Inferring processes of community assembly from macroscopic patterns: the case for inclusive and mechanistic approaches

Statistical techniques exist for inferring community assembly processes from community patterns. Habitat filtering, competition, and biogeographical effects have, for example, been inferred from signals in phenotypic and phylogenetic data. The usefulness of current inference techniques is, however, debated as the causal link between process and pattern is often lacking and processes known to be important are ignored. Here, we revisit current knowledge on community assembly across scales and, in line with several reviews that have outlined the features and challenges associated with current inference techniques, we identify a discrepancy between features of real communities and current inference techniques. We argue, that mechanistic eco-evolutionary models in combination with novel model fitting and model evaluation techniques can provide avenues for more accurate, reliable and inclusive inference. To exemplify, we implement a trait-based and spatially explicit dynamic eco-evolutionary model and discuss steps of model modification, fitting, and evaluation as an iterative approach enabling inference from diverse data sources. This suggested approach can be computationally intensive, and model fitting and parameter estimation can be challenging. We discuss optimization of model implementation, data requirements and availability, and Approximate Bayesian Computation (ABC) as potential solutions to challenges that may arise in our quest for better inference techniques

Boom‐bust dynamics in biological invasions: towards an improved application of the concept

Boom‐bust dynamics – the rise of a population to outbreak levels, followed by a dramatic decline – have been associated with biological invasions and offered as a reason not to manage troublesome invaders. However, boom‐bust dynamics rarely have been critically defined, analyzed, or interpreted. Here, we define boom‐bust dynamics and provide specific suggestions for improving the application of the boom‐bust concept. Boom‐bust dynamics can arise from many causes, some closely associated with invasions, but others occurring across a wide range of ecological settings, especially when environmental conditions are changing rapidly. As a result, it is difficult to infer cause or predict future trajectories merely by observing the dynamic. We use tests with simulated data to show that a common metric for detecting and describing boom‐bust dynamics, decline from an observed peak to a subsequent trough, tends to severely overestimate the frequency and severity of busts, and should be used cautiously if at all. We review and test other metrics that are better suited to describe boom‐bust dynamics. Understanding the frequency and importance of boom‐bust dynamics requires empirical studies of large, representative, long‐term data sets that use clear definitions of boom‐bust, appropriate analytical methods, and careful interpretations

Structures and processes of the initial ecosystem development phase in an artificial water catchment (Final report CRC/TR 38)

Objective of the Transregional Collaborative Research Centre (CRC/TR) 38 was the study of structures and processes of the initial ecosystem development. It was assumed that the initial phase is characterized by less structured and therefore less heterogeneous ecosystems. Thus, analysis of young ecosystems in their initial stages should provide better insights into ecosystem functioning. Following this basic concept, the idea of the CRC/TR 38 was to analyze the establishment of new structures and processes which lead to a growing structuring and in consequence to a growing complexity and heterogeneity in an artificially created watershed. Further, with the help of this step-by-step development of the ecosystem it was aimed to learn from occurring feedbacks, which appear between old and newly emerging structures and patterns in order to better understand also the behavior of more mature systems. Special emphasis was placed on the spatial and temporal dynamics of both evolving structures and related processes and their interactions. In summary, the CRC/TR 38 was able to identify a number of structures and processes that are considered to be relevant and specific for young systems.Ziel des Sonderforschungsbereichs/Transregio (SFB/TRR) 38 war die Untersuchung von Strukturen und Prozessen der initialen Ökosystemgenese. Es wurde angenommen, dass die initiale Entwicklungsphase durch geringere Strukturierung und damit durch eine geringere Heterogenität der Ökosysteme gekennzeichnet ist. Entsprechend sollte die Untersuchung von Ökosystemen in ihrer initialen Entwicklungsphase verbesserte Erkenntnisse zur Funktion von Ökosystemen bieten. Diesem Konzept folgend untersuchte der SFB/TRR 38 in einem künstlichen Wassereinzugsgebiet die Entwicklung von neuen Strukturen und Prozessen, die zu einer zunehmenden Strukturierung und damit zu einer zunehmenden Heterogenität führte. Weiterhin war beabsichtigt, mit Hilfe der schrittweisen Entwicklung des Ökosystems auftretende Rückkopplungsprozesse zwischen alten und sich neu etablierenden Strukturen und Mustern zu erkennen und damit auch das Verständnis der Funktionsweise gereifter Ökosysteme zu verbessern. Besonderes Augenmerk wurde auf die zeitliche und räumliche Dynamik sowohl der sich entwickelnden Strukturen als auch der damit verbundenen Prozesse und ihrer Interaktionen gelegt. Zusammenfassend kann gesagt werden, dass der SFB/TRR 38 in der Lage war, zahlreiche Strukturen und Prozesse zu identifizieren, die als relevant und spezifisch für junge Ökosysteme betrachtet werden können

Adaptation and diversification of <i>Escherichia coli</i> K12 MC1000 in a complex environment

Complexiteit is inherent aan natuurlijke zowel als industriele habitats. Voorgaand wetenschappelijk werk heeft duidelijk het flexibele (genotypische en fenotypische) aanpassingsvermogen van microorganismen aan complexiteit laten zien. De meeste experimenten zijn echter onder relatief simpele (uniforme) omstandigheden verricht. Derhalve richtte het huidige onderzoek zich op bacteriele evolutie in complex groeimedium, waarbij de nadruk lag op de analyse van de mate van genetische / fysiologische diversifiering naar fitnessverhoging en nichedifferentiatie.De lange-termijn-aanpassingen (~1000 generaties) van E. coli K12 MC1000 in Luria-Bertani (LB) bouillon onder aerobe, wisselende en anaerobe condities werden geevalueerd. Verschillende genetische wegen resulteerden in aanpassingen en een aantal metabole routes waren geactiveerd. De veranderingen waren reproduceerbaar met betrekking tot geselecteerde functie, waarbij habitat de belangrijkste selector bleek. Een specific response werd waargenomen in de genen die betrokken waren bij het metabolisme van galactose (galR en galE). Daarbij werd een hoge mate van heterogeniteit gevonden tussen en binnen populaties. De verschillende fenotypische aanpassingen gaven ook aan dat parallele responses werden gestuurd door de verschillende genomen.De analyse van polymorfismen binnen een geevolueerde population toonde het bestaan van twee metabole and interactieve typen aan. Derhalve werd het voorkomen van additionele specifieke fenotypische eigenschappen (stress resistentie en metabole eigenschappen) bevestigd. De interactieve en stabiele coexistentie van deze vormen liet trade-offs in groei- en stress-eigenschappen tussen de vormen, en nicheverdeling, zien. De complexiteit van de habitat kan derhalve de vorming van aangepaste coexisterende vormen sturen.An inherent characteristic of natural as well as industrial environments is complexity. Scientific studies have revealed the flexible genetic and phenotypic capacities of microorganisms to cope with such complexity. However, most experiments have been conceptually simple, as they compare populations adapting to rather uniform environments. Therefore, the present work addressed bacterial evolution in a complex environment. The emphasis was on unraveling the level of diversification in respect of the genetic and physiological changes that the organism underwent, which allowed it to either acquire superior fitness or occupy a different niche.The long-term (~1000 generations) adaptive responses of E. coli K12 MC1000 in Luria-Bertani (LB) broth under aerobic, fluctuating and anaerobic conditions were evaluated. Several genetic solutions led to adaptation and a number of metabolic pathways were activated. Reproducibility of changes on genuine targets of selection was observed in parallel populations, suggesting a response triggered by medium. A specific response occurred in genes related to the metabolisms of galactose (galR and galE). Considerable heterogeneity was also found between and within populations. Differential phenotypic outcomes, suggested that parallel responses were affected by differing genomic backgrounds. Analysis of the polymorphisms in one evolved population revealed the existence of two main metabolic and interactive types. The emergence of additional specific phenotypic traits (stress resistance and metabolic properties) was confirmed. The interactive and stable coexistence of these forms revealed the presence of trade-offs and niche partitioning. The complexity of the environment has the potential to trigger the establishment of adapted and coexisting forms