Genotypic diversity effects on the performance of Taraxacum officinale populations increase with time and environmental favorability

Genotypic Diversity Improves Photosynthetic Traits of Hydrocotyle vulgaris and Alters Soil Organic Matter and N2O Emissions of Wetland Microecosystems

In plant communities, genotypic diversity can impact the plant community structure and ecosystem functions, but related research has focused on native plants. Therefore, whether genotypic diversity affects the growth of invasive plants and then changes the wetland microecosystem remains unresolved. In this study, six different genotypes of Hydrocotyle vulgaris, a common invasive plant in China, were selected to construct populations with three different genotypic diversity levels (one, three, and six genotype combinations, respectively) to explore the effects of different genotypic diversity levels on the growth and physiological traits of H. vulgaris, and soil nutrients and greenhouse gas emissions of the wetland microecosystem under flooding conditions. We found that genotypic diversity improved the leaf area, root to shoot ratio and photosynthetic physiological traits of H. vulgaris, especially under flooding. Moreover, genotypic diversity increased soil organic matter (SOM) contents in the wetland microecosystem, while it reduced the cumulative nitrous oxide emissions under flooding conditions. Overall, genotype diversity improved photosynthetic traits of H. vulgaris, further increased SOM, and reduced the N2O emissions of the wetland microecosystem. The results of this study can provide a theoretical basis for exploring how genotypic diversity levels affect the invasiveness of invasive plants and ecosystems in wetland microecosystems.

Comparison of ARIMA, ES, GRNN and ARIMA–GRNN hybrid models to forecast the second wave of COVID-19 in India and the United States

As acute infectious pneumonia, the coronavirus disease-2019 (COVID-19) has created unique challenges for each nation and region. Both India and the United States (US) have experienced a second outbreak, resulting in a severe disease burden. The study aimed to develop optimal models to predict the daily new cases, in order to help to develop public health strategies. The autoregressive integrated moving average (ARIMA) models, generalised regression neural network (GRNN) models, ARIMA–GRNN hybrid model and exponential smoothing (ES) model were used to fit the daily new cases. The performances were evaluated by minimum mean absolute per cent error (MAPE). The predictive value with ARIMA (3, 1, 3) (1, 1, 1)₁₄ model was closest to the actual value in India, while the ARIMA–GRNN presented a better performance in the US. According to the models, the number of daily new COVID-19 cases in India continued to decrease after 27 May 2021. In conclusion, the ARIMA model presented to be the best-fit model in forecasting daily COVID-19 new cases in India, and the ARIMA–GRNN hybrid model had the best prediction performance in the US. The appropriate model should be selected for different regions in predicting daily new cases. The results can shed light on understanding the trends of the outbreak and giving ideas of the epidemiological stage of these regions.

Toward Unifying Evolutionary Ecology and Genomics to Understand Positive Plant-Plant Interactions Within Wild Species

In a local environment, plant networks include interactions among individuals of different species and among genotypes of the same species. While interspecific interactions are recognized as main drivers of plant community patterns, intraspecific interactions have recently gained attention in explaining plant community dynamics. However, an overview of intraspecific genotype-by-genotype interaction patterns within wild plant species is still missing. From the literature, we identified 91 experiments that were mainly designed to investigate the presence of positive interactions based on two contrasting hypotheses. Kin selection theory predicts partisan help given to a genealogical relative. The rationale behind this hypothesis relies on kin/non-kin recognition, with the positive outcome of kin cooperation substantiating it. On the other hand, the elbow-room hypothesis supports intraspecific niche partitioning leading to positive outcome when genetically distant genotypes interact. Positive diversity-productivity relationship rationalizes this hypothesis, notably with the outcome of overyielding. We found that both these hypotheses have been highly supported in experimental studies despite their opposite predictions between the extent of genetic relatedness among neighbors and the level of positive interactions. Interestingly, we identified a highly significant effect of breeding system, with a high proportion of selfing species associated with the presence of kin cooperation. Nonetheless, we identified several shortcomings regardless of the species considered, such as the lack of a reliable estimate of genetic relatedness among genotypes and ecological characterization of the natural habitats from which genotypes were collected, thereby impeding the identification of selective drivers of positive interactions. We therefore propose a framework combining evolutionary ecology and genomics to establish the eco-genomic landscape of positive GxG interactions in wild plant species.

Plant genotypic diversity effects on soil nematodes vary with trophic level

At local spatial scales, loss of genetic diversity within species can lead to species loss. Few studies, however, have examined plant genotypic diversity effects across trophic levels. We investigated genotypic diversity effects of Phragmites australis on belowground biomass and soil nematode communities. Our results revealed that belowground plant biomass and nematode abundance responses to plant genotypic diversity were uncoupled. Decreasing plant genotypic diversity decreased the abundance of lower, but not higher trophic level nematodes. Low plant genotypic diversity also decreased the structural footprint and functional indices of nematodes, indicating lowered metabolic functioning of higher trophic level nematodes and decreased soil food web stability. Our study suggests that plant genotypic diversity effects differ across trophic levels, taxonomic groups and ecosystem functions and that decreasing plant genotypic diversity could destabilise belowground food webs. This highlights the importance of conserving intraspecific plant diversity.

Effects of genomic and functional diversity on stand-level productivity and performance of non-native Arabidopsis

Biodiversity can affect the properties of groups of organisms, such as ecosystem function and the persistence of colonizing populations. Genomic data offer a newly available window to diversity, complementary to other measures like taxonomic or phenotypic diversity. We tested whether native genetic diversity in field experimental stands of Arabidopsis thaliana affected their aboveground biomass and fecundity in their colonized range. We constructed some stands of genotypes that we a priori predicted would differ in performance or show overyielding. We found no relationship between genetic diversity and stand total biomass. However, increasing stand genetic diversity increased fecundity in high-resource conditions. Polyculture (multiple genotype) stands consistently yielded less biomass than expected based on the yields of component genotypes in monoculture. This under-yielding was strongest in stands with late-flowering and high biomass genotypes, potentially due to interference competition by these genotypes. Using a new implementation of association mapping, we identified genetic loci whose diversity was associated with stand-level yield, revealing a major flowering time locus associated with under-yielding of polycultures. Our field experiment supports community ecology studies that find a range of diversity-function relationships. Nevertheless, our results suggest diversity in colonizing propagule pools can enhance population fitness. Furthermore, interference competition among genotypes differing in flowering time might limit the advantages of polyculture.

Genetic richness affects trait variation but not community productivity in a tree diversity experiment

Biodiversity-ecosystem functioning experiments found that productivity generally increases with species richness, but less is known about effects of within-species genetic richness and potential interactions between the two. While functional differences between species can explain species richness effects, empirical evidence regarding functional differences between genotypes within species and potential consequences for productivity is largely lacking. We therefore measured within- and among-species variation in functional traits and growth and determined stand-level tree biomass in a large forest experiment factorially manipulating species and genetic richness in subtropical China. Within-species variation across genetic seed families, in addition to variation across species, explained a substantial amount of trait variation. Furthermore, trait responses to species and genetic richness varied significantly within and between species. Multivariate trait variation was larger among individuals from species mixtures than those from species monocultures, but similar among individuals from genetically diverse vs genetically uniform monocultures. Correspondingly, species but not genetic richness had a positive effect on stand-level tree biomass. We argue that identifying functional diversity within and among species in forest communities is necessary to separate effects of species and genetic diversity on tree growth and community productivity.

Genetic Divergence and Relationship Among Opisthopappus Species Identified by Development of EST-SSR Markers

Opisthopappus Shih is an endemic and endangered genus restricted to the Taihang Mountains that has important ornamental and economic value. According to the Flora Reipublicae Popularis Sinicae (FRPS, Chinese version), this genus contains two species (Opisthopappus longilobus and Opisthopappus taihangensis), whereas in the Flora of China (English version) only one species O. taihangensis is present. The interspecific phylogenetic relationship remains unclear and undefined, which might primarily be due to the lack of specific molecular markers for phylogenetic analysis. For this study, 2644 expressed sequence tag-simple sequence repeats (EST-SSRs) from 33,974 unigenes using a de novo transcript assembly of Opisthopappus were identified with a distribution frequency of 7.78% total unigenes. Thereinto, mononucleotides (1200, 45.39%) were the dominant repeat motif, followed by trinucleotides (992, 37.52%), and dinucleotides (410, 15.51%). The most dominant trinucleotide repeat motif was ACC/GGT (207, 20.87%). Based on the identified EST-SSRs, 245 among 1444 designed EST-SSR primers were selected for the development of potential molecular markers. Among these markers, 63 pairs of primers (25.71%) generated clear and reproducible bands with expected sizes. Eventually, 11 primer pairs successfully amplified all individuals from the studied populations. Through the EST-SSR markers, a high level of genetic diversity was detected between Opisthopappus populations. A significant genetic differentiation between the O. longilobus and O. taihangensis populations was found. All studied populations were divided into two clusters by UPGMA, NJ, STRUCTURE, and PCoA. These results fully supported the view of the FRPS, namely, that O. longilobus and O. taihangensis should be regarded as two distinct species. Our study demonstrated that transcriptome sequences, as a valuable tool for the quick and cost-effective development of molecular markers, was helpful toward obtaining comprehensive EST-SSR markers that could contribute to an in-depth assessment of the genetic and phylogenetic relationships between Opisthopappus species.

Does intrinsic light heterogeneity in Ricinus communis L. monospecific thickets drive species' population dynamics?

Ricinus communis L. colonizes heterogeneous urban landscapes as monospecific thickets. The ecological understanding on colonization success of R. communis population due to variable light availability is lacking. Therefore, to understand the effect of intrinsic light heterogeneity on species' population dynamics, R. communis populations exposed to variable light availability (low, intermediate, and high) were examined for performance strategies through estimation of key vegetative, eco-physiological, biochemical, and reproductive traits. Considerable variability existed in studied plant traits in response to available light. Individuals inhabiting high-light conditions exhibited high eco-physiological efficiency and reproductive performance that potentially confers population boom. Individuals exposed to low light showed poor performance in terms of eco-physiology and reproduction, which attribute to bust. However, individuals in intermediate light were observed to be indeterminate to light availability, potentially undergoing trait modulations with uncertainty of available light. Heterogeneous light availability potentially drives the boom and bust cycles in R. communis monospecific thickets. Such boom and bust cycles subsequently affect species' dominance, persistence, collapse, and/or resurgence as an aggressive colonizer in contrasting urban environments. The study fosters extensive monitoring of R. communis thickets to probe underlying mechanism(s) affecting expansions and/or collapses of colonizing populations.

Genet dynamics of a regenerating dwarf bamboo population across heterogeneous light environments in a temperate forest understorey

Despite the advantage of plant clonality in patchy environments, studies focusing on genet demography in relation to spatially heterogeneous environments remain scarce. Regeneration of bamboos in forest understoreys after synchronous die-off provides an opportunity for assessing how they come to proliferate across heterogeneous light environments. In a Japanese forest, we examined genet demography of a population of Sasa kurilensis over a 7-year period starting 10 years after die-off, shortly after which some genets began spreading horizontally by rhizomes. The aboveground biomass was estimated, and genets were discriminated in 9-m2 plots placed under both canopy gaps and closed canopies. Overall, the results suggest that the survival and spread of more productive genets and the spatial expansion of genets into closed canopies underlie the proliferation of S. kurilensis. Compared to canopy gaps, the recovery rate of biomass was much slower under closed canopies for the first 10 years after the die-off, but became accelerated during the next 7 years. Genet survival was greater for more productive genets (with greater initial number of culms), and the spaces occupied by genets that died were often colonized afterward by clonal growth of surviving genets. The number of genets decreased under canopy gaps due to greater mortality, but increased under closed canopies where greater number of genets colonized clonally from outside the plots than genets died. The colonizing genets were more productive (having larger culms) than those originally germinated within the plots, and the contribution of colonizing genets to the biomass was greater under closed canopies. Our study emphasizes the importance of investigating genet dynamics over relevant spatiotemporal scales to reveal processes underlying the success of clonal plants in heterogeneous habitats.

Genotypic and Phenotypic Diversity Does Not Affect Productivity and Drought Response in Competitive Stands of Trifolium repens

Clonal plants can form dense canopies in which plants of different genetic origin are competing for the uptake of essential resources. The competitive relationships among these clones are likely to be affected by extreme environmental conditions, such as prolonged drought spells, which are predicted to occur more frequently due to global climate change. This, in turn, may alter characteristics of the ecological system and its associated functioning. We hypothesized that the relative success of individual clones will depend on the size of the ramets as ramets with larger leaves and longer petioles (large ramets) were predicted to have a competitive advantage in terms of increased light interception over smaller-sized ramets. Under drier conditions the relative performances of genotypes were expected to change leading to a change in genotype ranking. We also hypothesized that increased genotypic and phenotypic diversity will increase stand performance and resistance to drought. These hypotheses and the mechanisms responsible for shifts in competitive relationships were investigated by subjecting genotypes of the important pasture legume Trifolium repens to competition with either genetically identical clones, genetically different but similarly sized clones, or genetically as well as morphologically different clones under well-watered and dry conditions. Competitive relationships were affected by ramet size with large genotypes outperforming small genotypes in diverse stands in terms of biomass production. However, large genotypes also produced relatively fewer ramets than small genotypes and could not benefit in terms of clonal reproduction from competing with smaller genotypes, indicating that evolutionary shifts in genotype composition will depend on whether ramet size or ramet number is under selection. In contrast to our hypotheses, diversity did not increase stand performance under different selection regimes and genotype ranking was hardly affected by soil moisture, indicating that increasing fluctuations in water availability result in few short-term effects on genotypic diversity in this stoloniferous grassland species. Communities dominated by stoloniferous herbs such as T. repens may be relatively resilient to environmental change and to low levels of genetic diversity.

Genotypic richness predicts phenotypic variation in an endangered clonal plant

Declines in genetic diversity within a species can affect the stability and functioning of populations. The conservation of genetic diversity is thus a priority, especially for threatened or endangered species. The importance of genetic variation, however, is dependent on the degree to which it translates into phenotypic variation for traits that affect individual performance and ecological processes. This is especially important for predominantly clonal species, as no single clone is likely to maximise all aspects of performance. Here we show that intraspecific genotypic diversity as measured using microsatellites is a strong predictor of phenotypic variation in morphological traits and shoot productivity of the threatened, predominantly clonal seagrass Posidonia australis, on the east coast of Australia. Biomass and surface area variation was most strongly predicted by genotypic richness, while variation in leaf chemistry (phenolics and nitrogen) was unrelated to genotypic richness. Genotypic richness did not predict tissue loss to herbivores or epiphyte load, however we did find that increased herbivore damage was positively correlated with allelic richness. Although there was no clear relationship between higher primary productivity and genotypic richness, variation in shoot productivity within a meadow was significantly greater in more genotypically diverse meadows. The proportion of phenotypic variation explained by environmental conditions varied among different genotypes, and there was generally no variation in phenotypic traits among genotypes present in the same meadows. Our results show that genotypic richness as measured through the use of presumably neutral DNA markers does covary with phenotypic variation in functionally relevant traits such as leaf morphology and shoot productivity. The remarkably long lifespan of individual Posidonia plants suggests that plasticity within genotypes has played an important role in the longevity of the species. However, the strong link between genotypic and phenotypic variation suggests that a range of genotypes is still the best case scenario for adaptation to and recovery from predicted environmental change.

Explaining microbial genomic diversity in light of evolutionary ecology

Comparisons of closely related microorganisms have shown that individual genomes can be highly diverse in terms of gene content. In this Review, we discuss several studies showing that much of this variation is associated with social and ecological interactions, which have an important role in the population biology of wild populations of bacteria and archaea. These interactions create frequency-dependent selective pressures that can either stabilize gene frequencies at intermediate levels in populations or promote fast gene turnover, which presents as low gene frequencies in genome surveys. Thus, interpretation of gene-content diversity requires the delineation of populations according to cohesive gene flow and ecology, as micro-evolutionary changes arise in response to local selection pressures and population dynamics.

Effects of genotypic diversity of Phragmites australis on primary productivity and water quality in an experimental wetland

An increasing number of studies have shown that genetic diversity within plant species can influence important ecological processes. Here, we report a two-year wetland mesocosm experiment in which genotypic richness of Phragmites australis was manipulated to examine its effects on primary productivity and nitrogen removal from water. We used six genotypes of P. australis, and compared primary productivity and nitrogen concentration in the outflow water of the mesocosms between monocultures and polycultures of all six genotypes. We also quantified the abundance of denitrifying bacteria, as denitrification is a primary mechanism of nitrogen removal in addition to the biotic uptake by P. australis. Plant productivity was significantly greater in genotypic polycultures compared to what was expected based on monocultures. This richness effect on productivity was driven by both complementary and competitive interactions among genotypes. In addition, nitrogen removal rates of mesocosms were generally greater in genotypic polycultures compared to those expected based on monocultures. This effect, particularly pronounced in autumn, may largely be attributable to the enhanced uptake of nitrogen by P. australis, as the abundance of nitrite reducers did not increase with plant genotypic diversity. Although our effect sizes were relatively small compared to previous experiments, our study emphasizes the effect of genotypic interactions in regulating multiple ecological processes.

DNA fingerprinting in botany: past, present, future

Almost three decades ago Alec Jeffreys published his seminal Nature papers on the use of minisatellite probes for DNA fingerprinting of humans (Jeffreys and colleagues Nature 1985, 314:67-73 and Nature 1985, 316:76-79). The new technology was soon adopted for many other organisms including plants, and when Hilde Nybom, Kurt Weising and Alec Jeffreys first met at the very First International Conference on DNA Fingerprinting in Berne, Switzerland, in 1990, everybody was enthusiastic about the novel method that allowed us for the first time to discriminate between humans, animals, plants and fungi on the individual level using DNA markers. A newsletter coined "Fingerprint News" was launched, T-shirts were sold, and the proceedings of the Berne conference filled a first book on "DNA fingerprinting: approaches and applications". Four more conferences were about to follow, one on each continent, and Alec Jeffreys of course was invited to all of them. Since these early days, methodologies have undergone a rapid evolution and diversification. A multitude of techniques have been developed, optimized, and eventually abandoned when novel and more efficient and/or more reliable methods appeared. Despite some overlap between the lifetimes of the different technologies, three phases can be defined that coincide with major technological advances. Whereas the first phase of DNA fingerprinting ("the past") was dominated by restriction fragment analysis in conjunction with Southern blot hybridization, the advent of the PCR in the late 1980s gave way to the development of PCR-based single- or multi-locus profiling techniques in the second phase. Given that many routine applications of plant DNA fingerprinting still rely on PCR-based markers, we here refer to these methods as "DNA fingerprinting in the present", and include numerous examples in the present review. The beginning of the third phase actually dates back to 2005, when several novel, highly parallel DNA sequencing strategies were developed that increased the throughput over current Sanger sequencing technology 1000-fold and more. High-speed DNA sequencing was soon also exploited for DNA fingerprinting in plants, either in terms of facilitated marker development, or directly in the sense of "genotyping-by-sequencing". Whereas these novel approaches are applied at an ever increasing rate also in non-model species, they are still far from routine, and we therefore treat them here as "DNA fingerprinting in the future".

Genetic diversity and ecosystem functioning in the face of multiple stressors

Species diversity is important for a range of ecosystem processes and properties, including the resistance to single and multiple stressors. It has been suggested that genetic diversity may play a similar role, but empirical evidence is still relatively scarce. Here, we report the results of a microcosm experiment where four strains of the marine diatom Skeletonema marinoi were grown in monoculture and in mixture under a factorial combination of temperature and salinity stress. The strains differed in their susceptibility to the two stressors and no strain was able to survive both stressors simultaneously. Strong competition between the genotypes resulted in the dominance of one strain under both control and salinity stress conditions. The overall productivity of the mixture, however, was not related to the dominance of this strain, but was instead dependent on the treatment; under control conditions we observed a positive effect of genetic richness, whereas a negative effect was observed in the stress treatments. This suggests that interactions among the strains can be both positive and negative, depending on the abiotic environment. Our results provide additional evidence that the biodiversity-ecosystem functioning relationship is also relevant at the level of genetic diversity.

The pattern of genetic variability in apomictic clones of Taraxacum officinale indicates the alternation of asexual and sexual histories of apomicts

Dandelions (genus Taraxacum) comprise a group of sexual diploids and apomictic polyploids with a complicated reticular evolution. Apomixis (clonal reproduction through seeds) in this genus is considered to be obligate, and therefore represent a good model for studying the role of asexual reproduction in microevolutionary processes of apomictic genera. In our study, a total of 187 apomictic individuals composing a set of nine microspecies (sampled across wide geographic area in Europe) were genotyped for six microsatellite loci and for 162 amplified fragment length polymorphism (AFLP) markers. Our results indicated that significant genetic similarity existed within accessions with low numbers of genotypes. Genotypic variability was high among accessions but low within accessions. Clustering methods discriminated individuals into nine groups corresponding to their phenotypes. Furthermore, two groups of apomictic genotypes were observed, which suggests that they had different asexual histories. A matrix compatibility test suggests that most of the variability within accession groups was mutational in origin. However, the presence of recombination was also detected. The accumulation of mutations in asexual clones leads to the establishment of a network of clone mates. However, this study suggests that the clones primarily originated from the hybridisation between sexual and apomicts.