New publication – Predicting species establishment using absent species and functional neighborhoods

Text by Meelis Pärtel and Jonathan Bennett

Understanding which species establish in which habitats is fundamental to community ecology and to more applied pursuits, such as the restoration of degraded sites and the prevention of invasion by exotic species. Jonathan Bennett and Meelis Pärtel from macroecology workgroup of the University of Tartu developed a method that compares the characteristics of species across the regional species list, the site-specific species pool and locally observed species to predict which other species will be able to establish. As part of this method, we developed a new way to measure dissimilarity among species which we call functional neighborhood distances. Using this method in Estonian grasslands, we were able to predict approximately 50% of species establishment from seed, indicating that the new method may be a robust means to predict establishment and potentially invasion.

Citation: Bennett, J. A., & Pärtel, M. (2017). Predicting species establishment using absent species and functional neighborhoods. Ecology and Evolution, DOI: 10.1002/ece3.2804 (link to full text)

bennett ja pärtel

FIG 2 from the paper: A hypothetical example showing how different functional distance measures may affect our interpretation of establishment probabilities. Panel (a) shows the distribution of species in functional space, where gray circles represent biotically excluded species and white circles species present in the community. The letters A and B represent two potential colonists. Both species are similarly distant from their nearest neighbor (b). As species A is closer to the mean trait value for the observed community than species B, species B has a higher mean distance to species within the community than A (c). Using the mean distance to species within the functional neighborhood (dashed circles), there is little difference between species A and B (d)

Species establishment within a community depends on their interactions with the local environment and resident community. Such environmental and biotic filtering is frequently inferred from functional trait and phylogenetic patterns within communities; these patterns may also predict which additional species can establish. However, differentiating between environmental and biotic filtering can be challenging, which may complicate establishment predictions. Creating a habitat-specific species pool by identifying which absent species within the region can establish in the focal habitat allows us to isolate biotic filtering by modeling dissimilarity between the observed and biotically excluded species able to pass environmental filters. Similarly, modeling the dissimilarity between the habitat-specific species pool and the environmentally excluded species within the region can isolate local environmental filters. Combined, these models identify potentially successful phenotypes and why certain phenotypes were unsuccessful. Here, we present a framework that uses the functional dissimilarity among these groups in logistic models to predict establishment of additional species. This approach can use multivariate trait distances and phylogenetic information, but is most powerful when using individual traits and their interactions. It also requires an appropriate distance-based dissimilarity measure, yet the two most commonly used indices, nearest neighbor (one species) and mean pairwise (all species) distances, may inaccurately predict establishment. By iteratively increasing the number of species used to measure dissimilarity, a functional neighborhood can be chosen that maximizes the detection of underlying trait patterns. We tested this framework using two seed addition experiments in calcareous grasslands. Although the functional neighborhood size that best fits the community’s trait structure depended on the type of filtering considered, selecting these functional neighborhood sizes allowed our framework to predict up to 50% of the variation in actual establishment from seed. These results indicate that the proposed framework may be a powerful tool for studying and predicting species establishment.
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EcolChange seminar – Ülo Mander about the consequences of man-made changes to nitrogen cyclon

Seminar of the Centre of Excellence EcolChange

Ülo Mander is professor at the Department of Geography, University of Tartu.

Man-made alterations of nitrogen cycling: global and regional consequences

Time: Thursday, 16. March 2017 at 15.15

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


Ülo Mander with couple of manuscripts (pic from here)


During the last 70 years, the reactive nitrogen cycling in the biosphere has been significantly intensifying. Globally, about a half of this cycling is caused by anthropogenic activities. Among several environmental consequences, nitrate contamination of water bodies and groundwater, as well as increasing emission of nitrous oxide (N2O), the dangerous greenhouse gas and the main ozone layer depletion agent, can be highlighted. In this presentation results from three projects will be presented: (1) the global effect of peatland drainage on nitrogen cycling, especially focusing on relations between the N2O emissions and controlling environmental and microbiological factors (denitrification genes); (2) nitrogen budget dynamics in full-drained peatland forests in Estonia; (3) mitigation of nitrate contamination of intensively managed agricultural catchments using artificial wetlands (the French experience).

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New paper published – Arbuscular mycorrhizal fungal communities in forest plant roots are simultaneously shaped by host characteristics and canopy-mediated light availability

Text by Kadri Koorem

Recent years have been ground-breaking in describing the diversity patterns of arbuscular mycorrhizal (AM) fungi. These microscopic fungi live in plant roots and receive carbon compounds from the plant in exchange of nutrients. In natural conditions, one plant individual can harbour more than ten taxa of AM fungi. Interestingly, AM fungal communities in the roots of plants in same habitat can be remarkably different. However, we have little information what determines the composition of AM fungi in plant roots and with this study we aimed to contribute to filling this gap.

In the presence of forest canopy, shade-avoidant plant species have been shown to harbour less diverse AM fungal community in their roots than shade-tolerant plant species. We hypothesized that this due to carbon deficiency and in the absence of forest canopy, shade-avoidant plant species can increase their photosynthetic capacity and become associated to more diverse AM fungal community, similarly to shade-tolerant plants. We sampled shade-tolerant and shade-avoidant plant species in the presence and absence of forest canopy. In all plant individuals, we recorded photosynthetic capacity and the composition of AM fungal communities in their roots.

Results of this study indicated that all, but especially shade-avoidant plants have higher photosynthetic capacity in the absence of forest canopy. AM fungal communities, associated to shade-avoidant and shade-tolerant species remained distinctive under the canopy and indeed become more similar in the absence of forest canopy. Interestingly the change in the AM fungal communities was bigger in the roots of shade-tolerant plants, which experienced smaller increase in photosynthetic capacity. Thus it seems that host plant characteristics as well as environment influence AM fungal communities in plant roots but the mechanisms need to be examined further.

Citation: Koorem, K., Tulva, I., Davison, J., Jairus, T., Öpik, M., Vasar, M., Zobel, M, & Moora, M. (2017). Arbuscular mycorrhizal fungal communities in forest plant roots are simultaneously shaped by host characteristics and canopy-mediated light availability. Plant and Soil, 410(1-2), 259-271. (link to full text)


Kadri explaining some research-related stuff (pic from here)


Background and Aims The majority of terrestrial plant species associate with arbuscular mycorrhizal (AM) fungi, to exchange carbon compounds with nutrients. However, the factors that determine the composition of AM fungal communities in individual plant roots remain poorly understood. We hypothesized that AM fungal communities are simultaneously influenced by environmental conditions, such as light availability, and the photosynthetic capacity of host plant species.

Methods We sampled individuals of shade-tolerant and shade-avoidant plant species, growing in the presence and absence of forest canopy, representing conditions of low and high light availability. We recorded photosynthetic parameters, shoot biomass and root AM fungal colonisation of these plant individuals and used 454-sequencing to characterise AM fungal communities in the roots of these plants.

Results Shade-avoidant plant species increased their photosynthetic capacity more than shade-tolerant plant species as a response to increased light availability due to canopy removal. Root AM fungal colonisation of all plants was higher when the forest canopy was absent, but canopy status had little influence on AM fungal richness in plant roots. The composition of AM fungal communities associating with shade-tolerant plants was significantly influenced by canopy status, while a less pronounced difference was observed among shade-avoidant plants.

Conclusions We suggest that both environmental conditions and the ability of plant species to exploit available resources determine the dynamics of mutualistic associations between host plant species and AM fungal taxa.

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EcolChange seminar – Carlos Carmona on trait probability densities

Seminar of the Centre of Excellence EcolChange

Carlos P. Carmona is researcher at the macroecology workgroup of the Department of Botany, University of Tartu.

Trait probability densities: probabilistic hypervolumes in ecology and beyond

Time: Thursday, 9nd. March 2017 at 15.15

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


Somehow all the niche memes out there are of Eltonian nature…


Hutchinson’s idea of niches as multidimensional hypervolumes has long inspired ecologists. However, practical use of hypervolumes has not been feasible until recent times, when advances in computational resources and data availability are allowing to estimate them. In particular, functional-trait based ecologists have been attempting to incorporate this appealing concept for more than a decade. In this seminar, I will present an overview of existing hypervolume-based methods to estimate the functional niche of species, along with their respective strengths and weaknesses. I will then show how the adoption of a probabilistic-based idea of the niche can serve to build a unified framework that allows estimating any aspect of functional diversity at all scales while also considering the role of intraspecific variability. Finally, I will provide some examples of practical uses of this framework in a purely ecological context as well as in other fields.

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Congratulations – Martin Zobel 60!

Text by Lauri Laanisto

A week ago, academician, and the professor of Plant ecology in the University of Tartu, and also one the team leaders in EcolChange, Martin Zobel, celebrated his 60th birthday. All the best wishes to him!

Incidentally, his seminal paper about species pool: “The relative of species pools in determining plant species richness: an alternative explanation of species coexistence?” (link to full text) was published in TREE exactly 20 years ago. So, back then he was 40. It´s his most cited first author paper, which to this day gets nearly 50 new citations annually.

And on a personal note – this text is the most influencial for me. It has more or less set the ground rules to what and how I have been studying stuff. Thanks!


i don´t know for sure but that picture of MZ is probably taken around late 1990s


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New paper published – Trait assembly in grasslands depends on habitat history and spatial scale

Text and pic by Liina Saar

Recently published paper by Liina Saar, Meelis Pärtel and Aveliina Helm together with Francesco de Bello from Czechia (University of South Bohemia) in Oecologia revealed that grasslands with regular and long management history are assembled differently from abandoned grasslands and young developing grasslands, although these habitats seem visually similar. Results of this study showed that long-term management of grasslands allows small-scale coexistence of many species with different life-history traits and habitat requirements, whereas in abandoned or young grasslands, species with more similar characteristics and requirements co-exist. Understanding the mechanisms behind species assembly and their relationship with land-use history is vital for habitat conservation and restoration, as well for mitigating the effects of global change.

Citation: Saar, L., de Bello, F., Pärtel, M., & Helm, A. (2017). Trait assembly in grasslands depends on habitat history and spatial scale. Oecologia, DOI: 10.1007/s00442-017-3812-9 (link to full text)


Although the theory used to infer the mechanisms behind assembly patterns has been widely discussed in the literature, the empirical results vary across different spatial scales, species pool sizes, habitat types or across studied traits. Less is known how assembly mechanisms vary in dynamic landscapes subjected to changes in land-use history.

What was done?

We studied the community assembly in grassland habitats with differing land-use history, from historical grasslands to dynamic ones, focusing on principal life-history traits and combining several spatial scales. We used novel functional species pool framework proposed by de Bello et al. (2012). This method tests the trait assembly patterns (divergence or convergence) at finer scales in comparison with the patterns at broader scales (species pool), which better distinguishes biotic and dispersal-related effects from environmental filtering. By analysing the trait distribution and mean trait values it is possible to detect main processes driving assembly. For different scales of observations, we used (1) plot scale, consisting of species from the 2×2 m sample plots, (2) local community scale, consisting of species in the area surrounding the 2×2 m plots, and (3) habitat-specific species pool at the broadest scale, compiled as cumulative list of species sampled from 35 sites of respective grassland type.

What was found and what it means?

Our study showed that species assembly patterns in grasslands depend both on habitat history and on the spatial scale considered (Figure 1). Mostly random or divergent co-occurrence patterns characterised diverse fine-scale vegetation in grasslands with long continuous management history. Strong convergence patterns were detected in former and developing grasslands, indicating filtering effects of biotic interactions (exclusion of weaker competitors) and dispersal limitation. Dominance of certain trait values in dynamic grasslands indicate the need for changes in management activity and necessity for more active conservation in order to improve habitat environmental conditions for allowing more species from species pool to co-exist in a habitat.

At broader scales, mostly convergence patterns prevailed in all grassland types (Figure 1b). Differing trait patterns at finer and broader spatial scales indicate different mechanisms governing species assembly at different scales and development stages.


Figure 1 The mean trait dissimilarity (indicated with the effect size) between species a filtered from the local community to 2 × 2 m plots and b from the habitat species pool to local communities in grasslands with different development histories across all analysed traits (dispersal mechanism, life span, main pollen vector, mean plant height, mean seed weight, mode of reproduction, specific leaf area, terminal velocity). The dotted line indicates that effect size is zero, results above zero indicate ‘divergence’, below zero ‘convergence’. Grey boxplots indicate that the effect size significantly differs from zero (P < 0.05). In box plots, the median for each data set is indicated by the heavy central line, and the first and third quartiles are the lower and upper edges of each box, which is known as the interquartile range (IQR). Individual points indicate outliers (within 1.5 times the interquartile range from the upper or lower quartile)



During the past century, grasslands in Europe have undergone marked changes in land-use, leading to a decline in plant diversity both at local and regional scales, thus possibly also affecting the mechanisms of species sorting into local communities. We studied plant species assembly in grasslands with differing habitat history and hypothesized that trait divergence prevails in historical grasslands due to niche differentiation and trait convergence prevails in more dynamic grasslands due to competitive exclusion and dispersal limitation. We tested these hypotheses in 35 grassland complexes in Estonia, containing neighbouring grassland habitats with different land-use histories: continuously managed open historical grassland, currently overgrown former grassland and young developing grassland. We assessed species assembly patterns in each grassland type for finer scale – a 2×2 m plot scale from a local community pool and for broader scale – a local community from the habitat species pool for that grassland stage and observed changes in trait means at finer scale. We found that grasslands with long management history are assembled differently from former grasslands or young developing grasslands. In historical grasslands, divergence or random patterns prevailed at finer scale species assembly while in former or developing grasslands, mostly convergence patterns prevailed. With increasing scale convergence patterns become more prevalent in all grassland types. We conclude that land-use history is an important factor to consider when assessing grassland functional trait assembly, particularly at small scales. Understanding the mechanisms behind species assembly and their relationship with land-use history is vital for habitat conservation and restoration.


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New paper published – Secondary succession in alvar grasslands – do changes in vascular plant and cryptogam communities correspond?

Text by Lauri Laanisto & Martin Zobel

Alvar grasslands are probably one of the better-studied ecosystems in Europe. They are narrowly distributed in Swedish islands, Estonia, and tiny bits also in western Russia near St Petersburg. (Though, rather similar ecosystems can be also found around the Great Lakes area, in Northern America.) And somehow it has also happened that the density of good plant ecologists is also high in aforementioned countries…

Although we already know quite a lot about how alvar ecosystems function – from historical and large-scale processes building up species richness (for example this one) to disturbance practices and short-term diversity dynamics (for example that one) -, there are still some blank spots in our knowledge. This particular study tried to cover one of these – secondary succession dynamics of often overlooked bryophytes and lichens in alvar communities, and how does it correspond with plant secondary succession dynamics in the same communities.

For that the covariation of plants, bryophyes and lichens was recorded in several alvars in different successional stages (young, intermediate, mature). The results indicate, as empirically predictable, that from the richness point of view plants have the fastest successional dynamics, then come bryophyes, and the lichens are the slowest. However, the changes in all life forms, whether in the abundance or diversity, happened rather concurrently. Different life forms seem to be associated in different successional stages, it´s just that bryophes and especially lichens need more time to arrive.

Citation: de León, D. G., Neuenkamp, L., Gerz, M., Oja, E., & Zobel, M. Secondary succession in alvar grasslands–do changes in vascular plant and cryptogam communities correspond?. Folia Geobotanica, DOI: 10.1007/s12224-016-9260-1 (link to full text)


There can be a lot of bryophytes and lichens in alvars – Atla alvar in Saaremaa island, Estonia (pic from here)


Although bryophytes and lichens are frequently vital components of aboveground communities, their interrelationships with vascular plant communities are poorly known. We addressed small-scale covariation of vascular plant and cryptogam (bryophytes and lichens) communities during secondary succession from abandoned gravel pit towards thin soil calcareous (alvar) grassland communities. The cover, richness and diversity of vascular plants, bryophytes and lichens were studied. Whereas vascular plants showed the fastest successional dynamics in terms of richness, bryophytes showed a fast successional dynamic in terms of cover and diversity; the establishment of lichens was the slowest. THe cover, richness and diversity of different life forms changed concurrently. There were significant associations among the species composition of all life forms considered. The strongest relationship was found between lichens and vascular plants in mature stages. We conclude that alvar grasslands are certainly an example of a community in which the association between the vascular plant and the cryptogam communities may influence the overall vegetation succession, and the strength of this association increases during secondary succession.

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EcolChange seminar on 2nd of March – Arne Sellin talks about the effect of air humidity on tree growth

Seminar of the Centre of Excellence EcolChange

Docent of plant ecophysiology and the head of the chair of ecophysiology at the Department of Botany, University of Tartu, Arne Sellin, will give a talk titled:

Growth of northern deciduous trees under increasing atmospheric humidity: possible mechanisms behind the growth retardation

Time: Thursday, 2nd. March 2017 at 15.15

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


Arne Sellin


The growth reduction in response to increasing air humidity appears to be species specific, with larger reductions for hybrid aspen than for silver birch. The impact of elevated humidity on tree functioning is complex; there is no certain single mechanism behind the growth retardation. The magnitude of the effects and dominating mechanism depend on particular conditions (and thus on other environmental drivers), especially weather conditions prevailing during the growing period. The expected climate-change-induced increase in the growth rate of trees in northern temperate and boreal areas due to an earlier start of the growing season and higher carbon assimilation rate could be smaller or absent if temperature rise is accompanied by a rise in atmospheric humidity.

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EcolChange seminar on 16th of February – Marju Himma about communicating science

Seminar of the Centre of Excellence EcolChange

Researcher and PhD student of media and communication at University of Tartu and Editor in Chief of Estonian Public Broadcasting, Marju Himma, will give a talk titled:

Communicating science

Time: Thursday, 16. February 2017 at 15.15

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


Marju himma (on the left) doing her daily job of communicating science (pic from here)


1) Triangulation of information between science, public sphere and policy makers. In the age of information/data overload the decision-making is getting more complex, which presents a challenge in communicating science in public and policy makers. Otherwise we face the situation of “alternative facts”, misleading information and poor decision making on all levels. One of the solutions in this situation is:

2) Empowerment of scientists and researchers in communication. I bring some examples where the voice of the scientists is essentially needed: Reaching the goal of 1 %of GDP in Estonian state budget was set in 2014, but in 2017 it was 0.86%; the transition of science and research into knowledge based society in Estonia is poor compared to e.g. Finland or other Scandinavian countries; people are making everyday decisions based on pseudo-scientific or fabricated information.

Advocacy is the buzzword we hear in political communication, journalism etc., but there are not too many examples in science and research. This places scientists in the position where their voice is less heard both in public and in the process of policy making. Therefore we need to empower scientists and researchers to communicate directly to public in order to change the previous examples.

3) In the light of the previous two statements I propose five practical suggestions for efficient science communication.

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New paper published – Community response to alkaline pollution as an adjusting re-assembly between alternative stable states

Text by Ave Suija and Jaan Liira

The schematic representation of community adaptive responses on environmental changes, supported by meta-pool of species (fig by Jaan Liira)

Man made disturbances and environmental pollution are the reality of contemporary world, however, such long-term created environmental gradients are handy to describe ecological processes (community dynamics) otherwise difficult to observe in natural conditions or test in experiments. We assumed that at regional scale, many community responses should not be always interpreted as a degradation, but as a part of the long-term dynamic equilibrium of various community states, if they are supported by different environment-specific species pools, harboured in different habitats. At the regional scale, such spatially clustered pool system forms a meta-pool of species. A community degradation should be declared only when the meta-pool cannot support the community’s switching between alternate states. The difficulty in applied ecology relies in adequate delineation and evaluation of these alternate states – usually, expert knowledge or species niche data have been used, but their accuracy has been sometimes questioned. A different approach is to compare new community states to other communities in the region, as they harbour alternative species pools within meta-pool.


Exteme pH of tree bark near the cement factory in Kunda, Estonia (pic by Jaan Liira)

We studied the re-assembly of lichen community on Scots pine (Pinus sylvestris) in response to the long-term alkaline dust pollution around a cement factory. Along pollution gradient we observed (1) the change of substrate (pine bark) pH from very acid to pH analogous to limestone, and (2) a respective alteration of natural community to unusual to pine lichen communities. The loss of diversity reflected the difference between source species pools. We found also that (3) expert knowledge (ecological indicator values) can reflect the overall trend, however, it does not describe humped variability of niche range of species, the divergence in alternate community states two different reference communities, add the revealed hidden interaction between limiting environmental drivers (specifically substrate pH and understorey density).

The study indicates that community responses to man-made disturbances should be interpreted with care, particularly as community reformations take long time assuming the availability of respective species sources. Still, as disturbance intensity may change over time by improving technologies or policies, such alterations can be reversed, if original pools are preserved somewhere in the neighbourhood.

Citation: Suija, A., & Liira, J. (2016). Community response to alkaline pollution as an adjusting reassembly between alternative stable states. Journal of Vegetation Science, DOI: 10.1111/jvs.12506 (link to full text)


Exposed thick layer of accumulated cement dust inside the moss layer in Kunda, Estonia (pic by Jaan Liira)



We hypothesize that the community response to disturbances can be interpreted as a large-scale dynamic equilibrium between multiple alternate states stemming from different species pools within a regional meta-pool and being limited by species’ multi-dimensional niches. We explore this hypothesis by examining the re-assembly of an acidophilous lichen community in response to long-term alkaline dust pollution, assuming understorey as a potential side-factor.


Around a cement factory in Kunda, Estonia.


Lichen communities on Scots pine (Pinus sylvestris) trunks in 40 stands around a cement factory and in nine distant limestone habitats were assessed.


The formed bark pH gradient from pH 2.4 to 8.1 was reflected in a continuum of lichen communities on pines from acidophilous to basidophilous communities. Besides suppressing species richness, understorey density more evidently caused the compositional divergence from neutral bark conditions. The effect of hidden interactions among drivers was explained through reactions of individual species – almost all species across the pollution gradient were pH-limited, whereas species adapted to neutral or alkaline substrate were additionally sensitive to understorey conditions. The hump-shaped distribution of pH niche ranges along the observed niche optima, rather than ecological indicator values, showed that the shape of species’ multi-dimensional niche-space still needs to be quantified.


Each alternative community state along the disturbance gradient represents a realization of its specific species pool within the meta-pool. Degradation can be defined if the community state is not supported by a meta-pool. Species infiltration during community re-assembly can be predicted using species source communities as cost-efficient proxies.

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