Publications by authors named "Martin Kopecký"

41 Publications

Response to Comment on "Forest microclimate dynamics drive plant responses to warming".

Science 2020 12;370(6522)

Museum of Natural History, University of Wrocław, PL-50-335 Wroclaw, Poland.

Schall and Heinrichs question our interpretation that the climatic debt in understory plant communities is locally modulated by canopy buffering. However, our results clearly show that the discrepancy between microclimate warming rates and thermophilization rates is highest in forests where canopy cover was reduced, which suggests that the need for communities to respond to warming is highest in those forests.
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http://dx.doi.org/10.1126/science.abf2939DOI Listing
December 2020

Response to Comment on "Forest microclimate dynamics drive plant responses to warming".

Science 2020 11;370(6520)

Museum of Natural History, University of Wrocław, PL-50-335 Wroclaw, Poland.

Bertrand question our interpretation about warming effects on the thermophilization in forest plant communities and propose an alternative way to analyze climatic debt. We show that microclimate warming is a better predictor than macroclimate warming for studying forest plant community responses to warming. Their additional analyses do not affect or change our interpretations and conclusions.
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http://dx.doi.org/10.1126/science.abd6193DOI Listing
November 2020

Topographic Wetness Index calculation guidelines based on measured soil moisture and plant species composition.

Sci Total Environ 2021 Feb 14;757:143785. Epub 2020 Nov 14.

Institute of Botany of the Czech Academy of Sciences, Zámek 1, CZ-252 43 Průhonice, Czech Republic; Faculty of Environmental Sciences, Czech University of Life Sciences Prague, Kamýcká 129, CZ-165 21, Prague 6, Suchdol, Czech Republic.

Soil moisture controls environmental processes and species distributions, but it is difficult to measure and interpolate across space. Topographic Wetness Index (TWI) derived from digital elevation model is therefore often used as a proxy for soil moisture. However, different algorithms can be used to calculate TWI and this potentially affects TWI relationship with soil moisture and species assemblages. To disentangle insufficiently-known effects of different algorithms on TWI relation with soil moisture and plant species composition, we measured the root-zone soil moisture throughout a growing season and recorded vascular plants and bryophytes in 45 temperate forest plots. For each plot, we calculated 26 TWI variants from a LiDAR-based digital terrain model and related these TWI variants to the measured soil moisture and moisture-controlled species assemblages of vascular plants and bryophytes. A flow accumulation algorithm determined the ability of the TWI to predict soil moisture, while the flow width and slope algorithms had only a small effects. The TWI calculated with the most often used single-flow D8 algorithm explained less than half of the variation in soil moisture and species composition explained by the TWI calculated with the multiple-flow FD8 algorithm. Flow dispersion used in the FD8 algorithm strongly affected the TWI performance, and a flow dispersion close to 1.0 resulted in the TWI best related to the soil moisture and species assemblages. Using downslope gradient instead of the local slope gradient can strongly decrease TWI performance. Our results clearly showed that the method used to calculate TWI affects study conclusion. However, TWI calculation is often not specified and thus impossible to reproduce and compare among studies. We therefore provide guidelines for TWI calculation and recommend the FD8 flow algorithm with a flow dispersion close to 1.0, flow width equal to the raster cell size and local slope gradient for TWI calculation.
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http://dx.doi.org/10.1016/j.scitotenv.2020.143785DOI Listing
February 2021

Forest microclimate dynamics drive plant responses to warming.

Science 2020 05;368(6492):772-775

Museum of Natural History, University of Wrocław, PL-50-335 Wrocław. Poland.

Climate warming is causing a shift in biological communities in favor of warm-affinity species (i.e., thermophilization). Species responses often lag behind climate warming, but the reasons for such lags remain largely unknown. Here, we analyzed multidecadal understory microclimate dynamics in European forests and show that thermophilization and the climatic lag in forest plant communities are primarily controlled by microclimate. Increasing tree canopy cover reduces warming rates inside forests, but loss of canopy cover leads to increased local heat that exacerbates the disequilibrium between community responses and climate change. Reciprocal effects between plants and microclimates are key to understanding the response of forest biodiversity and functioning to climate and land-use changes.
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http://dx.doi.org/10.1126/science.aba6880DOI Listing
May 2020

SoilTemp: A global database of near-surface temperature.

Glob Chang Biol 2020 Nov 24;26(11):6616-6629. Epub 2020 Jun 24.

A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia.

Current analyses and predictions of spatially explicit patterns and processes in ecology most often rely on climate data interpolated from standardized weather stations. This interpolated climate data represents long-term average thermal conditions at coarse spatial resolutions only. Hence, many climate-forcing factors that operate at fine spatiotemporal resolutions are overlooked. This is particularly important in relation to effects of observation height (e.g. vegetation, snow and soil characteristics) and in habitats varying in their exposure to radiation, moisture and wind (e.g. topography, radiative forcing or cold-air pooling). Since organisms living close to the ground relate more strongly to these microclimatic conditions than to free-air temperatures, microclimatic ground and near-surface data are needed to provide realistic forecasts of the fate of such organisms under anthropogenic climate change, as well as of the functioning of the ecosystems they live in. To fill this critical gap, we highlight a call for temperature time series submissions to SoilTemp, a geospatial database initiative compiling soil and near-surface temperature data from all over the world. Currently, this database contains time series from 7,538 temperature sensors from 51 countries across all key biomes. The database will pave the way toward an improved global understanding of microclimate and bridge the gap between the available climate data and the climate at fine spatiotemporal resolutions relevant to most organisms and ecosystem processes.
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http://dx.doi.org/10.1111/gcb.15123DOI Listing
November 2020

Replacements of small- by large-ranged species scale up to diversity loss in Europe's temperate forest biome.

Nat Ecol Evol 2020 06 13;4(6):802-808. Epub 2020 Apr 13.

Department of Botany, Faculty of Biological Sciences, University of Wrocław, Wrocław, Poland.

Biodiversity time series reveal global losses and accelerated redistributions of species, but no net loss in local species richness. To better understand how these patterns are linked, we quantify how individual species trajectories scale up to diversity changes using data from 68 vegetation resurvey studies of seminatural forests in Europe. Herb-layer species with small geographic ranges are being replaced by more widely distributed species, and our results suggest that this is due less to species abundances than to species nitrogen niches. Nitrogen deposition accelerates the extinctions of small-ranged, nitrogen-efficient plants and colonization by broadly distributed, nitrogen-demanding plants (including non-natives). Despite no net change in species richness at the spatial scale of a study site, the losses of small-ranged species reduce biome-scale (gamma) diversity. These results provide one mechanism to explain the directional replacement of small-ranged species within sites and thus explain patterns of biodiversity change across spatial scales.
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http://dx.doi.org/10.1038/s41559-020-1176-8DOI Listing
June 2020

Seasonal drivers of understorey temperature buffering in temperate deciduous forests across Europe.

Glob Ecol Biogeogr 2019 Dec 22;28(12):1774-1786. Epub 2019 Aug 22.

Forest & Nature Lab, Department of Environment Ghent University Melle-Gontrode Belgium.

Aim: Forest understorey microclimates are often buffered against extreme heat or cold, with important implications for the organisms living in these environments. We quantified seasonal effects of understorey microclimate predictors describing canopy structure, canopy composition and topography (i.e., local factors) and the forest patch size and distance to the coast (i.e., landscape factors).

Location: Temperate forests in Europe.

Time Period: 2017-2018.

Major Taxa Studied: Woody plants.

Methods: We combined data from a microclimate sensor network with weather-station records to calculate the difference, or offset, between temperatures measured inside and outside forests. We used regression analysis to study the effects of local and landscape factors on the seasonal offset of minimum, mean and maximum temperatures.

Results: The maximum temperature during the summer was on average cooler by 2.1 °C inside than outside forests, and the minimum temperatures during the winter and spring were 0.4 and 0.9 °C warmer. The local canopy cover was a strong nonlinear driver of the maximum temperature offset during summer, and we found increased cooling beneath tree species that cast the deepest shade. Seasonal offsets of minimum temperature were mainly regulated by landscape and topographic features, such as the distance to the coast and topographic position.

Main Conclusions: Forest organisms experience less severe temperature extremes than suggested by currently available macroclimate data; therefore, climate-species relationships and the responses of species to anthropogenic global warming cannot be modelled accurately in forests using macroclimate data alone. Changes in canopy cover and composition will strongly modulate the warming of maximum temperatures in forest understories, with important implications for understanding the responses of forest biodiversity and functioning to the combined threats of land-use change and climate change. Our predictive models are generally applicable across lowland temperate deciduous forests, providing ecologically important microclimate data for forest understories.
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http://dx.doi.org/10.1111/geb.12991DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6900070PMC
December 2019

A meta-analysis of global fungal distribution reveals climate-driven patterns.

Nat Commun 2019 11 13;10(1):5142. Epub 2019 Nov 13.

Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic.

The evolutionary and environmental factors that shape fungal biogeography are incompletely understood. Here, we assemble a large dataset consisting of previously generated mycobiome data linked to specific geographical locations across the world. We use this dataset to describe the distribution of fungal taxa and to look for correlations with different environmental factors such as climate, soil and vegetation variables. Our meta-study identifies climate as an important driver of different aspects of fungal biogeography, including the global distribution of common fungi as well as the composition and diversity of fungal communities. In our analysis, fungal diversity is concentrated at high latitudes, in contrast with the opposite pattern previously shown for plants and other organisms. Mycorrhizal fungi appear to have narrower climatic tolerances than pathogenic fungi. We speculate that climate change could affect ecosystem functioning because of the narrow climatic tolerances of key fungal taxa.
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http://dx.doi.org/10.1038/s41467-019-13164-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6853883PMC
November 2019

Functionally distinct assembly of vascular plants colonizing alpine cushions suggests their vulnerability to climate change.

Ann Bot 2019 03;123(4):569-578

Institute of Botany, The Czech Academy of Sciences, Průhonice, Czech Republic.

Background And Aims: Alpine cushion plants can initially facilitate other species during ecological succession, but later on can be negatively affected by their development, especially when beneficiaries possess traits allowing them to overrun their host. This can be reinforced by accelerated warming favouring competitively strong species over cold-adapted cushion specialists. However, little empirical research has addressed the trait-based mechanisms of these interactions. The ecological strategies of plants colonizing the cushion plant Thylacospermum caespitosum (Caryophyllaceae), a dominant pioneer of subnival zones, were studied in the Western Himalayas.

Methods: To assess whether the cushion colonizers are phylogenetically and functionally distinct, 1668 vegetation samples were collected, both in open ground outside the cushions and inside their live and dead canopies, in two mountain ranges, Karakoram and Little Tibet. More than 50 plant traits related to growth, biomass allocation and resource acquisition were measured for target species, and the phylogenetic relationships of these species were studied [or determined].

Key Results: Species-based trait-environment analysis with phylogenetic correction showed that in both mountain ranges Thylacospermum colonizers are phylogenetically diverse but functionally similar and are functionally different from species preferring bare soil outside cushions. Successful colonizers are fast-growing, clonal graminoids and forbs, penetrating the cushion by rhizomes and stolons. They have higher root-to-shoot ratios, leaf nitrogen and phosphorus concentrations, and soil moisture and nutrient demands, sharing the syndrome of competitive species with broad elevation ranges typical of the late stages of primary succession. In contrast, the species from open ground have traits typical of stress-tolerant specialists from high and dry environments.

Conclusion: Species colonizing tight cushions of T. caespitosum are competitively strong graminoids and herbaceous perennials from alpine grasslands. Since climate change in the Himalayas favours these species, highly specialized subnival cushion plants may face intense competition and a greater risk of decline in the future.
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http://dx.doi.org/10.1093/aob/mcy207DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6417476PMC
March 2019

Environmental drivers interactively affect individual tree growth across temperate European forests.

Glob Chang Biol 2019 01 22;25(1):201-217. Epub 2018 Nov 22.

Forest & Nature Lab, Department of Environment, Ghent University, Melle-Gontrode, Belgium.

Forecasting the growth of tree species to future environmental changes requires a better understanding of its determinants. Tree growth is known to respond to global-change drivers such as climate change or atmospheric deposition, as well as to local land-use drivers such as forest management. Yet, large geographical scale studies examining interactive growth responses to multiple global-change drivers are relatively scarce and rarely consider management effects. Here, we assessed the interactive effects of three global-change drivers (temperature, precipitation and nitrogen deposition) on individual tree growth of three study species (Quercus robur/petraea, Fagus sylvatica and Fraxinus excelsior). We sampled trees along spatial environmental gradients across Europe and accounted for the effects of management for Quercus. We collected increment cores from 267 trees distributed over 151 plots in 19 forest regions and characterized their neighbouring environment to take into account potentially confounding factors such as tree size, competition, soil conditions and elevation. We demonstrate that growth responds interactively to global-change drivers, with species-specific sensitivities to the combined factors. Simultaneously high levels of precipitation and deposition benefited Fraxinus, but negatively affected Quercus' growth, highlighting species-specific interactive tree growth responses to combined drivers. For Fagus, a stronger growth response to higher temperatures was found when precipitation was also higher, illustrating the potential negative effects of drought stress under warming for this species. Furthermore, we show that past forest management can modulate the effects of changing temperatures on Quercus' growth; individuals in plots with a coppicing history showed stronger growth responses to higher temperatures. Overall, our findings highlight how tree growth can be interactively determined by global-change drivers, and how these growth responses might be modulated by past forest management. By showing future growth changes for scenarios of environmental change, we stress the importance of considering multiple drivers, including past management and their interactions, when predicting tree growth.
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http://dx.doi.org/10.1111/gcb.14493DOI Listing
January 2019

Understanding context dependency in the response of forest understorey plant communities to nitrogen deposition.

Environ Pollut 2018 Nov 23;242(Pt B):1787-1799. Epub 2018 Jul 23.

Forest & Nature Lab, Department of Environment, Faculty of Bioscience Engineering, Ghent University, Geraardsbergsesteenweg 267, 9090, Melle-Gontrode, Belgium.

Understorey communities can dominate forest plant diversity and strongly affect forest ecosystem structure and function. Understoreys often respond sensitively but inconsistently to drivers of ecological change, including nitrogen (N) deposition. Nitrogen deposition effects, reflected in the concept of critical loads, vary greatly not only among species and guilds, but also among forest types. Here, we characterize such context dependency as driven by differences in the amounts and forms of deposited N, cumulative deposition, the filtering of N by overstoreys, and available plant species pools. Nitrogen effects on understorey trajectories can also vary due to differences in surrounding landscape conditions; ambient browsing pressure; soils and geology; other environmental factors controlling plant growth; and, historical and current disturbance/management regimes. The number of these factors and their potentially complex interactions complicate our efforts to make simple predictions about how N deposition affects forest understoreys. We review the literature to examine evidence for context dependency in N deposition effects on forest understoreys. We also use data from 1814 European temperate forest plots to test the ability of multi-level models to characterize context-dependent understorey responses across sites that differ in levels of N deposition, community composition, local conditions and management history. This analysis demonstrated that historical management, and plot location on light and pH-fertility gradients, significantly affect how understorey communities respond to N deposition. We conclude that species' and communities' responses to N deposition, and thus the determination of critical loads, vary greatly depending on environmental contexts. This complicates our efforts to predict how N deposition will affect forest understoreys and thus how best to conserve and restore understorey biodiversity. To reduce uncertainty and incorporate context dependency in critical load setting, we should assemble data on underlying environmental conditions, conduct globally distributed field experiments, and analyse a wider range of habitat types.
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http://dx.doi.org/10.1016/j.envpol.2018.07.089DOI Listing
November 2018

Global environmental change effects on plant community composition trajectories depend upon management legacies.

Glob Chang Biol 2018 04 18;24(4):1722-1740. Epub 2018 Jan 18.

Botany Department, School of Natural Sciences, Trinity College Dublin, Dublin 2, Ireland.

The contemporary state of functional traits and species richness in plant communities depends on legacy effects of past disturbances. Whether temporal responses of community properties to current environmental changes are altered by such legacies is, however, unknown. We expect global environmental changes to interact with land-use legacies given different community trajectories initiated by prior management, and subsequent responses to altered resources and conditions. We tested this expectation for species richness and functional traits using 1814 survey-resurvey plot pairs of understorey communities from 40 European temperate forest datasets, syntheses of management transitions since the year 1800, and a trait database. We also examined how plant community indicators of resources and conditions changed in response to management legacies and environmental change. Community trajectories were clearly influenced by interactions between management legacies from over 200 years ago and environmental change. Importantly, higher rates of nitrogen deposition led to increased species richness and plant height in forests managed less intensively in 1800 (i.e., high forests), and to decreases in forests with a more intensive historical management in 1800 (i.e., coppiced forests). There was evidence that these declines in community variables in formerly coppiced forests were ameliorated by increased rates of temperature change between surveys. Responses were generally apparent regardless of sites' contemporary management classifications, although sometimes the management transition itself, rather than historic or contemporary management types, better explained understorey responses. Main effects of environmental change were rare, although higher rates of precipitation change increased plant height, accompanied by increases in fertility indicator values. Analysis of indicator values suggested the importance of directly characterising resources and conditions to better understand legacy and environmental change effects. Accounting for legacies of past disturbance can reconcile contradictory literature results and appears crucial to anticipating future responses to global environmental change.
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http://dx.doi.org/10.1111/gcb.14030DOI Listing
April 2018

The paradox of long-term ungulate impact: increase of plant species richness in a temperate forest.

Appl Veg Sci 2017 Apr 8;20(2):282-292. Epub 2017 Feb 8.

The Forest Management Institute, Vrázova 1, 616 00 Brno, Czech Republic.

Questions: Did high densities of wild ungulates cause a decline in plant species richness in a temperate oakwood? How did species composition change after nearly five decades? Did ungulates facilitate the spread of ruderal species and supress endangered species? Did dispersal strategies play a role in these processes?

Location: Krumlov Wood, SE Czech Republic.

Methods: In 2012, we resampled 58 quasi-permanent vegetation plots first surveyed in 1960s. Between the surveys, 36 plots were enclosed in a game preserve with artificially high density of ungulates (mostly deer, mouflon and wild boar; ca. 55 animals per square km). We analysed the differences in temporal changes between plots inside and outside the game preserve, focusing on species diversity and composition. We assessed species characteristics relevant to grazing to understand compositional changes.

Results: Ungulates significantly increased alpha and gamma diversity and caused significant vegetation homogenization inside the game preserve. Vegetation homogenization and the increase in species richness resulted from massive enrichment by ruderal species. However, richness of endangered species decreased. Species dispersed by animals internally (endozoochory) increased, while species dispersed externally (epizoochory) or by wind (anemochory) decreased.

Conclusions: Contrary to our expectations, our long-term data showed that artificially high ungulate densities substantially increased plant species richness. Apparently, the establishment of ruderal herbs was supported by frequent disturbances and ungulate-mediated dispersal. At the same time, species richness of non-ruderal plants did not change, probably because ungulates hindered the regeneration of woody species and maintained an open forest canopy. In conclusion, high ungulate density led to the spread of ruderal species, which in turn strongly contributed to the observed shift towards nutrient-richer conditions and taxonomically more homogenous communities.
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http://dx.doi.org/10.1111/avsc.12289DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5726491PMC
April 2017

Fungal root symbionts of high-altitude vascular plants in the Himalayas.

Sci Rep 2017 07 26;7(1):6562. Epub 2017 Jul 26.

Faculty of Science, University of South Bohemia, Branišovská 1760, 370 05, České Budějovice, Czech Republic.

Arbuscular mycorrhizal fungi (AMF) and dark septate endophytes (DSE) form symbiotic relationships with plants influencing their productivity, diversity and ecosystem functions. Only a few studies on these fungi, however, have been conducted in extreme elevations and none over 5500 m a.s.l., although vascular plants occur up to 6150 m a.s.l. in the Himalayas. We quantified AMF and DSE in roots of 62 plant species from contrasting habitats along an elevational gradient (3400-6150 m) in the Himalayas using a combination of optical microscopy and next generation sequencing. We linked AMF and DSE communities with host plant evolutionary history, ecological preferences (elevation and habitat type) and functional traits. We detected AMF in elevations up to 5800 m, indicating it is more constrained by extreme conditions than the host plants, which ascend up to 6150 m. In contrast, DSE were found across the entire gradient up to 6150 m. AMF diversity was unimodally related to elevation and positively related to the intensity of AMF colonization. Mid-elevation steppe and alpine plants hosted more diverse AMF communities than plants from deserts and the subnival zone. Our results bring novel insights to the abiotic and biotic filters structuring AMF and DSE communities in the Himalayas.
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http://dx.doi.org/10.1038/s41598-017-06938-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5529584PMC
July 2017

Life and death of Picea abies after bark-beetle outbreak: ecological processes driving seedling recruitment.

Ecol Appl 2017 01;27(1):156-167

Geobotany, Department of Ecology and Ecosystem Management, Center of Life and Food Sciences, Technische Universität München TUM, Hans-Carl-von-Carlowitz-Platz 2, D-85354, Freising, Germany.

The severity and spatial extent of bark-beetle outbreaks substantially increased in recent decades worldwide. The ongoing controversy about natural forest recovery after these outbreaks highlights the need for individual-based long-term studies, which disentangle processes driving forest regeneration. However, such studies have been lacking. To fill this gap, we followed the fates of 2,552 individual seedlings for 12 years after a large-scale bark-beetle outbreak that caused complete canopy dieback in mountain Norway spruce (Picea abies) forests in southeast Germany. We explore the contribution of advance, disturbance-related, and post-disturbance regeneration to forest recovery. Most seedlings originated directly within the three-year dieback of canopy trees induced by bark-beetle outbreak. After complete canopy dieback, the establishment of new seedlings was minimal. Surprisingly, advance regeneration formed only a minor part of all regeneration. However, because it had the highest survival rate, its importance increased over time. The most important factor influencing the survival of seedlings after disturbance was their height. Survival was further modified by microsite: seedlings established on dead wood survived best, whereas almost all seedlings surrounded by graminoids died. For 5 cm tall seedlings, annual mortality ranged from 20 to 50% according to the rooting microsite. However, for seedlings taller than 50 cm, annual mortality was below 5% at all microsites. While microsite modified seedling mortality, it did not affect seedling height growth. A model of regeneration dynamics based on short-term observations accurately predicts regeneration height growth, but substantially underestimates mortality rate, thus predicting more surviving seedlings than were observed. We found that P. abies forests were able to regenerate naturally even after severe bark-beetle outbreaks owing to advance and particularly disturbance-related regeneration. This, together with microsite-specific mortality, yields structurally and spatially diverse forests. Our study thus highlights the so far unrecognized importance of disturbance-related regeneration for stand recovery after bark-beetle outbreaks.
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http://dx.doi.org/10.1002/eap.1429DOI Listing
January 2017

Combining community resurvey data to advance global change research.

Bioscience 2016 Dec;67(1):73-83

Department of Phytology, Faculty of Forestry, Technical University in Zvolen, T. G. Masaryka 24, 960 53 Zvolen, Slovakia,

More and more ecologists have started to resurvey communities sampled in earlier decades to determine long-term shifts in community composition and infer the likely drivers of the ecological changes observed. However, to assess the relative importance of, and interactions among, multiple drivers joint analyses of resurvey data from many regions spanning large environmental gradients are needed. In this paper we illustrate how combining resurvey data from multiple regions can increase the likelihood of driver-orthogonality within the design and show that repeatedly surveying across multiple regions provides higher representativeness and comprehensiveness, allowing us to answer more completely a broader range of questions. We provide general guidelines to aid implementation of multi-region resurvey databases. In so doing, we aim to encourage resurvey database development across other community types and biomes to advance global environmental change research.
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http://dx.doi.org/10.1093/biosci/biw150DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6136644PMC
December 2016

Resurveying historical vegetation data - opportunities and challenges.

Appl Veg Sci 2016 Oct;20(2):164-171

Department of Biology, University of Bergen, Thormøhlensgate 53A, 5020 Bergen, Norway.

Background: Resurveying historical vegetation plots has become more and more popular in recent years as it provides a unique opportunity to estimate vegetation and environmental changes over the past decades. Most historical plots, however, are not permanently marked and uncertainty in plot location, in addition to observer bias and seasonal bias, may add significant error to temporal change. These errors may have major implications for the reliability of studies on long-term environmental change and deserve closer attention of vegetation ecologists.

Material & Methods: Vegetation data obtained from the resurveying of non-permanently marked plots are assessed for their potential to study environmental-change effects on plant communities and the challenges the use of such data have to meet. We describe the properties of vegetation resurveys distinguishing basic types of plots according to relocation error, and we highlight the potential of such data types for studying vegetation dynamics and their drivers. Finally, we summarise the challenges and limitations of resurveying non-permanently marked vegetation plots for different purposes in environmental change research.

Results And Conclusions: Resampling error is caused by three main independent sources of error: error caused by plot relocation, observer bias, and seasonality bias. For relocation error, vegetation plots can be divided into permanent and non-permanent plots, while the latter are further divided into quasi-permanent (with approximate relocation) and non-traceable (with random relocation within a sampled area) plots. To reduce the inherent sources of error in resurvey data, the following precautions should be followed: (i) resurvey historical vegetation plots whose approximate plot location within a study area is known; (ii) consider all information available from historical studies in order to keep plot relocation errors low; (iii) resurvey at times of the year when vegetation development is comparable to the historical survey to control for seasonal variability in vegetation; (iv) keep a high level of experience of the observers to keep observer bias low; and (v) edit and standardise datasets before analyses.
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http://dx.doi.org/10.1111/avsc.12269DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6145442PMC
October 2016

Measuring size and composition of species pools: a comparison of dark diversity estimates.

Ecol Evol 2016 06 20;6(12):4088-101. Epub 2016 May 20.

Institute of Ecology and Earth Sciences University of Tartu Lai 40 51005 Tartu Estonia.

Ecological theory and biodiversity conservation have traditionally relied on the number of species recorded at a site, but it is agreed that site richness represents only a portion of the species that can inhabit particular ecological conditions, that is, the habitat-specific species pool. Knowledge of the species pool at different sites enables meaningful comparisons of biodiversity and provides insights into processes of biodiversity formation. Empirical studies, however, are limited due to conceptual and methodological difficulties in determining both the size and composition of the absent part of species pools, the so-called dark diversity. We used >50,000 vegetation plots from 18 types of habitats throughout the Czech Republic, most of which served as a training dataset and 1083 as a subset of test sites. These data were used to compare predicted results from three quantitative methods with those of previously published expert estimates based on species habitat preferences: (1) species co-occurrence based on Beals' smoothing approach; (2) species ecological requirements, with envelopes around community mean Ellenberg values; and (3) species distribution models, using species environmental niches modeled by Biomod software. Dark diversity estimates were compared at both plot and habitat levels, and each method was applied in different configurations. While there were some differences in the results obtained by different methods, particularly at the plot level, there was a clear convergence, especially at the habitat level. The better convergence at the habitat level reflects less variation in local environmental conditions, whereas variation at the plot level is an effect of each particular method. The co-occurrence agreed closest the expert estimate, followed by the method based on species ecological requirements. We conclude that several analytical methods can estimate species pools of given habitats. However, the strengths and weaknesses of different methods need attention, especially when dark diversity is estimated at the plot level.
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http://dx.doi.org/10.1002/ece3.2169DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4877358PMC
June 2016

The Root-Associated Microbial Community of the World's Highest Growing Vascular Plants.

Microb Ecol 2016 08 31;72(2):394-406. Epub 2016 May 31.

Institute of Botany, The Czech Academy of Sciences, Zámek 1, 25243, Průhonice, Czech Republic.

Upward migration of plants to barren subnival areas is occurring worldwide due to raising ambient temperatures and glacial recession. In summer 2012, the presence of six vascular plants, growing in a single patch, was recorded at an unprecedented elevation of 6150 m.a.s.l. close to the summit of Mount Shukule II in the Western Himalayas (Ladakh, India). Whilst showing multiple signs of stress, all plants have managed to establish stable growth and persist for several years. To learn about the role of microbes in the process of plant upward migration, we analysed the root-associated microbial community of the plants (three individuals from each) using microscopy and tagged amplicon sequencing. No mycorrhizae were found on the roots, implying they are of little importance to the establishment and early growth of the plants. However, all roots were associated with a complex bacterial community, with richness and diversity estimates similar or even higher than the surrounding bare soil. Both soil and root-associated communities were dominated by members of the orders Sphingomonadales and Sphingobacteriales, which are typical for hot desert soils, but were different from communities of temperate subnival soils and typical rhizosphere communities. Despite taxonomic similarity on the order level, the plants harboured a unique set of highly dominant operational taxonomic units which were not found in the bare soil. These bacteria have been likely transported with the dispersing seeds and became part of the root-associated community following germination. The results indicate that developing soils act not only as a source of inoculation to plant roots but also possibly as a sink for plant-associated bacteria.
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http://dx.doi.org/10.1007/s00248-016-0779-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4937074PMC
August 2016

Vegetation dynamics at the upper elevational limit of vascular plants in Himalaya.

Sci Rep 2016 05 4;6:24881. Epub 2016 May 4.

Swiss Federal Research Institute WSL, Birmensdorf, Switzerland.

A rapid warming in Himalayas is predicted to increase plant upper distributional limits, vegetation cover and abundance of species adapted to warmer climate. We explored these predictions in NW Himalayas, by revisiting uppermost plant populations after ten years (2003-2013), detailed monitoring of vegetation changes in permanent plots (2009-2012), and age analysis of plants growing from 5500 to 6150 m. Plant traits and microclimate variables were recorded to explain observed vegetation changes. The elevation limits of several species shifted up to 6150 m, about 150 vertical meters above the limit of continuous plant distribution. The plant age analysis corroborated the hypothesis of warming-driven uphill migration. However, the impact of warming interacts with increasing precipitation and physical disturbance. The extreme summer snowfall event in 2010 is likely responsible for substantial decrease in plant cover in both alpine and subnival vegetation and compositional shift towards species preferring wetter habitats. Simultaneous increase in summer temperature and precipitation caused rapid snow melt and, coupled with frequent night frosts, generated multiple freeze-thaw cycles detrimental to subnival plants. Our results suggest that plant species responses to ongoing climate change will not be unidirectional upward range shifts but rather multi-dimensional, species-specific and spatially variable.
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http://dx.doi.org/10.1038/srep24881DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4855180PMC
May 2016

Gardening in the zone of death: an experimental assessment of the absolute elevation limit of vascular plants.

Sci Rep 2016 Apr 13;6:24440. Epub 2016 Apr 13.

Institute of Botany, The Czech Academy of Sciences, Třeboň, Czech Republic.

Vascular plants in the western Tibetan Plateau reach 6000 m--the highest elevation on Earth. Due to the significant warming of the region, plant ranges are expected to shift upwards. However, factors governing maximum elevational limits of plant are unclear. To experimentally assess these factors, we transplanted 12 species from 5750 m to 5900 m (upper edge of vegetation) and 6100 m (beyond range) and monitored their survival for six years. In the first three years (2009-2012), there were plants surviving beyond the regional upper limit of vegetation. This supports the hypothesis of dispersal and/or recruitment limitation. Substantial warming, recorded in-situ during this period, very likely facilitated the survival. The survival was ecologically a non-random process, species better adapted to repeated soil freezing and thawing survived significantly better. No species have survived at 6100 m since 2013, probably due to the extreme snowfall in 2013. In conclusion, apart from the minimum heat requirements, our results show that episodic climatic events are decisive determinants of upper elevational limits of vascular plants.
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http://dx.doi.org/10.1038/srep24440DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4829891PMC
April 2016

Life stage, not climate change, explains observed tree range shifts.

Glob Chang Biol 2016 May 29;22(5):1904-14. Epub 2016 Feb 29.

Faculty of Forestry, Technical University in Zvolen, T.G. Masaryka 24, SK-960 53, Zvolen, Slovak Republic.

Ongoing climate change is expected to shift tree species distribution and therefore affect forest biodiversity and ecosystem services. To assess and project tree distributional shifts, researchers may compare the distribution of juvenile and adult trees under the assumption that differences between tree life stages reflect distributional shifts triggered by climate change. However, the distribution of tree life stages could differ within the lifespan of trees, therefore, we hypothesize that currently observed distributional differences could represent shifts over ontogeny as opposed to climatically driven changes. Here, we test this hypothesis with data from 1435 plots resurveyed after more than three decades across the Western Carpathians. We compared seedling, sapling and adult distribution of 12 tree species along elevation, temperature and precipitation gradients. We analyzed (i) temporal shifts between the surveys and (ii) distributional differences between tree life stages within both surveys. Despite climate warming, tree species distribution of any life stage did not shift directionally upward along elevation between the surveys. Temporal elevational shifts were species specific and an order of magnitude lower than differences among tree life stages within the surveys. Our results show that the observed range shifts among tree life stages are more consistent with ontogenetic differences in the species' environmental requirements than with responses to recent climate change. The distribution of seedlings substantially differed from saplings and adults, while the distribution of saplings did not differ from adults, indicating a critical transition between seedling and sapling tree life stages. Future research has to take ontogenetic differences among life stages into account as we found that distributional differences recently observed worldwide may not reflect climate change but rather the different environmental requirements of tree life stages.
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http://dx.doi.org/10.1111/gcb.13210DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5424071PMC
May 2016

Drivers of temporal changes in temperate forest plant diversity vary across spatial scales.

Glob Chang Biol 2015 Oct 27;21(10):3726-37. Epub 2015 Jul 27.

Department Silviculture and Forest Ecology of the Temperate Zones, Burckhardt-Institute, Georg-August University Göttingen, Büsgenweg 1, D-37077, Göttingen, Germany.

Global biodiversity is affected by numerous environmental drivers. Yet, the extent to which global environmental changes contribute to changes in local diversity is poorly understood. We investigated biodiversity changes in a meta-analysis of 39 resurvey studies in European temperate forests (3988 vegetation records in total, 17-75 years between the two surveys) by assessing the importance of (i) coarse-resolution (i.e., among sites) vs. fine-resolution (i.e., within sites) environmental differences and (ii) changing environmental conditions between surveys. Our results clarify the mechanisms underlying the direction and magnitude of local-scale biodiversity changes. While not detecting any net local diversity loss, we observed considerable among-site variation, partly explained by temporal changes in light availability (a local driver) and density of large herbivores (a regional driver). Furthermore, strong evidence was found that presurvey levels of nitrogen deposition determined subsequent diversity changes. We conclude that models forecasting future biodiversity changes should consider coarse-resolution environmental changes, account for differences in baseline environmental conditions and for local changes in fine-resolution environmental conditions.
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http://dx.doi.org/10.1111/gcb.12993DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6136642PMC
October 2015

Vegetation resurvey is robust to plot location uncertainty.

Divers Distrib 2015 Mar;21(3):322-330

Department of Botany, Faculty of Science, Charles University, Benátská 2, CZ-128 01, Praha, Czech Republic.

Aim: Resurveys of historical vegetation plots are increasingly used for the assessment of decadal changes in plant species diversity and composition. However, historical plots are usually relocated only approximately. This potentially inflates temporal changes and undermines results.

Location: Temperate deciduous forests in Central Europe.

Methods: To explore if robust conclusions can be drawn from resurvey studies despite location uncertainty, we compared temporal changes in species richness, frequency, composition and compositional heterogeneity between exactly and approximately relocated plots. We hypothesized that compositional changes should be lower and changes in species richness should be less variable on exactly relocated plots, because pseudo-turnover inflates temporal changes on approximately relocated plots.

Results: Temporal changes in species richness were not more variable and temporal changes in species composition and compositional heterogeneity were not higher on approximately relocated plots. Moreover, the frequency of individual species changed similarly on both plot types.

Main Conclusions: The resurvey of historical vegetation plots is robust to uncertainty in original plot location and, when done properly, provides reliable evidence of decadal changes in plant communities. This provides important background for other resurvey studies and opens up the possibility for large-scale assessments of plant community change.
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http://dx.doi.org/10.1111/ddi.12299DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5424074PMC
March 2015

Experimental restoration of coppice-with-standards: Response of understorey vegetation from the conservation perspective.

For Ecol Manage 2013 Dec 13;310:234-241. Epub 2013 Sep 13.

Ministry of Environment of the Czech Republic, Vršovická 1442, Prague 10, 100 10, Czech Republic.

A substantial part of European lowland woodlands was managed as coppices or wood pastures for millennia. However, traditional management forms were almost completely abandoned in Central Europe by the middle of the 20th century. Combined with the effects of nitrogen deposition and herbivore pressure, shifts in management resulted in biodiversity loss affecting particularly light-demanding oligotrophic plant species. Experimental thinning was applied in a former oak coppice-with-standards in an attempt to restore vanishing understorey plant communities. Two levels of thinning intensity and zero management as control were used on 90 plots. Ten years after the treatment, significant changes in species composition and diversity were observed in heavily thinned plots, while moderate thinning had mostly insignificant effects. Light-demanding oligotrophic species significantly increased, indicating positive consequences of restoration. However, heavy thinning also brought about the expansion of native ruderal species. Alien species remained unchanged. We conclude that the restoration of coppice-with-standards can be an efficient tool to support vanishing light-demanding woodland species. Combined with biodiversity benefits, the increasing demand for biofuel may contribute to the renaissance of traditional management forms in forestry.
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http://dx.doi.org/10.1016/j.foreco.2013.07.056DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5777631PMC
December 2013

LONGWOOD - integrating woodland history and ecology in a geodatabase through an interdisciplinary approach.

Proc SPIE Int Soc Opt Eng 2013 Aug;8795

Institute of Botany, Academy of Sciences of the Czech Republic, 252 43 Průhonice, Czech Republic.

Forests in Europe have been shaped considerably by human activities during most of the Holocene. Changes in forest structure, distribution of tree species and forest biodiversity are partly driven by management history, and many current forest types result from former management. The interdisciplinary project "Long-term woodland dynamics in Central Europe: from estimations to a realistic model" (LONGWOOD) aims to reconstruct long-term dynamics of woodland cover, structure and management in the eastern Czech Republic (Moravia, ca. 27,000 km), compare the historical and present state of forests, and analyze general patterns of changes and stability of woodlands as well as the role of humans in these processes. In the LONGWOOD project, palaeoecological, archaeological, historical and ecological sources of information on woodland cover, species composition, and human activities (management, settlement density) over the past 7500 years are collected and integrated in the form of a geodatabase. Combining data of different origin, scale, degree of spatial precision and detail into a single geodatabase is a challenging task. The level of detail, information content, and spatio-temporal distribution of data varies between layers as well as individual records according to the nature of the data source and the data itself. The limited and incomplete sources of information until ca. 1100 AD provide a coarser view on forest history while the historical period (especially the past ca. 250 years) is covered by large amounts of precisely located ecological and historical data enabling detailed spatial and temporal analyses. Data on forest structure, history and management will be related to environmental factors (soil type, climate, elevation and other topographic variables derived from DEM) and social historical data (settlement distribution, population density, landuse). A spatio-temporal forest landscape model will be built to assess the forest changes and the main drivers of change.
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http://dx.doi.org/10.1117/12.2027650DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5726494PMC
August 2013

Community structure of soil phototrophs along environmental gradients in arid Himalaya.

Environ Microbiol 2013 Sep 6;15(9):2505-16. Epub 2013 May 6.

Institute of Botany, Academy of Sciences of the Czech Republic, Dukelská 135, 37982, Třeboň, Czech Republic.

The well-developed biological soil crusts cover up to 40% of the soil surface in the alpine and subnival zones of the Tibetan Plateau, accounting for a vast area of Asia. We investigated the diversity and biomass of the phototrophic part (Cyanobacteria) of the microbial community inhabiting biological soil crusts and uncrusted soils in their surroundings on the elevation gradient of 5200-5900 m a.s.l. The influence of soil physico-chemical properties on phototrophs was studied. The ability of high-altitude phototrophs to fix molecular nitrogen was also determined under laboratory conditions. The biological soil crust phototroph community did not differ from that living in uncrusted soil in terms of the species composition, but the biomass is three-to-five times higher. An increasing trend in the cyanobacterial biomass from the biological soil crusts with elevation was observed, with the genera Nostoc spp., Microcoleus vaginatus and Phormidium spp. contributing to this increase. Based on the laboratory experiments, the highest nitrogenase activity was recorded in the middle elevations, and the rate of nitrogen fixation was not correlated with the cyanobacterial biomass.
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http://dx.doi.org/10.1111/1462-2920.12132DOI Listing
September 2013

Tree-rings mirror management legacy: dramatic response of standard oaks to past coppicing in Central Europe.

PLoS One 2013 6;8(2):e55770. Epub 2013 Feb 6.

Institute of Botany of the Academy of Sciences of the Czech Republic, Průhonice, Czech Republic.

Background: Coppicing was one of the most important forest management systems in Europe documented in prehistory as well as in the Middle Ages. However, coppicing was gradually abandoned by the mid-20(th) century, which has altered the ecosystem structure, diversity and function of coppice woods.

Methodology/principal Findings: Our aim was to disentangle factors shaping the historical growth dynamics of oak standards (i.e. mature trees growing through several coppice cycles) in a former coppice-with-standards in Central Europe. Specifically, we tried to detect historical coppicing events from tree-rings of oak standards, to link coppicing events with the recruitment of mature oaks, and to determine the effects of neighbouring trees on the stem increment of oak standards. Large peaks in radial growth found for the periods 1895-1899 and 1935-1939 matched with historical records of coppice harvests. After coppicing, the number of newly recruited oak standards markedly grew in comparison with the preceding or following periods. The last significant recruitment of oak standards was after the 1930s following the last regular coppicing event. The diameter increment of oak standards from 1953 to 2003 was negatively correlated with competition indices, suggesting that neighbouring trees (mainly resprouting coppiced Tilia platyphyllos) partly suppressed the growth of oak standards. Our results showed that improved light conditions following historical coppicing events caused significant increase in pulses of radial growth and most probably maintained oak recruitment.

Conclusions/significance: Our historical perspective carries important implications for oak management in Central Europe and elsewhere. Relatively intense cutting creating open canopy woodlands, either as in the coppicing system or in the form of selective cutting, is needed to achieve significant radial growth in mature oaks. It is also critical for the successful regeneration and long-term maintenance of oak populations.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0055770PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3565998PMC
August 2013

Non-random extinctions dominate plant community changes in abandoned coppices.

J Appl Ecol 2013 Feb;50(1):79-87

Department of Vegetation Ecology, Institute of Botany, Academy of Sciences of the Czech Republic, Lidická 25/27, CZ-602 00 Brno, Czech Republic.

The plant community structure of European lowland forests has changed dramatically in the 20 century, leading to biodiversity decline at various spatial scales. However, due to methodological difficulties associated with simultaneous changes in species diversity and composition, ecological processes behind the changes are still poorly understood. We analysed temporal changes in forest plant community after the mid-20 century abandonment of coppicing in a typical Central European forest, which had been managed as coppice for centuries. We used 122 semi-permanent plots first surveyed in the 1950s shortly after the last coppicing and again in the 2000s after half a century of natural succession. We used a novel Temporal Nestedness Analysis to disentangle the immigration and extinction processes underlying temporal changes in community structure and tested whether species gains and losses were ecologically random. The studied vegetation has shifted from the species-rich assemblages of a relatively open and low-nutrient forest towards the impoverished flora of a closed-canopy forest dominated by a few shade-adapted species. The significant reduction of beta diversity, i.e. compositional heterogeneity among plots, indicated taxonomic homogenization of the forest understorey. Temporal species turnover was only a minor component of the community change and recent assemblages are nested subsets of the former ones. Ecologically non-random extinctions dominated these changes. Light-demanding species with a persistent seed-bank were the most prone to extinction, while species with high specific leaf area substantially increased in frequency. The dominant process after the abandonment of coppicing was the ecologically non-random extinction of light-demanding species leading to an impoverished, temporally nested plant community structure. This development is typical for many abandoned lowland coppice forests and poses a significant threat to forest biodiversity in Europe. If forestry and conservation policies continue to prefer closed-canopy stands, many endangered species are likely to pay their extinction debts. To restore declining or even locally extinct species, canopy opening in abandoned coppices is urgently needed.
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http://dx.doi.org/10.1111/1365-2664.12010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6176902PMC
February 2013

Testing the stress-gradient hypothesis at the roof of the world: effects of the cushion plant Thylacospermum caespitosum on species assemblages.

PLoS One 2013 10;8(1):e53514. Epub 2013 Jan 10.

Section of Plant Ecology, Institute of Botany, Academy of Sciences of the Czech Republic, Třeboň, Czech Republic.

Many cushion plants ameliorate the harsh environment they inhabit in alpine ecosystems and act as nurse plants, with significantly more species growing within their canopy than outside. These facilitative interactions seem to increase with the abiotic stress, thus supporting the stress-gradient hypothesis. We tested this prediction by exploring the association pattern of vascular plants with the dominant cushion plant Thylacospermum caespitosum (Caryophyllaceae) in the arid Trans-Himalaya, where vascular plants occur at one of the highest worldwide elevational limits. We compared plant composition between 1112 pair-plots placed both inside cushions and in surrounding open areas, in communities from cold steppes to subnival zones along two elevational gradients (East Karakoram: 4850-5250 m and Little Tibet: 5350-5850 m). We used PERMANOVA to assess differences in species composition, Friedman-based permutation tests to determine individual species habitat preferences, species-area curves to assess whether interactions are size-dependent and competitive intensity and importance indices to evaluate plant-plant interactions. No indications for net facilitation were found along the elevation gradients. The open areas were not only richer in species, but not a single species preferred to grow exclusively inside cushions, while 39-60% of 56 species detected had a significant preference for the habitat outside cushions. Across the entire elevation range of T. caespitosum, the number and abundance of species were greater outside cushions, suggesting that competitive rather than facilitative interactions prevail. This was supported by lower soil nutrient contents inside cushions, indicating a resource preemption, and little thermal amelioration at the extreme end of the elevational gradient. We attribute the negative associations to competition for limited resources, a strong environmental filter in arid high-mountain environment selecting the stress-tolerant species that do not rely on help from other plants during their life cycle and to the fact the cushions do not provide a better microhabitat to grow in.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0053514PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3542354PMC
July 2013