Evolutionary Community Ecology: Time to Think Outside the (Taxonomic) Box

Eco-Evolutionary Dynamics in Microbial Communities from Spontaneous Fermented Foods

Eco-evolutionary forces are the key drivers of ecosystem biodiversity dynamics. This resulted in a large body of theory, which has partially been experimentally tested by mimicking evolutionary processes in the laboratory. In the first part of this perspective, we outline what model systems are used for experimental testing of eco-evolutionary processes, ranging from simple microbial combinations and, more recently, to complex natural communities. Microbial communities of spontaneous fermented foods are a promising model system to study eco-evolutionary dynamics. They combine the complexity of a natural community with extensive knowledge about community members and the ease of manipulating the system in a laboratory setup. Due to rapidly developing sequencing techniques and meta-omics approaches incorporating data in building ecosystem models, the diversity in these communities can be analysed with relative ease while hypotheses developed in simple systems can be tested. Here, we highlight several eco-evolutionary questions that are addressed using microbial communities from fermented foods. These questions relate to analysing species frequencies in space and time, the diversity-stability relationship, niche space and community coalescence. We provide several hypotheses of the influence of these factors on community evolution specifying the experimental setup of studies where microbial communities of spontaneous fermented food are used.

Can functional genomic diversity provide novel insights into mechanisms of community assembly? A pilot study from an invaded alpine streambed

An important focus of community ecology, including invasion biology, is to investigate functional trait diversity patterns to disentangle the effects of environmental and biotic interactions. However, a notable limitation is that studies usually rely on a small and easy-to-measure set of functional traits, which might not immediately reflect ongoing ecological responses to changing abiotic or biotic conditions, including those that occur at a molecular or physiological level. We explored the potential of using the diversity of expressed genes-functional genomic diversity (FGD)-to understand ecological dynamics of a recent and ongoing alpine invasion. We quantified FGD based on transcriptomic data measured for 26 plant species occurring along adjacent invaded and pristine streambeds. We used an RNA-seq approach to summarize the overall number of expressed transcripts and their annotations to functional categories, and contrasted this with functional trait diversity (FTD) measured from a suite of characters that have been traditionally considered in plant ecology. We found greater FGD and FTD in the invaded community, independent of differences in species richness. However, the magnitude of functional dispersion was greater from the perspective of FGD than from FTD. Comparing FGD between congeneric alien-native species pairs, we did not find many significant differences in the proportion of genes whose annotations matched functional categories. Still, native species with a greater relative abundance in the invaded community compared with the pristine tended to express a greater fraction of genes at significant levels in the invaded community, suggesting that changes in FGD may relate to shifts in community composition. Comparisons of diversity patterns from the community to the species level offer complementary insights into processes and mechanisms driving invasion dynamics. FGD has the potential to illuminate cryptic changes in ecological diversity, and we foresee promising avenues for future extensions across taxonomic levels and macro-ecosystems.

Identifying "Useful" Fitness Models: Balancing the Benefits of Added Complexity with Realistic Data Requirements in Models of Individual Plant Fitness

AbstractDirect species interactions are commonly included in individual fitness models used for coexistence and local diversity modeling. Though widely considered important for such models, direct interactions alone are often insufficient for accurately predicting fitness, coexistence, or diversity outcomes. Incorporating higher-order interactions (HOIs) can lead to more accurate individual fitness models but also adds many model terms, which can quickly result in model overfitting. We explore approaches for balancing the trade-off between tractability and model accuracy that occurs when HOIs are added to individual fitness models. To do this, we compare models parameterized with data from annual plant communities in Australia and Spain, varying in the extent of information included about the focal and neighbor species. The best-performing models for both data sets were those that grouped neighbors based on origin status and life form, a grouping approach that reduced the number of model parameters substantially while retaining important ecological information about direct interactions and HOIs. Results suggest that the specific identity of focal or neighbor species is not necessary for building well-performing fitness models that include HOIs. In fact, grouping neighbors by even basic functional information seems sufficient to maximize model accuracy, an important outcome for the practical use of HOI-inclusive fitness models.

Occurrence data uncover patterns of allopatric divergence and interspecies interactions in the evolutionary history of Sceloporus lizards

As shown from several long-term and time-intensive studies, closely related, sympatric species can impose strong selection on one another, leading to dramatic examples of phenotypic evolution. Here, we use occurrence data to identify clusters of sympatric Sceloporus lizard species and to test whether Sceloporus species tend to coexist with other species that differ in body size, as we would expect when there is competition between sympatric congeners. We found that Sceloporus species can be grouped into 16 unique bioregions. Bioregions that are located at higher latitudes tend to be larger and have fewer species, following Rapoport's rule and the latitudinal diversity gradient. Species richness was positively correlated with the number of biomes and elevation heterogeneity of each bioregion. Additionally, most bioregions show signs of phylogenetic underdispersion, meaning closely related species tend to occur in close geographic proximity. Finally, we found that although Sceloporus species that are similar in body size tend to cluster geographically, small-bodied Sceloporus species are more often in sympatry with larger-bodied Sceloporus species than expected by chance alone, whereas large-bodied species cluster with each other geographically and phylogenetically. These results suggest that community composition in extant Sceloporus species is the result of allopatric evolution, as closely related species move into different biomes, and interspecies interactions, with sympatry between species of different body sizes. Our phyloinformatic approach offers unique and detailed insights into how a clade composed of ecologically and morphologically disparate species are distributed over large geographic space and evolutionary time.

The Evolution of 'Ecological Release' into the 21st Century

Ecological release, originally conceived as niche expansion following a reduction in interspecific competition, may prompt invasion success, morphological evolution, speciation, and other ecological and evolutionary outcomes. However, the concept has not been recently reviewed. Here, we trace the study of 'ecological release' from its inception through the present day and find that current definitions are broad and highly varied. Viewing this development as a potential impediment to clear communication and hypothesis testing, we suggest a consensus definition for ecological release: niche expansions and shifts when a constraining interspecific interaction is reduced or removed. In rationalizing this definition, we highlight the various ways ecological release can unfold and address its potential evolutionary consequences.

Convergent evolution of specialized generalists: Implications for phylogenetic and functional diversity of carabid feeding groups

Closely related species are often assumed to be functionally similar. Phylogenetic information is thus widely used to infer functional diversity and assembly of communities. In contrast, evolutionary processes generating functional similarity of phylogenetically distinct taxa are rarely addressed in this context.To investigate the impact of convergent evolution on functional diversity (FD) and phylogenetic diversity (PD), we reconstructed the phylogenetic structure of carabid trophic groups. We then analyzed the mandible shapes using geometric morphometrics to link specialization in functional morphology with feeding specialization among herbivores, generalist carnivores, and specialized consumers of Collembola.Our results show that carabid feeding groups are paraphyletic. Herbivory evolved at least twice and specialization to Collembola predation at least three times. Species within feeding groups share a remarkably similar mandible morphology, which evolved convergently. While specialized mandibles of herbivores and collembolan specialists represent an adaptation to their main food source, the particular mandible morphologies do not necessarily reflect the degree of food specialization within feeding groups. Only a few species with a specialized herbivorous mandible may occasionally feed on animals, but the range of specific food resources in generalist carnivore species is large, despite an almost identical mandible shape.Thus, convergent evolution in specialized feeding groups reverses the relationship between PD and functional similarity compared with generalist carnivores. We conclude that phylogenetic relationship is a poor proxy of FD in carabids. Moreover, the inconsistencies between relatedness, morphological adaptation, and ecological function require caution in the characterization of functional groups. Rather than assuming general relationships between PD and FD, we suggest integrating the analysis of evolutionary processes into functional community analyses.

Phylogeny and ecological processes influence grass coexistence at different spatial scales within the steppe biome

Phylogenetic analyses are essential for disentangling how environmental filtering and competition determine species coexistence across spatial scales. Inner Mongolia steppe has strong environmental gradients, but how the phylogenetic relatedness of co-occurring species and phylogenetic signals of functional traits change across spatial scales remains unclear. We investigated the phylogenetic structure of grass assemblages along environmental gradients from regional to local scales, and measured functional traits within assemblages. We compared phylogenetic signals of plant traits between the same numbers of species randomly selected from the regional pool and species observed at the local scale, did phylogenetic principal component analysis to infer the main factors driving species coexistence, and examined the key plant trait-environment relationships across the phylogeny to reveal ecological adaptation mechanisms. Regionally, grass species were phylogenetically clustered with contrasting climate preferences. With decreasing spatial scales, species richness declined, changing from phylogenetically clustered to overdispersed, and phylogenetic signals of plant traits became weaker. At the local scale, grass assemblages were structured by soil water content and neighbor density, and the trait-environment relationships were less clear than those at the regional scale. This study demonstrated that at smaller scales, co-occurring grass species in the steppe tended to be more phylogenetically overdispersed, and that phylogenetic signals of plant functional traits became weaker with increasing abiotic and biotic interactions. Our findings contributed evidence for understanding species coexistence and maintenance at scales spanning regional to local communities in the East Asia steppe biome.

Reciprocal facilitation between large herbivores and ants in a semi-arid grassland

While positive interactions have been well documented in plant and sessile benthic marine communities, their role in structuring mobile animal communities and underlying mechanisms has been less explored. Using field removal experiments, we demonstrated that a large vertebrate herbivore (cattle; Bos tarurs) and a much smaller invertebrate (ants; Lasius spp.), the two dominant animal taxa in a semi-arid grassland in Northeast China, facilitate each other. Cattle grazing led to higher ant mound abundance compared with ungrazed sites, while the presence of ant mounds increased the foraging of cattle during the peak of the growing season. Mechanistically, these reciprocal positive effects were driven by habitat amelioration and resource (food) enhancement by cattle and ants (respectively). Cattle facilitated ants, probably by decreasing plant litter accumulation by herbivory and trampling, allowing more light to reach the soil surface leading to microclimatic conditions that favour ants. Ants facilitated cattle probably by increasing soil nutrients via bioturbation, increasing food (plant) biomass and quality (nitrogen content) for cattle. Our study demonstrates reciprocal facilitative interactions between two animal species from phylogenetically very distant taxa. Such reciprocal positive interactions may be more common in animal communities than so far assumed, and they should receive more attention to improve our understanding of species coexistence and animal community assembly.