Modeling potential habitats and predicting habitat connectivity for Leucanthemum vulgare Lam. in northwestern rangelands of Iran.

Invasive plants can alter the function and structure of ecosystems resulting in social, economic, and ecological damage. Effective methods to reduce the dominance of invasive plants are needed. The present study was aimed at modeling the invasive species Leucanthemum vulgare Lam. in the rangelands of the Namin region in northwest Iran, as well as predicting the habitat connectivity of this species to detect areas with high habitat connectivity. Modeling of potential habitats was performed using logistic regression (LR) and maximum entropy (MaxEnt); the ensemble map which resulted from these was used to predict habitat connectivity using the electrical circuit method. Topography (elevation, slope, and aspect), climate (precipitation and temperature), and soil (acidity, electrical conductivity, soil texture, calcium, magnesium, sodium, phosphorus, potassium, organic carbon, organic matter, saturation percentage, and total neutralizing value) were used in this study. The presence and absence points of the L. vulgare were recorded using a stratified-random sampling method by means of a global positioning system. Soil samples were collected at a depth of 0 to 30 cm where L. vulgare was present and also where it was absent. According to the results, in LR, the variables of temperature, phosphorus, organic matter, and sand and in the MaxEnt, the variables of sand, total neutralizing value (TNV), and silt were the most influential factors on the distribution of L. vulgare. The appraisal of the MaxEnt performance and the precision of the model prediction were 0.97. The Kappa indices for the predicted map obtained from the LR and MaxEnt models were 0.80 and 0.73, respectively. The models' evaluation indicated that both models were able to predict the distribution of L. vulgare habitats with a high level of accuracy; however, LR was more reliable. According to the LR prediction, 9.91% (10,556.25 ha) of the Namin region was attacked by L. vulgare. Connectivity assessment showed that the current density spread of L. vulgare continued from the northeast of the Namin region toward the southeast. On the other hand, the higher current density spread was demonstrated in the eastern region (rangelands adjacent to Fandoghlu forests), and other rangelands which are more threatened by the invasion of L. vulgare. Identifying sites exposed to invasive species can help implement programs to prevent invasive species from invading areas where management and prevention should be implanted to prevent and/or reduce the spread.

Ecological restoration of habitats invaded by Leucanthemum vulgare that alters key ecosystem functions.

Precise assessment of the impacts of invasive alien species (IAS) on ecosystem structure and functions is paramount for implementing appropriate management and restoration strategies. Here we investigated the impacts of Leucanthemum vulgare (ox-eye daisy), an aggressive invader in Kashmir Himalaya, on species diversity and primary productivity. We also evaluated bunch of strategies for the ecological restoration of the habitats invaded by this species. We found that uninvaded plots harbored on an average of 6.11 (±2.92) more species per 1m2 of quadrat than invaded plots. At multivariate scale, the ordination (nMDS) and ANOSIM exhibited significant differences between invaded and uninvaded plots with R = 0.7889 and p < 0.001. The decrease in diversity indices in invaded as compared to uninvaded plots was associated with more productive plant communities due to Leucanthemum invasion. Higher altitude Gulmarg site was more affected by Leucanthemum invasion than lower altitude Drung site. We tested different approaches for restoration and management of invaded habitats that include herbicide treatment at seedling stage, herbicide treatment before and after flowering stage, mowing and herbicide treatment together, joint mowing, digging and herbicide treatment and Leucanthemum uprooting. Among these treatments, uprooting and combined digging, mowing and herbicide treatment proved to be most effective in controlling Leucanthemum invasion. The implications of these results for effective management of ecologically sensitive and socio-culturally important landscapes are discussed.

ALLCOPOL: inferring allele co-ancestry in polyploids.

BACKGROUND: Inferring phylogenetic relationships of polyploid species and their diploid ancestors (leading to reticulate phylogenies in the case of an allopolyploid origin) based on multi-locus sequence data is complicated by the unknown assignment of alleles found in polyploids to diploid subgenomes. A parsimony-based approach to this problem has been proposed by Oberprieler et al. (Methods Ecol Evol 8:835-849, 2017), however, its implementation is of limited practical value. In addition to previously identified shortcomings, it has been found that in some cases, the obtained results barely satisfy the applied criterion. To be of better use to other researchers, a reimplementation with methodological refinement appears to be indispensable. RESULTS: We present the AllCoPol package, which provides a heuristic method for assigning alleles from polyploids to diploid subgenomes based on the Minimizing Deep Coalescences (MDC) criterion in multi-locus sequence datasets. An additional consensus approach further allows to assess the confidence of phylogenetic reconstructions. Simulations of tetra- and hexaploids show that under simplifying assumptions such as completely disomic inheritance, the topological errors of reconstructed phylogenies are similar to those of MDC species trees based on the true allele partition. CONCLUSIONS: AllCoPol is a Python package for phylogenetic reconstructions of polyploids offering enhanced functionality as well as improved usability. The included methods are supplied as command line tools without the need for prior programming knowledge.

Biological effects of the free and embedded metribuzin and tribenuron-methyl herbicides on various cultivated weed species.

The present study addresses the herbicidal activity and biological effects of the metribuzin (MET) and tribenuron-methyl (TBM) herbicides used to control various weed species (Amaranthus retroflexus, Sinapis arvensis, and Leucanthemum maximum). The effects of the free herbicides and the herbicides embedded in granules of degradable polymer poly-3-hydroxybutyrate [P(3HB)] blended with birch wood flour were compared. Metribuzin, regardless of the form, caused 100% mortality of the three weeds by day 21. The herbicidal activity of tribenuron-methyl was lower than that of metribuzin, but the embedded TBM was superior to the free herbicide in the length and strength of its action on the weeds. Both metribuzin forms dramatically decreased the main parameters of fluorescence: maximum quantum yield of photosystem-II [Y(II)max], maximum quantum yield of non-photochemical quenching [Y(NPQ)max], and maximum rate of non-cyclic electron transport [ETRmax] and concentrations of chlorophyll a and b. The effect of the embedded TBM on the photosynthetic activity of the weeds was lower in the first two weeks of the growth of herbicide-treated plants but lasted longer than the effect of the free TBM and increased over time. Embedding of metribuzin in the matrix of degradable blend did not decrease its herbicidal activity.

Can we use it? On the utility of de novo and reference-based assembly of Nanopore data for plant plastome sequencing.

The chloroplast genome harbors plenty of valuable information for phylogenetic research. Illumina short-read data is generally used for de novo assembly of whole plastomes. PacBio or Oxford Nanopore long reads are additionally employed in hybrid approaches to enable assembly across the highly similar inverted repeats of a chloroplast genome. Unlike for PacBio, plastome assemblies based solely on Nanopore reads are rarely found, due to their high error rate and non-random error profile. However, the actual quality decline connected to their use has rarely been quantified. Furthermore, no study has employed reference-based assembly using Nanopore reads, which is common with Illumina data. Using Leucanthemum Mill. as an example, we compared the sequence quality of seven chloroplast genome assemblies of the same species, using combinations of two sequencing platforms and three analysis pipelines. In addition, we assessed the factors which might influence Nanopore assembly quality during sequence generation and bioinformatic processing. The consensus sequence derived from de novo assembly of Nanopore data had a sequence identity of 99.59% compared to Illumina short-read de novo assembly. Most of the errors detected were indels (81.5%), and a large majority of them is part of homopolymer regions. The quality of reference-based assembly is heavily dependent upon the choice of a close-enough reference. When using a reference with 0.83% sequence divergence from the studied species, mapping of Nanopore reads results in a consensus comparable to that from Nanopore de novo assembly, and of only slightly inferior quality compared to a reference-based assembly with Illumina data. For optimal de novo assembly of Nanopore data, appropriate filtering of contaminants and chimeric sequences, as well as employing moderate read coverage, is essential. Based on these results, we conclude that Nanopore long reads are a suitable alternative to Illumina short reads in plastome phylogenomics. Few errors remain in the finalized assembly, which can be easily masked in phylogenetic analyses without loss in analytical accuracy. The easily applicable and cost-effective technology might warrant more attention by researchers dealing with plant chloroplast genomes.

Plant invasion alters the physico-chemical dynamics of soil system: insights from invasive Leucanthemum vulgare in the Indian Himalaya.

Understanding the impact of plant invasions on the terrestrial ecosystems, particularly below-ground soil system dynamics can be vital for successful management and restoration of invaded landscapes. Here, we report the impacts of a global plant invader, Leucanthemum vulgare Lam. (ox-eye daisy), on the key physico-chemical soil properties across four sites selected along an altitudinal gradient (1600-2550 m) in Kashmir Himalaya, India. At each site, two types of spatially separated but environmentally similar sampling plots: invaded (IN) and uninvaded (UN) were selected for soil sampling. The results revealed that invasion by L. vulgare had a significant impact on key soil properties in the IN plots. The soil pH, water content, organic carbon and total nitrogen were significantly higher in the IN plots as compared with the UN plots. In contrast, the electrical conductivity, phosphorous and micronutrients, viz. iron, copper, manganese and zinc, were significantly lower in the IN plots as compared with the UN plots. These changes in the soil system dynamics associated with L. vulgare invasion were consistent across all the sites. Also, among the sites, soil properties of low-altitude site (1600 m) were different from the rest of the sampling sites. Overall, the results of the present study indicate that L. vulgare, by altering key properties of the soil system, is likely to influence nutrient cycling processes and facilitates positive feedback for itself. Furthermore, the research insights from this study have wide management implications in the effective ecological restoration of the invaded landscapes.

Global distribution modelling, invasion risk assessment and niche dynamics of Leucanthemum vulgare (Ox-eye Daisy) under climate change.

In an era of climate change, biological invasions by alien species represent one of the main anthropogenic drivers of global environmental change. The present study, using an ensemble modelling approach, has mapped current and future global distribution of the invasive Leucanthemum vulgare (Ox-eye Daisy) and predicted the invasion hotspots under climate change. The current potential distribution of Ox-eye Daisy coincides well with the actual distribution records, thereby indicating robustness of our model. The model predicted a global increase in the suitable habitat for the potential invasion of this species under climate change. Oceania was shown to be the high-risk region to the potential invasion of this species under both current and future climate change scenarios. The results revealed niche conservatism for Australia and Northern America, but contrastingly a niche shift for Africa, Asia, Oceania and Southern America. The global distribution modelling and risk assessment of Ox-eye Daisy has immediate implications in mitigating its invasion impacts under climate change, as well as predicting the global invasion hotspots and developing region-specific invasion management strategies. Interestingly, the contrasting patterns of niche dynamics shown by this invasive plant species provide novel insights towards disentangling the different operative mechanisms underlying the process of biological invasions at the global scale.

'At the crossroads towards polyploidy': genomic divergence and extent of homoploid hybridization are drivers for the formation of the ox-eye daisy polyploid complex (Leucanthemum, Compositae-Anthemideae).

Polyploidy plays a paramount role in phytodiversity, but the causes of this evolutionary pathway require further study. Here, we use phylogenetic methods to examine possible polyploidy-promoting factors by comparing diploid representatives of the comprehensive European polyploid complex Leucanthemum with members of its strictly diploid North African counterpart Rhodanthemum. We investigate genetic divergence and gene flow among all diploid lineages of both genera to evaluate the role of genomic differentiation and hybridization for polyploid speciation. To test whether hybridization in Leucanthemum has been triggered by the geological conditions during its diversification, we additionally generate a time-calibrated phylogeny of 46 species of the subtribe Leucantheminae. Leucanthemum shows a significantly higher genetic divergence and hybridization signal among diploid lineages compared with Rhodanthemum, in spite of a similar crown age and diversification pattern during the Quaternary. Our study demonstrates the importance of genetic differentiation among diploid progenitors and their concurrent affinity for natural hybridization for the formation of a polyploid complex. Furthermore, the role of climate-induced range overlaps on hybridization and polyploid speciation during the Quaternary is discussed.

Leucanthemum vulgare lam. crude oil phytoremediation.

Sites with crude oil pollution have been successfully treated using phytoremediation, but expanding the range of plants that can be used and understanding how exposure impacts the plants are two areas of study that are important to continue. Leucanthemum vulgare has been shown to grow well under a variety of stressful conditions. To examine L. vulgare's ability to both survive crude oil exposure and to reduce crude oil concentrations in soil, plants were placed in soil containing 0, 2.5, 5, 7.5, or 10% w/w crude oil. Total petroleum hydrocarbons (TPH) concentration, peroxidase and catalase activity, proline and phenol content in roots and leaves were determined at the start of planting and every 2 months for 6 months. L. vulgare roots were successfully colonized with mycorrhizae under all conditions. Results showed positive correlation between antioxidant compound concentration and crude oil contamination. Also, a significant reduction occurred in TPH content of soil over time in planted pots as compared to controls. The lowest TPH content was recorded after 6 months under all treatments. Results showed L. vulgare could survive crude oil exposure and enhance reducing of crude oil from soil.

Isolate identity determines plant tolerance to pathogen attack in assembled mycorrhizal communities.

Arbuscular mycorrhizal fungi (AMF) are widespread soil microorganisms that associate mutualistically with plant hosts. AMF receive photosynthates from the host in return for various benefits. One of such benefits is in the form of enhanced pathogen tolerance. However, this aspect of the symbiosis has been understudied compared to effects on plant growth and its ability to acquire nutrients. While it is known that increased AMF species richness positively correlates with plant productivity, the relationship between AMF diversity and host responses to pathogen attack remains obscure. The objective of this study was to test whether AMF isolates can differentially attenuate the deleterious effects of a root pathogen on plant growth, whether the richest assemblage of AMF isolates provides the most tolerance against the pathogen, and whether AMF-induced changes to root architecture serve as a mechanism for improved plant disease tolerance. In a growth chamber study, we exposed the plant oxeye daisy (Leucanthemum vulgare) to all combinations of three AMF isolates and to the plant root pathogen Rhizoctonia solani. We found that the pathogen caused an 81% reduction in shoot and a 70% reduction in root biomass. AMF significantly reduced the highly deleterious effect of the pathogen. Mycorrhizal plants infected with the pathogen produced 91% more dry shoot biomass and 72% more dry root biomass relative to plants solely infected with R. solani. AMF isolate identity was a better predictor of AMF-mediated host tolerance to the pathogen than AMF richness. However, the enhanced tolerance response did not result from AMF-mediated changes to root architecture. Our data indicate that AMF communities can play a major role in alleviating host pathogen attack but this depends primarily on the capacity of individual AMF isolates to provide this benefit.