New publication – Plant diversity in oceanic archipelagos: realistic patterns emulated by an agent-based computer simulation

Text by Madli Jõks

Simulated islands help to untangle the secrets of biodiversity

Volcanic islands emerge empty from the sea and thus, offer a unique change to study how plant- and animal species colonize new areas. They have been in the focus on interest of biogeographers for centuries and are known as hotspots for biodiversity as well as for extinctions. Unfortunately, even several centuries are a time too short to observe evolution and dispersal processes in live. That often makes difficult to study the mechanisms behind the curious patterns of island biodiversity.

Computer simulations, which allow us to emulate the possible processes responsible for insular biodiversity development, might come in handy in this situation. Scientist of the macroecology workgroup in University of Tartu Madli Jõks and Meelis Pärtel used a computer simulation to study the plant communities of Hawaii, Galapagos, Canary Islands, Azores and Cape Verde. Their aim was to understand, which factors design species richness and composition on the islands: is it mainly island area, habitat diversity or the position in the archipelago?

The aim was approached by altering archipelago maps to create realistic and less realistic situations in which island biodiversity might have developed during the millions of years. These maps were then used as arena for simulations which emulated immigration and dispersal processes, as well as competition between the species, evolution and extinction. As these simulations are more than an ordinary computer can handle, the help of the High Performance Computing Centre of the University of Tartu was used.

It became apparent that the results were more realistic when the virtual islands contained many different habitats; scenarios where the islands were covered with one consistent habitat didn’t give results quite as accurate. From the results, it can be concluded that the diversity of the habitats has been a more important factor of island biodiversity than had been previously assumed.

To test the importance of the spatial configuration of islands, simulations with randomly relocated islands were used. The right positioning of the islands was found to be important for getting a realistic composition of species only in more elongated archipelagos: in Hawaii, Azores and Canary Islands. That also makes perfect sense: when the configuration of islands is randomly changed in an elongated archipelago, the islands are likely to be further away from their actual neighbours, and islands which were initially further away will become their new neighbours.

But why study oceanic islands in Estonia? Islands, especially oceanic islands, are primarily great model systems. Knowledge about how species disperse between habitat fragments or diverge due to geographic barriers can be applied to the study and protection of other island-like communities, e.g., patches of forest left between clear-cut areas.

Citation: Jõks. M, & Pärtel, M. (2018). Plant diversity in oceanic archipelagos: realistic patterns emulated by an agent-based computer simulation, Ecography, (link to full text)


Current primary dispersal corridors to Canary Islands (pic from here)


Although islands as natural laboratories have held the attention of scientists for centuries, they continue to offer new study questions, especially in the context of the current biodiversity crisis. To date, habitat diversity on islands and spatial configuration of archipelagos have received less attention than classical island area and isolation. Moreover, in the field where experiments are impossible, correlative methods have dominated, despite the call for more mechanistic approaches. We developed an agent‐based computer simulation to study the effect of habitat diversity and archipelago configuration on plant species richness and composition in five archipelagos worldwide (Hawaii, Galapagos, Canary Islands, Cape Verde and Azores) and compared simulated diversity patterns to the empirical data. Habitat diversity proved to be an important factor to achieve realistic simulation results in all five archipelagos, whereas spatial structure of archipelagos was important in more elongated archipelagos. In most cases, simulation results correlate stronger with spermatophyte than with pteridophyte data, which we suggest can be attributed to the different dispersal and evolution rates of the two species groups. Correlation strength between simulated and observed diversity also varied among archipelagos, suggesting that geological and biogeographic histories of archipelagos have affected the species richness and composition on the islands. Our study demonstrates that a relatively simple computer simulation involving just a few essential processes can largely emulate patterns of archipelagic species richness and composition and serve as a powerful additional method to complement empirical approaches.

Posted in New publication | Tagged , , , , , , , , , , , | Leave a comment

Andres Metspalu about biobanks and personalized medicine

Seminar of Department of Botany and Centre of Excellence EcolChange

Speaker: Andres Metspalu is professor of biotechnology at the Institute of Molecular and Cell Biology, University of Tartu, and head of Estonian Genome Centre.

Title of the talk: From biobanking to personalized medicine

Time: Thursday, 15. November 2018 at 15.15

Place: Tartu, Lai 40-218 (Vaga auditorium)


Andres Metspalu (pic from

Posted in Event | Tagged , , , | Leave a comment

DOI codes will be used parallel to species names

Text from Research in Estonia page (link to the original post)

Scientists at the University of Tartu created a new method for communicating species. The classification initiated by Carl von Linné, which has lasted for over 200 years, does not take current scientific methods into account.

The mycologists and taxonomists working under the Natural History Museum and the Botanical Garden of the University of Tartu have so far been known as the creators of the eBiodiversity portal and the PlutoF platform. But now we can say that 10 years of work has resulted in the creation of a new international system that facilitates the classification of species.

Let’s start from the beginning. When a new species is discovered and being described, it is given a scientific name in Latin (e.g., the Brachyzapus greengoblin discovered recently by scientists from Tartu), the species will belong to some specific genus and family, etc. Often, it later becomes apparent that the initial classification was incorrect and the species name has to be changed – more trouble than necessary.

Furthermore, new modern work methods are now being used to search for species in an environment without catching them. For example, a water sample from one lake contains the DNA of all the fish living there (through faeces, fish slime as well as other excretions). Thus, describing the species living in an environment through a DNA analysis of a sample from this environment is becoming the most common work method used by scientists.

This is also the work method for mycologists, for example, studying the fungi that form symbiotic relationships with plant roots. The amount of microfungi found in soil is immense and they can all be found by simply separating their DNAs from the soil sample in a laboratory. In its essence, DNA is only a code, a nucleotide sequence. However, knowing this code is not that helpful as not all the DNA sequences of the world’s species have been correlated with the species names and there is no database that would let you know the name of the species by entering the DNA sequence.

The research group led by the professor of mycology, Urmas Kõljalg, at the University of Tartu, developed a database just for this purpose. However, this database is initially only for fungi. “We created a communication system so these species found via DNA could be communicated without knowing the names of the taxon (e.g., species, genus, etc. – ed.)”, explained Kõljalg. “Many species are only known based on their DNA: for example, analysing microfungi in soil. A large part of these have also not been described for science. Some have been described between 50 and 100 years ago but only based on their visible portion and this cannot be connected to the DNA collected from the sample.”

To associate a DNA sample with a specific species, you will need to assign this sample a unique name or code as the DNA sequence itself is too cumbersome – long and varying. The DOI (Digital Object Identifier) code known from scientific literature was chosen as this code. Every research ever published has its own unique DOI code that is constant in time, so this code can always be used to find the one specific research from the databases of scientific literature all over the world. DOI codes are given out by the International Certification Centre and the right of issuing DOI codes (in this instance, to fungal species or more specifically to their DNA samples instead of articles) was also granted to the Natural History Museum.

“For this purpose, we have a separate global database named ‘UNITE’, which we started and manage, and employs hundreds of people. Certain gene sequences have been gathered together from all over the world, and based on these, species and DNA-based species have been calculated. Then we simply built a communication system on top of it, which is an alternative to Linné’s system and based on DOIs, the same as journal articles. Every species has its own DOI code, which is an identifier that is stable in time.”

Scientists basically managed to develop a tool, which will tell the researcher who lives in the environment they are studying solely on the basis of DNA samples.

“That’s right”, said Kõljalg. “And it works almost on all fungi in the world. Little by little, we will start with other groups as well.”

The receipt of the right to issue DOI codes is also an interesting story – it happened as recently as during the years 2013–2014.

“Before DOIs, we created our own unique and stable identifiers. But the internationally recognised system is much better. And when we got the right to issue an indefinite number of DOIs, we issued half a million of them at the first go. And then these went to the headquarters in Germany, where they register these DOIs, and it was silent for a while. These DOIs are meant for scientific data and at that time there were only a couple of thousands of codes issued for scientific data in the world. And then we barged in with half a million. And then they looked at it for a while and said that ‘oh, this is a clever idea indeed’ (Urmas laughs).”

The DOI codes issued to species (and to be precise, to species hypothesis) enable the scientists working with wildlife classification to enter the modern world of data. Systematists constantly work with species names and the definition of one species often changes a couple of times a year. Now, however, every DOI code marks one definition made at a given moment in time, and all the old and new definitions are linked in databases.

“For example, if someone carries out a study of soil biota today and finds out who (whose DNA) is found in the soil somewhere, and then, 10 years later, someone conducts the same study and wants to compare the results of the two studies, then it is possible, because even if the species have been relocated in the interim, the digital connections between the new and old species have been retained. All of this is possible thanks to digital solutions”, exclaimed Urmas Kõljalg with anticipation for the use of the new system.

'Turn right at the Robinia pseudoacacia, pass the garden with the salvia officinalis, cross the road when you see the stranvaesia davidinia and the pub is on the left!'

DOIs will be DOIs! (pic from here)


Posted in Other news | Tagged , , , , | Leave a comment

EcolChange seminar – Melissa McCormick about orchid mycorrhiza

Seminar of Department of Botany and Centre of Excellence EcolChange

Speaker: Melissa McCormick is ecologist at the Smithsonian Environmental Research Center, USA. She visitis Department of Botany to act as opponent at the PhD defence of Jane Oja on November 8th, at 9.15 AM in Vaga auditorium, Lai 40-218, Tartu.

Title of the talk: The fungal half of the mycorrhizal equation: how fungi affect orchid population dynamics

Time: Wednesday, 7. November 2018 at 16.15

Place: Tartu, Lai 40-218 (Vaga auditorium)

Say it with Flowers: 'Late - daffs. Drunk - roses. Stag party - carnations. Adultery - orchids.'

Some orchid-related semiotics (pic from here)

Posted in Event | Tagged , , , , , | Leave a comment

EcolChange seminar – Ebe Merilo about stomatal regulation of crops

Seminar of Department of Botany and Centre of Excellence EcolChange

Speaker: Ebe Merilo is senior researcher at the Institute of Technology, University of Tartu.

Title of the talk: Stomatal regulation of crops

Time: Thursday, 25. October 2018 at 15.15

Place: Tartu, Lai 40-218 (Vaga auditorium)

Posted in Event | Tagged , , , , , | Leave a comment

New publication – Conceptual differences lead to divergent trait estimates in empirical and taxonomic approaches to plant mycorrhizal trait assignment

Text by Guillermo Bueno

How plant mycorrhizal traits are estimated?

As plant trait measurements are increasingly available, more complete plant trait datasets are compiled allowing to formulate more mechanistic and complex questions in plant ecology. One of the plant functional aspect that are lagging behind is related to plant’s biotic interactions. Mycorrhizal symbiosis is increasingly recognized as a key plant biotic interactions, directly involved in plant survival and distribution. However, little advances have been done in the way these traits are estimated, and thus relative little amount of data is available. Recently, an alternative method (taxonomic approach) to the classical collation and revision of empirical evidences (hereafter empirical approach) was proposed. The taxonomic approach is based on an expert-based extrapolation from often unreferenced background mycorrhizal information at the species-level, to plant family level, or exceptionally extrapolated to genus level. Despite the taxonomic approach has been claimed to be almost definitive, no quantitative comparisons have been made to support this claim. A group of researchers from the University of Tartu have prepared the first quantitative comparison between these two approaches to clarify their differences, identify their weaknesses and discuss further improvements in their estimation. This comparison has been just published in the Journal Mycorrhiza. The main findings are that the key differences in the output of both approaches are due to two main causes: 1) the taxonomic extrapolation to family level might not be appropriate systematically, as some of the plant mycorrhizal traits can be highly variable within plant families. Second and even more relevant, 2) both approaches use different conceptual frameworks. For instance, the concepts of arbuscular mycorrhizal, facultatively mycorrhizal or non-mycorrhizal plants significantly differed between the approaches. Overall this paper highlights the need to discuss basic concepts in the field for paving the way for more solid plant mycorrhizal trait approaches to come.

bueno 2018 octB

Figure. Graphs with the percentages of matching (blue) and mismatching plant species (red) in a comparison of plant mycorrhizal traits derived using taxonomic and empirical approaches (the empirical approach is used as reference), more details in the paper.

Citation: Bueno, C. G., Gerz, M., Zobel, M., & Moora, M. (2018). Conceptual differences lead to divergent trait estimates in empirical and taxonomic approaches to plant mycorrhizal trait assignment. Mycorrhiza, (link to full text)


Empirical and taxonomic approaches are the two main methods used to assign plant mycorrhizal traits to species lists. While the empirical approach uses only available empirical information, the taxonomic approach extrapolates certain core information about plant mycorrhizal types and statuses to related species. Despite recent claims that the taxonomic approach is now almost definitive, with little benefit to be gained from further empirical data collection, it has not been thoroughly compared with the empirical approach. Using the most complete available plant mycorrhizal trait information for Europe and both assignment approaches, we calculate the proportion of species for each trait, and model environmental drivers of trait distribution across the continent. We found large degrees of mismatch between approaches, with consequences for biogeographical interpretation, among facultatively mycorrhizal (FM; 91% of species mismatched), non-mycorrhizal (NM; 45%), and to a lesser extent arbuscular mycorrhizal (AM; 16%) plant species. This can partly be attributed to the taxonomic precision of the taxonomic approach and the use of different AM, NM, and FM concepts. Our results showed that the extrapolations of the taxonomic approach do not consistently match with empirical information and indicate that more empirical data are needed, in particular for FM, NM, and AM plant species. Clarifying certain concepts underlying mycorrhizal traits and empirically describing NM, AM, and FM species within plant families can greatly improve our understanding of the biogeography of mycorrhizal symbiosis.


Posted in New publication | Tagged , , , , , , , | Leave a comment

EcolChange seminar – Bengt-Gunnar Jonsson about the forest cover changes in Scandinavia

Seminar of Department of Botany and Centre of Excellence EcolChange

Speaker: Bengt-Gunnar Jonsson is Professor of Plant Ecology at Mid Sweden University. His research focuses on forest history and dynamics and its role in maintaining forest biodiversity. He has played an active role in several national conservation projects initiated by the Swedish Environmental Protection Agency and the Swedish Forest Agency. He is the author and editor of number of books, including “Biodiversity in dead wood“. Prof. Jonsson is also a lead author of IPBES (Intergovermental Science-Policy Platform on Biodiversity and Ecosystem Services) European and Central Asia assessment, focusing on topics of forestry and forest land use.

Title of the talk: Coping with the loss of the last – the Scandinavian Green Belt and boreal forest green infrastructure in the northern Sweden

Time: Wednesday, 17. October 2018 at 15.15

Place: Tartu, Lai 40-218 (Vaga auditorium)


Boreal forest (pic from here)

Posted in Event | Tagged , , , , , | Leave a comment

Two more global citizen science networks calling for participants – FunLeaf and FunHome

Last week we had a post about DarkDivNet, a global network to explore the dark diversity of plant communities, instigated by Meelis Pärtel´s macroecology workgroup in the University of Tartu.

Now the Natural History Museum in Tartu, led by Urmas Kõljalg, has started with two global citizen science networks: FunLeaf to study the diversity of fungi and bacteria living in and on plant leaves; and FunHome to study the diversity of microscopic organisms living in the dusty corners of our homes.

Below you can find a little overview of both projects, for more information click the links to project web pages.

Cleaner dusts the letters of a book.

This is literally how you can do science, although not all the are nucleotides depicted with the right letter symbols… (pic from here)

FunLeaf (link to project page)

All parts of plants harbour many microscopic organisms. Especially plant leaves are an important habitat for many fungal and bacterial species that live inside or on the surface of these organs. Yet, very little is known about the diversity and distribution of these microorganisms in relation to habitat, seasonality and geographical space.

This citizen science project, led by well-recognized researchers, aims to describe the biodiversity of organisms associated with plant leaves across the globe. By using DNA-based methods for identification, scientists aim to determine the environmental features that lead to increase or loss of leaf biodiversity. Mathematical models enable to estimate total species richness of microorganisms on leaves to add one piece to the puzzle of global biodiversity.

This project seeks for volunteers who wish to contribute to understanding of complexity of life on the Earth. Participants are given simple protocols for collecting and sterilizing and posting leaf samples. The DNA of dead organisms is analysed only for identification purpose in one or more central laboratories. The results are communicated to participants over the web in each major analysis step. The principal idea of involving citizen science is to bridge frontline research and common people and to shed light on global issues among the public.


FunHome (link to project page)

Households of families harbour dust, which is comprised of particles of fibers and skin and many other biological components including pollen, parts of arthropods and various microscopic organisms. These nutrient-rich substances serve as a substrate for mites and moulds, many of which are severe allergens. Some information exists about the diversity of bacteria and fungi in dust in US homes (doi:10.1073/pnas.1420815112), but information about other organisms and from the entire world is almost lacking (doi:10.1073/pnas.1000454107).

The FunHome citizen science project extends from another public project focused on homes in USA (, which has received abundant public feedback and resulted in international scientific publications. The FunHome project is initiated by leading researchers in microbial ecology, with an objective to describe the biodiversity of microbes, plants and animals in household dust across the globe. By using DNA-based methods for identification, scientists aim to determine the global distribution patterns of dust-associated organisms with a focus on particularly toxin-producing species.

Hereby, the project leaders invite volunteers to contribute to a global understanding about the biological composition of dust in the home environment. Participants are provided simple protocols for collecting and storing and posting dust samples. The DNA from dust is analysed in a single central laboratory in the University of Tartu, Estonia. The results are communicated to participants over the web after major analysis steps.


Posted in Fieldwork/Experiment | Tagged , , , , , , , , | Leave a comment

New publication – Non-native species led to marked shifts in functional diversity of the world freshwater fish faunas

Text by Aurele Toussaint

The biodiversity of freshwater fish fauna disturbed by invasive species

Non-native species introductions are recognized as one of the major drivers responsible of the ongoing sixth biodiversity crisis, along with climate change, pollution and habitat loss. However, this factor is most often only addressed in terms of increasing or decreasing in number of species, leaving unclear its impact on the functional diversity of communities (i.e. the diversity of ecological roles provide by species in ecosystems). An international team of researchers from the Institute of Ecology and Earth Sciences (Department of Botany/ University of Tartu/ Estonia), the Evolution and Biodiversity Laboratory (EDB – CNRS / University of Toulouse III Paul Sabatier / IRD) and the Center for Marine Biodiversity, Exploitation and Conservation (MARBEC – CNRS / University Montpellier / IRD / Ifremer) has just shown that while the number of fish species per river increased on average by 15% in the world’s rivers, the diversity of their functional attributes increased on average by 150% under the pressure of non-native fish introductions. These results, published in the November issue of the journal Ecology Letters, highlight the need to consider different facets of biodiversity in order to evaluate the impact of biological invasions on ecosystems.

Human activities has promoted biotic exchanges between regions for centuries, for food, commercial, ornamental and even involuntary purposes by carrying organisms unknowingly. As a result, several hundreds of species of freshwater fish are now established outside their native area. The survey of these introductions in the rivers of the world is rather well known and has already shown that the non-natives species introductions have resulted in an increase of about 15%, on average, of the number of species per river. However, it remained to be tested whether these non-native species share or not similar ecological characteristics to the species already present (native species) and therefore have or not led to an increase in the functional diversity of the communities. Toward this goal researchers have measured the morphological traits associated with locomotion and nutrition for more than 9,000 species of freshwater fish out of the 13,000 currently known. We demonstrated in this study that the 15% average increase in the number of species per river simultaneously caused an unexpected 150% increase of the functional diversity of the community!

While the very large rivers, such as the Amazon or Mississippi, have undergone few functional changes under the introduction of non-native species, the small rivers have undergone an explosion of their functional diversity because the introduced species have very different ecological traits from those of the species already present. This trend is particularly striking in arid and Mediterranean rivers, which naturally host few highly specialized species. Thus, in the Alpes-Maritimes for example, the Siagne river hosts historically 9 fish native species, but received under the effect of the human activities 6 non-native species. Among them the Carp, originating from Asia and Black Bass native to North America which have multiplied the original functional diversity of the community by more than 40.

More generally, at the world scale, we observed an increase in the average body size of fishes and an overrepresentation of laterally flattened species (such as carp or black bass) in communities under the introduction pressure. These functional changes are probably related to the effects of dams that favor the establishment of non-native species able to move and survive in a stagnant environment.

As conclusion of this study, we already knew that non-native species have a strong impact on the taxonomic diversity worldwide but we here demonstrate that considering the functional role of organisms is clearly a key point in order to better understand the impact of non-native species on biological communities.

aurele fish

World maps representing the changes in biodiversity due to non-native species introductions in terms of number of species (top) and in functional diversity (low)

Citation: Toussaint, A., Charpin, N., Beauchard, O., Grenouillet, G., Oberdorff, T., Tedesco, P. A., … & Villéger, S. (2018). Non‐native species led to marked shifts in functional diversity of the world freshwater fish faunas. Ecology Letters, 21: 1649–1659 (link to full text)



Global spread of non‐native species profoundly changed the world biodiversity patterns, but how it translates into functional changes remains unanswered at the world scale. We here show that while in two centuries the number of fish species per river increased on average by 15% in 1569 basins worldwide, the diversity of their functional attributes (i.e. functional richness) increased on average by 150%. The inflation of functional richness was paired with changes in the functional structure of assemblages, with shifts of species position toward the border of the functional space of assemblages (i.e. increased functional divergence). Non‐native species moreover caused shifts in functional identity toward higher body sized and less elongated species for most of assemblages throughout the world. Although varying between rivers and biogeographic realms, such changes in the different facets of functional diversity might still increase in the future through increasing species invasion and may further modify ecosystem functioning.

Posted in New publication | Tagged , , , , , , , , | Leave a comment

New publication – Didymocyrtis trassii sp. nov. and other lichenicolous fungi on Cetraria aculeata

Text by Lauri Laanisto

Time for another taxonomy paper about fungi. (The previous blogpost about that can be found from here.) This time about new species that grow on lichens, specifically Cetraria aculeata. Genus Cetraria is called cuckoo´s ear in Estonian, by the way… One of the species that was found from these cuckoo ears in Ukranian sand dunes appeared to be new to species. And this species is now called Didymocyrtis trassii. Another trivia fact about names – Didymocyrtis is both a genus of fungi, but also a genus of Radiolaria (protozoa).


Didymocyrtis the radiolara (pic from here)


Didymocyrtisthe fungus (pic from here)

But in our case, the most important name here is trassii, the epithet of the new fungus species. The species is named after recently deceased Hans Trass (1928-2017), a renowned Estonian lichenologist. By the way he was first to publish how certain lichen species indicate air quality – e.g. bioindicators. Hans Trass was also the head of Botany and Ecology department for more than 30 years, and most of the PIs of EcolChange still work or have previously worked in this department under the Peremees – this was his nickname. (Including yours truly.)


Hans Trass (pic from here)

Citation: Khodosovtsev, A., Darmostuk, V., Suija, A., & Ordynets, A. (2018). Didymocyrtis trassii sp. nov. and other lichenicolous fungi on Cetraria aculeata. The Lichenologist, 50(5), 529-540. (link to full text)


Recently, nine species of lichenicolous fungi were found growing on Cetraria aculeata (Parmeliaceae) in a sand dune system in the Ukraine. One of them, Didymocyrtis trassii, is described here as new to science. This species is similar to D. pseudeverniae but differs in having smaller pycnidia, smaller obpyriform to clavate conidia as well as its DNA sequence. The new monotypic lichenicolous genus Katherinomyces is described here. Acremonium lichenicola s. l., Eonema pyriforme, Didymocyrtis cladoniicola and Lichenoconium erodensare reported for the first time on Cetraria aculeata. Furthermore, E. pyriforme is reported for the first time from lichen thalli. Acremonium lichenicola, E. pyriforme and Taeniolella rolfiiare new for the mycobiota of the Ukraine. A key to the eleven known lichenicolous species on Cetraria aculeata is provided.

Posted in New publication | Tagged , , , , , , , | Leave a comment