Revealing uncertainty in the status of biodiversity change.

Biodiversity faces unprecedented threats from rapid global change1. Signals of biodiversity change come from time-series abundance datasets for thousands of species over large geographic and temporal scales. Analyses of these biodiversity datasets have pointed to varied trends in abundance, including increases and decreases. However, these analyses have not fully accounted for spatial, temporal and phylogenetic structures in the data. Here, using a new statistical framework, we show across ten high-profile biodiversity datasets2-11 that increases and decreases under existing approaches vanish once spatial, temporal and phylogenetic structures are accounted for. This is a consequence of existing approaches severely underestimating trend uncertainty and sometimes misestimating the trend direction. Under our revised average abundance trends that appropriately recognize uncertainty, we failed to observe a single increasing or decreasing trend at 95% credible intervals in our ten datasets. This emphasizes how little is known about biodiversity change across vast spatial and taxonomic scales. Despite this uncertainty at vast scales, we reveal improved local-scale prediction accuracy by accounting for spatial, temporal and phylogenetic structures. Improved prediction offers hope of estimating biodiversity change at policy-relevant scales, guiding adaptive conservation responses.

Crop diversification and parasitic weed abundance: a global meta-analysis.

Parasitic weeds cause huge annual losses to food production globally. A small number of species from the genera Cuscuta, Orobanche, Phelipanche and Striga have proliferated across many agroecological zones. Their control is compromised due to the lack of efficacy of conventional herbicides and their rapid adaptation to new resistant crop cultivars. A broad range of studies suggest consistent reductions in parasitic weed densities owing to increased spatial (intercropping) and temporal diversity (crop rotation). However, to date, no synthesis of this body of research has been published. Here we report the results of a meta-analysis using 1525 paired observations from 67 studies across 24 countries, comparing parasitic weed density and crop yields from monocrop and more diverse cropping systems. We found both spatial and temporal crop diversification had a significant effect on parasitic weed density reduction. Furthermore, our results show effects of spatial diversification are stronger in suppressing parasitic weeds than temporal effects. Furthermore, the analysis indicates intercrops which alter both microclimate and soil chemistry (e.g. Crotalaria, Stylosanthes, Berseem clover and Desmodium) are most effective in parasitic weed management. This analysis serves to underline the viability of crop diversification as a tool to enhance food security globally.

Evaluating the potential of Unmanned Aerial Systems for mapping weeds at field scales: a case study with Alopecurus myosuroides.

Mapping weed densities within crops has conventionally been achieved either by detailed ecological monitoring or by field walking, both of which are time-consuming and expensive. Recent advances have resulted in increased interest in using Unmanned Aerial Systems (UAS) to map fields, aiming to reduce labour costs and increase the spatial extent of coverage. However, adoption of this technology ideally requires that mapping can be undertaken automatically and without the need for extensive ground-truthing. This approach has not been validated at large scale using UAS-derived imagery in combination with extensive ground-truth data. We tested the capability of UAS for mapping a grass weed, Alopecurus myosuroides, in wheat crops. We addressed two questions: (i) can imagery accurately measure densities of weeds within fields and (ii) can aerial imagery of a field be used to estimate the densities of weeds based on statistical models developed in other locations? We recorded aerial imagery from 26 fields using a UAS. Images were generated using both RGB and Rmod (Rmod 670-750 nm) spectral bands. Ground-truth data on weed densities were collected simultaneously with the aerial imagery. We combined these data to produce statistical models that (i) correlated ground-truth weed densities with image intensity and (ii) forecast weed densities in other fields. We show that weed densities correlated with image intensity, particularly Rmod image data. However, results were mixed in terms of out of sample prediction from field-to-field. We highlight the difficulties with transferring models and we discuss the challenges for automated weed mapping using UAS technology.

Why care? Inferring the evolution of complex social behaviour.

Phylogenetic comparative analyses of complex traits often reduce the traits of interests into a single (or a few) component variables. Here, we show that this may be an over-simplification, because components of a complex trait may evolve independently from each other. Using eight components of parental care in 400 bird species from 89 avian families that represent the relative contribution of male vs. female to a particular type of care, we show that some components evolve in a highly correlated manner, whereas others exhibit low (or no) phylogenetic correlation. Correlations were stronger within types of parental activity (brooding, feeding, guarding) than within stages of the breeding cycle (incubation, prefledging care, post-fledging care). A phylogenetically corrected cluster analysis identified two groups of parental care components that evolved in a correlated fashion: one group included incubation and brooding, whereas the other group comprised of the remaining components. The two groups of components provide working hypotheses for follow-up studies to test the underlying genetic, developmental and ecological co-evolutionary mechanism between male and female care. Furthermore, the components within each group are expected to respond consistently to different ambient and social environments.

Phylogenetic comparative approaches for studying niche conservatism.

Analyses of phylogenetic niche conservatism (PNC) are becoming increasingly common. However, each analysis makes subtly different assumptions about the evolutionary mechanism that generates patterns of niche conservatism. To understand PNC, analyses should be conducted with reference to a clear underlying model, using appropriate methods. Here, we outline five macroevolutionary models that may underlie patterns of PNC (drift, niche retention, phylogenetic inertia, niche filling/shifting and evolutionary rates) and link these to published phylogenetic comparative methods. For each model, we give recent examples from the literature and suggest how the methods can be practically applied. We hope that this will help clarify the niche conservatism literature and encourage people to think about the evolutionary models underlying niche conservatism in their study group.

The seven deadly sins of comparative analysis.

Phylogenetic comparative methods are extremely commonly used in evolutionary biology. In this paper, I highlight some of the problems that are frequently encountered in comparative analyses and review how they can be fixed. In broad terms, the problems boil down to a lack of appreciation of the underlying assumptions of comparative methods, as well as problems with implementing methods in a manner akin to more familiar statistical approaches. I highlight that the advent of more flexible computing environments should improve matters and allow researchers greater scope to explore methods and data.

Are parental care trade-offs in shorebirds driven by parental investment or sexual selection?

Sexual selection, mating systems and parental behaviour are closely linked, although the exact nature of their relationship is controversial. The parental investment hypothesis (PIH) states that parental care disparity drives sexual selection intensity, because the sex providing less care competes for the sex that provides more. In contrast, the sexual selection hypothesis (SSH) asserts that more intense sexual selection on males leads to reduced male parental investment. We tested these hypotheses using directional phylogenetic comparative methods in shorebirds, which have an unusually diverse array of breeding systems. Changes in parental care and sexual selection intensity were tightly correlated, and we carried out three sets of analyses focusing on changes in male behaviour, female behaviour and in either sex. The results from the analyses were consistent with both PIH and SSH, although the patterns in male transition were sensitive to model values. We propose two explanations for these results. First, phylogenetic transitions may be idiosyncratic so that they depend on the ecological circumstances of individual species. Second, transitions in social traits, such as breeding systems, may be rapid and take place in ecological time, so directional phylogenetic methods that work through longer time scales may not infer accurately the timing and direction of all changes.

Parental conflict in birds: comparative analyses of offspring development, ecology and mating opportunities.

Parents often conflict over how much care to provide to their offspring. This conflict is expected to produce a negative relationship between male and female parental care, the strength of which may be mediated by both ecological and life-history variables. Previous studies have observed such trade-offs, but it is not known how generally they occur. Traditional views of sexual conflict place great importance on ecological factors in determining levels of parental care, whereas alternative views propose that the key determinant is mating opportunity. We carried out a broad-scale comparative study of parental conflict using 193 species from 41 families of birds. Using phylogenetic comparative analysis, we establish the generality of intersexual parental care conflict. We also show that parental conflict, as indicated by the disparity in care between the male and the female, depends on offspring development and mating opportunities, since in precocial species both males and females responded to increased mating opportunities. Altricial birds, however, failed to show these relationships. We also found little influence of breeding climate on parental conflict. Taken together, our results suggest that sexual conflict is a key element in the evolution of parental care systems. They also support the view that the major correlates of the intersexual conflict are mating opportunities for both sexes, rather than the breeding environment.

Amelioration of biodiversity impacts of genetically modified crops: predicting transient versus long-term effects.

It has been suggested that genetically modified herbicide-tolerant crops may benefit biodiversity because spraying of crops may be delayed until later in the growing season, allowing weeds to grow during the early part of the year. This provides an enhanced resource for arthropods, and potentially benefits birds that feed on these. Thus, this technology could enhance biodiversity. Using a review of weed phenologies and a population model, we show that many weeds are unlikely to benefit because spraying is generally delayed insufficiently late in the season to allow most to set seed. The positive effects on biodiversity observed in trials lasting one or two seasons are thus likely to be transient. For one weed of particular significance (Chenopodium album, fat hen) we show that it is unlikely that the positive effects observed could be maintained by inputs of seed during other parts of the rotation. However, we find preliminary evidence that if spraying can be ceased earlier in the season, then a viable population of late-emerging weeds could be maintained. This strategy could benefit weeds in both genetically modified (GM) and non-GM crops, but would probably lead to reduced inputs in GM systems compared with conventional ones.

Phylogenetic analysis and comparative data: a test and review of evidence.

The question is often raised whether it is statistically necessary to control for phylogenetic associations in comparative studies. To investigate this question, we explore the use of a measure of phylogenetic correlation, lambda, introduced by Pagel (1999), that normally varies between 0 (phylogenetic independence) and 1 (species' traits covary in direct proportion to their shared evolutionary history). Simulations show lambda to be a statistically powerful index for measuring whether data exhibit phylogenetic dependence or not and whether it has low rates of Type I error. Moreover, lambda is robust to incomplete phylogenetic information, which demonstrates that even partial information on phylogeny will improve the accuracy of phylogenetic analyses. To assess whether traits generally show phylogenetic associations, we present a quantitative review of 26 published phylogenetic comparative data sets. The data sets include 103 traits and were chosen from the ecological literature in which debate about the need for phylogenetic correction has been most acute. Eighty-eight percent of data sets contained at least one character that displayed significant phylogenetic dependence, and 60% of characters overall (pooled across studies) showed significant evidence of phylogenetic association. In 16% of tests, phylogenetic correlation could be neither supported nor rejected. However, most of these equivocal results were found in small phylogenies and probably reflect a lack of power. We suggest that the parameter lambda be routinely estimated when analyzing comparative data, since it can also be used simultaneously to adjust the phylogenetic correction in a manner that is optimal for the data set, and we present an example of how this may be done.

Nonmanipulative determination of plant community dynamics.

Knowledge of the strengths of interactions between species in plant communities is of fundamental importance to our understanding of how communities are structured, although they are notoriously difficult to quantify. Techniques have recently been developed that allow the detailed enumeration of the strength of interactions between plant species within unmanipulated multispecies communities. Nonlinear regression analysis is used to fit competition models to long-term census data using natural variations in plant densities in lieu of manipulation. The models generated have been used to infer the intensity and importance of interactions as well as to analyse the effects of spatial and temporal variability. Theoretical work has begun to look at how different techniques for measuring competition perform in a range of systems, highlighting the importance of spatial scale. The lessons learned from applying these methods will enable improved estimation of the strength of competition in natural communities.

Predictions of biodiversity response to genetically modified herbicide-tolerant crops.

We simulated the effects of the introduction of genetically modified herbicide-tolerant (GMHT) crops on weed populations and the consequences for seed-eating birds. We predict that weed populations might be reduced to low levels or practically eradicated, depending on the exact form of management. Consequent effects on the local use of fields by birds might be severe, because such reductions represent a major loss of food resources. The regional impacts of GMHT crops are shown to depend on whether the adoption of GMHT crops by farmers covaries with current weed levels.

Determinants of the abundance of invasive annual weeds: community structure and non-equilibrium dynamics.

The dynamics of an annual pasture community are described from a five-year experimental and monitoring study. The community was dominated by two grasses (Lolium rigidum and Vulpia bromoides) and a legume (Trifolium subterraneum). Fits of population dynamic models to per capita rates of population change indicate that interactions between the grasses were generally strong, while interactions between the grasses and legumes were weaker. Most, but not all, of the net effects of competition on population growth could be attributed to interactions occurring during plant growth. Phase-plane analysis indicated that, for a constant environment, a joint equilibrium of the two grasses is unstable since interspecific competition between Lolium and Vulpia is stronger than intraspecific competition. Consequently, the community will tend to a mixture of only one or other of the grass species and T. subterraneum, depending on the founding composition of the pasture. Analysis of data taken from a year in which a drought occurred (1993-1994) demonstrated profound effects on all three species. Modelling of the long-term impacts of the effects of repeated droughts showed that disturbance of this form overrides the founder effect observed under constant conditions. Consequently, Vulpia is ultimately able to invade any mixture of the other species in environments where stochastic disturbances occur.