To predict the threat of biological invasions to native species, it is critical that we understand how increasing abundance of invasive alien species (IAS) affects native populations and communities. The form of this relationship across taxa and ecosystems is unknown, but is expected to depend strongly on the trophic position of the IAS relative to the native species. Using a global metaanalysis based on 1,258 empirical studies presented in 201 scientific publications, we assessed the shape, direction, and strength of native responses to increasing invader abundance. We also tested how native responses varied with relative trophic position and for responses at the population vs. community levels. As IAS abundance increased, native populations declined nonlinearly by 20%, on average, and community metrics declined linearly by 25%. When at higher trophic levels, invaders tended to cause a strong, nonlinear decline in native populations and communities, with the greatest impacts occurring at low invader abundance. In contrast, invaders at the same trophic level tended to cause a linear decline in native populations and communities, while invaders at lower trophic levels had no consistent impacts. At the community level, increasing invader abundance had significantly larger effects on species evenness and diversity than on species richness. Our results show that native responses to invasion depend critically on invasive species’ abundance and trophic position. Further, these general abundance–impact relationships reveal how IAS impacts are likely to develop during the invasion process and when to best manage them.

Amplified fragment length polymorphism (AFLP) fingerprint data are now commonly collected using DNA sequencers. AFLP genotypes are still often scored by eye from such data - a time-consuming, error-prone and subjective process. We present a semi-automated method of genotyping sequencer-collected AFLPs at predefined fragment locations (loci) within the fingerprint. Our method uses thresholds of AFLP-polymerase chain reaction-product fluorescence intensity (peak height) in order to: (i) exclude AFLP loci that are likely to contribute high rates of error to data sets, and (ii) determine the AFLP phenotype (fragment presence or absence) at the retained loci. Error rate analysis is an integral part of this process and is used to determine optimal thresholds that minimize genotyping error, while maximizing the numbers of retained loci. We show that application of this method to a large AFLP data set allows genotype calls that are rapid, objective and repeatable, facilitating the extraction of reliable genotype data for molecular ecological studies.

Summary 1.A recent experiment varied the genetic diversity of model grassland communities under standardized soil and management conditions and at constant initial species diversity. After 5 years' growth, genetically diverse communities retained more species diversity and became more similar in species composition than genetically impoverished communities. 2.Here we present the results of further investigation within this experimental system. We proposed that two mechanisms -the first invoking genetically determined and constant differences in plant phenotypes and the second invoking genotype-environment interactions -could each underpin these results. This mechanistic framework was used as a tool to interpret our findings. 3. We used inter-simple sequence repeat (ISSR) DNA markers to confirm which of the individuals of six study species initially included in the model communities were unique genotypes. We then used the molecular markers to assess the survival and abundance of each genotype at the end of the 5-year experimental period. 4. The DNA marker data were used to create, for the first time, a genotype abundance hierarchy describing the structure of a community at the level of genotypes. This abundance hierarchy revealed wide variation in the abundance of genotypes within species, and large overlaps in the performance of the genotypes of different species. 5. Each genotype achieved a consistent level of abundance within genetically diverse communities, which differed from that attained by other genotypes of the same species. The abundance hierarchy of genotypes within species also showed consistency across communities differing in their initial level of genetic diversity, such that species abundance in genetically impoverished communities could be predicted, in part, by genotypic identity. 6. Three species (including two canopy-dominants) experienced shifts in their communitylevel genotype abundance hierarchies that were consistent with an increased influence of genotype-environment interactions in genetically impoverished communities. 7. Our results indicate that under relatively constant environmental conditions the species abundance structure of plant communities can in part be predicted from the genotypic composition of their component populations. Genotype-environment interactions also appear to shape the structure of communities under such conditions, although further experiments are needed to clarify the magnitude and mechanism of these effects.

Understanding the effects of intraspecific genetic diversity on the structure and functioning of ecological communities is a fundamentally important part of evolutionary ecology and may also have conservation relevance in identifying the situations in which genetic diversity coincides with species-level diversity.Early studies within this field documented positive relationships between genetic diversity and ecological structure, but recent studies have challenged these findings. Conceptual synthesis has been hampered because studies have used different measures of intraspecific variation (phenotypically adaptive vs. neutral) and have considered different measures of ecological structure in different ecological and spatial contexts. The aim of this study is to strengthen conceptual understanding by providing an empirical synthesis quantifying the relationship between genetic diversity and ecological structure.Here, I present a meta-analysis of the relationship between genetic diversity within plant populations and the structure and functioning of associated ecological communities (including 423 effect sizes from 70 studies). I used Bayesian meta-analyses to examine (i) the strength and direction of this relationship, (ii) the extent to which phenotypically adaptive and neutral (molecular) measures of diversity differ in their association with ecological structure and (iii) variation in outcomes among different measures of ecological structure and in different ecological contexts.Effect sizes measuring the relationship between adaptive diversity (genotypic richness) and both community- and ecosystem-level ecological responses were small, but significantly positive. These associations were supported by genetic effects on species richness and productivity, respectively.There was no overall association between neutral genetic diversity and measures of ecological structure, but a positive correlation was observed under a limited set of demographic conditions. These results suggest that adaptive and neutral genetic diversity should not be treated as ecologically equivalent measures of intraspecific variation.Synthesis. This study advances the debate over whether relationships between genetic diversity and ecological structure are either simply positive or negative, by showing how the strength and direction of these relationships changes with different measures of diversity and in different ecological contexts. The results provide a solid foundation for assessing when and where an expanded synthesis between ecology and genetics will be most fruitful.

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