The comment by Gamisch (2020) draws the attention of users of the R-package RPANDA (Morlon et al. 2016) on situations when properly interpreting the results of linear diversification dependencies requires caution. Here we provide clarifications to help users interpreting their results when using any type of functional diversification dependencies with time or the environment.

Hydraulic properties control plant responses to climate and are likely to be under strong selective pressure, but their macro-evolutionary history remains poorly characterized. To fill this gap, we compiled a global dataset of hydraulic traits describing xylem conductivity (Ks), xylem resistance to embolism (P50), sapwood allocation relative to leaf area (Hv) and drought exposure (ψmin), and matched it with global seed plant phylogenies. Individually, these traits present medium to high levels of phylogenetic signal, partly related to environmental selective pressures shaping lineage evolution. Most of these traits evolved independently of each other, being co-selected by the same environmental pressures. However, the evolutionary correlations between P50 and ψmin and between Ks and Hv show signs of deeper evolutionary integration because of functional, developmental or genetic constraints, conforming to evolutionary modules. We do not detect evolutionary integration between conductivity and resistance to embolism, rejecting a hardwired trade-off for this pair of traits.

We develop a novel approach to trophic metacommunities which allows us to explore how progressive habitat loss affects food webs. Our method combines classic metapopulation models on fragmented landscapes with a Bayesian network representation of trophic interactions for calculating local extinction rates. This means we can repurpose known results from classic metapopulation theory for trophic metacommunities, such as ranking the habitat patches of the landscape with respect to their importance to the persistence of the metacommunity as a whole. We use this to study the effects of habitat loss, both on model communities and the plant-mammal Serengeti food web dataset as a case study. Combining straightforward parameterizability with computational efficiency, our method permits the analysis of species-rich food webs over large landscapes, with hundreds or even thousands of species and habitat patches, while still retaining much of the flexibility of explicit dynamical models.

There is a rich amount of information in co-occurrence data that could be used to understand community assembly. This proposition first envisioned by Forbes (1907) and then Diamond (1975) prompted the development of numerous modelling approaches (e.g. null model analysis, co-occurrence networks and, more recently, joint species distribution models). Both theory and experimental evidence support the idea that ecological interactions may affect co-occurrence, but it remains unclear to what extent the signal of interaction can be captured in observational data. The time is now ripe to step back from the statistical developments and critically assess whether co-occurrence data really is a proxy for ecological interactions. In this paper we present a series of arguments based on probability, sampling, food web and coexistence theories supporting that significant spatial associations between species (or the lack of) is a poor proxy for ecological interactions. We discuss appropriate interpretations of co-occurrence, along with potential avenues to extract as much information as possible from such data.

Grassland ecosystems account for more than 10% of the global CH4 sink in soils. A 4-year field experiment found that addition of P alone did not affect CH4 uptake and experimental addition of N alone significantly suppressed CH4 uptake, while concurrent N and P additions suppressed CH4 uptake to a lesser degree. A meta-analysis including 382 data points in global grasslands corroborated these findings. Global extrapolation with an empirical modeling approach estimated that contemporary N addition suppresses CH4 sink in global grassland by 11% and concurrent N and P deposition alleviates this suppression by 6%. The P alleviation of N-suppressed CH4 sink is primarily attributed to substrate competition, defined as the competition between ammonium and CH4 for the methane monooxygenase enzyme. The N and P impacts on CH4 uptake indicate that projected increases in N and P depositions might substantially affect CH4 uptake and alter the global CH4 cycle.

Pathogen persistence in host communities is influenced by a hierarchy of heterogeneities from individual host to landscape-level attributes, but isolating the relative contributions of these heterogeneities is challenging. We developed theory to partition the influence of host species, habitat patches, and landscape connectivity on pathogen persistence within host-pathogen metacommunities. We used the framework to quantify the contributions of host species composition and habitat patch identity on the persistence of an amphibian pathogen across the landscape. By sampling over 11,000 hosts of six amphibian species, we found that a single host species could maintain the pathogen in 91% of the metacommunities we observed. Moreover, this dominant maintenance species contributed, on average, twice as much to landscape-level pathogen persistence compared to the most influential source patch in a metacommunity. Our analysis demonstrates substantial inequality in how species and patches contribute to pathogen persistence, with important implications for targeted disease management.

Plant-soil feedback is commonly pointed out as driver of plant community dynamics and species co-existence. However, experimental evidence for soil legacy effects of conditioning plant communities on responding plant communities under natural conditions is lacking. We conditioned 192 grassland plots with plant communities with different ratios of grasses and forbs and fast and slow-growing plants. Soil microbial legacies were most evident for soil fungi. Soil abiotic parameters did not change in response to conditioning. The soil legacies affected the composition of the succeeding vegetation. Plant communities of a specific functional type caused negative feedbacks on succeeding plants when they belonged to the same functional type. Richness, relative species cover and belowground biomass of the responding vegetation were all influenced by the growth rate of the conditioning community. We conclude that plant-soil feedbacks play an important role in vegetation assembly of natural communities.

Underpinnings of the distribution of allopolyploid species (hybrids with duplicated genome) along spatial and ecological gradients are elusive. As allopolyploid speciation combines the range of genetic and ecological characteristics of divergent diploids, allopolyploids initially show their additivity and are predicted to evolve differentiated ecological niches to establish in face of their competition. Here, we use four diploid wild wheats that differentially combined into four independent allopolyploid species to test for such additivity and assess the impact of ecological constraints on species ranges. Divergent genetic variation from diploids being fixed in heterozygote allopolyploids supports their genetic additivity. Spatial integration of comparative phylogeography and modeling of climatic niches supports ecological additivity of locally adapted diploid progenitors into allopolyploid species which subsequently colonized wide ranges. Allopolyploids fill suitable range to a larger extent than diploids and conservative evolution following the combination of divergent species appears to support their expansion under environmental changes.

Ecological processes in food webs depend on species interactions. By identifying broad-scaled interaction patterns, important information on species ecological roles may be revealed. Here, we use the group model to examine how spatial resolution and proximity influence the group structure. We examine a dataset from the Barents Sea, with species occurrences for both the whole region and 25 subregions. Specifically, we test how the group structure in the networks differ comparing i) the regional metaweb to subregions and ii) subregion to subregion. We find that more than half the species in the metaweb change groups when compared to subregions. Between subregions, networks with similar group structure are usually spatially related. Interestingly, although species overlap is important for similarity in group structure, there are notable exceptions. Our results highlight that species ecological roles differ depending on fine-scaled differences in patterns of interactions, and that local network characteristics are important to consider.

Long-distance migrations by marine fish have long fascinated scientists, but are difficult to track by visual surveys. Here, we propose a new method to easily and precisely track such migrations using stable nitrogen isotopic composition at the base of the food web (δ15NBase), which can be estimated by using compound-specific isotope analysis. δ15NBase exclusively reflects the δ15N of nitrate in the ocean at a regional scale and is not affected by the trophic position of sampled organisms. We initially constructed a δ15NBase isoscape in the northern North Pacific, and determined retrospective δ15NBase values of chum salmon (Oncorhynchus keta) from their vertebral centra. Then, we estimated the migration routes of chum salmon during their skeletal growth by using a state-space model. Our isotope tracking method successfully reproduced a known chum salmon migration route between the Okhotsk and Bering seas, and indicates the presence of a novel migration route to the eastern Bering Sea Shelf during a later growth stage.