Genotypic selection shapes patterns of within-species diversity in experimental plant populations

1.  An increasing body of evidence suggests that within-species diversity plays an important role for community and ecosystem functioning, alters complex trophic interactions and affects patterns of species diversity and coexistence. Nonetheless, we lack a good understanding of how genotypic trait variation translates into shifts in the relative abundance of genotypes within populations.
2.  In this study, we show that genotypic selection strongly alters dominance relationships among genotypes over a period of 5 years. This resulted in remarkably consistent changes in the proportional representation of genotypes, and in a concomitant decline of diversity and evenness in our experimental populations.
3.  High growth rates and the production of large offspring were positively associated with genotypic performance. Vegetative abundances of genotypes translated monotonically into flowering frequencies.
4.   Synthesis . We conclude that genotypic selection markedly affects patterns of diversity and consistently alters genotypic abundance and mean trait distributions in plant populations over a relatively short period of time.     

Strain-specific colonization patterns and serum modulation of multi-species oral biofilm development

Periodontitis results from an ecological shift in the composition of subgingival biofilms. Subgingival community maturation is modulated by inter-organismal interactions and the relationship of communities with the host. In an effort to better understand this process, we evaluated biofilm formation, with oral commensal species, by three strains of the subgingivally prevalent microorganism Fusobacterium nucleatum and four strains of the periodontopathogen Porphyromonas gingivalis. We also tested the effect of serum, which resembles gingival exudates, on subgingival biofilms. Biofilms were allowed to develop in flow cells using salivary medium. We found that although not all strains of F. nucleatum were able to grow in mono-species biofilms, forming a community with health-associated partners Actinomyces oris and Veillonella parvula promoted biofilm growth of all F. nucleatum strains. Strains of P. gingivalis also showed variable ability to form mono-species biofilms. P. gingivalis W50 and W83 did not form biofilms, while ATCC 33277 and 381 formed biofilm structures, but only strain ATCC 33277 grew over time. Unlike the enhanced growth of F. nucleatum with the two health-associated species, no strain of P. gingivalis grew in three-species communities with A. oris and V. parvula. However, addition of F. nucleatum facilitated growth of P. gingivalis ATCC 33277 with health-associated partners. Importantly, serum negatively affected the adhesion of F. nucleatum, while it favored biofilm growth by P. gingivalis. This work highlights strain specificity in subgingival biofilm formation. Environmental factors such as serum alter the colonization patterns of oral microorganisms and could impact subgingival biofilms by selectively promoting pathogenic species.     

Asymmetric competition in plant populations

Recently there has been much interest in the hypothesis that competition between individual plants is asymmetric or onesided: larger individuals obtain a disproportionate share of the resources (for their relative size) and suppress the growth of smaller individuals. This has important implications for population structure, for the analysis of competition between plants at the individual, population and community levels, and for our understanding of competition as a selective force in the evolution of plant populations.     

Group selection in plant populations

Summary Several mechanisms have been proposed for group selection, to account for the evolution of altruistic traits. One type, Neighbourhood models, suggests that individuals react with those immediately around them, but with no recognition mechanism. The organization of plant populations seems especially favorable for this type of selection. The possibility of Neighbourhood selection was investigated by simulating a plant population. It was possible for an altruistic trait to evolve, though only under restricted conditions. The main requirement was gene flow only by very restricted pollen dispersal, and a high benefit : cost ratio in the altruistic relationship. Under conditions favourable for such evolution, the starting frequency of the allele, the initial pattern, and the population size, had little effect. Inbreeding tended to prevent the increase of the altruism allele, though this depended on the mechanism of selfing. Known ecological features of plants are discussed that could be considered altruistic and hence require some form of group selection for their evolution, and whether the benefit : cost requirements are likely to be met. Neighbourhood models of group selection are a possibility in plant populations, and we therefore cannot exclude the possibility of altruism in plants. However, Neighbourhood selection is weak force, unlikely to be effective in the face of opposing individual selection. It may be more important as reinforcement of individual selection.     

Definition of plant functional groups for informing implementation scenarios in resource-limited multi-species recovery planning

We describe an approach to multi-species recovery planning and bio-regional biodiversity assessment that uses trait-based plant functional groups as the basis for developing threat/risk assessments for rare, threatened and ‘of concern’ species. Multi-variate methods were used to extract and test emergent groups, and additional information fields related to species life history and distributional data were added to develop a species-level information assessment matrix in spreadsheet format. Relating emergent trait-based plant functional groups to habitat was found to be the most informative approach for the subsequent development of management recommendations and landscape scale threat/risk assessment to inform recovery planning. Examples on the use of the identified groups in a management context are provided. These include higher and lower resource and data availability scenarios, and the role of selected traits in adding to or ameliorating threats and risk of extinction.     

Detection of process-related changes in plant patterns at extended spatial scales during early dryland desertification

Arid and semiarid shrublands occupy extensive land areas over the world, are susceptible to desertification by anthropic use and can contribute to regional climate change. These prompt the interest to monitor and evaluate these lands adequately in order to detect early stages of degradation. Evaluation topics must refer to biology‐relevant characteristics of these systems, while simultaneously satisfying sampling consistency over extended landscape areas. We present an analysis of process‐relevant parameters related to changes in the spatial arrangement of the plant canopy of shrublands inferred from high‐resolution panchromatic aerial photos and Interferometric Synthetic Aperture Radar imagery. We obtained low‐altitude images systematically located along several gradients of land‐use intensity in a Patagonian Monte shrubland in Argentina. Images were digitized to spatial resolutions ranging from 0.09 to 0.72 m (pixel size) and the average values and an‐isotropic characteristics of the plant canopy patterns were quantified by means of a Fourier metric. We used radar‐derived imagery to overlay the panchromatic images on a digital elevation model in order to study the correspondence of potential runoff patterns and the spatial arrangement of plants. We related an‐isotropic features of the plant canopy images to the prevailing wind regime. Observed trends were further interpreted on the basis of a spatial‐explicit simulation model describing the dynamics of the main functional groups in the plant community. We conclude that early stages of anthropic‐driven dryland degradation in the Patagonian Monte can be characterized by the incipient un‐coupling of spatial vegetation patterns from those of runoff at a landscape scale, and a progressive coupling to the spatial pattern of the wind regime. The method and metrics we present can be used to quantify early desertification changes in other similar drylands at extended spatial scales.     

Cyclic dynamics in simulated plant populations

Despite the general interest in nonlinear dynamics in animal populations, plant populations are supposed to show a stable equilibrium that is attributed to fundamental differences compared with animals. Some studies find more complex dynamics, but empirical studies usually are too short and most modelling studies ignore important spatial aspects of local competition and establishment. Therefore, we used a spatially explicit individual-based model of a hypothetical, non-clonal perennial to explore which mechanisms might generate complex dynamics, i.e. cycles. The model is based on the field-of-neighbourhood approach that describes local competition and establishment in a phenomenological manner. We found cyclic population dynamics for a wide spectrum of model variants, provided that mortality is determined by local competition and recruitment is virtually completely suppressed within the zone of influence of established plants. This destabilizing effect of local processes within plant populations might have wide-ranging implications for the understanding of plant community dynamics and coexistence.     

Modelling the spatio-temporal dynamics of multi-species host-parasitoid interactions: heterogeneous patterns and ecological implications

A mathematical model of the spatio-temporal dynamics of a two host, two parasitoid system is presented. There is a coupling of the four species through parasitism of both hosts by one of the parasitoids. The model comprises a system of four reaction-diffusion equations. The underlying system of ordinary differential equations, modelling the host-parasitoid population dynamics, has a unique positive steady state and is shown to be capable of undergoing Hopf bifurcations, leading to limit cycle kinetics which give rise to oscillatory temporal dynamics. The stability of the positive steady state has a fundamental impact on the spatio-temporal dynamics: stable travelling waves of parasitoid invasion exhibit increasingly irregular periodic travelling wave behaviour when key parameter values are increased beyond their Hopf bifurcation point. These irregular periodic travelling waves give rise to heterogeneous spatio-temporal patterns of host and parasitoid abundance. The generation of heterogeneous patterns has ecological implications and the concepts of temporary host refuge and niche formation are considered.     

Dynamics of size structure in plant populations

The size structure of populations is important for the study of the life histories and evolution of plant species. Many aspects of the dynamics of size structure as affected by species characteristics and environmental conditions have been interpreted well by recent models.     

Reconstruction of pedigrees in clonal plant populations

We present a Bayesian method for the reconstruction of pedigrees in clonal populations using co-dominant genomic markers such as microsatellites and single nucleotide polymorphisms (SNPs). The accuracy of the algorithm is demonstrated for simulated data. We show that the joint estimation of parameters of interest such as the rate of self-fertilization is possible with high accuracy even with marker panels of moderate power. Classical methods can only assign a very limited number of statistically significant parentages in this case and would therefore fail. Statistical confidence is estimated by Markov Chain Monte Carlo (MCMC) sampling. The method is implemented in a fast and easy to use open source software that scales to large datasets with many thousand individuals.     

Discriminating multi-species populations in biofilms with peptide nucleic acid fluorescence in situ hybridization (PNA FISH)

Background

Our current understanding of biofilms indicates that these structures are typically composed of many different microbial species. However, the lack of reliable techniques for the discrimination of each population has meant that studies focusing on multi-species biofilms are scarce and typically generate qualitative rather than quantitative data.

Methodology/Principal Findings

We employ peptide nucleic acid fluorescence in situ hybridization (PNA FISH) methods to quantify and visualize mixed biofilm populations. As a case study, we present the characterization of Salmonella enterica/Listeria monocytogenes/Escherichia coli single, dual and tri-species biofilms in seven different support materials. Ex-situ, we were able to monitor quantitatively the populations of ∼56 mixed species biofilms up to 48 h, regardless of the support material. In situ, a correct quantification remained more elusive, but a qualitative understanding of biofilm structure and composition is clearly possible by confocal laser scanning microscopy (CLSM) at least up to 192 h. Combining the data obtained from PNA FISH/CLSM with data from other established techniques and from calculated microbial parameters, we were able to develop a model for this tri-species biofilm. The higher growth rate and exopolymer production ability of E. coli probably led this microorganism to outcompete the other two [average cell numbers (cells/cm²) for 48 h biofilm: E. coli 2,1×10⁸ (±2,4×10⁷); L. monocytogenes 6,8×10⁷ (±9,4×10⁶); and S. enterica 1,4×10⁶ (±4,1×10⁵)]. This overgrowth was confirmed by CSLM, with two well-defined layers being easily identified: the top one with E. coli, and the bottom one with mixed regions of L. monocytogenes and S. enterica.

Significance

While PNA FISH has been described previously for the qualitative study of biofilm populations, the present investigation demonstrates that it can also be used for the accurate quantification and spatial distribution of species in polymicrobial communities. Thus, it facilitates the understanding of interspecies interactions and how these are affected by changes in the surrounding environment.     

Genomic patterns of homozygosity in worldwide human populations

Genome-wide patterns of homozygosity runs and their variation across individuals provide a valuable and often untapped resource for studying human genetic diversity and evolutionary history. Using genotype data at 577,489 autosomal SNPs, we employed a likelihood-based approach to identify runs of homozygosity (ROH) in 1,839 individuals representing 64 worldwide populations, classifying them by length into three classes—short, intermediate, and long—with a model-based clustering algorithm. For each class, the number and total length of ROH per individual show considerable variation across individuals and populations. The total lengths of short and intermediate ROH per individual increase with the distance of a population from East Africa, in agreement with similar patterns previously observed for locus-wise homozygosity and linkage disequilibrium. By contrast, total lengths of long ROH show large interindividual variations that probably reflect recent inbreeding patterns, with higher values occurring more often in populations with known high frequencies of consanguineous unions. Across the genome, distributions of ROH are not uniform, and they have distinctive continental patterns. ROH frequencies across the genome are correlated with local genomic variables such as recombination rate, as well as with signals of recent positive selection. In addition, long ROH are more frequent in genomic regions harboring genes associated with autosomal-dominant diseases than in regions not implicated in Mendelian diseases. These results provide insight into the way in which homozygosity patterns are produced, and they generate baseline homozygosity patterns that can be used to aid homozygosity mapping of genes associated with recessive diseases.     

Diversity of topological digital patterns in Iranian populations

We analyzed bilateral finger prints of 3158 individuals from 13 Iranian populations of diverse origins, for digital patterns, using the topological method. Some male/female differences, and a great deal of heterogeneity in interpopulational variation was observed. Distance analysis, and the resultant dendrograms separated the populations studied, but the separation was not in agreement with the known ethnohistory of this region. Comparison of the obtained results with those based on the traditional methodology showed that the traditional methodology gives better results in measuring population distances.     

Diversity of topological palmar patterns in Iranian populations

The bilateral palmar prints of 3,158 females and males from 13 Iranian populations of diverse origins were analyzed to see how well topological palmar pattern frequencies reflect population distances. The results showed bimanual variation among most of the populations studied. Sex variation showed significant differences among all of the populations studied. Distance analysis and constructed dendrograms showed separation between the populations studied. These distances were frequently in agreement with the known ethnohistoric background of the populations studied. The male data gave better results. It appears that topological palmar patterns are a better indicator of population distance than topological finger patterns.