Summary: Fundamental ecological research is both intrinsically interesting and provides the basic knowledge required to answer applied questions of importance to the management of the natural world. The 100th anniversary of the British Ecological Society in 2013 is an opportune moment to reflect on the current status of ecology as a science and look forward to high‐light priorities for future work. To do this, we identified 100 important questions of fundamental importance in pure ecology. We elicited questions from ecologists working across a wide range of systems and disciplines. The 754 questions submitted (listed in the online appendix) from 388 participants were narrowed down to the final 100 through a process of discussion, rewording and repeated rounds of voting. This was done during a two‐day workshop and thereafter. The questions reflect many of the important current conceptual and technical pre‐occupations of ecology. For example, many questions concerned the dynamics of environmental change and complex ecosystem interactions, as well as the interaction between ecology and evolution. The questions reveal a dynamic science with novel subfields emerging. For example, a group of questions was dedicated to disease and micro‐organisms and another on human impacts and global change reflecting the emergence of new subdisciplines that would not have been foreseen a few decades ago. The list also contained a number of questions that have perplexed ecologists for decades and are still seen as crucial to answer, such as the link between population dynamics and life‐history evolution. Synthesis. These 100 questions identified reflect the state of ecology today. Using them as an agenda for further research would lead to a substantial enhancement in understanding of the discipline, with practical relevance for the conservation of biodiversity and ecosystem function.

Studies of evolutionary responses to novel environments typically consider single species or perhaps pairs of interacting species. However, all organisms co-occur with many other species, resulting in evolutionary dynamics that might not match those predicted using single species approaches. Recent theories predict that species interactions in diverse systems can influence how component species evolve in response to environmental change. In turn, evolution might have consequences for ecosystem functioning. We used experimental communities of five bacterial species to show that species interactions have a major impact on adaptation to a novel environment in the laboratory. Species in communities diverged in their use of resources compared with the same species in monocultures and evolved to use waste products generated by other species. This generally led to a trade-off between adaptation to the abiotic and biotic components of the environment, such that species evolving in communities had lower growth rates when assayed in the absence of other species. Based on growth assays and on nuclear magnetic resonance (NMR) spectroscopy of resource use, all species evolved more in communities than they did in monocultures. The evolutionary changes had significant repercussions for the functioning of these experimental ecosystems: communities reassembled from isolates that had evolved in polyculture were more productive than those reassembled from isolates that had evolved in monoculture. Our results show that the way in which species adapt to new environments depends critically on the biotic environment of co-occurring species. Moreover, predicting how functioning of complex ecosystems will respond to an environmental change requires knowing how species interactions will evolve. Understanding how species adapt to new environments is important both for evolutionary theory and for predicting and managing ecosystem responses to changing environments. However, most research into adaptation to new environments has considered species in isolation. Whether results from these systems apply to more realistically diverse groups of species remains unclear. We exposed five species of bacteria, collected from pools around the roots of beech trees, to a novel laboratory environment either in isolation or in species mixtures for approximately 70 generations. We found that each species evolved more in diverse species mixtures than it did when cultured in isolation. Moreover, species diverged in their use of resources and how they used the waste products of other species. These changes meant that the community of bacteria that evolved together used more of the available resources and were thereby more productive than the same group of species that evolved in isolation. Our findings show that species interactions can have a major effect on evolutionary dynamics, which can in turn influence ecosystem functioning.

A characteristic signature of adaptive radiation is a slowing of the rate of speciation toward the present. On the basis of molecular phylogenies, studies of single clades have frequently found evidence for a slowdown in diversification rate and have interpreted this as evidence for density dependent speciation. However, we demonstrated via simulation that large clades are expected to show stronger slowdowns than small clades, even if the probability of speciation and extinction remains constant through time. This is a consequence of exponential growth: clades, which, by chance, diversify at above the average rate early in their history, will tend to be large. They will also tend to regress back to the average diversification rate later on, and therefore show a slowdown. We conducted a meta-analysis of the distribution of speciation events through time, focusing on sequence-based phylogenies for 45 clades of birds. Thirteen of the 23 clades (57%) that include more than 20 species show significant slowdowns. The high frequency of slowdowns observed in large clades is even more extreme than expected under a purely stochastic constant-rate model, but is consistent with the adaptive radiation model. Taken together, our data strongly support a model of density-dependent speciation in birds, whereby speciation slows as ecological opportunities and geographical space place limits on clade growth. It is probable that the number of species that a given region can support is limited; however, it is unclear whether the limit is approached sufficiently in nature such that the rate at which new species form slows down. Using the pattern of phylogenetic branching, a technique that estimates evolutionary relationships based on molecular data, we demonstrate that in large clades of birds, there is a decrease in the per-lineage probability of speciation as the number of species in the clade increase. We also show that this pattern can arise even if speciation and extinction occur randomly through time. This is because large clades are likely, by chance, to have rapidly speciated early in their history, and will relax back to the average speciation rate later on. We account for this effect, and we still find evidence that, as a clade grows to large size, the per-lineage probability of speciation declines. These results strongly suggest that speciation rates are slowed as environments fill up with competitors.

The branching times of molecular phylogenies allow us to infer speciation and extinction dynamics even when fossils are absent. Troublingly, phylogenetic approaches usually return estimates of zero extinction, conflicting with fossil evidence. Phylogenies and fossils do agree, however, that there are often limits to diversity. Here, we present a general approach to evaluate the likelihood of a phylogeny under a model that accommodates diversity-dependence and extinction. We find, by likelihood maximization, that extinction is estimated most precisely if the rate of increase in the number of lineages in the phylogeny saturates towards the present or first decreases and then increases. We demonstrate the utility and limits of our approach by applying it to the phylogenies for two cases where a fossil record exists (Cetacea and Cenozoic macroperforate planktonic foraminifera) and to three radiations lacking fossil evidence ( Dendroica , Plethodon and Heliconius ). We propose that the diversity-dependence model with extinction be used as the standard model for macro-evolutionary dynamics because of its biological realism and flexibility.

The taxonomic rank of subspecies remains highly contentious, largely because traditional subspecies boundaries have sometimes been contradicted by molecular phylogenetic data. The most complete meta-analysis to date, for instance, found that only 3% of traditional avian subspecies represented distinct phylogenetic lineages. However, the global generality of this phenomenon remains unclear due to this previous study's narrow geographic focus on continental Nearctic and Palearctic subspecies. Here, we present a new global analysis of avian subspecies and show that 36% of avian subspecies are, in fact, phylogenetically distinct. Among biogeographic realms we find significant differences in the proportion of subspecies that are phylogenetically distinct, with Nearctic/Palearctic subspecies showing significantly reduced levels of differentiation. Additionally, there are differences between island and continental subspecies, with continental subspecies significantly less likely to be genetically distinct. These results indicate that the overall level of congruence between taxonomic subspecies and molecular phylogenetic data is greater than previously thought. We suggest that the widespread impression that avian subspecies are not real arises from a predominance of studies focusing on continental subspecies in North America and Eurasia, regions which show unusually low levels of genetic differentiation. The broader picture is that avian subspecies often provide an effective short-cut for estimating patterns of intraspecific genetic diversity, thereby providing a useful tool for the study of evolutionary divergence and conservation.

Ecology letters (2011) 14: 552–560 Abstract Islands acquire species through immigration and speciation. Models of island biogeography should capture both processes; however quantitative island biogeography theory has either neglected speciation or treated it unrealistically. We introduce a model where the dominance of immigration on small and near islands gives way to an increasing role for speciation as island area and isolation increase. We examine the contribution of immigration and speciation to the avifauna of 35 archipelagoes and find, consistent with our model, that the zone of radiation comprises two regions: endemic species diverged from mainland sister-species at intermediate isolation and from insular sister-species at higher levels of isolation. Our model also predicts species–area curves in accord with existing research and makes new predictions about species ages and abundances. We argue that a paucity of data and theory on species abundances on isolated islands highlights the need for island biogeography to be reconnected with mainstream ecology.