Erosion of global functional diversity across the tree of life

Low level of anthropization linked to harsh vertebrate biodiversity declines in Amazonia

Assessing the impact of human activity on ecosystems often links local biodiversity to disturbances measured within the same locality. However, remote disturbances may also affect local biodiversity. Here, we used environmental DNA metabarcoding to evaluate the relationships between vertebrate biodiversity (fish and mammals) and disturbance intensity in two Amazonian rivers. Measurements of anthropic disturbance -here forest cover losses- were made from the immediate vicinity of the biodiversity sampling sites to up to 90 km upstream. The findings suggest that anthropization had a spatially extended impact on biodiversity. Forest cover losses of <11% in areas up to 30 km upstream from the biodiversity sampling sites were linked to reductions of >22% in taxonomic and functional richness of both terrestrial and aquatic fauna. This underscores the vulnerability of Amazonian biodiversity even to low anthropization levels. The similar responses of aquatic and terrestrial fauna to remote disturbances indicate the need for cross-ecosystem conservation plans that consider the spatially extended effects of anthropization.

It is unclear how far the impact of deforestation can spread. Here the authors analyse freshwater eDNA data along two rivers in the Amazon forest, and find that low levels of deforestation are linked to substantial reductions of fish and mammalian diversity downstream.

A global ecological signal of extinction risk in terrestrial vertebrates

To determine the distribution and causes of extinction threat across functional groups of terrestrial vertebrates, we assembled an ecological trait data set for 18,016 species of terrestrial vertebrates and utilized phylogenetic comparative methods to test which categories of habitat association, mode of locomotion, and feeding mode best predicted extinction risk. We also examined the individual categories of the International Union for Conservation of Nature Red List extinction drivers (e.g., agriculture and logging) threatening each species and determined the greatest threats for each of the four terrestrial vertebrate groups. We then quantified the sum of extinction drivers threatening each species to provide a multistressor perspective on threat. Cave dwelling amphibians (p < 0.01), arboreal quadrupedal mammals (all of which are primates) (p < 0.01), aerial and scavenging birds (p < 0.01), and pedal (i.e., walking) squamates (p < 0.01) were all disproportionately threatened with extinction in comparison with the other assessed ecological traits. Across all threatened vertebrate species in the study, the most common risk factors were agriculture, threatening 4491 species, followed by logging, threatening 3187 species, and then invasive species and disease, threatening 2053 species. Species at higher risk of extinction were simultaneously at risk from a greater number of threat types. If left unabated, the disproportionate loss of species with certain functional traits and increasing anthropogenic pressures are likely to disrupt ecosystem functions globally. A shift in focus from species- to trait-centric conservation practices will allow for protection of at-risk functional diversity from regional to global scales.

Life history mediates the trade-offs among different components of demographic resilience

Accelerating rates of biodiversity loss underscore the need to understand how species achieve resilience-the ability to resist and recover from a/biotic disturbances. Yet, the factors determining the resilience of species remain poorly understood, due to disagreements on its definition and the lack of large-scale analyses. Here, we investigate how the life history of 910 natural populations of animals and plants predicts their intrinsic ability to be resilient. We show that demographic resilience can be achieved through different combinations of compensation, resistance and recovery after a disturbance. We demonstrate that these resilience components are highly correlated with life history traits related to the species' pace of life and reproductive strategy. Species with longer generation times require longer recovery times post-disturbance, whilst those with greater reproductive capacity have greater resistance and compensation. Our findings highlight the key role of life history traits to understand species resilience, improving our ability to predict how natural populations cope with disturbance regimes.

A trait database and updated checklist for European subterranean spiders

Species traits are an essential currency in ecology, evolution, biogeography, and conservation biology. However, trait databases are unavailable for most organisms, especially those living in difficult-to-access habitats such as caves and other subterranean ecosystems. We compiled an expert-curated trait database for subterranean spiders in Europe using both literature data (including grey literature published in many different languages) and direct morphological measurements whenever specimens were available to us. We started by updating the checklist of European subterranean spiders, now including 512 species across 20 families, of which at least 192 have been found uniquely in subterranean habitats. For each of these species, we compiled 64 traits. The trait database encompasses morphological measures, including several traits related to subterranean adaptation, and ecological traits referring to habitat preference, dispersal, and feeding strategies. By making these data freely available, we open up opportunities for exploring different research questions, from the quantification of functional dimensions of subterranean adaptation to the study of spatial patterns in functional diversity across European caves.

Diversity patterns of lizard assemblages from a protected habitat mosaic in the Brazilian Cerrado savanna

Differences in habitat complexity and structure can directly influence the composition, diversity, and structure of species assemblages. Measurements of functional and phylogenetic diversity complement the commonly used measurements of taxonomic diversity, elucidating the relationships between species, their traits, and their evolutionary history. In this study, we evaluated how the mosaic of open and forested formations in a federal conservation unit in the western portion of the Brazilian Cerrado savanna influences the taxonomic, functional, and phylogenetic structure of lizard assemblages. Lizards were sampled for 15 months using pitfall traps set in open and forested formations. We recorded 292 lizards distributed among 16 species from eight families, with species composition differing among the formations. Richness was greater in the assemblages from open formations, while functional diversity and phylogenetic variability were greater in those of forested formations. Lizard assemblages in open formations were functionally and phylogenetically clustered, probably as a result of environmental filters acting on species, while the assemblages from forested formations were randomly structured. Different environmental and historical mechanisms have apparently shaped the current diversity of lizards in the region. This study shows that Cerrado vegetation mosaics can promote wide variation in different aspects of the taxonomic, functional, and phylogenetic structure from the lizard assemblages.

Rare and common species contribute disproportionately to the functional variation within tropical forests

Understanding how functional traits and functional entities (FEs, i.e., unique combinations of functional traits) are distributed within plant communities can contribute to the understanding of vegetation properties and changes in species composition. We utilized investigation data on woody plants (including trees, shrubs and lianas) from 17 1-ha plots across six old-growth tropical forest types on Hainan island, China. Plant species were categorized as common (>1 individuals/ha) and rare species (≤1 individuals/ha) according to their abundance to determine how they contributed to different ecosystem functions. First, we assessed the differences in traits between common and rare species, and second, we examined functional redundancy, functional over-redundancy, and functional vulnerability for common and rare species of the forests. We found that both common species and rare species in each of the forest types were placed into just a few FEs, leading to functional over-redundancy and resulting in functional vulnerability. Rare species tended to have different trait values than those of common species, and were differently distributed among FEs, indicating different contributions to ecosystem functioning. Our results highlighted the disproportionate contribution of rare species in all of the studied forests. Rare species are more likely than common species to possess unique FEs, and thus, they have a disproportionately large contribution to community trait space. The loss of such species may impact the functioning, redundancy, and resilience of tropical forests.

Profiling insular vertebrates prone to biological invasions: What makes them vulnerable?

Invasive alien species (IAS) are a major threat to insular vertebrates, although the ecological characteristics that make insular communities vulnerable to IAS are poorly understood. After describing the ecological strategies of 6015 insular amphibians, birds, lizards, and mammals, we assessed the functional and ecological features of vertebrates exposed to IAS. We found that at least 50% of insular amphibian functional richness was hosted by IAS-threatened amphibians and up to 29% for birds. Moreover, all IAS-threatened groups except birds harbored a higher functional richness than species groups threatened by other threats. Disentangling the ecological strategies threatened by IAS, compared to those associated with other threats, we showed that birds, lizards, and mammals were more likely to be terrestrial foragers and amphibians to have larval development. By contrast, large-bodied species and habitat specialists were universally threatened. By considering the functional aspect of threatened insular diversity, our work improves our understanding of global IAS impacts. This new dimension proves essential for undertaking relevant and effective conservation actions.

The macroecology of plant populations from local to global scales

Population ecologists develop theoretical and pragmatic knowledge of how and why populations change or remain stable, how life histories evolve and devise management strategies for populations of concern. However, forecasting the effects of global change or recommending management strategies is often urgent, requiring ecologists to work without detailed local evidence while using data and models from outside the focal location or species. Here we explore how the comparative ecology of populations, population macroecology, can be used to develop generalisations within and between species across different scales, using available demographic, environmental, life history, occurrence and trait data. We outline the strengths and weaknesses of using broad climatic variables and suitability inferred from probability of occupancy models to represent environmental variation in comparative analyses. We evaluate the contributions of traits, environment and their interaction as drivers of life history strategy. We propose that insights from life history theory, together with the adaptive capacity of populations and individuals, can inform on 'persist in place' vs 'shift in space' responses to changing conditions. As demographic data accumulate at landscape and regional scales for single species, and throughout plant phylogenies, we will have new opportunities for testing macroecological generalities within and across species.

Characterizing the spatial signal of environmental DNA in river systems using a community ecology approach

Environmental DNA (eDNA) is gaining a growing popularity among scientists but its applicability to biodiversity research and management remains limited in river systems by the lack of knowledge about the spatial extent of the downstream transport of eDNA. Here, we assessed the ability of eDNA inventories to retrieve spatial patterns of fish assemblages along two large and species-rich Neotropical rivers. We first examined overall community variation with distance through the distance decay of similarity and compared this pattern to capture-based samples. We then considered previous knowledge on individual species distributions, and compared it to the eDNA inventories for a set of 53 species. eDNA collected from 28 sites in the Maroni and 25 sites in the Oyapock rivers permitted to retrieve a decline of species similarity with increasing distance between sites. The distance decay of similarity derived from eDNA was similar and even more pronounced than that obtained with capture-based methods (gill-nets). In addition, the species upstream-downstream distribution range derived from eDNA matched to the known distribution of most species. Our results demonstrate that environmental DNA does not represent an integrative measure of biodiversity across the whole upstream river basin but provides a relevant picture of local fish assemblages. Importantly, the spatial signal gathered from eDNA was therefore comparable to that gathered with local capture-based methods, which describes fish fauna over a few hundred metres.

Fine-root traits in the global spectrum of plant form and function

Plant traits determine how individual plants cope with heterogeneous environments. Despite large variability in individual traits, trait coordination and trade-offs^1,2 result in some trait combinations being much more widespread than others, as revealed in the global spectrum of plant form and function (GSPFF³) and the root economics space (RES⁴) for aboveground and fine-root traits, respectively. Here we combine the traits that define both functional spaces. Our analysis confirms the major trends of the GSPFF and shows that the RES captures additional information. The four dimensions needed to explain the non-redundant information in the dataset can be summarized in an aboveground and a fine-root plane, corresponding to the GSPFF and the RES, respectively. Both planes display high levels of species aggregation, but the differentiation among growth forms, families and biomes is lower on the fine-root plane, which does not include any size-related trait, than on the aboveground plane. As a result, many species with similar fine-root syndromes display contrasting aboveground traits. This highlights the importance of including belowground organs to the GSPFF when exploring the interplay between different natural selection pressures and whole-plant trait integration.

Extinction of threatened vertebrates will lead to idiosyncratic changes in functional diversity across the world

Although species with larger body size and slow pace of life have a higher risk of extinction at a global scale, it is unclear whether this global trend will be consistent across biogeographic realms. Here we measure the functional diversity of terrestrial and freshwater vertebrates in the six terrestrial biogeographic realms and predict their future changes through scenarios mimicking a gradient of extinction risk of threatened species. We show vastly different effects of extinctions on functional diversity between taxonomic groups and realms, ranging from almost no decline to deep functional losses. The Indo-Malay and Palearctic realms are particularly inclined to experience a drastic loss of functional diversity reaching 29 and 31%, respectively. Birds, mammals, and reptiles regionally display a consistent functional diversity loss, while the projected losses of amphibians and freshwater fishes differ across realms. More efficient global conservation policies should consider marked regional losses of functional diversity across the world.

Anthropogenic extinctions are driving functional shifts in biological communities, but these changes might differ considerably among taxa and biogeographic regions. Here the authors show that projected losses of functional diversity among land and freshwater vertebrates are unevenly distributed across the world.

How do lizard niches conserve, diverge or converge? Further exploration of saurian evolutionary ecology

Background

Environmental conditions on Earth are repeated in non-random patterns that often coincide with species from different regions and time periods having consistent combinations of morphological, physiological and behavioral traits. Observation of repeated trait combinations among species confronting similar environmental conditions suggest that adaptive trait combinations are constrained by functional tradeoffs within or across niche dimensions. In an earlier study, we assembled a high-resolution database of functional traits for 134 lizard species to explore ecological diversification in relation to five fundamental niche dimensions. Here we expand and further examine multivariate relationships in that dataset to assess the relative influence of niche dimensions on the distribution of species in 6-dimensional niche space and how these may deviate from distributions generated from null models. We then analyzed a dataset with lower functional-trait resolution for 1023 lizard species that was compiled from our dataset and a published database, representing most of the extant families and environmental conditions occupied by lizards globally. Ordinations from multivariate analysis were compared with null models to assess how ecological and historical factors have resulted in the conservation, divergence or convergence of lizard niches.

Results

Lizard species clustered within a functional niche volume influenced mostly by functional traits associated with diet, activity, and habitat/substrate. Consistent patterns of trait combinations within and among niche dimensions yielded 24 functional groups that occupied a total niche space significantly smaller than plausible spaces projected by null models. Null model tests indicated that several functional groups are strongly constrained by phylogeny, such as nocturnality in the Gekkota and the secondarily acquired sit-and-wait foraging strategy in Iguania. Most of the widely distributed and species-rich families contained multiple functional groups thereby contributing to high incidence of niche convergence.

Conclusions

Comparison of empirical patterns with those generated by null models suggests that ecological filters promote limited sets of trait combinations, especially where similar conditions occur, reflecting both niche convergence and conservatism. Widespread patterns of niche convergence following ancestral niche diversification support the idea that lizard niches are defined by trait-function relationships and interactions with environment that are, to some degree, predictable and independent of phylogeny.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12862-021-01877-8.

Iberian Protected Areas Capture Regional Functional, Phylogenetic and Taxonomic Diversity of Most Tetrapod Groups

Protected areas (PAs) have been created with the purpose of preserving biodiversity, acting as refuges from anthropogenic pressures. Traditionally, PAs have been designed and managed to represent mainly taxonomic diversity, ignoring other diversity facets such as its functional and phylogenetic components. Yet, functional and phylogenetic diversity are, respectively, connected with species’ roles on ecosystems and evolutionary history held within communities. Here, we focused on the amphibian, reptile, resident breeding bird, and non-flying mammal faunas of the national and natural parks of the Iberian Peninsula, to evaluate whether these PAs are adequately representing regional functional, phylogenetic, and taxonomic diversity of each group. Specifically, we computed functional and phylogenetic diversity within each PA, and then compared those values to the ones obtained from a random assembly of species from the regional pool, that was defined as the region encompassing the PA and a neighboring area of 50 km beyond its boundary. We also calculated the proportion of species in each regional pool that were present within the PAs. In general, the functional and phylogenetic diversity of amphibians, reptiles and non-flying mammals found within PAs did not differ significantly from random expectations generated from the species pertaining to the regional pool, although a few PAs showed a higher diversity. In contrast, resident breeding birds presented lower functional and phylogenetic diversity than expected by chance in many of the PAs, which could relate to climatic variables and the habitat specificity of some species. The proportion of species from the regional pools that are present in the PAs was high for amphibians, reptiles and mammals, and slightly lower for birds. These results suggest that the Iberian natural and national parks are effectively capturing the functional, phylogenetic and taxonomic diversity of most tetrapod assemblages present at the regional level. Future studies should identify priority areas to expand the representation of these biodiversity components, and assess potential effects of climate and land-use changes on current patterns.