Items 1-20 of 1324

• Journal Article

#### Regeneration Dynamics Following the Formation of Understory Gaps in a Slovakian Beech Virgin Forest ﻿

Forests 2020; 11(5) p.1-20: Art. 585
The frequency and size of canopy gaps largely determine light transmission to lower canopy strata, controlling structuring processes in the understory. However, quantitative data from temperate virgin forests on the structure of regeneration in gaps and its dynamics over time are scarce. We studied the structure and height growth of tree regeneration by means of sapling density, shoot length growth and cumulative biomass in 17 understory gaps (29 to 931 m2 in size) in a Slovakian beech (Fagus sylvatica L.) virgin forest, and compared the gaps with the regeneration under closed-canopy conditions. Spatial differences in regeneration structure and growth rate within a gap and in the gap periphery were analyzed for their dependence on the relative intensities of direct and diffuse radiation (high vs. low). We tested the hypotheses that (i) the density and cumulative biomass of saplings are higher in gaps than in closed-canopy patches, (ii) the position in a gap influences the density and height growth of saplings, and (iii) height growth of saplings increases with gap size. Sapling density and biomass were significantly higher in understory gaps than under closed canopy. Density of saplings was positively affected by comparatively high direct, but low diffuse radiation, resulting in pronounced spatial differences. In contrast, sapling shoot length growth was positively affected by higher levels of diffuse radiation and also depended on sapling size, while direct radiation intensity was not influential. Conclusively, in this forest, regeneration likely becomes suppressed after a short period by lateral canopy expansion in small gaps (<100 m2), resulting in a heterogeneous understory structure. In larger gaps (≥100 m2) saplings may be capable even at low plant densities to fill the gap, often forming a cohort-like regeneration layer. Thus, gaps of different sizes imprint on the resulting canopy structure in different ways, enhancing spatial heterogeneity.
• Journal Article

#### Modeling and Measuring Pre-Service Teachers’ Assessment Literacy Regarding Experimentation Competences in Biology ﻿

Education Sciences 2020; 10(5) p.1-27: Art. 140
Assessment literacy is a crucial aspect of teachers’ professional knowledge and relevant to fostering students’ learning. Concerning experimentation, teachers have to be able to assess student achievement when students form hypotheses, design experiments, and analyze data. Therefore, teachers need to be familiar with criteria for experimentation as well as student conceptions of experimentation. The present study modeled and measured 495 German pre-service teachers’ knowledge of what to assess regarding experimentation competences in biology. We applied an open-answer format for the measurement instrument. For modeling we used item response theory (IRT). We argue that knowledge of what to assess regarding experimentation competences is a one-dimensional construct and we provide evidence for the validity of the measurement. Furthermore, we describe qualitative findings of pre-service teachers’ knowledge of what to assess, in particular difficulties concerning the assessment of student conceptions as well as the use of scientific terms in the assessments. We discuss the findings in terms of implications for science teacher education and further research perspectives.
• Journal Article

#### Sexual modulation in a polyploid grass: a reproductive contest between environmentally inducible sexual and genetically dominant apomictic pathways ﻿

Scientific Reports 2020; 10(1) p.1-14: Art. 8319
In systems alternating between sexual and asexual reproduction, sex increases under unfavorable environmental conditions. In plants producing sexual and asexual (apomictic) seeds, studies on the influence of environmental factors on sex are equivocal. We used Paspalum intermedium to study environmental effects on the expression of sexual and apomictic developments, and on resulting reproductive fitness variables. Flow cytometric and embryological analyses were performed to characterize ploidy and reproductive modes, and effects of local climatic conditions on sexual and apomictic ovule and seed frequencies were determined. Seed set and germination data were collected and used to estimate reproductive fitness. Frequencies of sexual and apomictic ovules and seeds were highly variable within and among populations. Apomictic development exhibited higher competitive ability but lower overall fitness. Frequencies of sexual reproduction in facultative apomictic plants increased at lower temperatures and wider mean diurnal temperature ranges. We identified a two-fold higher fitness advantage of sexuality and a Tug of War between factors intrinsic to apomixis and environmental stressors promoting sexuality which influence the distribution of sex in apomictic populations. This points toward a crucial role of local ecological conditions in promoting a reshuffling of genetic variability that may be shaping the adaptative landscape in apomictic P. intermedium plants.
• Journal Article

#### Epigenetic Patterns and Geographical Parthenogenesis in the Alpine Plant Species Ranunculus kuepferi (Ranunculaceae) ﻿

International Journal of Molecular Sciences 2020; 21(9) p.1-20: Art. 3318
Polyploidization and the shift to apomictic reproduction are connected to changes in DNA cytosine-methylation. Cytosine-methylation is further sensitive to environmental conditions. We, therefore, hypothesize that DNA methylation patterns would differentiate within species with geographical parthenogenesis, i.e., when diploid sexual and polyploid apomictic populations exhibit different spatial distributions. On natural populations of the alpine plant Ranunculus kuepferi, we tested differences in methylation patterns across two cytotypes (diploid, tetraploid) and three reproduction modes (sexual, mixed, apomictic), and their correlation to environmental data and geographical distributions. We used methylation-sensitive amplified fragment-length polymorphism (methylation-sensitive AFLPs) and scored three types of epiloci. Methylation patterns differed independently between cytotypes versus modes of reproduction and separated three distinct combined groups (2x sexual + mixed, 4x mixed, and 4x apomictic), with differentiation of 4x apomicts in all epiloci. We found no global spatial autocorrelation, but instead correlations to elevation and temperature gradients in 22 and 36 epiloci, respectively. Results suggest that methylation patterns in R. kuepferi were altered by cold conditions during postglacial recolonization of the Alps, and by the concomitant shift to facultative apomixis, and by polyploidization. Obligate apomictic tetraploids at the highest elevations established a distinct methylation profile. Methylation patterns reflect an ecological gradient rather than the geographical differentiation.
• Journal Article

#### Encoding Information From Rotations Too Rapid To Be Consciously Perceived as Rotating: A Replication of the Motion Bridging Effect on a Liquid Crystal Display ﻿

i-Perception 2020; 11(3) p.1-11: Art. 204166952092511
A ring of points that is rotated so rapidly is perceived as a stationary outline circle that can induce an illusory rotation with the same spin direction in a subsequently presented ring of stationary points. This motion bridging effect (MBE) demonstrates that motion information can be conveyed by temporal frequencies generally thought to exceed the processing capabilities of the human visual system. It was first described in displays shown with an analog oscilloscope, but the rapid rotation rates needed to produce the MBE have heretofore prevented it from being investigated with conventional raster scan monitors. Here, we demonstrate the MBE can be reliably generated using the new generation of 240 Hz LCD gaming monitors, and exhibits basic characteristics similar to those reported previously. These monitors therefore provide a readily available resource for research on the MBE and the studies of the visual processing rapid motions in general.
• Journal Article

#### Apomixis Technology: Separating the Wheat from the Chaff ﻿

Genes 2020; 11(4) p.1-24: Art. 411
Projections indicate that current plant breeding approaches will be unable to incorporate the global crop yields needed to deliver global food security. Apomixis is a disruptive innovation by which a plant produces clonal seeds capturing heterosis and gene combinations of elite phenotypes. Introducing apomixis into hybrid cultivars is a game-changing development in the current plant breeding paradigm that will accelerate the generation of high-yield cultivars. However, apomixis is a developmentally complex and genetically multifaceted trait. The central problem behind current constraints to apomixis breeding is that the genomic configuration and molecular mechanism that initiate apomixis and guide the formation of a clonal seed are still unknown. Today, not a single explanation about the origin of apomixis o er full empirical coverage, and synthesizing apomixis by manipulating individual genes has failed or produced little success. Overall evidence suggests apomixis arise from a still unknown single event molecular mechanism with multigenic e ects. Disentangling the genomic basis and complex genetics behind the emergence of apomixis in plants will require the use of novel experimental approaches benefiting from Next Generation Sequencing technologies and targeting not only reproductive genes, but also the epigenetic and genomic configurations associated with reproductive phenotypes in homoploid sexual and apomictic carriers. A comprehensive picture of most regulatory changes guiding apomixis emergence will be central for successfully installing apomixis into the target species by exploiting genetic modification techniques.
• Journal Article

#### Effects of Temperature Treatments on Cytosine-Methylation Profiles of Diploid and Autotetraploid Plants of the Alpine Species Ranunculus kuepferi (Ranunculaceae) ﻿

Frontiers in Plant Science 2020; 11 p.1-13: Art. 435
The exposure to environmental stress can trigger epigenetic variation, which may have several evolutionary consequences. Polyploidy seems to affect the DNA methylation profiles. Nevertheless, it abides unclear whether temperature stress can induce methylations changes in different cytotypes and to what extent a treatment shift is translated to an epigenetic response. A suitable model system for studying these questions is Ranunculus kuepferi, an alpine perennial herb. Diploid and autotetraploid individuals of R. kuepferi were exposed to cold (+7°C day/+2°C night; frost treatment −1° C cold shocks for 3 nights per week) and warm (+15° day/+10°C night) conditions in climate growth chambers for two consecutive flowering periods and shifted from one condition to the other after the first flowering period. Methylation-sensitive amplified fragment-length polymorphism markers were applied for both years, to track down possible alterations induced by the stress treatments. Patterns of methylation suggested that cytotypes differed significantly in their profiles, independent from year of treatment. Likewise, the treatment shift had an impact on both cytotypes, resulting in significantly less epiloci, regardless the shift's direction. The AMOVAs revealed higher variation within than among treatments in diploids. In tetraploids, internally-methylated loci had a higher variation among than within treatments, as a response to temperature's change in both directions, and support the hypothesis of temperature stress affecting the epigenetic variation. Results suggest that the temperature-sensitivity of DNA methylation patterns shows a highly dynamic phenotypic plasticity in R. kuepferi, as both cytotypes responded to temperature shifts. Furthermore, ploidy level, even without effects of hybridization, has an important effect on epigenetic background variation, which may be correlated with the DNA methylation dynamics during cold acclimation.
• Journal Article

#### A Comparison of the Affectiva iMotions Facial Expression Analysis Software With EMG for Identifying Facial Expressions of Emotion ﻿

Frontiers in Psychology 2020; 11 p.1-9: Art. 329
Human faces express emotions, informing others about their affective states. In order to measure expressions of emotion, facial Electromyography (EMG) has widely been used, requiring electrodes and technical equipment. More recently, emotion recognition software has been developed that detects emotions from video recordings of human faces. However, its validity and comparability to EMG measures is unclear. The aim of the current study was to compare the Affectiva Affdex emotion recognition software by iMotions with EMG measurements of the zygomaticus mayor and corrugator supercilii muscle, concerning its ability to identify happy, angry and neutral faces. Twenty participants imitated these facial expressions while videos and EMG were recorded. Happy and angry expressions were detected by both the software and by EMG above chance, while neutral expressions were more often falsely identified as negative by EMG compared to the software. Overall, EMG and software values correlated highly. In conclusion, Affectiva Affdex software can identify facial expressions and its results are comparable to EMG findings.
• Journal Article

#### Ploidy-Dependent Effects of Light Stress on the Mode of Reproduction in the Ranunculus auricomus Complex (Ranunculaceae) ﻿

Frontiers in Plant Science 2020; 11 p.1-11: Art. 104
Polyploidy in angiosperms is an influential factor to trigger apomixis, the reproduction of asexual seeds. Apomixis is usually facultative, which means that both sexual and apomictic seeds can be formed by the same plant. Environmental abiotic stress, e.g. light stress, can change the frequency of apomixis. Previous work suggested effects of stress treatments on meiosis and megasporogenesis. We hypothesized that polyploidy would alter the stress response and hence reproductive phenotypes of different cytotypes. The main aims of this research were to explore with prolonged photoperiods, whether polyploidy alters proportions of sexual ovule and sexual seed formation under light stress conditions. We used three facultative apomictic, pseudogamous cytotypes of the Ranunculus auricomus complex (diploid, tetraploid, and hexaploid). Stress treatments were applied by extended light periods (16.5 h) and control (10 h) in climate growth chambers. Proportions of apomeiotic vs. meiotic development in the ovule were evaluated with clearing methods, and mode of seed formation was examined by single seed flow cytometric seed screening (ssFCSS). We further studied pollen stainability to understand effects of pollen quality on seed formation. Results revealed that under extended photoperiod, all cytotypes produced significantly more sexual ovules than in the control, with strongest effects on diploids. The stress treatment affected neither the frequency of seed set nor the proportion of sexual seeds nor pollen quality. Successful seed formation appears to be dependent on balanced maternal: paternal genome contributions. Diploid cytotypes had mostly sexual seed formation, while polyploid cytotypes formed predominantly apomictic seeds. Pollen quality was in hexaploids better than in diploids and tetraploids. These findings confirm our hypothesis that megasporogenesis is triggered by light stress treatments. Comparisons of cytotypes support the hypothesis that ovule development in polyploid plants is less sensitive to prolonged photoperiods and responds to a lesser extent with sexual ovule formation. Polyploids may better buffer environmental stress, which releases the potential for aposporous ovule development from somatic cells, and may facilitate the establishment of apomictic seed formation.
• Journal Article

#### Characterization of an Immunoglobulin Binding Protein (IbpM) From $\text{Mycoplasma pneumoniae}$ ﻿

Frontiers in Microbiology 2020; 11 p.1-12: Art. 685
Bacteria evolved many ways to invade, colonize and survive in the host tissue. Such complex infection strategies of other bacteria are not present in the cell-wall less $\textit{Mycoplasmas}$. Due to their strongly reduced genomes, these bacteria have only a minimal metabolism. $\textit{Mycoplasma pneumoniae}$ is a pathogenic bacterium using its virulence repertoire very efficiently, infecting the human lung. $\textit{M. pneumoniae}$ can cause a variety of conditions including fever, inflammation, atypical pneumoniae, and even death. Due to its strongly reduced metabolism, $\textit{M. pneumoniae}$ is dependent on nutrients from the host and aims to persist as long as possible, resulting in chronic diseases. $\textit{Mycoplasmas}$ evolved strategies to subvert the host immune system which involve proteins fending off immunoglobulins (Igs). In this study, we investigated the role of MPN400 as the putative factor responsible for Ig-binding and host immune evasion. MPN400 is a cell-surface localized protein which binds strongly to human IgG, IgA, and IgM. We therefore named the protein MPN400 immunoglobulin binding protein of $\textit{Mycoplasma}$ (IbpM). A strain devoid of IbpM is slightly compromised in cytotoxicity. Taken together, our study indicates that $\textit{M. pneumoniae}$ uses a refined mechanism for immune evasion.
• Journal Article

#### The Economy of Canopy Space Occupation and Shade Production in Early- to Late-Successional Temperate Tree Species and Their Relation to Productivity ﻿

Forests 2020; 11(3) p.1-18: Art. 317
Light capture is linked to occupation of canopy space by tree crowns, which requires investment of carbon and nutrients. We hypothesize that (i) late-successional trees invest more in casting shade than in occupying space than early-successional trees, and (ii) shade production and crown volume expansion are generally greater in more productive species. For six Central European early-successional (Betula pendula, Pinus sylvestris), mid/late-successional (Quercus petraea, Carpinus betulus), and late-successional tree species (Tilia cordata, Fagus sylvatica), we measured through full-tree harvests (1) crown volume, (2) the costs of canopy space exploration (carbon (C) and nutrients invested to fill crown volume), of space occupation (annual foliage production per volume), and of shade production (foliage needed to reduce light transmittance), and (3) related the costs to aboveground productivity (ANPP). The C and nutrient costs of canopy volume exploration and occupation were independent of the species’ seral stage, but increased with ANPP. In contrast, the cost of shade production decreased from early-to late-successional species, suggesting that the economy of shade production is more decisive for the competitive superiority of late-successional species than the economy of canopy space exploration and occupation.
• Journal Article

#### Biomass, Morphology, and Dynamics of the Fine Root System Across a 3,000-M Elevation Gradient on Mt. Kilimanjaro ﻿

Frontiers in Plant Science 2020; 11 p.1-16: Art. 13
Fine roots (≤2 mm) consume a large proportion of photosynthates and thus play a key role in the global carbon cycle, but our knowledge about fine root biomass, production, and turnover across environmental gradients is insufficient, especially in tropical ecosystems. Root system studies along elevation transects can produce valuable insights into root trait-environment relationships and may help to explore the evidence for a root economics spectrum (RES) that should represent a trait syndrome with a trade-off between resource acquisitive and conservative root traits. We studied fine root biomass, necromass, production, and mean fine root lifespan (the inverse of fine root turnover) of woody plants in six natural tropical ecosystems (savanna, four tropical mountain forest types, tropical alpine heathland) on the southern slope of Mt. Kilimanjaro (Tanzania) between 900 and 4,500 m a.s.l. Fine root biomass and necromass showed a unimodal pattern along the slope with a peak in the moist upper montane forest (~2,800 m), while fine root production varied little between savanna and upper montane forest to decrease toward the alpine zone. Root:shoot ratio (fine root biomass and production related to aboveground biomass) in the tropical montane forest increased exponentially with elevation, while it decreased with precipitation and soil nitrogen availability (decreasing soil C:N ratio). Mean fine root lifespan was lowest in the ecosystems with pronounced resource limitation (savanna at low elevation, alpine heathland at high elevation) and higher in the moist and cool forest belt (~1,800–3,700 m). The variation in root traits across the elevation gradient fits better with the concept of a multi-dimensional RES, as root tissue density and specific root length showed variable relations to each other, which does not agree with a simple trade-off between acquisitive and conservative root traits. In conclusion, despite large variation in fine root biomass, production, and morphology among the different plant species and ecosystems, a general belowground shift in carbohydrate partitioning is evident from 900 to 4,500 m a.s.l., suggesting that plant growth is increasingly limited by nutrient (probably N) shortage toward higher elevations.
• Journal Article

#### Notes on the leaf insects of the genus Phyllium of Sumatra and Java, Indonesia, including the description of two new species with purple coxae (Phasmatodea, Phylliidae) ﻿

ZooKeys 2020; 913 p.89-126
Within the last two years, the leaf insects of the genus Phyllium of both the islands of Java and Sumatra have been reviewed extensively based on morphological observations. However, cryptic species which cannot be differentiated morphologically may be present among the various populations. Since it has frequently been demonstrated that analyses based on molecular data can bring clarity in such cases, we conducted a phylogenetic analysis based on three genes (nuclear gene 28S and mitochondrial genes COI and 16S) from the Phyllium species of these islands. The results show distinct molecular divergence for several populations and suggest the presence of two new cryptic species, morphologically inseparable from Phyllium hausleithneri Brock, 1999. From Sumatra, the population originally thought to be a range expansion for Phyllium hausleithneri, is now here described as Phyllium nisus sp. nov., with the only consistent morphological difference being the color of the eggs between the two populations (dark brown in P. hausleithneri and tan in P. nisus sp. nov.). Further, an additional population with purple coxae from Java was morphologically examined and found to have no consistent features to separate it morphologically from the other purple coxae species. This cryptic species from Java was however shown to be molecularly distinct from the other purple coxae populations from Sumatra and Peninsular Malaysia and is here described as Phyllium gardabagusi sp. nov. In addition, Phyllium giganteum is here officially reported from Java for the first time based on both historic and modern records of male specimens.
• Journal Article

#### Dbp5/DDX19 between Translational Readthrough and Nonsense Mediated Decay ﻿

International Journal of Molecular Sciences 2020; 21(3) p.1-13: Art. 1085
The DEAD-box protein Dbp5 (human DDX19) remodels RNA-protein complexes. Dbp5 functions in ribonucleoprotein export and translation termination. Termination occurs, when the ribosome has reached a stop codon through the Dbp5 mediated delivery of the eukaryotic termination factor eRF1. eRF1 contacts eRF3 upon dissociation of Dbp5, resulting in polypeptide chain release and subsequent ribosomal subunit splitting. Mutations in DBP5 lead to stop codon readthrough, because the eRF1 and eRF3 interaction is not controlled and occurs prematurely. This identifies Dbp5/DDX19 as a possible potent drug target for nonsense suppression therapy. Neurodegenerative diseases and cancer are caused in many cases by the loss of a gene product, because its mRNA contained a premature termination codon (PTC) and is thus eliminated through the nonsense mediated decay (NMD) pathway, which is described in the second half of this review. We discuss translation termination andNMDin the light of Dbp5/DDX19 and subsequently speculate on reducing Dbp5/DDX19 activity to allow readthrough of the PTC and production of a full-length protein to detract the RNA from NMD as a possible treatment for diseases.
• Journal Article

#### A Collection of 13 Archaeal and 46 Bacterial Genomes Reconstructed from Marine Metagenomes Derived from the North Sea ﻿

Data 2020; 5(1) p.1-5: Art. 15
Marine bacteria are key drivers of ocean biogeochemistry. Despite the increasing number of studies, the complex interaction of marine bacterioplankton communities with their environment is still not fully understood. Additionally, our knowledge about prominent marine lineages is mostly based on genomic information retrieved from single isolates, which do not necessarily represent these groups. Consequently, deciphering the ecological contributions of single bacterioplankton community members is one major challenge in marine microbiology. In the present study, we reconstructed 13 archaeal and 46 bacterial metagenome-assembled genomes (MAGs) from four metagenomic data sets derived from the North Sea. Archaeal MAGs were a liated to Marine Group II within the Euryarchaeota. Bacterial MAGs mainly belonged to marine groups within the Bacteroidetes as well as alpha- and gammaproteobacteria. In addition, two bacterial MAGs were classified as members of the Actinobacteria and Verrucomicrobiota, respectively. The reconstructed genomes contribute to our understanding of important marine lineages and may serve as a basis for further research on functional traits of these groups.
• Journal Article

#### Stochastic and Arbitrarily Generated Input Patterns to the Mushroom Bodies Can Serve as Conditioned Stimuli in Drosophila ﻿

Frontiers in Physiology 2020; 11 p.1-15: Art. 53
Single neurons in the brains of insects often have individual genetic identities and can be unambiguously identified between animals. The overall neuronal connectivity is also genetically determined and hard-wired to a large degree. Experience-dependent structural and functional plasticity is believed to be superimposed onto this more-or-less fixed connectome. However, in Drosophila melanogaster, it has been shown that the connectivity between the olfactory projection neurons (OPNs) and Kenyon cells, the intrinsic neurons of the mushroom body, is highly stochastic and idiosyncratic between individuals. Ensembles of distinctly and sparsely activated Kenyon cells represent information about the identity of the olfactory input, and behavioral relevance can be assigned to this representation in the course of associative olfactory learning. Previously, we showed that in the absence of any direct sensory input, artificially and stochastically activated groups of Kenyon cells could be trained to encode aversive cues when their activation coincided with aversive stimuli. Here, we have tested the hypothesis that the mushroom body can learn any stochastic neuronal input pattern as behaviorally relevant, independent of its exact origin. We show that fruit flies can learn thermogenetically generated, stochastic activity patterns of OPNs as conditioned stimuli, irrespective of glomerular identity, the innate valence that the projection neurons carry, or inter-hemispheric symmetry.
• Journal Article

#### Predictive context biases binocular rivalry in children and adults with no positive relation to two measures of social cognition ﻿

Scientific Reports 2020; 10 p.1-12: Art. 2059
Integration of prior experience and contextual information can help to resolve perceptually ambiguous situations and might support the ability to understand other peoples’ thoughts and intentions, called Theory of Mind. We studied whether the readiness to incorporate contextual information for resolving binocular rivalry is positively associated with Theory-of-Mind-related social cognitive abilities. In children (12 to 13 years) and adults (18 to 25 years), a predictive temporal context reliably modulated the onset of binocular rivalry to a similar degree. In contrast, adult participants scored better on measures of Theory of Mind compared to children. We observed considerable interindividual differences regarding the influence of a predictive context on binocular rivalry, which were associated with differences in sensory eye dominance. The absence of a positive association between predictive effects on perception and Theory of Mind performance suggests that predictive effects on binocular rivalry and higher-level Theory-of-Mind-related abilities stem from different neurocognitive mechanisms. We conclude that the influence of predictive contextual information on basic visual processes is fully developed at an earlier age, whereas social cognitive skills continue to evolve from adolescence to adulthood.
• Journal Article

#### Parenchyma Abundance in Wood of Evergreen Trees Varies Independently of Nutrients ﻿

Frontiers in Plant Science 2020; 11 p.1-15: Art. 86
The abundance of living cells in wood—mainly as interconnected axial and ray parenchyma networks—varies widely between species. However, the functional significance of this variation and its role in plant ecological strategies is poorly understood, as is the extent to which different parenchyma fractions are favored in relation to soil nutrients and hydraulic functions. We analyzed wood tissue fractions of 16 Australian angiosperm species sampled from two nearby areas with similar climate but very different soil nutrient profiles and investigated structure-function links with soil and tissue nutrient concentrations and other plant traits. We expected the variation in parenchyma fractions to influence nutrient concentrations in wood xylem, and to find species with lower parenchyma fractions and accordingly lower nutrient requirements on lower-nutrient soils. Surprisingly, both axial and ray parenchyma fractions were mostly unrelated to tissue and soil nutrient concentrations, except for nitrogen concentration in stem sapwood. Species from low nutrient soils showed higher fractional P translocation from both leaves and sapwood, but little patterning with respect to tissue nitrogen. While species from high and low nutrient soils clearly clustered along the soil-fertility axis, their tissue composition varied independently from plant functional traits related to construction costs and hydraulic anatomy. Our findings imply that there is considerable variation among species in the nutrient concentrations within different parenchyma tissues. The anatomical composition of wood tissue seems unrelated to plant nutrient requirements. Even though xylem parenchyma is involved in metabolic functions such as nutrient translocation and storage, parenchyma abundance on its own does not directly explain variation in these functions, even in co-occurring species. While parenchyma is highly abundant in wood of angiosperm trees, we are still lacking a convincing ecological interpretation of its variability and role in whole-tree nutrient budgets.
• Journal Article

#### The number of k-mer matches between two DNA sequences as a function of k and applications to estimate phylogenetic distances ﻿

PLOS ONE 2020; 15(2) p.1-18: Art. e0228070
We study the number $N_k$ of length-k word matches between pairs of evolutionarily related DNA sequences, as a function of k. We show that the Jukes-Cantor distance between two genome sequences—i.e. the number of substitutions per site that occurred since they evolved from their last common ancestor—can be estimated from the slope of a function $F$ that depends on $N_k$ and that is affine-linear within a certain range of $k$. Integers kmin and $k_{max}$ can be calculated depending on the length of the input sequences, such that the slope of $F$ in the relevant range can be estimated from the values $F(k_{min})$ and $F(k_{max})$. This approach can be generalized to so-called $Spaced-word$ $Matches$ $(SpaM)$, where mismatches are allowed at positions specified by a user-defined binary pattern. Based on these theoretical results, we implemented a prototype software program for alignment-free sequence comparison called $Slope-SpaM$. Test runs on real and simulated sequence data show that $Slope-SpaM$ can accurately estimate phylogenetic distances for distances up to around 0.5 substitutions per position. The statistical stability of our results is improved if spaced words are used instead of contiguous words. Unlike previous alignment-free methods that are based on the number of (spaced) word matches, $Slope-SpaM$ produces accurate results, even if sequences share only local homologies.
• Journal Article

#### The Rise of Apomixis in Natural Plant Populations ﻿

Frontiers in Plant Science 2019; 10: Art. 358
Apomixis, the asexual reproduction via seed, has many potential applications for plant breeding by maintaining desirable genotypes over generations. Since most major crops do not express natural apomixis, it is useful to understand the origin and maintenance of apomixis in natural plant systems. Here, we review the state of knowledge on origin, establishment and maintenance of natural apomixis. Many studies suggest that hybridization, either on diploid or polyploid cytotypes, is a major trigger for the formation of unreduced female gametophytes, which represents the ﬁrst step toward apomixis, and must be combined to parthenogenesis, the development of an unfertilized egg cell. Nevertheless, fertilization of endosperm is still needed for most apomictic plants. Coupling of these three steps appears to be a major constraint for shifts to natural apomixis. Adventitious embryony is another developmental pathway toward apomixis. Establishment of a newly arisen apomictic lineage is often fostered by side- effects of polyploidy. Polyploidy creates an immediate reproductive barrier against the diploid parental and progenitor populations; it can cause a breakdown of genetic self- incompatibility (SI) systems which is needed to establish self-fertility of pseudogamous apomictic lineages; and ﬁnally, polyploidy could indirectly help to establish an apomictic cytotype in a novel ecological niche by increasing adaptive potentials of the plants. This step may be followed by a phase of diversiﬁcation and range expansion, mostly described as geographical parthenogenesis. The utilization of apomixis in crops must consider the potential risks of pollen transfer and introgression into sexual crop ﬁelds, which might be overcome by using pollen-sterile or cleistogamous variants. Another risk is the escape into natural vegetation and potential invasiveness of apomictic plants which needs careful management and consideration of ecological conditions.