Steep increase in red-listed lichens of Estonia Tiina Randlane, Inga Jüriado, Kristiina Mark, Liis Marmor-Ohtla, Ede Oja, et al. Lichenologist, 2024 National Red Lists are useful tools in establishing local conservation priorities. The threat status of Estonian lichens based on the IUCN system has been assessed twice, in 2008 and 2023. In the latest Red List, the proportion of species of elevated conservation concern, that is taxa belonging to the Near Threatened and threatened categories or having become regionally extinct in Estonia, was high (58%) while Least Concern (LC) species represented one-third (36%) of all taxa. Macrolichens were more threatened than microlichens. The Red List Index (RLI), illustrating the trends of species in their projected extinction risk, was calculated. The values were low (< 0.7 in 2023), thus indicating a heightened risk both for the set of all species and for macrolichens. More than half of all Estonian lichens are associated with woodlands and 54% of these species are of elevated conservation concern. Lichens preferring broad-leaved deciduous trees included more threatened than LC species, while among lichens preferring other deciduous or coniferous trees the proportion of LC species was higher than that of threatened taxa. Lichens inhabiting calcareous grasslands had the highest share (69%) of taxa of elevated conservation concern. Comparisons of national red-listed data with four selected countries (Czech Republic, Denmark, Finland and Sweden) revealed that the biggest overlaps of Estonian taxa of elevated conservation concern were with the Czech Republic and Finland.
Desiccation-rehydration measurements in bryophytes: current status and future insights José Ángel Morales-Sánchez, Kristiina Mark, João Paulo S Souza, Ülo Niinemets Journal of Experimental Botany, 2022 Desiccation–rehydration experiments have been employed over the years to evaluate desiccation tolerance of bryophytes (Bryophyta, Marchantiophyta, and Anthocerotophyta). Researchers have applied a spectrum of protocols to induce desiccation and subsequent rehydration, and a wide variety of techniques have been used to study desiccation-dependent changes in bryophyte molecular, cellular, physiological, and structural traits, resulting in a multifaceted assortment of information that is challenging to synthesize. We analysed 337 desiccation–rehydration studies, providing information for 351 species, to identify the most frequent methods used, analyse the advances in desiccation studies over the years, and characterize the taxonomic representation of the species assessed. We observed certain similarities across methodologies, but the degree of convergence among the experimental protocols was surprisingly low. Out of 52 bryophyte orders, 40% have not been studied, and data are lacking for multiple remote or difficult to access locations. We conclude that for quantitative interspecific comparisons of desiccation tolerance, rigorous standardization of experimental protocols and measurement techniques, and simultaneous use of an array of experimental techniques are required for a mechanistic insight into the different traits modified in response to desiccation. New studies should also aim to fill gaps in taxonomic, ecological, and spatial coverage of bryophytes.
Analyzing the causes of method-to-method variability among Rubisco kinetic traits: From the first to the current measurements Concepción Iñiguez, Ülo Niinemets, Kristiina Mark, Jeroni Galmés Journal of Experimental Botany, 2021 Due to the importance of Rubisco in the biosphere, its kinetic parameters have been measured by different methodologies in a large number of studies over the last 60 years. These parameters are essential to characterize the natural diversity in the catalytic properties of the enzyme and they are also required for photosynthesis and cross-scale crop modeling. The present compilation of Rubisco kinetic parameters in model species revealed a wide intraspecific laboratory-to-laboratory variability, which was partially solved by making corrections to account for differences in the assay buffer composition and in the acidity constant of dissolved CO2, as well as for differences in the CO2 and O2 solubilities. Part of the intraspecific variability was also related to the different analytical methodologies used. For instance, significant differences were found between the two main methods for the determination of the specificity factor (Sc/o), and also between Rubisco quantification methods, Rubisco purification versus crude extracts, and single-point versus CO2 curve measurements for the carboxylation turnover rate (kcatc) determination. Causes of the intraspecific laboratory-to-laboratory variability for Rubisco catalytic traits are discussed. This study provides a normalized kinetic dataset for model species to be used by the scientific community. Corrections and recommendations are also provided to reduce measurement variability, allowing the comparison of kinetic data obtained in different laboratories using different assay conditions.
Response to Clerc & Naciri (2021) Usnea dasopoga (Ach.) Nyl. And U. barbata (L.) F. H. Wigg. (Ascomycetes, Parmeliaceae) are two different species: A plea for reliable identifications in molecular studies Tiina Randlane, Kristiina Mark Lichenologist, 2021 During the last thirty years phylogenetic analyses based on molecular characters have developed from simple single-locus studies into complicated surveys containing multi-locus phylogenies, species trees and possibilities to evaluate the evolutionary history of characters. This has been an exciting era for systematists, including fungal taxonomists. The majority of lichenized taxa have originally been described using morphological characters s. lat. (i.e. traits related to morphology, anatomy and chemistry), and thus the congruence between traditional species description and species delimitation based on their molecular evolutionary history remains a challenge. The use of morphological characters has not been abandoned, as predicted or advocated by some researchers (Lumbsch & Leavitt 2011; Hibbett et al. 2016). However, we now know that the morphology-based approach to species recognition has also been demonstrated in several cases to substantially misrepresent diversity, as it either underestimates the occurrence of cryptic species (Altermann et al. 2014; Boluda et al. 2016) or, on the contrary, overestimates the true diversity due to high levels of intra-specific morphological and chemical variation (Leavitt et al. 2011; Velmala et al. 2014). Therefore, morphological characters continue to be useful for the delimitation of species, but only if their discriminative ability has been verified using phylogenetic analyses. Phenotypic species recognition in the genus Usnea is particularly complicated; the species are delimited by distinctive combinations of diagnostic morphological traits (Clerc 1998, 2011) which may, however, in certain cases be poorly developed or even absent (Clerc 2011). This is aggravated by the fact that there are a great number of Usnea species and high intra-specific variation, leading to a situation where most lichenologists are not able to identify Usnea species or do not undertake the task at all. This drives researchers to find other solutions. An alternative and modern way for the identification of species is DNA barcoding (Schindel & Miller 2005). A test of the success of DNA barcoding with ITS as the barcoding marker in a case study of 112 Usnea specimens from the British Isles (Kelly et al. 2011) was encouraging as the method assigned a high percentage of samples to correct species. Recent thorough analysis (Lücking et al. 2020) found usage of ITS to be a good first approximation to assess species delimitation and recognition in Usnea; however, species boundaries can be reliably established using several markers and different phylogenetic tools. Our main interest in the paper by Mark et al. (2016) focused on phylogenetic issues as we attempted to reconstruct evolutionary relationships in sect. Usnea using DNA data from six markers of 144 specimens, and to determine evolutionarily independent lineages using multiple coalescent-based species delimitation approaches. To perform these tasks, we also followed a traditional approach using morphological characters to identify the samples. Clerc & Naciri (2021) revise the traditional identification of 35 samples used in our analyses (table 1 in Clerc & Naciri (2021)) and present the details of their morphological and chemical characters. Of these, 11 samples appeared to be misidentified in Mark et al. (2016). The main disparity arose from our identification of nine U. dasopoga specimens as U. barbata. Indeed, the distinction between the two species caused difficulties for us, partly because some of the samples used appeared to be atypical or young. It is encouraging to learn that a new, previously unused character, the ratio of medulla/cortex (M/C), has proved to be the most useful discriminant in separating U. barbata and U. dasopoga (fig. 2 in Clerc & Naciri (2021)). Accepting the new morphological identifications, the interpretation of two clades (viz. barbata-chaetophora-dasypoga-diplotypus clade and barbata-intermedia-lapponica-substerilis clade) on our phylogenetic tree (fig. 1b in Mark et al. (2016)) must be reconsidered. The first of the two clades, now the dasopoga clade in Clerc & Naciri (2021), contains only U. dasopoga specimens. However, the clade has low support on the Bayesian and maximum likelihood consensus tree, on account of which the U. dasopoga monophyly is not statistically supported and its sister relationships are unresolved in our analyses. The composition of species in the second, strongly supported clade remains variable, containing samples of U. barbata, U. intermedia, U. perplexans (= U. lapponica) and U. substerilis. The subclades within this clade do not have strong support and morphological species are intermixed between them. We want to point out that the synonymization of U. substerilis under U. perplexans (= U. lapponica) proposed by us was not based merely on the well-supported sister relationship of two samples (SBS15 and LAP5), and thus the reidentification of the latter does not refute the synonymization. This synonymy was also reasonably supported by Lücking et al. (2020). It can be inferred from our phylogenetic tree with new expert identifications based on Author for correspondence: Tiina Randlane. E-mail: tiina.randlane@ut.ee Cite this article: Randlane T and Mark K (2021) Response to Clerc & Naciri (2021) Usnea dasopoga (Ach.) Nyl. and U. barbata (L.) F. H. Wigg. (Ascomycetes, Parmeliaceae) are two different species: a plea for reliable identifications in molecular studies. Lichenologist 53, 231–232. https://doi.org/10.1017/S0024282921000189
Contrasting co-occurrence patterns of photobiont and cystobasidiomycete yeast associated with common epiphytic lichen species Kristiina Mark, Lauri Laanisto, C. Guillermo Bueno, Ülo Niinemets, Christine Keller, et al. New Phytologist, 2020 Summary The popular dual definition of lichen symbiosis is under question with recent findings of additional microbial partners living within the lichen body. Here we compare the distribution and co‐occurrence patterns of lichen photobiont and recently described secondary fungus (Cyphobasidiales yeast) to evaluate their dependency on lichen host fungus (mycobiont). We sequenced the nuclear internal transcribed spacer (ITS) strands for mycobiont, photobiont, and yeast from six widespread northern hemisphere epiphytic lichen species collected from 25 sites in Switzerland and Estonia. Interaction network analyses and multivariate analyses were conducted on operational taxonomic units based on ITS sequence data. Our study demonstrates the frequent presence of cystobasidiomycete yeasts in studied lichens and shows that they are much less mycobiont‐specific than the photobionts. Individuals of different lichen species growing on the same tree trunk consistently hosted the same or closely related mycobiont‐specific Trebouxia lineage over geographic distances while the cystobasidiomycete yeasts were unevenly distributed over the study area – contrasting communities were found between Estonia and Switzerland. These results contradict previous findings of high mycobiont species specificity of Cyphobasidiales yeast at large geographic scales. Our results suggest that the yeast might not be as intimately associated with the symbiosis as is the photobiont.
Photosynthetic acclimation of the lichen Parmelia sulcata to a forest light gradient through structural, chemical and physiological alterations U Sharma, K Mark, JPS Souza, JÁ Morales-Sánchez, JJ Rikisahedew, ... Symbiosis, 1-15 , 2026 2026
Initial improvement of photosynthetic activity and desiccation tolerance in bryophytes is quickly lost in long-term elevated CO2 in vitro conditions JÁ Morales-Sánchez, JPS Souza, Ü Niinemets, K Mark Planta 263 (4), 81 , 2026 2026
Tracing Rubisco evolution across Earth paleo-atmospheric records through ancestral kinetic reconstruction S Capó-Bauçà, C Iñiguez, K Mark, Ü Niinemets, J Galmés 2025
Steep increase in red-listed lichens of Estonia T Randlane, I Jüriado, K Mark, L Marmor-Ohtla, E Oja, A Saag, ... The Lichenologist 56 (5), 329-343 , 2024 2024 Citations: 7
Extremely thin but very robust: Surprising cryptogam trait combinations at the end of the leaf economics spectrum T Wuyun, L Zhang, T Tosens, B Liu, K Mark, JÁ Morales-Sánchez, ... Plant Diversity 46 (5), 621-629 , 2024 2024 Citations: 5
Improved monitoring of cryptogam gas-exchange and volatile emissions during desiccation-rehydration cycles with a within-chamber hydration method JÁ Morales-Sánchez, K Mark, E Talts, B Rasulov, Ü Niinemets Plant Science 333, 111745 , 2023 2023 Citations: 5
Desiccation-rehydration measurements in bryophytes: current status and future insights (vol 73, pg 4338, 2022) JA Morales-Sanchez, K Mark, JPS Souza, U Niinemets JOURNAL OF EXPERIMENTAL BOTANY 74 (3), 1158-1158 , 2023 2023
Desiccation–rehydration measurements in bryophytes: current status and future insights JÁM Morales-Sánchez, K Mark, JPS Souza, Ü Niinemets Journal of Experimental Botany 73 (13), 4338-4361 , 2022 2022 Citations: 25
Interplay among environmental factors, development of CO2 concentrating mechanisms and phylogenetic constraints shaping Rubisco evolution across aquatic photosynthetic organisms C Íñiguez Moreno, Ü Niinemets, K Mark, L Laanisto, J Galmés 2022
Analyzing the causes of method-to-method variability among Rubisco kinetic traits: from the first to the current measurements C Iñiguez, Ü Niinemets, K Mark, J Galmés Journal of Experimental Botany 72 (22), 7846-7862 , 2021 2021 Citations: 14
Barcoding lichen-forming fungi using 454 pyrosequencing is challenged by artifactual and biological sequence variation (vol 59, pg 685, 2016) K Mark, C Cornejo, C Keller, D Fluck, C Scheidegger GENOME 64 (6), 591-594 , 2021 2021
Response to Clerc & Naciri (2021) Usnea dasopoga (Ach.) Nyl. and U. barbata (L.) FH Wigg.(Ascomycetes, Parmeliaceae) are two different species: a plea for reliable … T Randlane, K Mark The Lichenologist 53 (3), 231-232 , 2021 2021 Citations: 1
Analyzing the causes of method-to-method variability among Rubisco kinetic traits: from the first to the current measurements C Íñiguez Moreno, Ü Niinemets, K Mark, J Galmés Oxford University Press , 2021 2021
Correction: Barcoding lichen-forming fungi using 454 pyrosequencing is challenged by artifactual and biological sequence variation K Mark, C Cornejo, C Keller, D Flück, C Scheidegger Genome 64 (6), 591-594 , 2021 2021 Citations: 4
Low genetic differentiation between apotheciate Usnea florida and sorediate Usnea subfloridana (Parmeliaceae, Ascomycota) based on microsatellite data P Degtjarenko, K Mark, R Moisejevs, D Himelbrant, I Stepanchikova, ... Fungal Biology 124 (10), 892-902 , 2020 2020 Citations: 11
Contrasting co‐occurrence patterns of photobiont and cystobasidiomycete yeast associated with common epiphytic lichen species K Mark, L Laanisto, CG Bueno, Ü Niinemets, C Keller, C Scheidegger New Phytologist 227 (5), 1362-1375 , 2020 2020 Citations: 93
Anatomical constraints to nonstomatal diffusion conductance and photosynthesis in lycophytes and bryophytes M Carriquí, M Roig‐Oliver, TJ Brodribb, R Coopman, W Gill, K Mark, ... New Phytologist 222 (3), 1256-1270 , 2019 2019 Citations: 121
Lichen chemistry is concordant with multilocus gene genealogy in the genus Cetrelia (Parmeliaceae, Ascomycota) K Mark, T Randlane, G Thor, JS Hur, W Obermayer, A Saag Fungal biology 123 (2), 125-139 , 2019 2019 Citations: 23
Anatomical constraints to nonstomatal diffusion conductance and photosynthesis in lycophytes and bryophytes M Carriqui Alcover, M Roig-Oliver, T Brodribb, R Coopman, W Gill, K Mark, ... University Of Tasmania , 2019 2019
Evaluation of traditionally circumscribed species in the lichen-forming genus Usnea , section Usnea (Parmeliaceae, Ascomycota) using a six-locus dataset K Mark, L Saag, SD Leavitt, S Will-Wolf, MP Nelsen, T Tõrra, A Saag, ... Organisms Diversity & Evolution 16 (3), 497-524 , 2016 2016 Citations: 66
MOST CITED SCHOLAR PUBLICATIONS
Evolution of complex symbiotic relationships in a morphologically derived family of lichen‐forming fungi PK Divakar, A Crespo, M Wedin, SD Leavitt, DL Hawksworth, L Myllys, ... New Phytologist 208 (4), 1217-1226 , 2015 2015 Citations: 163
Anatomical constraints to nonstomatal diffusion conductance and photosynthesis in lycophytes and bryophytes M Carriquí, M Roig‐Oliver, TJ Brodribb, R Coopman, W Gill, K Mark, ... New Phytologist 222 (3), 1256-1270 , 2019 2019 Citations: 121
Contrasting co‐occurrence patterns of photobiont and cystobasidiomycete yeast associated with common epiphytic lichen species K Mark, L Laanisto, CG Bueno, Ü Niinemets, C Keller, C Scheidegger New Phytologist 227 (5), 1362-1375 , 2020 2020 Citations: 93
Evaluation of traditionally circumscribed species in the lichen-forming genus Usnea , section Usnea (Parmeliaceae, Ascomycota) using a six-locus dataset K Mark, L Saag, SD Leavitt, S Will-Wolf, MP Nelsen, T Tõrra, A Saag, ... Organisms Diversity & Evolution 16 (3), 497-524 , 2016 2016 Citations: 66
Barcoding lichen-forming fungi using 454 pyrosequencing is challenged by artifactual and biological sequence variation K Mark, C Cornejo, C Keller, D Flück, C Scheidegger Genome 59 (9), 685-704 , 2016 2016 Citations: 48
Species delimitation in the lichenized fungal genus Vulpicida (Parmeliaceae, Ascomycota) using gene concatenation and coalescent‐based species tree approaches L Saag, K Mark, A Saag, T Randlane American journal of botany 101 (12), 2169-2182 , 2014 2014 Citations: 38
Diversification and species delimitation of lichenized fungi in selected groups of the family Parmeliaceae (Ascomycota) K Mark University of Tartu Press , 2016 2016 Citations: 26
Desiccation–rehydration measurements in bryophytes: current status and future insights JÁM Morales-Sánchez, K Mark, JPS Souza, Ü Niinemets Journal of Experimental Botany 73 (13), 4338-4361 , 2022 2022 Citations: 25
Lichen chemistry is concordant with multilocus gene genealogy in the genus Cetrelia (Parmeliaceae, Ascomycota) K Mark, T Randlane, G Thor, JS Hur, W Obermayer, A Saag Fungal biology 123 (2), 125-139 , 2019 2019 Citations: 23
Analyzing the causes of method-to-method variability among Rubisco kinetic traits: from the first to the current measurements C Iñiguez, Ü Niinemets, K Mark, J Galmés Journal of Experimental Botany 72 (22), 7846-7862 , 2021 2021 Citations: 14
Low genetic differentiation between apotheciate Usnea florida and sorediate Usnea subfloridana (Parmeliaceae, Ascomycota) based on microsatellite data P Degtjarenko, K Mark, R Moisejevs, D Himelbrant, I Stepanchikova, ... Fungal Biology 124 (10), 892-902 , 2020 2020 Citations: 11
Testing morphology-based delimitation of Vulpicida juniperinus and V. tubulosus (Parmeliaceae) using three molecular markers M Kristiina, S Lauri, S Andres, A Thell, T Randlane The Lichenologist 44 (6), 757-772 , 2012 2012 Citations: 11
Steep increase in red-listed lichens of Estonia T Randlane, I Jüriado, K Mark, L Marmor-Ohtla, E Oja, A Saag, ... The Lichenologist 56 (5), 329-343 , 2024 2024 Citations: 7
Extremely thin but very robust: Surprising cryptogam trait combinations at the end of the leaf economics spectrum T Wuyun, L Zhang, T Tosens, B Liu, K Mark, JÁ Morales-Sánchez, ... Plant Diversity 46 (5), 621-629 , 2024 2024 Citations: 5
Improved monitoring of cryptogam gas-exchange and volatile emissions during desiccation-rehydration cycles with a within-chamber hydration method JÁ Morales-Sánchez, K Mark, E Talts, B Rasulov, Ü Niinemets Plant Science 333, 111745 , 2023 2023 Citations: 5
Correction: Barcoding lichen-forming fungi using 454 pyrosequencing is challenged by artifactual and biological sequence variation K Mark, C Cornejo, C Keller, D Flück, C Scheidegger Genome 64 (6), 591-594 , 2021 2021 Citations: 4
Response to Clerc & Naciri (2021) Usnea dasopoga (Ach.) Nyl. and U. barbata (L.) FH Wigg.(Ascomycetes, Parmeliaceae) are two different species: a plea for reliable … T Randlane, K Mark The Lichenologist 53 (3), 231-232 , 2021 2021 Citations: 1
Barcoding the Swiss lichens and associated fungal communities using barcoded amplicon 454 pyrosequencing K Mark, C Cornejo, C Keller, C Scheidegger GENOME 58 (5), 252-252 , 2015 2015 Citations: 1
Phylogeny of the genus Vulpicida and delimitation of the species. L Saag, K Mark, A Thell, T Randlane Lichens: from genome to ecosystems in a changing world. Book of abstracts … , 2012 2012 Citations: 1
Photosynthetic acclimation of the lichen Parmelia sulcata to a forest light gradient through structural, chemical and physiological alterations U Sharma, K Mark, JPS Souza, JÁ Morales-Sánchez, JJ Rikisahedew, ... Symbiosis, 1-15 , 2026 2026