Data from: Logging, exotic plant invasions, and native plant reassembly in a lowland tropical rain forest

Habitat modification and biological invasions are key drivers of global environmental change. However, the extent and impact of exotic plant invasions in modified tropical landscapes remains poorly understood. We examined whether logging drives exotic plant invasions, and whether their combined influences alter understory plant community composition in lowland rain forests in Borneo. We tested the relationship between understory communities and local- and landscape-scale logging intensity, using leaf area index (LAI) and above-ground biomass (AGB) data from 192 plots across a logging-intensity gradient from primary to repeatedly-logged forests. Overall, we found relatively low levels of exotic plant invasions, despite an intensive logging history. Exotic species were more speciose, had greater cover, and more biomass in sites with more local-scale canopy loss. Surprisingly, though, exotic species invasion was not related to either landscape-scale canopy loss nor road configuration. Moreover, logging and invasion did not seem to be acting synergistically on native plant composition, except that seedlings of the canopy-dominant Dipterocarpaceae family were less abundant in areas with higher exotic plant biomass. Current low levels of invasion, and limited association with native understory community change, suggest there is a window of opportunity to manage invasive impacts. We caution about potential lag effects and the possibly severe negative impacts of exotic plant invasions on the long-term quality of tropical forest, particularly where agricultural plantations function as permanent seed sources for recurrent dispersal along logging roads. We therefore urge prioritization of strategic management plans to counter the growing threat of exotic plant invasions in modified tropical landscapes

Plot characteristics for understorey vegetation plots in Borneo

This csv file contains the full database of characteristics for each of 180 vegetation plots including logging metrics, environmental variables as well as taxonomic, functional and phylogenetic diversity indices for understorey plants in Borneo

Species trait data for understorey plant species in Borneo

This csv file contains the complete list of species (691) sampled across 180 vegetation plots (2 x 2m) located at the Stability of Altered Forest Ecosystems (SAFE) project in Sabah, Malaysia, including their allocation to a range of plant functional traits as well as a distinction between native or exotic species origin

Matrix of biomass values for 691 species in 180 understorey vegetation plots in Borneo

This csv file contains a matrix of biomass values for 691 plant taxa sampled across 180 vegetation plots (2 x 2m) located at the Stability of Altered Forest Ecosystems (SAFE) project in Sabah, Malaysia

Data from: Logging increases the functional and phylogenetic dispersion of understorey plant communities in tropical lowland rainforest

1. Logging is a major driver of tropical forest degradation, with severe impacts on plant richness and composition. Rarely have these effects been considered in terms of their impact on the functional and phylogenetic diversity of understorey plant communities, despite the direct relevance to community reassembly trajectories. Here, we test the effects of logging on functional traits and evolutionary relatedness, over and above effects that can be explained by changes in species richness alone. We hypothesised that strong environmental filtering will result in more clustered (under-dispersed) functional and phylogenetic structures within communities as logging intensity increases. 2. We surveyed understorey plant communities at 180 locations across a logging intensity gradient from primary to repeatedly-logged tropical lowland rainforest in Sabah, Malaysia. For the 691 recorded plant taxa, we generated a phylogeny to assess plot-level phylogenetic relatedness. We quantified 10 plant traits known to respond to disturbance (dispersal mode, fruit type, life-history mode, pollination syndrome, reproduction strategy and seed number) and affect ecosystem functioning (plant growth form, plant height, specific leaf area and wood density), and tested the influence of logging on functional and phylogenetic structure. 3. We found no significant effect of local- or landscape-scale forest canopy loss, or configuration of logging roads on species richness. By contrast, both the trait dispersion index (FDis) and net relatedness index (NRI) for phylogenetic dispersion showed strong gradients from clustered towards more randomly-assembled communities at higher logging intensity, independent of variation in species richness. All functional traits showed significant phylogenetic signals, indicating strong concordance between functional and phylogenetic dispersion. 4. Synthesis. We found a strong logging signal in the functional and phylogenetic structure of understorey plant communities, over and above species richness, but this effect was opposite to that predicted. Logging increased, rather than decreased, functional and phylogenetic dispersion in understorey plant communities. This effect was particularly pronounced for functional response traits, which directly link disturbance with plant community reassembly. Our study provides novel insight into the way logging affects understorey plant communities in tropical rainforest and highlights the importance of trait-based approaches to improve our understanding of the broad range of logging-associated impacts

SpeciesDataBiotropica

This csv file contains the complete list of species (723) sampled across 192 vegetation plots (2 x 2m) located at the Stability of Altered Forest Ecosystems (SAFE) project in Sabah, Malaysia, including a distinction between native and exotic species origin

PlotDataBiotropica

This csv file contains the full database of characteristics for each of 159 vegetation plots including logging metrics, environmental variables as well as specific data on native and exotic plants

PlotSpeciesDataBiotropica

This csv file contains a matrix of biomass values for 723 plant taxa sampled across 192 vegetation plots (2 x 2m) located at the Stability of Altered Forest Ecosystems (SAFE) project in Sabah, Malaysia

Same data, different analysts: variation in effect sizes due to analytical decisions in ecology and evolutionary biology

Gould E, Fraser H, Parker T, et al. Same data, different analysts: variation in effect sizes due to analytical decisions in ecology and evolutionary biology. 2023.Although variation in effect sizes and predicted values among studies of similar phenomena is inevitable, such variation far exceeds what might be produced by sampling error alone. One possible explanation for variation among results is differences among researchers in the decisions they make regarding statistical analyses. A growing array of studies has explored this analytical variability in different (mostly social science) fields, and has found substantial variability among results, despite analysts having the same data and research question. We implemented an analogous study in ecology and evolutionary biology, fields in which there have been no empirical exploration of the variation in effect sizes or model predictions generated by the analytical decisions of different researchers. We used two unpublished datasets, one from evolutionary ecology (blue tit, Cyanistes caeruleus, to compare sibling number and nestling growth) and one from conservation ecology (Eucalyptus, to compare grass cover and tree seedling recruitment), and the project leaders recruited 174 analyst teams, comprising 246 analysts, to investigate the answers to prespecified research questions. Analyses conducted by these teams yielded 141 usable effects for the blue tit dataset, and 85 usable effects for the Eucalyptus dataset. We found substantial heterogeneity among results for both datasets, although the patterns of variation differed between them. For the blue tit analyses, the average effect was convincingly negative, with less growth for nestlings living with more siblings, but there was near continuous variation in effect size from large negative effects to effects near zero, and even effects crossing the traditional threshold of statistical significance in the opposite direction. In contrast, the average relationship between grass cover and Eucalyptus seedling number was only slightly negative and not convincingly different from zero, and most effects ranged from weakly negative to weakly positive, with about a third of effects crossing the traditional threshold of significance in one direction or the other. However, there were also several striking outliers in the Eucalyptus dataset, with effects far from zero. For both datasets, we found substantial variation in the variable selection and random effects structures among analyses, as well as in the ratings of the analytical methods by peer reviewers, but we found no strong relationship between any of these and deviation from the meta-analytic mean. In other words, analyses with results that were far from the mean were no more or less likely to have dissimilar variable sets, use random effects in their models, or receive poor peer reviews than those analyses that found results that were close to the mean. The existence of substantial variability among analysis outcomes raises important questions about how ecologists and evolutionary biologists should interpret published results, and how they should conduct analyses in the future