New publication – The Taxon Hypothesis Paradigm—On the Unambiguous Detection and Communication of Taxa

Text by Urmas Kõljalg

In this paper we described the taxon hypothesis (TH) paradigm, which covers the construction, identification, and communication of taxa as datasets. Defining taxa as datasets of individuals and their traits will make taxon identification and most importantly communication of taxa precise and reproducible. This will allow datasets with standardized and atomized traits to be used digitally in identification pipelines and communicated through persistent identifiers. Such datasets are particularly useful in the context of formally undescribed or even physically undiscovered species if data such as sequences from samples of environmental DNA (eDNA) are available. Implementing the TH paradigm will to some extent remove the impediment to hastily discover and formally describe all extant species in that the TH paradigm allows discovery and communication of new species and other taxa also in the absence of formal descriptions. The TH datasets can be connected to a taxonomic backbone providing access to the vast information associated with the tree of life. In parallel to the description of the TH paradigm, we demonstrated how it is implemented in the UNITE digital taxon communication system. UNITE TH datasets include rich data on individuals and their rDNA ITS sequences. These datasets are equipped with digital object identifiers (DOI) that serve to fix their identity in our communication. All datasets are also connected to a GBIF taxonomic backbone. Researchers processing their eDNA samples using UNITE datasets will, thus, be able to publish their findings as taxon occurrences in the GBIF data portal. UNITE species hypothesis (species level THs) datasets are increasingly utilized in taxon identification pipelines and even formally undescribed species can be identified and communicated by using UNITE. The TH paradigm seeks to achieve unambiguous, unique, and traceable communication of taxa and their properties at any level of the tree of life. It offers a rapid way to discover and communicate undescribed species in identification pipelines and data portals before they are lost to the sixth mass extinction.

Reference: Kõljalg, U., Nilsson, H. R., Schigel, D., Tedersoo, L., Larsson, K. H., May, T. W., … & Põldmaa, K. (2020). The Taxon Hypothesis Paradigm—On the Unambiguous Detection and Communication of Taxa. Microorganisms, 8(12), 1910. (link to paper)

Pic from here

Abstract:

Here, we describe the taxon hypothesis (TH) paradigm, which covers the construction, identification, and communication of taxa as datasets. Defining taxa as datasets of individuals and their traits will make taxon identification and most importantly communication of taxa precise and reproducible. This will allow datasets with standardized and atomized traits to be used digitally in identification pipelines and communicated through persistent identifiers. Such datasets are particularly useful in the context of formally undescribed or even physically undiscovered species if data such as sequences from samples of environmental DNA (eDNA) are available. Implementing the TH paradigm will to some extent remove the impediment to hastily discover and formally describe all extant species in that the TH paradigm allows discovery and communication of new species and other taxa also in the absence of formal descriptions. The TH datasets can be connected to a taxonomic backbone providing access to the vast information associated with the tree of life. In parallel to the description of the TH paradigm, we demonstrate how it is implemented in the UNITE digital taxon communication system. UNITE TH datasets include rich data on individuals and their rDNA ITS sequences. These datasets are equipped with digital object identifiers (DOI) that serve to fix their identity in our communication. All datasets are also connected to a GBIF taxonomic backbone. Researchers processing their eDNA samples using UNITE datasets will, thus, be able to publish their findings as taxon occurrences in the GBIF data portal. UNITE species hypothesis (species level THs) datasets are increasingly utilized in taxon identification pipelines and even formally undescribed species can be identified and communicated by using UNITE. The TH paradigm seeks to achieve unambiguous, unique, and traceable communication of taxa and their properties at any level of the tree of life. It offers a rapid way to discover and communicate undescribed species in identification pipelines and data portals before they are lost to the sixth mass extinction.

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EcolChange seminar – Tanel Vahter about fungal diversity in cropfields

Seminars of Department of Botany and Centre of Excellence EcolChange

Speaker: Tanel Vahter is a PhD student in the Plant Ecology group in our Department, Tartu University. His research focuses on the application of arbuscular mycorrhizal fungi for vegetation restoration but also on fungal communities in Estonian fields and grasslands.

Title of the talk: Fungal diversity in Estonian agricultural soils

Time: Thursday, 10. Decmber 2020 at 14.15

Place: Tartu, Lai 40-218 (Vaga auditorium), or virtual link in the MS Teams group (link for seeing the seminar online, without any logging in etc.).

Summary: While large-scale studies of soil fungal diversity have vastly increased our breadth of knowledge about the ecology of soil fungi, there is still little known about the effects of management where “the rubber meets the road”. Agricultural soils represent a real-life living laboratory, where manipulations of the soil ecosystem can highlight processes and factors important for natural systems alike. In this seminar, i will be presenting the results of a recent soil fungal diversity study in Estonian agricultural fields, linking realised diversity patterns with management and environmental subsidy.

The event is virtual. The link to join the team: https://teams.microsoft.com/l/team/19%3ae3b94de81e5743abbacf128f50404a78%40thread.tacv2/conversations?groupId=f24fbdc9-665c-4756-af7c-fbabada99223&tenantId=6d356317-0d04-4abc-b6b6-8c9773885bb0

After the official seminar, you are welcome to stay longer in the video call to chat with colleagues during a virtual cake and coffee/tea. Please bring your own “sweet supplies” though.

Tanel in lab. (pic from Postimees)

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EcolChange seminar – Timo Maran about semiotics in ecology

Seminars of Department of Botany and Centre of Excellence EcolChange

Speaker: Prof. Timo Maran is Professor in Ecosemiotics and Environmental Humanities at Tartu University. His research focuses on the connection between ecology and semiotics, for example in multispecies environments (e.g. urban nature) and their effect on nature protection and communication.

Title of the talk: Semiotics in Ecology and Environmental Studies

Time: Thursday, 26. November 2020 at 14.15

Place: Tartu, Lai 40-218 (Vaga auditorium), or virtual link in the MS Teams group (link for seeing the seminar online, without any logging in etc.).

Summary: The fundamental connection between ecology and semiotics is that both fields give to relations a principal ontological position. In this presentation, I will give an overview of different ways how semiotics has been incorporated into ecological studies and what could be future perspectives of such synthesis. Most notably, Italian semiotician and landscape ecologist Almo Farina has developed the method of ecofield analysis that combines Umwelt theory with spatial description of landscapes and allocation of resources. From a semiotic perspective we could also describe interspecies communicative regularities and conventions in ecosystems as ecoacoustic codes or ecological codes. System ecology have further argued about the role of informational layer (Søren N. Nielsen’s semiotype) and feedback cycles in retaining stability and resilience of ecosystems. In environmental studies a number of concepts (e.g. semiotic pollution, dissent) have been applied for critical treatment of human effects of the environment. These developments have led to the formation of ecosemiotics (also semiotic ecology) starting from in 1990ties as an explicit synthesis of ecology and semiotics.

For everyone to stay as healthy as possible, please be reminded that wearing a face mask is mandatory. Please bring your own mask. Most importantly, don’t attend when you feel sick.

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EcolChange seminar – Eveli Otsing about the richness patterns of trees and fungi

Seminars of Department of Botany and Centre of Excellence EcolChange

Speaker: Eveli Otsing is a PhD student in our Department in the Ecology of Biological Interactions workgroup. Her research aims to shed more light onto the connections between trees (i.e. their species richness) and fungal community richness. Eveli Otsing will defend her PhD thesis this December.

Title of the talk: Tree species effects on fungal richness and community structure

Time: Thursday, 5. November 2020 at 14.15

Place: Tartu, Lai 40-218 (Vaga auditorium), or virtual link in the MS Teams group (link for seeing the seminar online, without any logging in etc.).

Summary: Tree species are expected to affect fungal communities through direct biotic interactions and litter quality. Plant–fungal interactions play important roles in the ecosystem functioning, but still little is known about the functional importance of tree species diversity on fungal diversity. Richness and community structure of biotrophic fungi are most strongly controlled by tree species identity, but tree species richness and composition may also influence richness and community structure of ectomycorrhizal fungi and plant pathogens in mixed forest stands.

For everyone to stay as healthy as possible, please be reminded that wearing a face mask is mandatory. Please bring your own mask. Most importantly, don’t attend when you feel sick.

Functionality is always formal… (pic from here)
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EcolChange seminar – Giacomo Puglielli about the triangle of abiotic stress tolerance of woody plants

Seminars of Department of Botany and Centre of Excellence EcolChange

Speaker: Dr. Giacomo Puglielli is a postdoctoral researcher at the Estonian University of Life Sciences, Institute of Agriculture and Environmental Sciences in Tartu. His work focuses on stress responses of woody plant species to abiotic factors such as water and light.

Title of the talk: The abiotic stress tolerance space of woody species

Time: Thursday, 29. October 2020 at 14.15

Place: Tartu, Lai 40-218 (Vaga auditorium), or virtual link in the MS Teams group (link for seeing the seminar online, without any logging in etc.).

Summary: Woody plant species’ ability to tolerate multiple abiotic stress factors is thought to be constrained by biological trade-offs among tolerances. However, there is still considerable uncertainty about the relationship between tolerances, and the limits on tolerance combinations. In this presentation, I propose a framework that partly resolves these uncertainties. (Link to the NewPhyt paper about the triangle, and also link to the accompanying blog post.)

For everyone to stay as healthy as possible, please be reminded that wearing a face mask is mandatory. Please bring your own mask. Most importantly, don’t attend when you feel sick.

The world´s first love triangle. And every love triangle is also a stress triangle… (pic from here)
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New publication – Global patterns of biomass allocation in woody species with different tolerance of shade and drought: evidence for multiple strategies

Text by Giacomo Puglielli

Can we solve a long-standing debate in plant ecology?

Plants are known to allocate the greatest proportion of biomass to the organs involved in the acquisition of the most limiting resource for growth. For example, if light is limiting plant growth then plants are expected to allocate more biomass to aboveground parts (i.e. leaves and stems) and less to roots. Conversely, when soil water is the limiting factor, then biomass allocation to roots is expected to be greater compared to that allocated to aboveground parts. Such model is also known as Optimal Partitioning Theory (OPT), and its first formulation dates back to 1960s. OPT has been formulated and it is valid at the intraspecific level, when a single species is exposed to different environmental conditions.

Plant species inherently differ in their habitat affinity, so that there are species that consistently perform the best in shaded or in dry environments. A long-standing debate in plant ecology is if OPT predictions can equally apply when addressing interspecific differences in biomass allocation between species differing in their habitat affinity. Nevertheless, results are scattered and often not consistent across studies. The greatest limitations of previous studies are: i) the sample size (differences among few species from a single ecosystem type are evaluated); ii) the considered range of total plant biomass that strongly influences biomass allocation patterns. Also differences between plant functional types could have further blurred previous results.

We used the most extensive database of biomass allocation available for woody species (Poorter et al., 2015) spanning more than 10 orders of magnitude in plant size, and complemented it with information on species ecological tolerance of shade and drought (i.e. habitat affinity in response to light and water availability), and on plant functional type (deciduous and evergreen broad-leaf and evergreen needle-leaf). The final dataset included 7377 observations of biomass allocation to leaves, stems and roots spanning 604 species worldwide from tropical to boreal ecosystems. We used this dataset to test if OPT predictions are equally valid at the interspecific level independently of developmental stages and plant functional types.

The main and most novel result we obtained is that plant functional type is the major determinant of biomass allocation patterns independently of the considered tolerance. Ifanything, differences between tolerant and intolerant species often run in opposite directions compared to OPT predictions. Also the total plant size at which the comparison was made strongly influenced the observed differences. We conclude that the detection of a given difference between tolerant and intolerant species strongly depends on the size at which the comparison has been made within each plant functional type.

Biomass allocation fractions to: (a-c) leaves (LMF); (d-f) stems (SMF); and (g-i) roots (RMF) at different shade tolerance levels (1 = intolerant; 3 = tolerant) at three fixed values of total plant dry mass at which differences were evaluated (Seedlings = 0.001 Kg; Small trees = 10 kg; Big trees = 1000 kg) for deciduous broad-leaf species.(Figure is from the paper.)

In the paper we also discuss other determinants of biomass allocation patterns between tolerant and intolerant species at the global scale, namely changes in organ morphology together with phenotypic plasticity and the effect of plant architecture on biomass allocation. Altogether, such factors allow tolerant and intolerant woody species to display multiple biomass allocation strategies in response to shade and drought.

While we partly solved a long-standing debate in plant ecology we could not challenge another one, biological patterns are not as easy as theory suggests….luckily for us!

Citation: Puglielli, G., Laanisto, L., Poorter, H., & Niinemets, Ü. (2020). Global patterns of biomass allocation in woody species with different tolerance of shade and drought: evidence for multiple strategies. New Phytologist, https://doi.org/10.1111/nph.16879

Abstract:

The optimal partitioning theory predicts that plants of a given species acclimate to different environments by allocating a larger proportion of biomass to the organs acquiring the most limiting resource. Are similar patterns found across species adapted to environments with contrasting levels of abiotic stress?

We tested the optimal partitioning theory by analysing how fractional biomass allocation to leaves, stems and roots differed between woody species with different tolerances of shade and drought in plants of different age and size (seedlings to mature trees) using a global dataset including 604 species.

No overarching biomass allocation patterns at different tolerance values across species were found. Biomass allocation varied among functional types as a result of phenological (deciduous vs evergreen broad‐leaved species) and broad phylogenetical (angiosperms vs gymnosperms) differences. Furthermore, the direction of biomass allocation responses between tolerant and intolerant species was often opposite to that predicted by the optimal partitioning theory.

We conclude that plant functional type is the major determinant of biomass allocation in woody species. We propose that interactions between plant functional type, ontogeny and species‐specific stress tolerance adaptations allow woody species with different shade and drought tolerances to display multiple biomass partitioning strategies.

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EcolChange seminar – Siim-Kaarel Sepp about soil biota and land use

Seminars of Department of Botany and Centre of Excellence EcolChange

Speaker: Siim-Kaarel Sepp is a PhD student at the Plant Ecology workgroup of our Department of Botany. His research focuses on mycorrhizal fungi, in particular the impact of land use on arbuscular mycorrhizal fungi. Siim-Kaarel Sepp will defend his PhD thesis in December.

Title of the talk: Responses of soil eukaryotic communities to land use and host identity

Time: Thursday, 22. October 2020 at 14.15

Place: Tartu, Lai 40-218 (Vaga auditorium), or virtual link in the MS Teams group.

Summary: Knowledge pertaining to diversity patterns of belowground organisms is piecemeal. On the one hand, we lack understanding of the behaviour of particular groups of organisms and the characteristics of the interactions they form. On the other hand, seldom are the effects of land use change studied on several groups in parallel. The presentation will shed light on correlated responses of belowground organisms and report the effects of human influence on a particularly important group of soil-dwelling microorganisms, the arbuscular mycorrhizal (AM) fungi. Further, we look at the properties of an AM interaction network and the implications of the revealed structure.

For everyone to stay as healthy as possible, please be reminded that wearing a face mask is mandatory. Please bring your own mask. Most importantly, don’t attend when you feel sick.

An early theoretical model of the density of soil biotic interactions. Every line represents one interaction. By Kazimir Malevich (pic from Wiki)
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EcolChange seminar – Marina Semchenko about plant-soil feedbacks

Seminars of Department of Botany and Centre of Excellence EcolChange

Speaker: Marina Semchenko is a senior researcher at our Department of Botany, in the Plant Ecology work group. Her main research focus is on biotic interactions between plants, including the role of root exudates and soil microbes in mediating plant-plant interactions, especially from an evolutionary point of view.

Title of the talk: Plant-soil feedbacks: current trends and known unknowns

Time: Thursday, 15. October 2020 at 14.15

Place: Tartu, Lai 40-218 (Vaga auditorium), or virtual link in the MS Teams group.

Summary: Environmental gradients and plant functional traits have been key to explaining local and global patterns of plant diversity and primary production. It is increasingly recognised that soil microorganisms also play a critical role in promoting plant species co-existence and regulating ecosystem functioning. Studies ranging from temperate grasslands to tropical forests suggest that these effects are driven by the accumulation of host-specific pathogenic fungi in soil and associated suppression of locally abundant plant species, a phenomenon known as negative plant-soil feedback. However, the identity and characteristics of pathogenic fungi involved in negative plant-soil feedback remain largely unknown, as do the links between plant-fungal interactions, plant traits and soil abiotic context.

For everyone to stay as healthy as possible, please be reminded that wearing a face mask is mandatory. Please bring your own mask. Most importantly, don’t attend when you feel sick.

Mugshot of the study object (pic from here)
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EcolChange seminar – Triin Reitalu about historical plant diversity analysis based on pollen data

Seminars of Department of Botany and Centre of Excellence EcolChange

Speaker:

Dr. Triin Reitalu is senior researcher at the Institute of Geology at Tallinn University of Technology. She works on the functional and phylogenetic diversity in sedimentary pollen and plant macrofossil data. Triin Reitalu was once a member of our Department during her bachelor and master studies as well as a research fellow and is still collaborating with colleagues from the Department.

Title of the talk: Reconstructing past plant diversity with the help of pollen data

Time: Thursday, 8. October 2020 at 14.15

Place: Tartu, Lai 40-218 (Vaga auditorium), or virtual link in the MS Teams group.

Summary: Pollen that is preserved in lake and mire sediments provides information about millennial-scale vegetation changes. Associations between pollen and plant data in current landscapes can be used to better understand the problems and possibilities in sediment pollen interpretation. Exploring different biodiversity indicators such as functional and phylogenetic diversity with the help of pollen data offers new perspectives on palaeoecological diversity reconstructions.

For everyone to stay as healthy as possible, please be reminded that wearing a face mask is mandatory. Please bring your own mask. Most importantly, don’t attend when you feel sick.

Pic from here
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New publication – Landscape context and plant population size affect morph frequencies in heterostylous Primula veris ‐ results of a nationwide citizen‐science campaign

Text and photos by Tsipe Aavik

Citizen scientists bring surprising insights into cowslip mating system

About half of the individuals of cowslip (Primula veris) have flowers with a short style, while the other half of individuals produce flowers with a long style. Recent discoveries have suggested that the loss and fragmentation of habitats may shake this optimal balance of morphologically different plants. This, in turn, decreases the reproductive success of plants and jeopardizes their future viability.

As the primary habitat, cowslips prefer semi-natural grasslands, which have experienced a dramatic area loss over the last hundred years throughout Europe. The study coordinated by the ecologists of the University of Tartu and the Estonian Fund for Nature aimed to examine whether this drastic landscape change has led to deviations in morph balance. To collect data across Estonia, they decided to implement a citizen science approach. A specifically designed web platform http://www.cowslips.eu facilitated an easy upload of data. “In addition, the task and importance of the cowslip observation campaign were explained in detailed guidelines, numerous videos, social media, and other communication platforms,” commented Tsipe Aavik, the lead researcher of the heterostyly project.

Cowslip is a distylous species with two morphologically different types of flowers. Plants with short-styled or S-morphs (photo A; sometimes referred to as thrum plants) carry flowers with a short style and long anthers, while long-styled L-morphs (or pin plants; photo B) have a long style and short anthers. Generally, successful fertilization takes place only in case of reciprocal pollen flow between different morphs, while within-morph crosses lead to no progenies.

Novel insight into fundamental research

Nearly 1,700 observations obtained during the campaign led to unexpected discoveries, is now published in the Journal of Ecology. First, data revealed a systematic dominance of short-styled morphs over long-styled morphs. Second, morph frequencies were more likely to deviate in smaller populations and deviations increased in landscapes with higher human population density.

“We are very thankful to all participants who helped to collect heterostyly data at such an unprecedented scale,” commented Tsipe Aavik. “Although the first discoveries on heterostyly were made already by Darwin more than 150 years ago, data obtained in the citizen science campaign has helped us to add novel aspects into this fascinating topic with a long history of research.”

The findings brought novel insights into fundamental research: the systematic dominance of the short-styled morphs is an intriguing but previously undescribed aspect in this otherwise well-studied plant mating system. However, perhaps even more important are the implications of these findings for conservation because deviating morph frequencies are likely to jeopardize the viability of heterostylous plants. The findings thus describe another threat in the list of negative consequences of habitat loss.

Perhaps Europe could be looking for cowslips one day

The surprising findings of the study have seeded an idea to widen the geographic scope of the study to examine whether the observed patterns are confirmed in other European countries. Furthermore, the discovery about the role of human population density altering morph balance encourages to look at the patterns of heterostyly in landscapes with more intense human impact than Estonia with its relatively low human population density. “In the spring of 2020, when we repeated the campaign, Latvian citizen scientists warmly welcomed the opportunity to contribute to heterostyly observations. But perhaps one day we all can participate in a project ‘Europe is looking for cowslips’,” adds Aavik with a hope that there still are places in Europe where one can find this beautiful and intriguing plant, cowslip.

Citation: Aavik, T., Carmona, C. P., Träger, S., Kaldra, M., Reinula, I., Conti, E., … & Kaisel, M. Landscape context and plant population size affect morph frequencies in heterostylous Primula veris‐results of a nationwide citizen‐science campaign. Journal of Ecology, https://doi.org/10.1111/1365-2745.13488

Abstract:

  1. Heterostyly is a genetically determined floral polymorphism of style length promoting outcrossing between individuals of different morphs, which usually coexist within populations at equal frequencies. Loss in the area and connectivity of suitable habitats may cause deviations from the expected equal morph frequencies. However, there is a need to evaluate the generality of this pattern at larger spatial extents and to identify possible underlying mechanisms.
  2. A citizen‐science approach was used to study morph frequencies in populations of the heterostylous grassland plant Primula veris across Estonia. We developed an online platform to facilitate an easy upload of the data. We examined the effect of the following variables in the surroundings of the study populations reflecting the landscape context on the deviation of morph ratios: (a) semi‐natural grasslands, (b) forests and shrubs, (c) human population density and (d) a proxy for plant population size.
  3. The citizen‐science approach provided unprecedented density of data from 1,700 localities. Nearly half of these observations, which were maintained for further analysis after data filtering, included over 62,000 short‐styled morphs and about 54,000 long‐styled morphs. Small populations were characterized by higher overall deviation of morph ratios from isoplethy (equal morph ratio). Deviation increased in semi‐natural grasslands located in regions with high human population density.
  4. The significant effect of human population density and plant population size on deviations of morph frequencies suggests the role of stochastic demographic effects of habitat fragmentation on morph ratios. Overall lower proportion of long‐styled morphs indicates that partial intra‐morph compatibility shown in long‐styled morphs may lead to higher inbreeding and related decline in fitness and abundance.
  5. Synthesis. Citizen‐science data about the morph type of Primula veris across Estonia obtained with the help of thousands of people demonstrates that in addition to plant population size, landscape context may affect plant reproductive traits, such as heterostyly. Larger population size of P. veris can help to buffer against random fluctuations in this trait. Increasing impact of human activities may have a negative impact on both small and large populations. The exact underlying mechanisms of the prevalence of one morph over the other, however, pose novel questions for further research.

This post was originally published in EurekAlert (link)

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