In legume-Rhizobium symbioses, specialised soil bacteria fix atmospheric nitrogen in return for carbon. However, ineffective strains can arise, making discrimination essential. Discrimination can occur via partner choice, where legumes prevent ineffective strains from entering, or via sanctioning, where plants provide fewer resources. Several studies have inferred that legumes exercise partner choice, but the rhizobia compared were not otherwise isogenic. To test when and how plants discriminate ineffective strains we developed sets of fixing and non-fixing strains that differed only in the expression of nifH – essential for nitrogen fixation – and could be visualised using marker genes. We show that the plant is unable to select against the non-fixing strain at the point of entry, but that non-fixing nodules are sanctioned. We also used the technique to characterise mixed nodules (containing both a fixing and a non-fixing strain), whose frequency could be predicted using a simple diffusion model. We discuss that sanctioning is likely to evolve in preference to partner choice in any symbiosis where partner quality cannot be adequately assessed until goods or services are actively exchanged.

Mutualistic interactions form the basis for many ecological processes and are often analyzed within the framework of ecological networks. These interactions can be sampled with a range of methods and first analyses of pollination networks sampled with different methods showed differences in common network metrics. However, it is yet unknown if metrics of seed dispersal networks are similarly affected by the sampling method and if different methods detect a complementary set of frugivores. This is necessary to better understand the (dis‐)advantages of each method and to identify the role of each frugivore for the seed dispersal process. Here, we compare seed removal networks based on the observation of 2189 frugivore visits on ten focal plant species with seed deposition networks constructed by DNA barcoding of plant seeds in 3094 frugivore scats. We were interested in whether both methods identify the same disperser species and if species‐level network metrics of plant species were correlated between network types. Both methods identified the same avian super‐generalist frugivores, which accounted for the highest number of dispersed seeds. However, only with DNA barcoding, we detected elusive but frequent mammalian seed dispersers. The overall networks created by both methods were congruent but the plant species' degree, their interaction frequency and their specialization index (d′) differed. Our study suggests that DNA barcoding of defecated and regurgitated seeds can be used to construct quantitative seed deposition networks similar to those constructed by focal observations. To improve the overall completeness of seed dispersal networks it might be useful to combine both methods to detect interactions by both birds and mammals. Most importantly, the DNA barcoding method provides information on the post‐dispersal stage and thus on the qualitative contribution of each frugivore for the plant community thereby linking species interactions to regeneration dynamics of fleshy‐fruited plant species.

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Forest degradation changes the structural heterogeneity of forests and species communities, with potential consequences for ecosystem functions including seed dispersal by frugivorous animals. While the quantity of seed dispersal may be robust towards forest degradation, changes in the effectiveness of seed dispersal through qualitative changes are poorly understood. Here, we carried out extensive field sampling on the structure of forest microhabitats, seed deposition sites and plant recruitment along three characteristics of forest microhabitats (canopy cover, ground vegetation and deadwood) in Europe's last lowland primeval forest (Białowieża, Poland). We then applied niche modelling to study forest degradation effects on multi-dimensional seed deposition by frugivores and recruitment of fleshy-fruited plants. Forest degradation was shown to (i) reduce the niche volume of forest microhabitat characteristics by half, (ii) homogenize the spatial seed deposition within and among frugivore species, and (iii) limit the regeneration of plants via changes in seed deposition and recruitment. Our study shows that the loss of frugivores in degraded forests is accompanied by a reduction in the complementarity and quality of seed dispersal by remaining frugivores. By contrast, structure-rich habitats, such as old-growth forests, safeguard the diversity of species interactions, forming the basis for high-quality ecosystem functions.