Kristiina Mark
@emu.ee
Researcher, Institute of Agricultural & Environmental Sciences
Estonian University of Life Sciences
RESEARCH, TEACHING, or OTHER INTERESTS
Plant Science, Ecology, Evolution, Behavior and Systematics, General Biochemistry, Genetics and Molecular Biology, Physiology
Scopus Publications
Scholar Citations
Scholar h-index
Scholar i10-index
Scopus Publications
José Ángel Morales-Sánchez, Kristiina Mark, Eero Talts, Bakhtier Rasulov, and Ülo Niinemets
Elsevier BV
José Ángel Morales-Sánchez, Kristiina Mark, João Paulo S Souza, and Ülo Niinemets
Oxford University Press (OUP)
AbstractDesiccation–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.
Concepción Iñiguez, Ülo Niinemets, Kristiina Mark, and Jeroni Galmés
Oxford University Press (OUP)
Abstract 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.
Tiina Randlane and Kristiina Mark
Cambridge University Press (CUP)
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
Polina Degtjarenko, Kristiina Mark, Rolands Moisejevs, Dmitry Himelbrant, Irina Stepanchikova, Andrei Tsurykau, Tiina Randlane, and Christoph Scheidegger
Elsevier BV
Kristiina Mark, Lauri Laanisto, C. Guillermo Bueno, Ülo Niinemets, Christine Keller, and Christoph Scheidegger
Wiley
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.
Marc Carriquí, Margalida Roig‐Oliver, Timothy J. Brodribb, Rafael Coopman, Warwick Gill, Kristiina Mark, Ülo Niinemets, Alicia V. Perera‐Castro, Miquel Ribas‐Carbó, Lawren Sack,et al.
Wiley
Summary Photosynthesis in bryophytes and lycophytes has received less attention than terrestrial plant groups. In particular, few studies have addressed the nonstomatal diffusion conductance to CO2 gnsd of these plant groups. Their lower photosynthetic rate per leaf mass area at any given nitrogen concentration compared with vascular plants suggested a stronger limitation by CO2 diffusion. We hypothesized that bryophyte and lycophyte photosynthesis is largely limited by low gnsd. Here, we studied CO2 diffusion inside the photosynthetic tissues and its relationships with photosynthesis and anatomical parameters in bryophyte and lycophyte species in Antarctica, Australia, Estonia, Hawaii and Spain. On average, lycophytes and, specially, bryophytes had the lowest photosynthetic rates and nonstomatal diffusion conductance reported for terrestrial plants. These low values are related to their very thick cell walls and their low exposure of chloroplasts to cell perimeter. We conclude that the reason why bryophytes lie at the lower end of the leaf economics spectrum is their strong nonstomatal diffusion conductance limitation to photosynthesis, which is driven by their specific anatomical characteristics.
Kristiina Mark, Tiina Randlane, Göran Thor, Jae-Seoun Hur, Walter Obermayer, and Andres Saag
Elsevier BV
Kristiina Mark, Lauri Saag, Steven D. Leavitt, Susan Will-Wolf, Matthew P. Nelsen, Tiiu Tõrra, Andres Saag, Tiina Randlane, and H. Thorsten Lumbsch
Springer Science and Business Media LLC
Kristiina Mark, Lauri Saag, Steven D. Leavitt, Susan Will-Wolf, Matthew P. Nelsen, Tiiu Tõrra, Andres Saag, Tiina Randlane, and H. Thorsten Lumbsch
Springer Science and Business Media LLC
Kristiina Mark, Carolina Cornejo, Christine Keller, Daniela Flück, and Christoph Scheidegger
Canadian Science Publishing
Kristiina Mark, Carolina Cornejo, Christine Keller, Daniela Flück, and Christoph Scheidegger
Canadian Science Publishing
Although lichens (lichen-forming fungi) play an important role in the ecological integrity of many vulnerable landscapes, only a minority of lichen-forming fungi have been barcoded out of the currently accepted ∼18 000 species. Regular Sanger sequencing can be problematic when analyzing lichens since saprophytic, endophytic, and parasitic fungi live intimately admixed, resulting in low-quality sequencing reads. Here, high-throughput, long-read 454 pyrosequencing in a GS FLX+ System was tested to barcode the fungal partner of 100 epiphytic lichen species from Switzerland using fungal-specific primers when amplifying the full internal transcribed spacer region (ITS). The present study shows the potential of DNA barcoding using pyrosequencing, in that the expected lichen fungus was successfully sequenced for all samples except one. Alignment solutions such as BLAST were found to be largely adequate for the generated long reads. In addition, the NCBI nucleotide database—currently the most complete database for lichen-forming fungi—can be used as a reference database when identifying common species, since the majority of analyzed lichens were identified correctly to the species or at least to the genus level. However, several issues were encountered, including a high sequencing error rate, multiple ITS versions in a genome (incomplete concerted evolution), and in some samples the presence of mixed lichen-forming fungi (possible lichen chimeras).
Pradeep K. Divakar, Ana Crespo, Mats Wedin, Steven D. Leavitt, David L. Hawksworth, Leena Myllys, Bruce McCune, Tiina Randlane, Jarle W. Bjerke, Yoshihito Ohmura,et al.
Wiley
Summary We studied the evolutionary history of the Parmeliaceae (Lecanoromycetes, Ascomycota), one of the largest families of lichen‐forming fungi with complex and variable morphologies, also including several lichenicolous fungi. We assembled a six‐locus data set including nuclear, mitochondrial and low‐copy protein‐coding genes from 293 operational taxonomic units (OTUs). The lichenicolous lifestyle originated independently three times in lichenized ancestors within Parmeliaceae, and a new generic name is introduced for one of these fungi. In all cases, the independent origins occurred c. 24 million yr ago. Further, we show that the Paleocene, Eocene and Oligocene were key periods when diversification of major lineages within Parmeliaceae occurred, with subsequent radiations occurring primarily during the Oligocene and Miocene. Our phylogenetic hypothesis supports the independent origin of lichenicolous fungi associated with climatic shifts at the Oligocene–Miocene boundary. Moreover, diversification bursts at different times may be crucial factors driving the diversification of Parmeliaceae. Additionally, our study provides novel insight into evolutionary relationships in this large and diverse family of lichen‐forming ascomycetes.
Lauri Saag, Kristiina Mark, Andres Saag, and Tiina Randlane
Wiley
• Premise of the study: Species boundaries in many organism groups are still in a state of flux, and for empirical species delimitation, finding appropriate character sets and analytical tools are among the greatest challenges. In the lichenized fungal genus Vulpicida, six morphologically circumscribed species have been distinguished, but phenotypic characters partly overlap for three of these and intermediate forms occur. We used a combination of phylogenetic strategies to delimit the species in this genus.• Methods: Five DNA loci were sequenced and analyzed. Single‐locus gene trees and a five‐locus concatenated phylogeny were constructed to assess current Vulpicida species. Species boundaries were inferred from molecular data using two coalescent‐based species delimitation methods (BP&P and Brownie) and from species trees reconstructed with three different algorithms (*BEAST, BEST, and STEM).• Key results: The two species restricted to North America, Vulpicida canadensis and V. viridis, are clearly distinct in all analyses. The four other traditionally accepted species form two strongly supported, closely related species‐level lineages within the core group of the genus. On the basis of these results, we propose four instead of the current six species in the genus: V. canadensis, V. juniperinus, V. pinastri, and V. viridis, while V. tilesii and V. tubulosus are reduced to synonymy under V. juniperinus.• Conclusions: Coalescent species delimitation and tree inference give consistent results for fully distinct Vulpicida species but not for diverging populations. Even the inconsistent results were informative, revealing developing isolation despite a complex history of recombination and incomplete lineage sorting.
Kristiina MARK, Lauri SAAG, Andres SAAG, Arne THELL, and Tiina RANDLANE
Cambridge University Press (CUP)
AbstractThe delimitation of two morphologically similar and not easily separable Vulpicida species, V. juniperinus and V. tubulosus, is analyzed using nuclear ITS and Mcm7, and mitochondrial SSU DNA sequences. Seventy-nine Vulpicida specimens, most from the two focal taxa, are included in the three-locus gene tree. The results from Bayesian and parsimony analyses are presented. There are strong conflicts between the single locus gene trees. Vulpicida juniperinus and V. tubulosus are divided into two clearly distinguished groups in the ITS and concatenated B/MCMC tree. However, these species are mixed in both clades, appearing polyphyletic. Currently accepted V. juniperinus and V. tubulosus are not distinct according to the loci studied. Vulpicida pinastri appears monophyletic based on the available sequences.