, stage of their transformation and environmental factors. This fact is a base to group communities by physiognomy in order to have an opportunity of comparative analysis of baidzharakh vegetation diversity in different regions of the Arctic. In total, 6 such groups for thermokarst mounds and trenches are proposed: “tundra-like” ― vegetation of flat polygonal mounds (or trenches) is similar to the plakor (zonal) communities; “eroded tundra-like” ― tundra-like vegetation is presented as fragments, open ground occupies the main part of flat polygonal mounds; “eroded mounds with nonassociated vegetation” ― eroded mounds of various shapes up to sharp conical with absent vegetation at the top and slopes, sparse pioneer vascular plants on a bare substrate and crustose lichens and chionophilous grasses at foots; “meadow-like” ― herb stands with a participation of tundra dwarf-shrubs, mosses, and lichens on elongated smooth-conical mounds and in moderately moist trenches; “communities in snowbeds” ― thin plant cover formed by small mosses, liverworts, crustose lichens, and sparse vascular plants in snowbed habitats on destroyed slightly convex mounds with a lumpy surface and in trenches; “communities of cotton grass” or others, depending on the dominant species ― in wet trenches where vegetation is similar to the arctic hypnum bogs with dominant hygrophyte graminoids as Eriophorum scheuchzeri, E. polystachion, Dupontia fischeri et al. This sheme according to physiognomic features of thermokarst mound and trench communities, as a simplier way to assess the current dynamic stage of the baidzharakh massifs, may be useful for monitoring the thermodenudation activity in different areas of the Arctic, particularly in connection with observed climate changes (ACIA, 2004) and a possible dramatic “cascade of their environmental consequences” (Fraser et al., 2018).


2019 ◽  
pp. 91-94
Author(s):  
T. M. Lysenko ◽  
V. Yu. Neshatayeva ◽  
Z. V. Dutova

The International conference “Flora and conservation in the Caucasus: history and current state of knowledge” dedicated to the 130-year anniversary of the Perkalsky Arboretum took place at 22–25 of May 2019 in Pyatigorsk (Stavropol Territory) on the base of the Pyatigorsk Museum of local lore and natural history. The participants were from 11 cities of Russia and 7 Republics of the Caucasus and represented 14 institutions. Proceedings of the conference were published by the beginning of the meeting the book of abstracts includes 49 papers on the study of vascular plants, bryophytes, lichens and fungi, plant communities, as well as the protection of rare and endangered species, unique plant communities, and ecological problems in the Caucasus. The following geobotanical topics were highlighted in 13 papers: forest communities (3 reports), meadow and steppe vegetation (2), xeric open forests (2), communities of ecotone areas (1), structure of populations of rare plant species (3), as well as the history and current status of nature protected areas (2). The great emphasis has been focused on the study of floristic composition and plant populations. Thus, the conference showed that very few studies от vegetation are currently carried out in the Caucasus, and a lot of districts are not affected by the research. The greatest attention is paid to forest vegetation while meadow, steppe, alpine heath and xerophytic communities are studied rather poorly. Besides, there are “white spots” — mire, floodplain and aquatic vegetation. In nowadays, when the anthropogenic impact on the plant cover of the Caucasus is intensively increasing, it is especially important to study natural undisturbed communities preserved in protected natural areas. Another important issue is the conservation of the unique vegetation cover of the whole Caucasus. Thus, the study of vegetation of this region opens a wide field for researchers using various methods of modern plant science.


2018 ◽  
pp. 107-130 ◽  
Author(s):  
T. V. Chernenkova ◽  
O. V. Morozova ◽  
N. G. Belyaeva ◽  
M. Yu. Puzachenko

This study aimed at an investigation of the structure, ecology and mapping of mixed communities with the participation of spruce, pine and broad-leave trees in one of the regions of broad-leave–coniferous zone. Despite the long history of the nature use of the study area, including forestry practices (Kurnayev, 1968; Rysin, Saveliyeva, 2007; Arkhipova, 2014; Belyaeva, Popov, 2016), the communities kept the main features of the indigenous forests of the broad-leave–coniferous zone ­— the tree species polydominance of the stands, the multilayer structure of communities and the high species diversity. In the course of field works in the southwestern part of the Moscow Region (2000–2016) 120 relevés were made. Spatial structure, species composition as well as cover values (%) of all vascular plants and bryophytes were recorded in each stand. The relevés were analysed following the ecology-phytocenotic classification approach and methods of multivariate statistical analysis that allowed correctly to differentiate communities according the broad-leave species participation. The accuracy of the classification based on the results of discriminant analysis was 95.8 %. Evaluation of the similarity of the selected units was carried out with the help of cluster analysis (Fig. 12). Clustering into groups is performed according to the activity index of species (A) (Malyshev, 1973) within the allocated syntaxon using Euclidean distance and Ward’s method. The classification results are corrected by DCA ordination in PC-ORD 5.0 (McCune, Mefford, 2006) (Fig. 1). Spatial mapping of forest cover was carried out on the basis of ground data, Landsat satellite images (Landsat 5 TM, 7 ETM +, 8 OLI_TIRS), digital elevation (DEM) and statistical methods (Puzachenko et al., 2014; Chernenkova et al., 2015) (Fig. 13 а, б). The obtained data and the developed classification refine the existing understanding of the phytocenotic structure of the forest cover of the broad-leave–coniferous zone. Three forest formation groups with different shares of broad-leave species in the canopy with seven groups of associations were described: a) coniferous forests with broad-leave species (small- and broad-herb spruce forests with oak and lime (1)); broad-herb spruce forests with oak and lime (2); small- and broad-herb pine forests with spruce, lime, oak and hazel (3); broad-herb pine forests with lime, oak and hazel (4)), b) broad-leave–coniferous forests (broad-herb spruce–broad-leave forests (5)), and c) broad-leave forests (broad-herb oak forests (6), broad-herb lime forests (7)). In the row of discussed syntaxa from 1 to 7 group, the change in the ratio of coniferous and broad-leave species of the tree layer (A) reflects re­gular decrease in the participation of spruce in the plant cover (from 66 to 6 %; Fig. 3 A1, A2) and an increase in oak and lime more than threefold (from 15 to 65 %; Fig. 4 a). Nemoral species predominate in the composition of ground layers, the cove­rage of which increases (from 40 to 80 %) in the range from 1 to 7 group, the coverage of the boreal group varies from 55 to 8 % (Fig. 11) while maintaining the presence of these species, even in nemoral lime and oak forests. In forests with equal share of broad-leave and coniferous trees (group 5) the nemoral species predominate in herb layer. In oak forests (group 6) the species of the nitro group are maximally represented, which is natural for oak forests occurring on rich soils, and also having abundant undergrowth of hazel. Practically in all studied groups the presence of both coniferous (in particular, spruce) and broad-leave trees in undergrowth (B) and ground layer (C) were present in equal proportions (Fig. 3). This does not confirm the unambiguity of the enrichment with nemoral species and increase in their cover in complex spruce and pine forests in connection with the climate warming in this region, but rather indicates on natural change of the main tree species in the cenopopulations. Further development of the stand and the formation of coni­ferous or broad-leave communities is conditioned by landscape. It is proved that the distribution of different types of communities is statistically significant due to the relief. According to the results of the analysis of remote information, the distribution areas of coniferous forests with broad-leave species, mixed and broad-leave forest areas for the study region are represented equally. The largest massifs of broad-leave–coniferous forests are located in the central and western parts of the study area, while in the eastern one the broad-leave forests predominate, that is a confirmation of the zonal ecotone (along the Pakhra River: Petrov, Kuzenkova, 1968) from broad-leave–coniferous forests to broad-leave forests.


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