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Data from: Vertebrate community composition and diversity declines along a defaunation gradient radiating from rural villages in Gabon

Anthropocene defaunation is the global phenomenon of human-induced animal biodiversity loss. Understanding the patterns and process of defaunation is critical to predict outcomes for wildlife populations and cascading consequences for ecosystem function and human welfare. We investigated a defaunation gradient in northeastern Gabon by establishing 24 transects at varying distances (2–30 km) to rural villages and surveying the abundance and composition of vertebrate communities. Distance from village was positively correlated with observations of hunting (shotgun shells, campfires, hunters), making it a good proxy for hunting pressure. Species diversity declined significantly with proximity to village, with mammal richness increasing by roughly 1.5 species every 10 km travelled away from a village. Compared to forest far from villages, the wildlife community near villages consisted of higher abundances of large birds and rodents and lower abundances of large mammals like monkeys and ungulates. Distance to nearest village emerged as a key driver of the relative abundance of five of the six taxonomic guilds, indicating that the top–down force of hunting strongly influences large vertebrate community composition and structure. Several measures of vegetation structure also explained animal abundance, but these varied across taxonomic guilds. Forest elephants were the exception: no measured variable or combination of variables explained variation in elephant abundances. Synthesis and applications. Hunting is concentrated within 10 km around villages, creating a hunting halo characterized by heavily altered animal communities composed of relatively small-bodied species. Although the strongest anthropogenic effects are relatively distance-limited, the linear increase in species richness shown here even at distances 30 km from villages suggests that hunting may have altered vertebrate abundances across the entire landscape. Central African forests store >25% of the carbon in tropical forests and are home to 3000 endemic species, but roughly 53% of the region lies within the village hunting halo. Resource management strategies should take into account this hunting-induced spatial variation in animal communities. Near villages, resource management should focus on sustainable community-led hunting programs that provide long-term supplies of wild meat to rural people. Resource management far from villages should focus on law enforcement and promoting industry practices that maintain remote tracts of land to preserve ecosystem services like carbon storage and biodiversity.

Data from: Niche construction by growth forms is as strong a predictor of species diversity as environmental gradients

We present a conceptual framework that describes how species belonging to a growth form collectively can be niche constructors (i.e. modify niches) and affect species diversity in plant communities. We use an empirical assessment of tundra plant communities to illustrate the framework's utility. In doing so, we make a first investigation of collective niche construction in ecological communities. In tundra plant communities, growth forms differently affect ecosystem process rates and cause environmental modifications; thus, growth forms are strong candidates for being niche constructors. To assess the impact of growth form niche construction on plant species diversity, we excluded the species of the growth form applied as niche constructor when estimating the community species diversity. We assessed niche construction in 70 tundra meadow communities and 1450 randomly selected tundra plant communities that are distributed along ecological gradients in temperature, resource availability, competitive interference and herbivory. These gradients allowed us to concomitantly assess to what extent the niche construction is independent of environmental conditions. Growth forms varied from strong positive to neutral predictors of both species richness and Simpson index in the order of forbs, grasses, sedges, deciduous shrubs and evergreen shrubs, suggesting that growth forms have important roles as niche constructors in tundra plant communities. Also, the environmental conditions were strong predictors of species diversity, but they did not interact with or confound the effects of growth forms. Forbs and grasses were the least abundant growth forms, yet they were the strongest positive predictors of species diversity. Therefore, our results suggest a particular niche-constructing role of these growth forms for enhancing species diversity in tundra plant communities. Synthesis. In this study, we provide conceptual and empirical evidence for collective niche construction as a powerful ecological process that affects species diversity and that can act independently of environmental conditions. Species sharing a single trait or species belonging to a growth form can act as collective niche constructors, and as exemplified for growth forms in this study, be important predictors of species diversity in ecological communities.

Data from: Shifts and linkages of functional diversity between above- and below-ground compartments along a flooding gradient

Trait-based approaches have the potential to reveal general and predictive relationships between organisms and ecosystem functioning. However, the mechanisms underlying the functional structure of communities are still unclear. Within terrestrial ecosystems, several studies have shown that many ecological processes are controlled by the interacting above- and below-ground compartments. However, few studies have used traits to reveal the functional relationships between plants and soil fauna. Mostly, research combining plants and soil fauna solely used the traits of one assemblage in predictive studies. Above-ground (plants) and below-ground (Collembola) compartments were sampled over a flooding gradient in northern France along the Seine River. First, we measured the effect of flooding on functional and taxonomic assembly within both communities. We then considered the linkages between plant and Collembolan species richness, community traits and assessed whether traits of both compartments converged at high flooding intensity (abiotic filtering) and diverged when this constraint is released (biotic filtering). Species richness of both taxa followed the same bell-shaped pattern along the gradient, while a similar significant pattern of functional richness was only observed for plants. Further analyses revealed a progressive shift from trait convergence to divergence for plants, but not for Collembola, as constraints intensity decreased. Instead, our results highlighted that Collembola traits were mainly linked to the variations in plant traits. This leads, within Collembola assemblages, to convergence of a subset of perception and habitat-related traits for which the relationship with plant traits was assessed. Synthesis. Using a trait-based approach, our study highlighted that functional relationships occur between above- and below-ground compartments. We underlined that functional composition of plant communities plays a key role in structuring Collembola assemblages in addition to the role of abiotic variables. Our study clearly shows that functional diversity provides a new approach to link the above- and below-ground compartments and might, therefore, be further considered when studying ecological processes at the interface between both compartments.

opencc-zeroDec 2011View details →

Data from: Global gradients in vertebrate diversity predicted by historical area-productivity dynamics and contemporary environment

Broad-scale geographic gradients in species richness have now been extensively documented, but their historical underpinning is still not well understood. While the importance of productivity, temperature, and a scale-dependence of the determinants of diversity is broadly acknowledged, we here argue that limitation to a single analysis scale and data pseudoreplication have impeded an integrated evolutionary and ecological understanding of diversity gradients. We develop and apply a hierarchical analysis framework for global diversity gradients that incorporates an explicit accounting of past environmental variation and provides an appropriate measurement of richness. Due to environmental niche conservatism organisms generally reside in climatically defined bioregions, or "evolutionary arenas", characterized by in situ speciation and extinction. These bioregions differ in age and their total productivity and have varied over time in area and energy available for diversification. We show that, consistently across the four major terrestrial vertebrate groups, current-day species richness of the world's main 32 bioregions is best explained by a model that integrates area and productivity over geological time together with temperature. Adding finer-scale variation in energy availability as an ecological predictor of within-bioregional patterns of richness explains much of the remaining global variation in richness at the 110km grain. These results highlight the separate evolutionary and ecological effects of energy availability and provide a first conceptual and empirical integration of the key drivers of broad-scale richness gradients. Avoiding the pseudo-replication that impedes the evolutionary interpretation of non-hierarchical macroecological analyses, our findings integrate evolutionary and ecological mechanisms at their most relevant scales and offer a new synthesis regarding global diversity gradients.

opencc-zeroJun 2019View details →

Data from: Beta diversity and specialization in plant-pollinator networks along an elevational gradient

Aim: To assess whether the reduced nutritional resources available for pollinators due to plant community simplification along an elevational plant-diversity gradient changes pollinator niche breadth and richness. Additionally, we evaluated how body size and proboscis length of pollinators shifted along the gradient, and whether these changes were related to pollinator niche breadth. Location: An elevational gradient (2,350-3,520 m a.s.l.) on the oceanic high-mountain strato-volcano of El Teide (Tenerife, Canary Islands). Taxon: Flowering plant and pollinator species. Methods: We compared quantitative plant–pollinator networks along the plant-diversity gradient. We calculated a set of niche-based topological metrics that capture the degree of specialization, niche breadth and niche overlap. Furthermore, we obtained β-diversity measures and the proportion of replacement and richness components. Results: There was an overall decline in species richness of pollinators with increasing elevation. This decline was mainly driven by the loss of species along the elevational gradient, which conformed a nested subset pattern. The whole network showed less specialization, greater connectance and lower modularity towards the summit. At high elevations, pollinators were more generalized and less selective in their flower choice, showing a greater trophic niche breadth compared to pollinators at lower elevations. Mean body size of pollinators increased with elevation, and species body size and proboscis length were positively associated with the number of plant species visited. Main conclusions. Overall, results indicated that the elevational gradient filters pollinator species, probably according to their thermal tolerance and ability to exploit a wide range of trophic resources. The finding that pollinators become more generalized and opportunistic at higher elevations is a novel result, which may have implications for new research into how ecological networks vary over environmental gradients. From an applied perspective, our results highlight the importance of considering the spatial variation of species assemblages when aiming to construct functionally reliable interaction networks along environmental gradients.

Data from: Diversity and composition of tropical butterflies along an Afromontane agricultural gradient in the Jimma Highlands, Ethiopia

Afromontane landscapes are typically characterized by a mosaic of smallholder farms and the biodiversity impacts of these practices will vary in accordance to local management and landscape context. Here, we assess how tropical butterfly diversity is maintained across an agricultural landscape in the Jimma Highlands of Ethiopia. We used transect surveys to sample understory butterfly communities within degraded natural forest, semi-managed coffee forest (SMCF), exotic timber plantations, open woodland, croplands and pasture. Surveys were conducted in 29 one-hectare plots and repeated five times between January and June 2013. We found that natural forest supports higher butterfly diversity than all agricultural plots (measured with Hill's numbers). SMCF and timber plantations retain relatively high abundance and diversity, but these metrics drop off sharply in open woodland, cropland and pasture. SMCF and timber plantations share the majority of their species with natural forest and support an equivalent abundance of forest-dependent species, with no increase in widespread species. There was some incongruence in the responses of families and sub-families, notably that Lycaenidae are strongly associated with open woodland and pasture. Adult butterflies clearly utilize forested agricultural practices such as SMCF and timber plantations, but species diversity declines steeply with distance from natural forest suggesting that earlier life-stages may depend on host plants and/or microclimatic conditions that are lost under agricultural management. From a management perspective, the protection of natural forest remains a priority for tropical butterfly conservation, but understanding functioning of the wider landscape mosaic is important as SMCF and timber plantations may act as habitat corridors that facilitate movement between forest fragments.

Data from: Genetic signatures of ecological diversity along an urbanization gradient

Despite decades of work in environmental science and ecology, estimating human influences on ecosystems remains challenging. This is partly due to complex chains of causation among ecosystem elements, exacerbated by the difficulty of collecting biological data at sufficient spatial, temporal, and taxonomic scales. Here, we demonstrate the utility of environmental DNA (eDNA) for quantifying associations between human land use and changes in an adjacent ecosystem. We analyze metazoan eDNA sequences from water sampled in nearshore marine eelgrass communities and assess the relationship between these ecological communities and the degree of urbanization in the surrounding watershed. Counter to conventional wisdom, we find strongly increasing richness and decreasing beta diversity with greater urbanization, and similar trends in the diversity of life histories with urbanization. We also find evidence that urbanization influences nearshore communities at local (hundreds of meters) rather than regional (tens of km) scales. Given that different survey methods sample different components of an ecosystem, we then discuss the advantages of eDNA—which we use here to detect hundreds of taxa simultaneously—as a complement to traditional ecological sampling, particularly in the context of broad ecological assessments where exhaustive manual sampling is impractical. Genetic data are a powerful means of uncovering human-ecosystem interactions that might otherwise remain hidden; nevertheless, no sampling method reveals the whole of a biological community.

opencc-zeroDec 2013View details →

Data from: Environmental filtering explains variation in plant diversity along resource gradients

The mechanisms that shape plant diversity along resource gradients remain unresolved because competing theories have been evaluated in isolation. By testing multiple theories simultaneously across a >2-million-year dune chronosequence in an Australian biodiversity hotspot, we show that variation in plant diversity is not explained by local resource heterogeneity, resource partitioning, nutrient stoichiometry, or soil fertility along this strong resource gradient. Rather, our results suggest that diversity is determined by environmental filtering from the regional flora, driven by soil acidification during long-term pedogenesis. This finding challenges the prevailing view that resource competition controls local plant diversity along resource gradients, and instead reflects processes shaping species pools over evolutionary time scales.

Data from: Speciation and the latitudinal diversity gradient: insights from the global distribution of endemic fish

The nearly universal pattern that species richness increases from the poles to the equator (the latitudinal diversity gradient [LDG]) has been of intense interest since its discovery by early natural-history explorers. Among the many hypotheses proposed to explain the LDG, latitudinal variation in (1) productivity, (2) time and area available for diversification, and (3) speciation and/or extinction rates have recently received the most attention. Because tropical regions are older and were formerly more widespread, these factors are often intertwined, hampering efforts to distinguish their relative contributions to the LDG. Here we examine the global distribution of endemic lake fishes to determine how lake age, area, and latitude each affect the probability of speciation and the extent of diversification occurring within a lake. We analyzed the distribution of endemic fishes worldwide (1,933 species and subspecies from 47 families in 2,746 lakes) and find that the probability of a lake containing an endemic species and the total number of endemics per lake increase with lake age and area and decrease with latitude. Moreover, the geographic locations of endemics in 34 of 41 families are found at lower latitudes than those of nonendemics. We propose that the greater diversification of fish at low latitudes may be driven in part by ecological opportunities promoted by tropical climates and by the coevolution of species interactions.

opencc-zeroDec 2016View details →

Data from: Great tits and the city: distribution of genomic diversity and gene-environment associations along an urbanization gradient

Urbanization is a growing concern challenging the evolutionary potential of wild populations by reducing genetic diversity and imposing new selection regimes affecting many key fitness traits. However, genomic footprints of urbanization have received little attention so far. Using RAD sequencing, we investigated the genome-wide effects of urbanization on neutral and adaptive genomic diversity in 140 adult great tits Parus major collected in locations with contrasted urbanization levels (from a natural forest to highly urbanized areas of a city (Montpellier, France). Heterozygosity was slightly lower in the more urbanized sites compared to the more rural ones. Low but significant effect of urbanization on genetic differentiation was found, at the site-level but not at the nest-level, indicative of the geographic scale of urbanization impact and of the potential for local adaptation despite gene flow. Gene-environment association tests identified numerous SNPs with small association scores to urbanization, distributed across the genome, from which a subset of 97 SNPs explained up to 81% of the variance in urbanization, overall suggesting a polygenic response to selection in the urban environment. These findings open stimulating perspectives for broader applications of high-resolution genomic tools on other cities and larger sample sizes to investigate the consistency of the effects of urbanization on the spatial distribution of genetic diversity and the polygenic nature of gene-urbanization association.

FIGURES 5A–E. Chrysometa petrasierwaldae n in The spider genus Chrysometa (Araneae, Tetragnathidae) from the Pico da Neblina and Serra do Tapirapecó mountains (Amazonas, Brazil): new species, new records, diversity and distribution along two altitudinal gradients

FIGURES 5A–E. Chrysometa petrasierwaldae n. sp. A. Male palp, ventral view. B. Same, retrolateral view. C. Epigynum, ventral view. D. Same, posterior view. E. Same, dorsal view. Scale bars: AB, 0.3 mm; CDE, 0.1 mm.

FIGURES 7A–D in The spider genus Chrysometa (Araneae, Tetragnathidae) from the Pico da Neblina and Serra do Tapirapecó mountains (Amazonas, Brazil): new species, new records, diversity and distribution along two altitudinal gradients

FIGURES 7A–D. Chrysometa spp. AB. Chrysometa candianii n. sp. A. Male palp, ventral view. B. Same, retrolateral view. CD. Chrysometa minuta (Keyserling). C. Male palp, ventral view. D. Same, retrolateral view. Scale bars: AB, 0.5mm; CD, 0.5 mm.

FIGURES 1. Study area. A in The spider genus Chrysometa (Araneae, Tetragnathidae) from the Pico da Neblina and Serra do Tapirapecó mountains (Amazonas, Brazil): new species, new records, diversity and distribution along two altitudinal gradients

FIGURES 1. Study area. A) South America; B) Northern South America (rectangle of map A enlarged). The mountain range at the left of the map represents the northern part of the Andes, and the mountainous region in the center of the map is the Guayana Shield, showing the study area in its southern part; C) Closer view of the study area (rectangle of map B enlarged), showing the two sampled sites, the Pico da Neblina (red circle) and the Serra do Tapirapecó (blue triangule). The white line represents the boundary between Brazil and Venezuela.

FIGURES 3A–E. Chrysometa saci n in The spider genus Chrysometa (Araneae, Tetragnathidae) from the Pico da Neblina and Serra do Tapirapecó mountains (Amazonas, Brazil): new species, new records, diversity and distribution along two altitudinal gradients

FIGURES 3A–E. Chrysometa saci n. sp. A. Male palp, ventral view. B. Same, retrolateral view. C. Epigynum, ventral view. D. Same, posterior view. E. Same, dorsal view. Scale bars: AB, 0.3 mm; CDE, 0.5 mm.

FIGURES 6A–I. Chrysometa spp. A–C. Chrysometa lomanhungae n in The spider genus Chrysometa (Araneae, Tetragnathidae) from the Pico da Neblina and Serra do Tapirapecó mountains (Amazonas, Brazil): new species, new records, diversity and distribution along two altitudinal gradients

FIGURES 6A–I. Chrysometa spp. A–C. Chrysometa lomanhungae n. sp. A. Epigynum, ventral view. B. Same, posterior view. C. Same, dorsal view. D–F. Chrysometa yanomami n. sp. D. Epigynum, ventral view. E. Same, posterior view. F. Same, dorsal view. G–I. Chrysometa santosi n. sp. G. Epigynum, ventral view. H. Same, posterior view. I. Same, dorsal view. Scale bars: A– C, 0.1 mm; D–F, 0.1 mm; G–I, 0.3 mm.

FIGURES 2A–E. Chrysometa nubigena n in The spider genus Chrysometa (Araneae, Tetragnathidae) from the Pico da Neblina and Serra do Tapirapecó mountains (Amazonas, Brazil): new species, new records, diversity and distribution along two altitudinal gradients

FIGURES 2A–E. Chrysometa nubigena n. sp. A. Male palp, ventral view. B. Same, retrolateral view. C. Epigynum, ventral view. D. Same, posterior view. E. Same, dorsal view. Scale bars: AB, 0.3 mm; CDE, 0.1 mm.

FIGURES 4A–E. Chrysometa waikoxi n in The spider genus Chrysometa (Araneae, Tetragnathidae) from the Pico da Neblina and Serra do Tapirapecó mountains (Amazonas, Brazil): new species, new records, diversity and distribution along two altitudinal gradients

FIGURES 4A–E. Chrysometa waikoxi n. sp. A. Male palp, ventral view. B. Same, retrolateral view. C. Epigynum, ventral view. D. Same, posterior view. E. Same, dorsal view. Scale bars: AB, 0.3 mm; CDE, 0.1 mm.

opencc-zeroNov 2021View details →

Depth and latitudinal diversity gradients in seamount benthic communities of the South Atlantic

Aim Although latitudinal and bathymetric species diversity gradients in the deep sea have been identified and investigated, studies have rarely considered these gradients across seamount and oceanic island ecosystems. This study aimed to identify whether the current understanding of latitudinal and bathymetric gradients in α-diversity (species richness) apply to South Atlantic seamount ecosystems, as well as ascertaining whether identifiable trends were present in seamount β-diversity along a bathymetric gradient. Location The South Atlantic Ocean. Time period 2013-2019 Major taxa studied Benthic communities. Methods Drop camera images from 39 transects, collected between 250 m and 950 m, were used to characterise species richness from within the Exclusive Economic Zones of Ascension Island, Saint Helena and Tristan da Cunha, spanning 8°S to 40°S. We subsequently applied linear modelling to test possible environmental drivers across latitudinal and bathymetric ranges (see transect metadata for variables). An Analysis of Similarity was employed to investigate the beta-diversity gradient, and the level of species turnover with depth. Results Surface primary productivity and substrate hardness both had significant positive effects on species richness, and there was significantly higher species richness at temperate latitudes. No significant relationship between species richness and depth was detected, but there was a significant species turnover with depth. Main conclusions Seamounts and oceanic islands do not conform to established depth-diversity relationships within the depth range studied. However, despite their isolation and small sizes, seamounts and oceanic islands in the South Atlantic appear to follow latitudinal patterns of deep-sea species richness established for specific taxonomic groups in different ecosystems.

opencc-zeroDec 2021View details →

Patterns and drivers of leaf-litter ant diversity along a tropical elevational gradient in Mexico

Aim: Given their high environmental variation over relatively short distances, mountains represent ideal systems for evaluating potential factors shaping diversity gradients. Despite a long-standing interest in ecological gradients, ant diversity patterns and their related mechanisms occurring on mountains are still not well understood. Here, we (i) describe species diversity patterns (α and β) of leaf-litter ants along the eastern slope of Cofre de Perote in Veracruz, Mexico, and (ii) evaluate climatic and spatial factors in determining these patterns. Location: Veracruz, Mexico Taxon: Leaf-litter ants Methods: We sampled 320 m2 of leaf litter spread across 8 equally-spaced sites from sea level to 3500 m of elevation. We used regression models to predict α-diversity patterns with climatic (temperature and precipitation) and spatial (geometric constraints) variables. We also assessed, through multiple regression based on distance matrices (MRM), the relative importance of habitat filtering and dispersal limitations for shaping total dissimilarity (βsor), turnover (βsim) or nestedness (βnes). Results: A hump-shaped pattern was observed in the α- diversity with a peak at 600-1000 meters above sea level. This pattern is best explained by the temperature gradient with around 80% of variance explanation. β-diversity showed a non-linear pattern along the elevational gradient with total dissimilarity and turnover components better explained by habitat filtering (i.e., temperature distances). Main conclusions: The importance of temperature on both α- and β-diversity patterns reinforces its widespread importance in shaping litter ant diversity patterns across elevational gradients. The hump-shaped pattern in species richness is probably the result of harsh abiotic conditions at the base and the top of the mountain combined with biotic attrition in lowland sites. Niche specialization of ant species in their optimal thermal zones may explain total dissimilarity and ant species replacement along the studied gradient. Taken all together, these results suggest a high relevance of temperature-driven mechanisms in the origin and maintenance of the biodiversity of ectothermic taxa.