Abundance-diversity relationship as a unique signature of temporal scaling in the fossil record

Species diversity increases with the temporal grain of samples according to the species-time relationship (STR), impacting palaeoecological analyses because the temporal grain (time averaging) of fossil assemblages varies by several orders of magnitude. We predict a positive relation between total abundance and sample size-independent diversity (ADR) in fossil assemblages because an increase in time averaging, determined by a decreasing sediment accumulation, should increase abundance and depress species dominance. We demonstrate that, in contrast to negative ADR of non-averaged living assemblages, the ADR of Holocene fossil assemblages is positive, unconditionally or when conditioned on the energy availability gradient. However, the positive fossil ADR disappears when conditioned on sediment accumulation, demonstrating that ADR is a signature of diversity scaling induced by variable time averaging. Conditioning ADR on sediment accumulation can identify and remove the scaling effect caused by time averaging, providing an avenue for unbiased biodiversity comparisons across space and time.

Unravelling the functional and phylogenetic dimensions of novel ecosystem assemblages

Human activities are causing taxonomic rearrangements across ecosystems that often result in the emergence of novel communities (assemblies with no historical representative). It is commonly assumed that these changes in the taxonomic makeup of ecosystems also inevitably lead to changes in other aspects of biodiversity, namely functional and phylogenetic diversity. However, this assumption is not always valid, as the changes in functional and phylogenetic composition resulting from taxonomic shifts depend on the level of redundancy in the evaluated community. Therefore, we need improved theoretical frameworks to predict when we can expect coordinated or decoupled responses among these three facets of biodiversity. To advance this understanding, we discuss the conceptual and methodological issues that complicate establishing a link between taxonomic rearrangements driven by human activities and the associated functional and phylogenetic changes. Here, we show that is crucial to consider the expected changes in functional and phylogenetic composition as communities are reshaped owing to human drivers of biodiversity loss to forecast the impacts of novel assemblages on ecosystem functions and the services they provide to humanity. This article is part of the theme issue 'Ecological novelty and planetary stewardship: biodiversity dynamics in a transforming biosphere'.

Metal nanoparticle-induced effects on green toads (Amphibia, Anura) under climate change: conservation implications

The toxicity of aluminum oxide (Al2O3), copper oxide (CuO), iron oxide (Fe3O4), nickel oxide (NiO), zinc oxide (ZnO), and titanium dioxide (TiO2) nanoparticles (NPs) on amphibians and their interaction with high temperatures, remain unknown. In this study, we investigated the survival, developmental, behavioral, and histological reactions of Bufotes viridis embryos and larvae exposed to different NPs for a duration of 10 days, using lethal concentrations (LC25%, LC50%, and LC75% mg/L) under both ambient (AT: 18 °C) and high (HT: 21 °C) temperatures. Based on LC, NiONPs > ZnONPs > CuONPs > Al2O3NPs > TiO2NPs > Fe3O4NPs showed the highest mortality at AT. A similar pattern was observed at HT, although mortality occurred at lower concentrations and Fe3O4NPs were more toxic than TiO2NPs. The results indicated that increasing concentrations of NPs significantly reduced hatching rates, except for TiO2NPs. Survival rates decreased, abnormality rates increased, and developmental processes slowed down, particularly for NiONPs and ZnONPs, under HT conditions. However, exposure to low concentrations of Fe3O4NPs for up to 7 days, CuONPs for up to 72 h, and NiO, ZnONPs, and TiO2NPs for up to 96 h did not have a negative impact on survival compared with the control group under AT. In behavioral tests with larvae, NPs generally induced hypoactivity at AT and hyperactivity at HT. Histological findings revealed liver and internal gill tissue lesions, and an increase in the number of melanomacrophage centers at HT. These results suggest that global warming may exacerbate the toxicity of metal oxide NPs to amphibians, emphasizing the need for further research and conservation efforts in this context.

What Can Evolutionary History Tell Us about the Functioning of Ecological Communities? The ASN Presidential Debate

AbstractIn January 2018, Sharon Strauss, then president of the American Society of Naturalists, organized a debate on the following topic: does evolutionary history inform the current functioning of ecological communities? The debaters-Ives, Lau, Mayfield, and Tobias-presented pro and con arguments, caricatured in standard debating format. Numerous examples show that both recent microevolutionary and longer-term macroevolutionary history are important to the ecological functioning of communities. On the other hand, many other examples illustrate that the evolutionary history of communities or community members does not influence ecological function, or at least not very much. This article aims to provide a provocative discussion of the consistent and conflicting patterns that emerge in the study of contemporary and historical evolutionary influences on community function, as well as to identify questions for further study. It is intended as a thought-provoking exercise to explore this complex field, specifically addressing (1) key assumptions and how they can lead us astray and (2) issues that need additional study. The debaters all agree that evolutionary history can inform us about at least some aspects of community function. The underlying question at the root of the debate, however, is how the fields of ecology and evolution can most profitably collaborate to provide a deeper and broader understanding of ecological communities.

The recovery of European freshwater biodiversity has come to a halt

Owing to a long history of anthropogenic pressures, freshwater ecosystems are among the most vulnerable to biodiversity loss1. Mitigation measures, including wastewater treatment and hydromorphological restoration, have aimed to improve environmental quality and foster the recovery of freshwater biodiversity2. Here, using 1,816 time series of freshwater invertebrate communities collected across 22 European countries between 1968 and 2020, we quantified temporal trends in taxonomic and functional diversity and their responses to environmental pressures and gradients. We observed overall increases in taxon richness (0.73% per year), functional richness (2.4% per year) and abundance (1.17% per year). However, these increases primarily occurred before the 2010s, and have since plateaued. Freshwater communities downstream of dams, urban areas and cropland were less likely to experience recovery. Communities at sites with faster rates of warming had fewer gains in taxon richness, functional richness and abundance. Although biodiversity gains in the 1990s and 2000s probably reflect the effectiveness of water-quality improvements and restoration projects, the decelerating trajectory in the 2010s suggests that the current measures offer diminishing returns. Given new and persistent pressures on freshwater ecosystems, including emerging pollutants, climate change and the spread of invasive species, we call for additional mitigation to revive the recovery of freshwater biodiversity.

Comparing temporal dynamics of compositional reorganization in long-term studies of birds and fish

The composition of ecological assemblages has changed rapidly over the past century. Compositional reorganization rates are high relative to rates of alpha diversity change, creating an urgent need to understand how this compositional reorganization is progressing. We developed a quantitative framework for comparing temporal trajectories of compositional reorganization and applied it to two long-term bird and marine fish datasets. We then evaluated how the number and magnitude of short-term changes relate to overall rates of change. We found varied trajectories of turnover across birds and fish, with linear directional change predominating in birds and non-directional change more common in fish. The number of changes away from the baseline was a more consistent correlate of the overall rate of change than the magnitude of such changes, but large unreversed changes were found in both fish and birds, as were time series with accelerating compositional change. Compositional reorganization is progressing through a complex mix of temporal trajectories, including both threshold-like behaviour and the accumulation of repeated, linear change.

Effective conservation planning of Iberian amphibians based on a regionalization of climate-driven range shifts

Amphibians are severely affected by climate change, particularly in regions where droughts prevail and water availability is scarce. The extirpation of amphibians triggers cascading effects that disrupt the trophic structure of food webs and ecosystems. Dedicated assessments of the spatial adaptive potential of amphibian species under climate change are, therefore, essential to provide guidelines for their effective conservation. I used predictions about the location of suitable climates for 27 amphibian species in the Iberian Peninsula from a baseline period to 2080 to typify shifting species' ranges. The time at which these range types are expected to be functionally important for the adaptation of a species was used to identify full or partial refugia; areas most likely to be the home of populations moving into new climatically suitable grounds; areas most likely to receive populations after climate adaptive dispersal; and climatically unsuitable areas near suitable areas. I implemented an area prioritization protocol for each species to obtain a cohesive set of areas that would provide maximum adaptability and where management interventions should be prioritized. A connectivity assessment pinpointed where facilitative strategies would be most effective. Each of the 27 species had distinct spatial requirements but, common to all species, a bottleneck effect was predicted by 2050 because source areas for subsequent dispersal were small in extent. Three species emerged as difficult to maintain up to 2080. The Iberian northwest was predicted to capture adaptive range for most species. My study offers analytical guidelines for managers and decision makers to undertake systematic assessments on where and when to intervene to maximize the persistence of amphibian species and the functionality of the ecosystems that depend on them.

Mussel parasite richness and risk of extinction

Parasite conservation is important for the maintenance of ecosystem diversity and function. Conserving parasites relies first on understanding parasite biodiversity and second on estimating the extinction risk to that biodiversity. Although steps have been taken independently in both these areas, previous studies have overwhelmingly focused on helminths in vertebrate hosts over broad scales, providing low resolution and excluding a large proportion of possible host and parasite diversity. We estimated both total obligate parasite richness and parasite extinction risk in freshwater mussels (Unionidae and Margaritiferidae) from Europe and the United States to provide a case study for considering parasite conservation in a severely understudied system. We used currently reported host-parasite relationships to extrapolate parasite diversity to all possible mussel hosts and then used the threat levels of those hosts to estimate the extinction risk for both described and undescribed parasites. An estimated 67% of parasite richness in freshwater mussels is undescribed and over 80% of the most host-specific groups (digenean trematodes and ciliates) are undescribed. We estimated that 21% of this total parasite fauna is at immediate risk of extinction, corresponding to 60 unique species, many of which will likely go extinct before being described. Given the important roles parasites play in community structure and function and the strong ecosystem engineering capacities of freshwater mussels, such extinctions are likely to severely affect freshwater ecosystems. Our detailed study of mussel parasites provides compelling evidence for the hidden conservation threat to parasites through extinction cascades and shows parasites are deserving of immediate attention.

The microbiome of a bacterivorous marine choanoflagellate contains a resource-demanding obligate bacterial associate

Microbial predators such as choanoflagellates are key players in ocean food webs. Choanoflagellates, which are the closest unicellular relatives of animals, consume bacteria and also exhibit marked biological transitions triggered by bacterial compounds, yet their native microbiomes remain uncharacterized. Here we report the discovery of a ubiquitous, uncultured bacterial lineage we name Candidatus Comchoanobacterales ord. nov., related to the human pathogen Coxiella and physically associated with the uncultured marine choanoflagellate Bicosta minor. We analyse complete ‘Comchoano’ genomes acquired after sorting single Bicosta cells, finding signatures of obligate host-dependence, including reduction of pathways encoding glycolysis, membrane components, amino acids and B-vitamins. Comchoano encode the necessary apparatus to import energy and other compounds from the host, proteins for host-cell associations and a type IV secretion system closest to Coxiella’s that is expressed in Pacific Ocean metatranscriptomes. Interactions between choanoflagellates and their microbiota could reshape the direction of energy and resource flow attributed to microbial predators, adding complexity and nuance to marine food webs.

Choanoflagellates are the closest living unicellular relatives of animals and are important bacterivorous predators in the ocean. Here the authors show that the microbiome of this predator includes an obligate, host resource-dependent bacterial associate.

Whole community invasions and the integration of novel ecosystems

The impact of invasion by a single non-native species on the function and structure of ecological communities can be significant, and the effects can become more drastic–and harder to predict–when multiple species invade as a group. Here we modify a dynamic Boolean model of plant-pollinator community assembly to consider the invasion of native communities by multiple invasive species that are selected either randomly or such that the invaders constitute a stable community. We show that, compared to random invasion, whole community invasion leads to final stable communities (where the initial process of species turnover has given way to a static or near-static set of species in the community) including both native and non-native species that are larger, more likely to retain native species, and which experience smaller changes to the topological measures of nestedness and connectance. We consider the relationship between the prevalence of mutualistic interactions among native and invasive species in the final stable communities and demonstrate that mutualistic interactions may act as a buffer against significant disruptions to the native community.

Emergence patterns of locally novel plant communities driven by past climate change and modern anthropogenic impacts

Anthropogenic disturbance and climate change can result in dramatic increases in the emergence of new, ecologically novel, communities of organisms. We used a standardised framework to detect local novel communities in 2135 pollen time series over the last 25,000 years. Eight thousand years of post‐glacial warming coincided with a threefold increase in local novel community emergence relative to glacial estimates. Novel communities emerged predominantly at high latitudes and were linked to global and local temperature change across multi‐millennial time intervals. In contrast, emergence of locally novel communities in the last 200 years, although already on par with glacial retreat estimates, occurred at midlatitudes and near high human population densities. Anthropogenic warming does not appear to be strongly associated with modern local novel communities, but may drive widespread emergence in the future, with legacy effects for millennia after warming abates.

A novel index to aid in prioritizing habitats for site-based conservation

Funding biodiversity conservation strategies are usually minimal, thus prioritizing habitats at high risk should be conducted. We developed and tested a conservation priority index (CPI) that ranks habitats to aid in prioritizing them for conservation. We tested the index using 1897 fish species from 273 African inland lakes and 34 countries. In the index, lake surface area, rarity, and their International Union for Conservation of Nature (IUCN) Red List status were incorporated. We retrieved data from the Global Biodiversity Information Facility (GBIF) and IUCN data repositories. Lake Nyasa had the highest species richness (424), followed by Tanganyika (391), Nokoué (246), Victoria (216), and Ahémé (216). However, lakes Otjikoto and Giunas had the highest CPI of 137.2 and 52.1, respectively. Lakes were grouped into high priority (CPI > 0.5; n = 56) and low priority (CPI < 0.5; n = 217). The median surface area between priority classes was significantly different (W = 11,768, p < .05, effect size = 0.65). Prediction accuracy of Random Forest (RF) and eXtreme Gradient Boosting (XGBoost) for priority classes were 0.912 and 0.954, respectively. Both models exhibited lake surface area as the variable with the highest importance. CPI generally increased with a decrease in lake surface area. This was attributed to less ecological substitutability and higher exposure levels of anthropogenic stressors such as pollution to a species in smaller lakes. Also, the highest species richness per unit area was recorded for high-priority lakes. Thus, smaller habitats or lakes may be prioritized for conservation although larger waterbodies or habitats should not be ignored. The index can be customized to local, regional, and international scales as well as marine and terrestrial habitats.

Advances in mixed cell deconvolution enable quantification of cell types in spatial transcriptomic data

Mapping cell types across a tissue is a central concern of spatial biology, but cell type abundance is difficult to extract from spatial gene expression data. We introduce SpatialDecon, an algorithm for quantifying cell populations defined by single cell sequencing within the regions of spatial gene expression studies. SpatialDecon incorporates several advancements in gene expression deconvolution. We propose an algorithm harnessing log-normal regression and modelling background, outperforming classical least-squares methods. We compile cell profile matrices for 75 tissue types. We identify genes whose minimal expression by cancer cells makes them suitable for immune deconvolution in tumors. Using lung tumors, we create a dataset for benchmarking deconvolution methods against marker proteins. SpatialDecon is a simple and flexible tool for mapping cell types in spatial gene expression studies. It obtains cell abundance estimates that are spatially resolved, granular, and paired with highly multiplexed gene expression data.

Learning from differences: Abiotic determinism of benthic communities in Northern Taiwan

Differences in the initial configuration of ecological communities may lead to contrasting trajectories when facing environmental changes. Here, we propose to uncover the determinism of benthic communities by carrying out a detailed investigation of their response to small-scale modification of environmental conditions, including physical, chemical, and geological factors. At ten locations (confounding site and depth) in Northern Taiwan, communities were delineated using a morpho-functional classification of the organisms. A k-means clustering was used to identify k homogenous groups among transects. Their environmental determinism was examined by combining this result with 16 environmental variables of transect conditions into a regression tree framework. Biotic and abiotic data were further analyzed with a Multivariate Regression Tree (MRT) to ascertain the hierarchical environmental determinism. The classifications produced by both approaches were compared using the Adjusted Rand index (ARI) to assess the predictive power of unsupervised clustering on its missing explanatory components (abiotic variables). k-means and MRT produced five clusters, respectively, with a similarity of 0.82 in ARI. Wave motion, followed by substrate types resolved most of the variance, while chemical factors in this study were uniform throughout the region. Comparable structures for both methods (clustering groups) demonstrated that the delineated clusters matched with contrasting environmental conditions which could be explained by the existence of various benthic communities. Further consideration of these different communities and their environmental context will be important in determining their trajectories under global changes and may help in the interpretation of community modifications with changing environmental conditions.

The rise of novelty in marine ecosystems: The Baltic Sea case

Global environmental changes have accelerated at an unprecedented rate in recent decades due to human activities. As a consequence, the incidence of novel abiotic conditions and biotic communities, which have been continuously emerging in the Earth system, has rapidly risen. Despite growing attention to the incidence and challenges posed by novelty in terrestrial ecosystems, novelty has not yet been quantified in marine ecosystems. Here, we measured for the rate of novelty (RoN) in abiotic conditions and community structure for three trophic levels, i.e., phytoplankton, zooplankton, and fish, in a large marine system - the Baltic Sea. We measured RoN as the degree of dissimilarity relative to a specific spatial and temporal baseline, and contrasted this with the rate of change as a measure of within-basin change over time. We found that over the past 35 years abiotic and biotic RoN showed complex dynamics varying in time and space, depending on the baseline conditions. RoN in abiotic conditions was smaller in the open Central Baltic Sea than in the Kattegat and the more enclosed Gulf of Bothnia, Gulf of Riga, and Gulf of Finland in the north. We found a similar spatial pattern for biotic assemblages, which resulted from changes in composition and stock size. We identified sea-surface temperature and salinity as key drivers of RoN in biotic communities. Hence, future environmental changes that are expected to affect the biogeochemistry of the Baltic Sea, may favor the rise of biotic novelty. Our results highlighted the need for a deeper understanding of novelty development in marine ecosystems, including interactions between species and trophic levels, ecosystem functioning under novel abiotic conditions, and considering novelty in future management interventions.

Ecophylogenetics redux

Species' evolutionary histories shape their present-day ecologies, but the integration of phylogenetic approaches in ecology has had a contentious history. The field of ecophylogenetics promised to reveal the process of community assembly from simple indices of phylogenetic pairwise distances - communities shaped by environmental filtering were composed of closely related species, whereas communities shaped by competition were composed of less closely related species. However, the mapping of ecology onto phylogeny proved to be not so straightforward, and the field remains mired in controversy. Nonetheless, ecophylogenetic methods provided important advances across ecology. For example the phylogenetic distances between species is a strong predictor of pest and pathogen sharing, and can thus inform models of species invasion, coexistence and the disease dilution/amplification effect of biodiversity. The phylogenetic structure of communities may also provide information on niche space occupancy, helping interpret patterns of facilitation, succession and ecosystem functioning - with relevance for conservation and restoration - and the dynamics among species within foodwebs and metacommunities. I suggest leveraging advances in our understanding of the process of evolution on phylogenetic trees would allow the field to progress further, while maintaining the essence of the original vision that proved so seductive.