Department of Geoecology

Head: Mgr. Martin Kopecký, Ph.D.

People ׀ Projects ׀ Publications ׀ Department website

Research topics

  • Microclimate measurement and modelling
  • Species distribution modelling
  • Forest disturbances
  • Plant community responses to global changes
  • Remote sensing in plant ecology

The department includes the Laboratory of GIS and Remote Sensing.

Selected recent results

1/ Prehistoric Settlement and Introduced Plants – A Bond That Endures?

A significant portion of the Czech flora consists of archaeophytes, plants that spread with human help in pre-Columbian times. In a collaborative effort among botanists, paleoecologists, and archaeologists, a study explored how the current presence of archaeophytes in local flora reflects past human settlement intensity and how much it is influenced by present landscape conditions. The study used extensive databases on plant occurrences in the Czech Republic (PLADIAS) and archaeological finds in Bohemia and Moravia. Despite the impact of current land use, areas with higher prehistoric settlement intensity still show a greater abundance of archaeophytes. Surprisingly, the size of the current range of these plants is more influenced by their ecological needs than the time of introduction.
The study explains this paradox by pointing out that introduced plants have an affinity for environments resembling those favored by prehistoric societies. Considering that the time since the introduction of archaeophytes is generally sufficient for them to colonize their potential range within the Czech Republic, this sheds light on the interesting relationship between human history and plant distribution.

  • Macek M., Abraham V., Tkáč P., Novák D. & Kolář J. 2023: The diversity and distribution of introduced plant species reflect 8000 years of settlement history. Journal of Ecology 111, 787 – 798. doi:10.1111/1365-2745.14060

Údaje o zastoupení archeofytů v české flóře na základě databáze PLADIAS (A), intenzita pravěkého osídlení modelovaná na základě archeologických nálezových databázi (B), nadmořská výška jako hlavní faktor řídící klima (C) a lesnatost území jako ukazatel využití krajiny (D).  

Representation of archaeophytes in the Czech flora from the PLADIAS database (A), intensity of prehistoric settlement modeled based on archaeological databases (B), elevation as the primary factor influencing climate (C), and forest cover as an indicator of landscape use (D).


2/myClim: Microclimate data handling and standardised analyses in R

With the increasing availability of microclimate dataloggers, there has been a massive expansion of their use in scientific research. Thanks to the continually shrinking dimensions of microclimate dataloggers, extended battery life, and increased memory capacity, it is now possible to measure microclimate even in hard-to-reach locations. However, this technological revolution brings not only great potential for gaining new insights but also new challenges like the management of the big microclimatic data and heterogenous methods of their processing. To address these challenges we developed an innovative software library myClim.
This library allows for the efficient reading, processing, visualization, and analyses of microclimate data in the environment of the popular scripting language R. In addition to simplifying the work with big microclimate data, myClim offers standardized calculations of ecologically relevant variables, their aggregation, and export. Such harmonization and standardization increase the comparability of results across microclimatic studies and facilitate data syntheses across different scales.

  • Man M., Kalčík V., Macek M., Brůna J., Hederová L., Wild J. & Kopecký M. 2023: myClim: Microclimate data handling and standardised analyses in R. Methods in Ecology and Evolution 14, 2308 – 2320. doi:1111/2041-210X.14192

 Detekce sněhové pokrývky na základě měření přízemní teploty s použitím knihovny myClim.  

Detection of snow cover from ground temperature measurements using the myClim library.


3/ DaLiBor: Database of Lichens and Bryophytes of the Czech Republic

The majority of bryophyte and lichen occurrences in the Czech Republic are not widely available in a standard and machine-readable form. Therefore, we created a Database of Lichens and Bryophytes (DaLiBor; DaLiBor provides an infrastructure for recording standardizing, validating, enhancing, and sharing data under Creative Commons license (CC-BY-SA). To the beginning of 2023 DaLiBor records (662 610) composed of 506 578 (76 %) bryophytes and 156 032 (24 %) lichens. DaLiBor data confirmed the importance of protected areas identified as the national biodiversity hotspots. On the biotope level the highest number of records, including Red-listed species, originates from natural beech and managed coniferous forests. On the substrate level the most important was the Fagus sylvatica, the tree with the highest number of recorded taxa. Benefiting from standardised DaLiBor data we computed the probability maps of suitable habitat distribution for locally important species in Bohemian Switzerland National Park. Based on the maps we found new localities for Dicranum majus and Polytrichastrum alpinum.

  • Man M., Malíček J., Kalčík V., Novotný P., Chobot K. & Wild J. (2022) DaLiBor: Database of Lichens and Bryophytes of the Czech Republic. – Preslia 94: 579–605

Záznamy o mechorostech (vlevo) z DaLiBor pokrývají rovnoměrně celou Českou republiku
Bryophytes records in DaLiBor (left) are distributed all arund the Czech Repiblic, but lichens records (right) are missing from many places. Red-listed (bottom; CR, EN, RE, VU) bryophytes distribution is concentrated in eastern prt of th country contrasting with western tendency of red-listed licehns.  


4/ Forest microclimate modelling: can drones replace fieldwork?

Forest canopy structure shapes understorey microclimate experienced by the forest plants. Here, we used detailed air and soil temperature measurements performed in the Czech Karst to compare three contrasting approaches how to obtain information about forest canopy structure according to their ability to predict understorey microclimate. We compared traditional field-based methods based on hemispherical photographs and tree height measurements with two remote sensing approaches – LiDAR scanning and photogrammetric Structure-from-Motion (SfM), both obtained with drones. We found that both remote sensing methods can replace field measurements and that the cheaper photogrammetric SfM can provide information about forest structure comparable to substantially more expensive LiDAR scanning. Our results also suggested that fine-scale modelling of soil temperatures is more challenging than air temperature modelling.

  • Kašpar V., Hederová L., Macek M., Müllerová J., Prošek J., Surový P., Wild J. & Kopecký M. 2021: Temperature buffering in temperate forests: Comparing microclimate models based on ground measurements with active and passive remote sensing. Remote Sensing of Environment 263, 1 – 10. doi:10.1016/j.rse.2021.112522

Podrost listnatého lesa představuje jemnozrnnou mosaiku teplejších a chladnějších míst.

Forest understorey is a fine-grained mosaic of warmer and cooler places. The occurrence of different plant species in the forest understorey reflects this mosaic sensitively, and a botanist studying the patterns of plant distribution therefore needs detailed information on the forest microclimate. In our paper, we compared different ways of obtaining this key information by both field measurements and remote sensing.


5/ Elevational gradients of plant diversity and distribution

The relationship between plant diversity and distribution mirrors the climatic tolerance of individual species, but it is formed also by other ecological processes related to geographic context and evolutionary history. Two original studies by members of the Department of GIS and RS together with the Department of Functional Ecology utilized data from their long-term research activities in Western Himalaya and revisit basic ecological rules and hypotheses concerning elevational patterns in plant diversity and distribution: the Elevational Rapoport’s rule (stating that species occurring in higher elevations tend to grow in a broader range of elevations) and the mid-domain effect (predicting middle-elevation diversity peak due to geometric constraints). With the use of advanced null models, we demonstrated that the tests of these ecological rules were confounded by geographic settings. Both ecological rules thus do not reflect plant ecological requirements properly and need to be thoroughly revisited.

  • Macek M., Dvorský M., Klimeš A., Wild J., Doležal J. & Kopecký M. 2021: Midpoint attractor models resolve the mid-elevation peak in Himalayan plant species richness. Ecography 44, 1665 – 1677. doi:10.1111/ecog.05901
  • Macek M., Dvorský M., Kopecký M., Wild J. & Doležal J. 2021. Elevational range size patterns of vascular plants in Himalaya contradict Rapoport’s rule. Journal of Ecology: 1-34. doi: 10.1111/1365-2745.13772

 LLadakh jako ideální přírodní laboratoř pro výzkum rostlinné diverzity

Steep elevational gradients, worldwide elevational maximum of vascular plant occurrence at 6150 m a.s.l. and relatively pristine nature makes the Himalayan region of Ladakh an ideal nature laboratory for plant diversity research.


6/ TMS microclimate logger

After 10 years of development and testing, we published the official description of the new TMS microclimate logger. TMS logger represents substantial innovation and overcomes several major drawbacks of other available microclimate loggers. TMS logger accurately measures air, surface and soil temperature, and soil moisture and has an extremely large memory and durable batteries. TMS logger is therefore highly suitable for long-term microclimate measurements in demanding field conditions.

Mikroklimatické čidlo TMS

TMS microclimate logger resembles a small herbaceous plant. This original design thus allows measuring air and soil temperatures and soil moisture at the plant-relevant scale.

  • Wild J., Kopecký M., Macek M., Šanda M., Jankovec J. & Haase T. (2019) Climate at ecologically relevant scales: A new temperature and soil moisture logger for long-term microclimate measurement. Agricultural and Forest Meteorology 268: 40–47.


7/ Life and death of Picea abies after bark-beetle outbreak

Large-scale stand-replacing disturbances are increasingly frequent, especially in vast coniferous forests of the Northern Hemisphere. Despite ongoing intensive research we still lack studies that disentangle processes driving forest regeneration and facilitate decision-making of forest managers, who are responsible for post-disturbance stand recovery. We followed the fate of 2552 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. We showed that most seedlings originated directly within the three-year dieback of canopy trees induced by bark-beetle outbreak. Our study thus highlights the so far unrecognized importance of “disturbance-related” regeneration at the expense of advance regeneration for stand recovery after bark-beetle outbreaks. We also showed that seedling mortality, and not the seedling growth rate, is the key process behind microsite specificity for tree regeneration.

Velkoplošný rozpad stromového patra v Bavorském Národním Parku, kde jsme podrobně studovali procesy smrkového lesa po kůrovcové kalamitě

Regenerating mountain spruce forest after large-scale bark beetle outbreak in the Bavarian Forest National Park where we studied tree regeneration after the stand-replacing disturbance.

  • Macek M., Wild J., Kopecký M., Červenka J., Svoboda M., Zenáhlíková J., Brůna J., Mosandl R., & Fischer A. (2017) Life and death of Picea abies after bark-beetle outbreak: ecological processes driving seedling recruitment. Ecological Applications, 27, 156–167.