Microclimates have been recognised as one of the key drivers in global change biology. Durable mi... more Microclimates have been recognised as one of the key drivers in global change biology. Durable microclimate loggers, detailed in‐situ measurements and sophisticated modelling tools are increasingly available, but a lack of standardised workflows for microclimate data handling hinders synthesis across the studies and thus progress in the global change biology. To overcome these limitations, we developed an R package myClim for microclimate data processing, storage and analyses. The myClim package supports complete workflow for microclimate data handling, including reading raw logger data files, their preprocessing and cleaning, time‐series' aggregation, calculation of ecologically relevant microclimatic variables, data export and storage. The myClim package stores data in a size‐efficient, hierarchical structure which respects the hierarchy of field microclimate measurement (locality > loggers > sensors). For imported microclimatic data, myClim provides an informative summa...
The methodology of processing hemispherialc photographs is a complex set of activities, starting ... more The methodology of processing hemispherialc photographs is a complex set of activities, starting with the creation of an image with a fish-eye lens, image editing in graphic editors and ending with analysis in specialized software. The obtained data indicate the amount of radiation falling into the undergrowth and the method of processing affects their quality. The procedure developed by the GIS and Remote Sensing Department of BU CAS integrates methods from various programmes into a script in R
in Czech Tato disertační práce se věnuje především využití dat dálkového průzkumu pro sledování a... more in Czech Tato disertační práce se věnuje především využití dat dálkového průzkumu pro sledování a studium změn vegetace. Díky archivním materiálům můžeme dnes provádět rozsáhlé studie na úrovni krajiny i celého světa bez potřeby rozsáhlých nebo archivních terénních dat. Od středověku se můžeme opřít o různé typy map, pro studium vegetace především lesnických. Od 30. let 20. století jsou v Evropě dostupné letecké snímky a od 70. let pak snímky satelitní, jejichž dostupnost a kvalita v době mého studia rapidně vzrostla. Nejnovějším příspěvkem v této oblasti jsou bezpilotní prostředky a metody jejich zpracování, které umožňují detailní mapování rozsáhlých ploch s nízkými náklady. Kromě výzkumných ekologických otázek, mají zde prezentované práce i environmentální rozměr a různou měrou přispívají k řešení aktuální problémů české ochrany životního prostředí od ochrany přírody v národních parcích a chráněných oblastech až po monitoring rostlinných invazí. Archivní lesnické mapy jsem využil...
Digitising and aggregating local floristic data is a critical step in the study of biodiversity. ... more Digitising and aggregating local floristic data is a critical step in the study of biodiversity. The integrative web-based platform Pladias, designed to cover a wide range of data on vascular plants, was recently developed in the Czech Republic. The combination of occurrence data with species characteristics opens many opportunities for data analysis and synthesis. This article describes the relational structure of the Pladias database service (PladiasDB) and the context of the platform architecture. The structure is relatively complex, as our goal was to cover: (i) species occurrence records, including their management, validation and export of revised species distribution maps, (ii) data on species characteristics with quality control tools using defined data types and (iii) separate user interfaces (UI) for professionals and the general public. We discuss the approaches chosen to model individual elements in PladiasDB and summarise the experience gained during the first five year...
Data from repeated field mapping of natural soil disturbances caused by wild boar. Sheet “Rooting... more Data from repeated field mapping of natural soil disturbances caused by wild boar. Sheet “Rooting_rerooting_history”: Columns: Rooted area (m2) = area of fragment of disturbance with certain history; Enclave = spatial parameter; Rooting history = history of certain disturbance fragment given by rooting and re-rootings. Sheet “Size (m2)”: Areas (in m2) of all disturbances mapped in certain years
4 Český abstrakt Práce se zabývá modelováním změny krajinného pokryvu způsobené opouštěním krajin... more 4 Český abstrakt Práce se zabývá modelováním změny krajinného pokryvu způsobené opouštěním krajiny. Studijní plocha o rozměrech 2,5 km × 2 km se nachází ve vojenském újezdu Hradiště, v okolí bývalé obce Tocov. Vzhledem k nedostatku historických dat o vegetaci na krajinné úrovni byly jako zdroj dat použity historické letecké snímky. Ty byly ortorektifikovány, mozaikovány a automaticky objektově klasifikovány do kategorií dřeviny a bezlesí. Postupné zarůstání krajiny bylo modelováno pomocí zobecněných lineárních modelů se smíšenými efekty (lmer) s použitím proměnných odvozených z digitálního výškového modelu, údajů o původním land use a prostorových proměnných získaných pomocí algoritmů na bázi celulárních automatů. Za účelem ověření predikce modelů se skutečným stavem, interpretace a vizualizace výsledků byla vytvořena aplikace PEMZOK Prostorově Explicitní Model Zarůstání Opuštěné Krajiny, která je jedním z výsledků této práce. Byla zjištěna stále rostoucí rychlost zarůstání zbylých ...
Ecological research heavily relies on coarse-gridded climate data based on standardized temperatu... more Ecological research heavily relies on coarse-gridded climate data based on standardized temperature measurements recorded at 2 m height in open landscapes. However, many organisms experience environmental conditions that differ substantially from those captured by these macroclimatic (i.e. free air) temperature grids. In forests, the tree canopy functions as a thermal insulator and buffers sub-canopy microclimatic conditions, thereby affecting biological and ecological processes. To improve the assessment of climatic conditions and climate-change-related impacts on forest-floor biodiversity and functioning, high-resolution temperature grids reflecting forest microclimates are thus urgently needed. Combining more than 1200 time series of in situ near-surface forest temperature with topographical, biological and macroclimatic variables in a machine learning model, we predicted the mean monthly offset between sub-canopy temperature at 15 cm above the surface and free-air temperature over the period 2000-2020 at a spatial resolution of 25 m across Europe. This offset was used to evaluate the difference between microclimate and macroclimate across space and seasons and finally enabled us to calculate mean annual and monthly temperatures for European forest understories. We found that sub-canopy air temperatures differ substantially from free-air temperatures, being on average 2.1°C (standard deviation ± 1.6°C) lower in summer and 2.0°C higher (±0.7°C) in winter across Europe. Additionally, our high-resolution maps expose considerable microclimatic variation within landscapes, not captured by the gridded macroclimatic products. The provided forest sub-canopy temperature maps will enable future research to model below-canopy biological processes and patterns, as well as species distributions more accurately.
Ladakh (Jammu & Kashmir State, NW. India) is a region in the Trans-Himalaya between the Great Him... more Ladakh (Jammu & Kashmir State, NW. India) is a region in the Trans-Himalaya between the Great Himalayan Range in the south and the eastern Karakoram in the north, at the southwestern edge of the Tibetan Plateau. Its flora, vegetation, ecology and climatic conditions were thoroughly studied by the late Leoš Klimeš. As regards the genus Taraxacum (Compositae-Crepidinae), Ladakh was an almost unexplored area. L. Klimeš accumulated an ample material (50 Ladakh species are exclusively based on his material), either as field samples or as cultivated specimens; together with further recent collections of other collectors, cultivated by JK & JŠ, and the historical herbarium material, it forms a basis for the present monograph. It presents a taxonomic treatment of all Taraxacum species documented from Ladakh, including notes on ecology and distribution, and notes on dandelions from adjacent regions, mainly Gilgit-Baltistan, Spiti, Lahaul and the cis-Himalayan Kashmir. Each species is charact...
Microclimates have been recognised as one of the key drivers in global change biology. Durable mi... more Microclimates have been recognised as one of the key drivers in global change biology. Durable microclimate loggers, detailed in‐situ measurements and sophisticated modelling tools are increasingly available, but a lack of standardised workflows for microclimate data handling hinders synthesis across the studies and thus progress in the global change biology. To overcome these limitations, we developed an R package myClim for microclimate data processing, storage and analyses. The myClim package supports complete workflow for microclimate data handling, including reading raw logger data files, their preprocessing and cleaning, time‐series' aggregation, calculation of ecologically relevant microclimatic variables, data export and storage. The myClim package stores data in a size‐efficient, hierarchical structure which respects the hierarchy of field microclimate measurement (locality > loggers > sensors). For imported microclimatic data, myClim provides an informative summa...
The methodology of processing hemispherialc photographs is a complex set of activities, starting ... more The methodology of processing hemispherialc photographs is a complex set of activities, starting with the creation of an image with a fish-eye lens, image editing in graphic editors and ending with analysis in specialized software. The obtained data indicate the amount of radiation falling into the undergrowth and the method of processing affects their quality. The procedure developed by the GIS and Remote Sensing Department of BU CAS integrates methods from various programmes into a script in R
in Czech Tato disertační práce se věnuje především využití dat dálkového průzkumu pro sledování a... more in Czech Tato disertační práce se věnuje především využití dat dálkového průzkumu pro sledování a studium změn vegetace. Díky archivním materiálům můžeme dnes provádět rozsáhlé studie na úrovni krajiny i celého světa bez potřeby rozsáhlých nebo archivních terénních dat. Od středověku se můžeme opřít o různé typy map, pro studium vegetace především lesnických. Od 30. let 20. století jsou v Evropě dostupné letecké snímky a od 70. let pak snímky satelitní, jejichž dostupnost a kvalita v době mého studia rapidně vzrostla. Nejnovějším příspěvkem v této oblasti jsou bezpilotní prostředky a metody jejich zpracování, které umožňují detailní mapování rozsáhlých ploch s nízkými náklady. Kromě výzkumných ekologických otázek, mají zde prezentované práce i environmentální rozměr a různou měrou přispívají k řešení aktuální problémů české ochrany životního prostředí od ochrany přírody v národních parcích a chráněných oblastech až po monitoring rostlinných invazí. Archivní lesnické mapy jsem využil...
Digitising and aggregating local floristic data is a critical step in the study of biodiversity. ... more Digitising and aggregating local floristic data is a critical step in the study of biodiversity. The integrative web-based platform Pladias, designed to cover a wide range of data on vascular plants, was recently developed in the Czech Republic. The combination of occurrence data with species characteristics opens many opportunities for data analysis and synthesis. This article describes the relational structure of the Pladias database service (PladiasDB) and the context of the platform architecture. The structure is relatively complex, as our goal was to cover: (i) species occurrence records, including their management, validation and export of revised species distribution maps, (ii) data on species characteristics with quality control tools using defined data types and (iii) separate user interfaces (UI) for professionals and the general public. We discuss the approaches chosen to model individual elements in PladiasDB and summarise the experience gained during the first five year...
Data from repeated field mapping of natural soil disturbances caused by wild boar. Sheet “Rooting... more Data from repeated field mapping of natural soil disturbances caused by wild boar. Sheet “Rooting_rerooting_history”: Columns: Rooted area (m2) = area of fragment of disturbance with certain history; Enclave = spatial parameter; Rooting history = history of certain disturbance fragment given by rooting and re-rootings. Sheet “Size (m2)”: Areas (in m2) of all disturbances mapped in certain years
4 Český abstrakt Práce se zabývá modelováním změny krajinného pokryvu způsobené opouštěním krajin... more 4 Český abstrakt Práce se zabývá modelováním změny krajinného pokryvu způsobené opouštěním krajiny. Studijní plocha o rozměrech 2,5 km × 2 km se nachází ve vojenském újezdu Hradiště, v okolí bývalé obce Tocov. Vzhledem k nedostatku historických dat o vegetaci na krajinné úrovni byly jako zdroj dat použity historické letecké snímky. Ty byly ortorektifikovány, mozaikovány a automaticky objektově klasifikovány do kategorií dřeviny a bezlesí. Postupné zarůstání krajiny bylo modelováno pomocí zobecněných lineárních modelů se smíšenými efekty (lmer) s použitím proměnných odvozených z digitálního výškového modelu, údajů o původním land use a prostorových proměnných získaných pomocí algoritmů na bázi celulárních automatů. Za účelem ověření predikce modelů se skutečným stavem, interpretace a vizualizace výsledků byla vytvořena aplikace PEMZOK Prostorově Explicitní Model Zarůstání Opuštěné Krajiny, která je jedním z výsledků této práce. Byla zjištěna stále rostoucí rychlost zarůstání zbylých ...
Ecological research heavily relies on coarse-gridded climate data based on standardized temperatu... more Ecological research heavily relies on coarse-gridded climate data based on standardized temperature measurements recorded at 2 m height in open landscapes. However, many organisms experience environmental conditions that differ substantially from those captured by these macroclimatic (i.e. free air) temperature grids. In forests, the tree canopy functions as a thermal insulator and buffers sub-canopy microclimatic conditions, thereby affecting biological and ecological processes. To improve the assessment of climatic conditions and climate-change-related impacts on forest-floor biodiversity and functioning, high-resolution temperature grids reflecting forest microclimates are thus urgently needed. Combining more than 1200 time series of in situ near-surface forest temperature with topographical, biological and macroclimatic variables in a machine learning model, we predicted the mean monthly offset between sub-canopy temperature at 15 cm above the surface and free-air temperature over the period 2000-2020 at a spatial resolution of 25 m across Europe. This offset was used to evaluate the difference between microclimate and macroclimate across space and seasons and finally enabled us to calculate mean annual and monthly temperatures for European forest understories. We found that sub-canopy air temperatures differ substantially from free-air temperatures, being on average 2.1°C (standard deviation ± 1.6°C) lower in summer and 2.0°C higher (±0.7°C) in winter across Europe. Additionally, our high-resolution maps expose considerable microclimatic variation within landscapes, not captured by the gridded macroclimatic products. The provided forest sub-canopy temperature maps will enable future research to model below-canopy biological processes and patterns, as well as species distributions more accurately.
Ladakh (Jammu & Kashmir State, NW. India) is a region in the Trans-Himalaya between the Great Him... more Ladakh (Jammu & Kashmir State, NW. India) is a region in the Trans-Himalaya between the Great Himalayan Range in the south and the eastern Karakoram in the north, at the southwestern edge of the Tibetan Plateau. Its flora, vegetation, ecology and climatic conditions were thoroughly studied by the late Leoš Klimeš. As regards the genus Taraxacum (Compositae-Crepidinae), Ladakh was an almost unexplored area. L. Klimeš accumulated an ample material (50 Ladakh species are exclusively based on his material), either as field samples or as cultivated specimens; together with further recent collections of other collectors, cultivated by JK & JŠ, and the historical herbarium material, it forms a basis for the present monograph. It presents a taxonomic treatment of all Taraxacum species documented from Ladakh, including notes on ecology and distribution, and notes on dandelions from adjacent regions, mainly Gilgit-Baltistan, Spiti, Lahaul and the cis-Himalayan Kashmir. Each species is charact...
The sixth part of the series on the distributions of vascular plants in the Czech Republic includ... more The sixth part of the series on the distributions of vascular plants in the Czech Republic includes grid maps of 112 taxa in the genera Athyrium, Carex, Centaurea, Chenopodium, Corispermum, Corrigiola, Crepis, Cystopteris, Glaucium, Hackelia, Hammarbya, Hippocrepis, Lappula, Lepidium, Liparis, Loranthus, Lycopus, Lythrum, Matteuccia, Osmunda, Plantago, Psephellus, Pteridium, Salvia, Scirpus and Viola. These maps were produced by taxonomic experts based on examined herbarium specimens, literature and field records. The native species include common and widespread plants such as Athyrium filix-femina, Carex acuta, Crepis biennis, Lycopus europaeus, Lythrum salicaria and Plantago lanceolata, as well as rare species such as Carex buxbaumii, Osmunda regalis and Viola alba. Almost 42{\%} of the mapped taxa are on the national Red List. Among themapped taxa there are rare mountain species (e.g. Carex aterrima, C. atrata, Centaurea mollis, C. montana, Crepis mollis subsp. mollis, C. sibirica and the endemic Plantago atrata subsp. sudetica), wetland orchids (Hammarbya paludosa, Liparis loeselii) and plants of dry grasslands (e.g. Crepis pannonica, Hippocrepis comosa, Lappula semicincta and Salvia aethiopis). Rare ecological specialists include Corrigiola litoralis from seasonally exposed sand and gravel bars in rivers, Plantago arenaria confined to dry open sandy habitats, and Chenopodium chenopodioides and Plantago maritima subsp. ciliata from saline habitats. Alien species mapped in this paper include both archaeophytes and neophytes, most of them from the genera Centaurea, Crepis and Lepidium. Salvia hispanica is recorded as a new alien species for this country's flora; its spontaneous occurrence was first detected in 2013, and since then this species has been found at about a dozen sites. Plantago coronopus has recently spread along the roads treated with de-icing salt. A number of species are at the limits of their distributions in the Czech Republic. The distribution maps of three interspecific hybrids are also included. Spatial distributions and often also temporal dynamics of individual taxa are shown in maps and documented by records included in the Pladias database and available in electronic appendices. The maps are accompanied by comments that include additional information on the distribution, habitats, taxonomy and biology of the taxa.
The second part of the publication series on the distributions of vascular plants in the Czech Re... more The second part of the publication series on the distributions of vascular plants in the Czech Republic includes grid maps of 87 taxa of the genera Antennaria, Aposeris, Astragalus, Avenula, Bidens, Carex, Cenchrus, Centunculus, Convallaria, Crocus, Cryptogramma, Cyperus, Dryopteris, Gladiolus, Gratiola, Helictochloa, Hierochlo{\"{e}}, Lindernia, Maianthemum, Myriophyllum, Notholaena, Nymphoides, Radiola, Schoenoplectus, Sisyrinchium, Spergularia, Tillaea, Veratrum and Veronica. The maps were produced by taxonomic experts based on all available herbarium, literature and field records. The plants studied include 56 taxa registered in the Red List of vascular plants of the Czech Republic, some of which showed remarkable declines. Astragalus arenarius, Hierochlo{\"{e}} odorata and H. repens, as representatives of vegetation of inland sand dunes, are critically threatened due to conversion of their habitats to arable land, local sand mining, afforestation, changes in landscape management and eutrophication followed by succession. Each of them survives at a few localities and their populations are poor. Competitively weak wetland annuals, confined to open habitats such as exposed fishpond littorals and river beds, abandoned sand-pits and wet arable fields, have considerably declined and disappeared from large areas as a result of agriculture and fish-farming intensification, in particular fertilization and restriction of summer drainage of fishponds, and other changes in land-use. These include Centunculus minimus, Cyperus flavescens, C. michelianus, Lindernia procumbens, Radiola linoides and Tillaea aquatica. Observed recently at a few sites only, they are all classified as critically threatened. A map is for the first time provided also for Spergularia kurkae, a newly recognized species and a central-European endemic. Astragalus asper, Schoenoplectus supinus and Veronica pumila are now extirpated from the country's flora. In contrast, Spergularia marina, until recently confined to natural saline habitats and very rare, has been spreading along roads that are treated by de-icing salts. Examination of an old herbarium voucher showed that the only record of Astragalus alopecuroides in the Czech flora actually refers to the species whose correct name is A. alopecurus. Further introduced casuals mapped in this paper include Bidens pilosus, Cenchrus echinatus, Gratiola neglecta and Lindernia dubia, each introduced to only a few sites. Bidens connatus was recorded at two dozen sites and appears to have spread as a consequence of the great floods in 2002. Typical examples of naturalized neophytes are Veronica filiformis and V. peregrina, both currently known from many parts of the country. Invasive aliens are represented by Bidens frondosus, which began to spread in the 1930s and now is frequent throughout the country. Spatial and temporal dynamics of individual species are shown in maps and documented by records included in the Pladias database and available in Electronic appendices. The maps are accompanied by comments, which include additional information on distribution, habitats, taxonomy and biology of the species.
Ladakh (Jammu {\&} Kashmir State, NW. India) is a region in the Trans-Himalaya between the Great ... more Ladakh (Jammu {\&} Kashmir State, NW. India) is a region in the Trans-Himalaya between the Great Himalayan Range in the south and the eastern Karakoram in the north, at the southwestern edge of the Tibetan Plateau. Its flora, vegetation, ecology and climatic conditions were thoroughly studied by the late Leo{\v{s}} Klime{\v{s}}. As regards the genus Taraxacum (Compositae-Crepidinae), Ladakh was an almost unexplored area. L. Klime{\v{s}} accumulated an ample material (50 Ladakh species are exclusively based on his material), either as field samples or as cultivated specimens; together with further recent collections of other collectors, cultivated by JK {\&} J{\v{S}}, and the historical herbarium material, it forms a basis for the present monograph. It presents a taxonomic treatment of all Taraxacum species documented from Ladakh, including notes on ecology and distribution, and notes on dandelions from adjacent regions, mainly Gilgit-Baltistan, Spiti, Lahaul and the cis-Himalayan Kashmir. Each species is characterized by a full description, photographs of involucre, capitulum and achenes, whenever available; species are arranged systematically in sections, the latter also with descriptions and identification keys including all the taxa from Ladakh and adjacent areas. Treatments of five sections include all or almost all of their members. Distribution maps and a complete list of specimens studied are given for all Ladakh dandelions. A comprehensive introduction in the vegetation of Ladakh, general features of the genus Taraxacum and the history of its exploration are also provided. As regards the Taraxacum diversity, the broader region covered by the present monograph includes representatives of one third of the world sectional diversity. One hundred and twenty one taxa, belonging to 19 sections, are given a full tratment in the monograph, including those from adjacent regions (the latter, 46 species, also with full descriptions and illustrations); the Ladakh proper harbours 76 taxa in 17 sections, one of which is described as new. Fifty one taxa are described as new for science, 42 from Ladakh, 9 from other regions. For all species, the mode of reproduction is given (mostly inferred from indirect indicators). Only seven species were found at least partly sexual (five of them outside the limits of the Ladakh proper); all the other taxa exhibit agamospermy. Ladakh and adjacent regions of Pakistan and India rank among the regions with the highest sectional and morphological Taraxacum diversities.
Projections of landscape dynamics are uncertain, partly due to uncertainties in model formulation... more Projections of landscape dynamics are uncertain, partly due to uncertainties in model formulations. However, quantitative comparative analyses of forest landscape models are lacking. We conducted a systematic comparison of all forest landscape models currently applied in temperate European forests (LandClim, TreeMig, LANDIS-II, iLand). We examined the uncertainty of model projections under several future climate, disturbance, and dispersal scenarios, and quantified uncertainties by variance partitioning. While projections under past climate conditions were in good agreement with observations, uncertainty under future climate conditions was high, with between-model biomass differences of up to 200 t ha−1. Disturbances strongly influenced landscape dynamics and contributed substantially to uncertainty in model projections ({\~{}}25–40{\%} of observed variance). Overall, model differences were the main source of uncertainty, explaining at least 50{\%} of observed variance. We advocate a more rigorous and systematic model evaluation and calibration, and a broader use of ensemble projections to quantify uncertainties in future landscape dynamics.
The severity and spatial extent of bark-beetle outbreaks substantially increased in recent decade... more 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 SE Germany. Here 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 Picea 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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Papers by Josef Brůna