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opencc-zeroDec 2018View details →

Data from: Functional diversity and composition of Caatinga woody flora are negatively impacted by chronic anthropogenic disturbance

Tropical plant assemblages can be taxonomically and phylogenetically impoverished by chronic anthropogenic disturbance (CAD), such as firewood collection and extensive grazing. However, to what extent the functional dimension responds to CAD is still unclear. Such knowledge is urgently required for predicting, preventing or even reversing the impacts of CAD. Chronic anthropogenic disturbance may operate as an ecological filter by selecting functional trait values (e.g. low wood density), thereby altering the functional composition and diversity of plant assemblages. We tested this hypothesis using 29 woody plant assemblages across three ontogenetic stages (seedlings, saplings and adults) in a 220‐km2 landscape of the Caatinga, northeast Brazil. We adopted a CAD index consisting of four indicators (proximity to urban centre and houses and the density of both people and livestock) and tested how well it explained the functional diversity and effect sizes (richness, evenness and dispersion) and composition (community‐weighted mean). Chronic anthropogenic disturbance affected several functional metrics across the three ontogenetic stages. However, CAD effects were stronger in adult communities by negatively affecting functional richness, dispersion and their effect sizes. CAD also altered the functional composition of leaf mass per area, woody density and leaf area of adult assemblages. Sapling communities were affected in terms of functional composition (leaf area, leaf dry matter and wood density), with positive and negative effects, while seedling assemblages responded positively to CAD only in terms of functional evenness and its effect size. Some changes in functional metrics were influenced by dominant Euphorbiaceae species across ontogenetic stages, especially in terms of leaf area and woody density. Synthesis. Chronic anthropogenic disturbance is an important driver of plant‐community functional organization across ontogenetic stages in the Caatinga. Adult assemblages are particularly sensitive and tend to lose functional niche space and support more acquisitive rather than conservative strategies as chronic anthropogenic disturbance increases. The proliferation of Euphorbiaceae disturbance‐adapted species can explain part of the community responses to chronic anthropogenic disturbance. Our findings highlight the ecological effects of chronic anthropogenic disturbance and show that it is a key influence on tropical biotas. Changes in plant functional traits associated with plant resource use are likely to affect ecosystem functioning and services provided by Caatinga.

opencc-zeroJun 2021View details →

Differential impacts of alternate primary producers on carbon cycling

Disturbance impacts the spatial distribution of primary producers, which can have cascading effects on ecosystem function. The lower-intertidal zone on the rocky shores of the Pacific Northwest is one such place where wave energy creates a mosaic-like distribution between two assemblages: surfgrass (Phyllospadix scouleri) meadows and macroalgal forests dominated by kelp. We simulated wave disturbance by experimentally removing patches of surfgrass monocultures, resulting in a macroalgal assemblage with increased diversity, biomass, and net primary productivity in the following year. While surfgrass had a higher C:N compared to macroalgal assemblages, macroalgal assemblages achieved a higher biomass, fixed carbon at a faster rate, and released more dissolved organic carbon (DOC) during photosynthesis. Thus, despite similar standing amounts of carbon, macroalgal assemblages have increased carbon turnover – from fixation to DOC release. Comparative photophysiology indicated that surfgrasses have a competitive advantage over other macrophytes at low-light levels, allowing them to persist when disturbance is reduced. Unexpectedly, disturbance in this system increased the potential for carbon sequestration when surfgrass monocultures were replaced by diverse macroalgae.

opencc-zeroDec 2015View details →

Data from: How persistent are the impacts of logging roads on Central African forest vegetation?

1. Logging roads can trigger tropical forest degradation by reducing the integrity of the ecosystem and providing access for encroachment. Therefore, road-management is crucial in reconciling selective logging and biodiversity conservation. Most logging roads are abandoned after timber harvesting, however little is known about their long-term impacts on forest vegetation and accessibility, especially in Central Africa. 2. In 11 logging concessions in the Congo Basin we field-sampled a chronosequence of roads that, judged by satellite images, had been abandoned between 1985 and 2015. We assessed recovery of timber resources, tree diversity and above-ground biomass in three zones: the road track, the road edge (where forest had been cleared during road construction) and the adjacent logged forest. 3. The density of commercial timber species ≤ 15 cm DBH was almost three times higher in the road track (327 individuals ha-1) and edge (278) than in the logged adjacent forest (111). Over time, tree species diversity converged to a comparable level between roads and adjacent forests, along with decreasing soil compaction and increasing canopy closure. 4. The average width of forest clearing for road construction was 20 m, covering a total 0.76% of the forest area inside concessions. After 15 years following abandonment, road tracks had recovered 24 Mg ha-1 of above-ground woody biomass, which was 6% of that in the adjacent forest, while road edges had accumulated 167 Mg ha-1 (42%). Ten years after abandonment, roads were no longer penetrable by poachers on motorcycles. Exotic herb species were fully replaced by dominant Marantaceae that have even higher abundance in the adjacent forest. 5. Synthesis and applications. Our evidence of vegetation recovery suggests that logging roads are mostly transient elements in forest landscapes. However, given the slow recovery of biomass on abandoned road tracks, we advocate both reducing the width of forest clearing for road construction and reopening old logging roads for future harvests, rather than building new roads in intact forests. Road edges seem suitable for post-logging silviculture which needs to be assisted by removing dominant herbs during the early years after abandonment while the road track is still accessible

opencc-zeroDec 2012View details →

Data from: The impact of spatial scale and habitat configuration on patterns of trait variation and local adaptation in a wild plant parasite

Theory indicates that spatial scale and habitat configuration are fundamental for coevolutionary dynamics and how diversity is maintained in host–pathogen interactions. Yet, we lack empirical data to translate the theory to natural host–parasite systems. In this study, we conduct a multiscale cross-inoculation study using the specialist wild plant pathogen Podosphaera plantaginis on its host plant Plantago lanceolata. We apply the same sampling scheme to a region with highly fragmented (Åland) and continuous (Saaremaa) host populations. Although theory predicts higher parasite virulence in continuous regions, we did not detect differences in traits conferring virulence among the regions. Patterns of adaptation were highly scale dependent. We detected parasite maladaptation among regions, and among populations separated by intermediate distances (6.0–40.0 km) within the fragmented region. In contrast, parasite performance did not vary significantly according to host origin in the continuous landscape. For both regions, differentiation among populations was much larger for genetic variation than for phenotypic variation, indicating balancing selection maintaining phenotypic variation within populations. Our findings illustrate the critical role of spatial scale and habitat configuration in driving host–parasite coevolution. The absence of more aggressive strains in the continuous landscape, in contrast to theoretical predictions, has major implications for long-term decision making in conservation, agriculture, and public health.

opencc-zeroDec 2018View details →

Data from: Altered leaf litter quality exacerbates the negative impact of climate change on decomposition

1.Leaf litter decomposition is a key component of global biogeochemical cycles that influences soil carbon storage, nutrient availability and plant productivity. Ongoing climate change will lead to warmer and drier conditions in many dryland regions, potentially affecting litter decomposition and nutrient dynamics. Climate change effects can be direct and/or indirect, e.g. through changes in litter quality, yet their relative importance on litter decomposition remains unclear. 2. We conducted a manipulative study in a semiarid shrubland to assess the effects of leaf litter quality, forecasted climate change, i.e. +2.5°C warming (W), 30% rainfall reduction (RR), as well as their interaction (W+RR) to elucidate their relative effects on litter decomposition. 3. Climatic effects alone reduced decomposition of a homogeneous control leaf litter collected from Helianthemum squamatum shrubs growing in unmanipulated plots by 23.4%, 18.1%, and 29.8% in the W, RR and W+RR treatments, respectively. Leaf litter quality was lower in shrubs that had been growing in warmed plots (W and W+RR), as they had lower nutrient concentrations (P, Fe) and higher C:N and C:P ratios than leaf litter produced under ambient (control) conditions. Lignin concentration was significantly lower in litter from W+RR plots, yet when both climate and litter quality were considered simultaneously, decomposition rates were 32.0%, 26.3% and 39.9% lower in W, RR and W+RR plots compared to controls. In addition, we found greater microbial N immobilization in leaf litter incubated within warmed (W and W+RR) than within non‐warmed plots (Control and RR). Structural equation modelling showed that higher litter moisture and microbial biomass contents stimulated decomposition. Simulated climate change (W, RR and W+RR) reduced decomposition indirectly by negatively affecting litter moisture contents and litter microbial biomass. Microbial nitrogen immobilization was stimulated by the lower quality (i.e. high C:N ratios) of the leaf litter collected in shrubs from warmed plots (W and W+RR). 4. Synthesis Our findings indicate that forecasted climate change conditions slow down C and N cycling in a dryland ecosystem, an effect that is further exacerbated by climate change‐induced reductions in litter quality and related reductions in bacterial and fungal biomass in litter.

opencc-zeroApr 2020View details →

Impact of smoking cessation, coffee and bread consumption on the intestinal microbial composition among Saudis: A cross-sectional study

The gut microbiota is often affected by the dietary and lifestyle habits of the host, resulting in a better efficacy that favors energy harvesting from the consumed food. Our objective was to characterize the composition of gut microbiota in adult Saudis and investigate possible association with lifestyle and dietary practices. Feces from 104 Saudi volunteers (48% males) were tested for microbiota by sequencing the V3-V4 region of bacterial 16S ribosomal RNA (rRNA). For all participants, data were collected related to their lifestyle habits and dietary practices. The relative abundance (RA) of Fusobacteria was significantly higher in normal weight Saudis ( p =0.005, FDR=0.014). Individuals who consumed more coffee presented marginally significant more RA of Fusobacteria ( p =0.02, FDR=0.20) in their gut microbiota compared to those reporting low or no coffee intake, but the RA of Fusobacteria was significantly higher in smokers compared to non-smokers p =0.009, FDR=0.027) . The RA of Fusobacteria was also significantly higher in those reporting daily consumption of bread ( p =0.005, FDR=0.015). At the species level, the gut microbiota of people who consumed coffee was dominated by Bacteroidetes thetaiotaomicron followed by Phascolarctobacterium faecium and Eubacteriumrectale . Similarly, the gut microbiota of smokers was also enriched by B. thetaiotaomicron and Lactobacillus amylovorus. Smoking cessation, bread and coffee consumption induce changes in the intestinal microbial composition of Saudis. This indicates the significance of diet and lifestyle practices in the determination of the composition of the gut microbiota, which could possibly lead later to changes in metabolic profile and weight.

opencc-zeroJan 2020View details →

Using cumulative impact mapping to prioritise marine conservation efforts in Equatorial Guinea

Marine biodiversity is under extreme pressure from anthropogenic activity globally, leading to calls to protect at least 10% of the world's oceans within marine protected areas (MPAs) and other effective area-based conservation measures by 2020. Fulfilling such commitments, however, requires a detailed understanding of the distribution of potentially detrimental human activities, and their predicted impacts. One such approach that is being increasingly used to strengthen our understanding of human impacts is cumulative impact mapping; as it can help identify economic sectors with the greatest potential impact on species and ecosystems in order to prioritise conservation management strategies, providing clear direction for intervention. In this paper, we present the first local cumulative utilisation impact mapping exercise for the Bioko-Corisco-Continental area of Equatorial Guinea's Exclusive Economic Zone – situated in the Gulf of Guinea one of the most important and least studied marine regions in the Eastern Central Atlantic. This study examines the potential impact of ten direct anthropogenic activities on a suite of key marine megafauna species and reveals that the most suitable habitats for these species, located on the continental shelf, are subject to the highest threat scores. However, in some coastal areas, the persistence of highly suitable habitat subject to lower threat scores suggests that there are still several strategic areas that are less impacted by human activity that may be suitable sites for protected area expansion. Highlighting both the areas with potentially the highest impact, and those with lower impact levels, as well as particularly damaging activities can inform the direction of future conservation initiatives in the region.

opencc-zeroDec 2013View details →

Data from: Impact on offspring methylation patterns of maternal gestational diabetes mellitus and intrauterine growth restraint suggest common genes and pathways linked to subsequent type 2 diabetes risk

Size at birth, postnatal weight gain, and adult risk for type 2 diabetes may reflect environmental exposures during developmental plasticity and may be mediated by epigenetics. Both low birth weight (BW), as a marker of fetal growth restraint, and high birth weight (BW), especially after gestational diabetes mellitus (GDM), have been linked to increased risk of adult type 2 diabetes. We assessed DNA methylation patterns using a bead chip in cord blood samples from infants of mothers with GDM (group 1) and infants with prenatal growth restraint indicated by rapid postnatal catch-up growth (group 2), compared with infants with normal postnatal growth (group 3). Seventy-five CpG loci were differentially methylated in groups 1 and 2 compared with the controls (group 3), representing 72 genes, many relevant to growth and diabetes. In replication studies using similar methodology, many of these differentially methylated regions were associated with levels of maternal glucose exposure below that defined by GDM [the Hyperglycemia and Adverse Pregnancy Outcome (HAPO) study] or were identified as changes observed after randomized periconceptional nutritional supplementation in a Gambian cohort characterized by maternal deprivation. These studies provide support for the concept that similar epigenetic modifications may underpin different prenatal exposures and potentially increase long-term risk for diseases such as type 2 diabetes.

opencc-zeroDec 2015View details →

Data from: Niche width impacts vertebrate diversification

Aim: The size of the climatic niche of a species is a major factor determining its distribution and evolution. In particular, it has been proposed that niche width should be associated with the rate of species diversification. Here, we test whether species niche width affects the speciation and extinction rates of three main clades of vertebrates: amphibians, mammals and birds. Location: Global. Methods: We obtained the time-calibrated phylogenies, IUCN conservation status, species distribution maps and climatic data for 2340 species of amphibians, 4563 species of mammals and 9823 species of birds. We computed the niche width for each species as the mean annual temperature across the species range. We estimated speciation, extinction and transition rates associated with lineages with either narrow (specialist) or wide (generalist) niches using phylogeny-based birth–death models. We also tested if current conservation status was correlated with the niche width of species. Results: We found higher net diversification rates in specialist species than in generalist species. This result was explained by both higher speciation rates (for the three taxonomic groups) and lower extinction rates (for mammals and birds only) in specialist than in generalist species. In contrast, current specialist species tended to be more threatened than generalist species. Main conclusions: Our diversification analysis shows that the width of the climatic niche is strongly associated with diversification rates and may thus be a crucial factor for understanding the emergence of diversity patterns in vertebrates. The striking difference between our diversification results and current conservation status suggests that the current extinction process may be different from extinction rates estimated from the whole history of the group.

opencc-zeroDec 2014View details →

Data from: Feed or fight: testing the impact of food availability and intraspecific aggression on the functional ecology of an island lizard

Body size often varies among insular populations relative to continental conspecifics – the 'island rule' – and functional, context-dependent morphological differences tend to track this body size variation on islands. Two hypotheses are often proposed as potential drivers of insular population differences in morphology: one relating to diet and the other involving intraspecific competition and aggression. We directly tested whether differences in morphology and maximum bite capacity were explained by interisland changes in hardness of both available and consumed prey, and levels of lizard-to-lizard aggression among small-island populations. Our study included 11 islands in the Greek Cyclades and made use of a gradient in island area spanning five orders of magnitude. We focused on the widespread lizard Podarcis erhardii. We found that on smaller islands, P. erhardii body size was larger, head height was larger relative to body size, and maximum bite capacity became proportionally stronger. This pattern in morphology and performance was not related to differences in diet, but was highly correlated with proxies of intraspecific aggression – bite scars and missing toes. Our findings suggest that critical functional traits such as body size and bite force in P. erhardii follow the predictions of the island rule and are changing in response to changes in the competitive landscape across islands of different sizes.

opencc-zeroDec 2014View details →

Data from: Impacts of grazing by different large herbivores in grassland depend on plant species diversity

1. It is well documented that large herbivores have pronounced effects on plant communities in grassland ecosystems, and the extent and course of their effects can largely depend on both plant and herbivore characteristics. Previous studies highlighted the importance of plant productivity in predicting the impact of herbivores on grasslands. Yet, there has been little consideration of how different herbivores affect plant communities that, in turn, differ in plant diversity. 2. In a 2-year grazing experiment, we tested the effects of large herbivores (cattle or sheep, or both together) on plant communities under high and low plant diversity levels in eastern Eurasian steppe. 3. We found that, for high plant diversity grassland, mixed grazing by cattle and sheep significantly increases plant diversity, but we found no effect of grazing by cattle or sheep alone. Grazing by cattle or sheep alone or mixed grazing by cattle and sheep did not significantly affect plant biomass in the high diversity grassland. However, for low plant diversity grassland, grazing by cattle alone and mixed grazing by cattle and sheep significantly increased plant diversity, but significantly decreased plant biomass. There was no significant impact on both plant diversity and biomass from sheep grazing. 4. Synthesis and applications. We conclude that the effects of grazing in grassland strongly depend on herbivore assemblages and pre-grazing plant diversity. Herbivore grazing might contribute more to the maintenance of grassland structure and ecosystem functioning under high plant diversity compared with low plant diversity. Furthermore, our data suggest that multiple-species mixed grazing regimes in grassland systems with high plant diversity could represent the optimal protocol for grazing management. This study emphasizes the importance of maintaining both plant and herbivore diversity to optimize ecosystem functioning.

opencc-zeroDec 2018View details →

Data from: Impact of prey occupancy and other ecological and anthropogenic factors on tiger distribution in Thailand's Western Forest Complex

1. Despite conservation efforts, large mammals such as tigers and their main prey, gaur, banteng, and sambar, are highly threatened and declining across their entire range. The only large viable source population of tigers in mainland Southeast Asia occurs in Thailand's Western Forest Complex (WEFCOM), an approximately 19,000 km2 landscape of 17 contiguous protected areas. 2. We used an occupancy modeling framework, which accounts for imperfect detection, to identify the factors that affect tiger distribution at the approximate scale of a female tiger's home range, 64 km2, and site use at a scale of 1 km2 in WEFCOM. At the larger scale, we estimated the proportion of sites occupied by tigers; at the finer scale, we identified the key variables that influence site-use and developed a predictive distribution map. At both scales, we examined key ecological and anthropogenic factors that help explain distribution and preferred habitat use. 3. WEFCOM is virtually only "half full" of tigers, it occupied 37% or 5,858 km2 of the landscape which was largely influenced by the combined presence of all three large prey species; in contrast, site use was most strongly influenced by presence of sambar. 4. By modeling occupancy while accounting for imperfect probability of detection, we established reliable benchmark data on the distribution of tigers. This study also identified factors that limit tiger distributions; which managers can then target to expand tiger distribution in WEFCOM and guide recovery elsewhere in Southeast Asia.

opencc-zeroDec 2015View details →

Data from: ECOALIM: a dataset of environmental impacts of feed ingredients used in French animal production

Feeds contribute highly to environmental impacts of livestock products. Therefore, formulating low-impact feeds requires data on environmental impacts of feed ingredients with consistent perimeters and methodology for life cycle assessment (LCA). We created the ECOALIM dataset of life cycle inventories (LCIs) and associated impacts of feed ingredients used in animal production in France. It provides several perimeters for LCIs (field gate, storage agency gate, plant gate and harbour gate) with homogeneously collected data from French R&D institutes covering the 2005–2012 period. The dataset of environmental impacts is available as a Microsoft® Excel spreadsheet on the ECOALIM website and provides climate change, acidification, eutrophication, non-renewable and total cumulative energy demand, phosphorus demand, and land occupation. LCIs in the ECOALIM dataset are available in the AGRIBALYSE® database in SimaPro® software. The typology performed on the dataset classified the 149 average feed ingredients into categories of low impact (co-products of plant origin and minerals), high impact (feed-use amino acids, fats and vitamins) and intermediate impact (cereals, oilseeds, oil meals and protein crops). Therefore, the ECOALIM dataset can be used by feed manufacturers and LCA practitioners to investigate formulation of low-impact feeds. It also provides data for environmental evaluation of feeds and animal production systems. Included in AGRIBALYSE® database and SimaPro®, the ECOALIM dataset will benefit from their procedures for maintenance and regular updating. Future use can also include environmental labelling of commercial products from livestock production.

Fig. 4 Latoniaseyfriedi von Meyer, 1843 in New discoveries in the frog Latonia seyfriedi (Anura: Alytidae) and their impact on taxonomy of the genus Latonia

Fig. 4 Latoniaseyfriedi von Meyer, 1843 (TMH 8438): exposed ventral surface of the skull roof. The braincase and palatal portion of skull are broken away

Fig. 1 Latoniaseyfriedi von Meyer, 1843 in New discoveries in the frog Latonia seyfriedi (Anura: Alytidae) and their impact on taxonomy of the genus Latonia

Fig. 1 Latoniaseyfriedi von Meyer, 1843 (specimen NHMUK 42739). Image by permission of the Natural History Museum in London

Fig. 6 in New discoveries in the frog Latonia seyfriedi (Anura: Alytidae) and their impact on taxonomy of the genus Latonia

Fig. 6 Reconstruction of the skull roof in Latonia seyfriedi von Meyer, 1843 in dorsal (a) and ventral (b) views. Based on TMH 8438 (reconstruction courtesy of Paula Muzzopappa)

Fig. 2 in New discoveries in the frog Latonia seyfriedi (Anura: Alytidae) and their impact on taxonomy of the genus Latonia

Fig. 2 Latonia gigantea (Lartet, 1851). a Frontoparietal in dorsal aspect (neotype MNHN Sa 13448); b anterior part of frontoparietal of slightly younger individual in dorsal aspect (MNHN Sa 13489); c posterior part of frontoparietal in young individual (MNHN Sa 13453). All from the Sansan locality. See also Roček (1994: fig. 7a, e, f) and Rage and Hossini (2000: figs. 8, 11)

Fig. 5 Latoniaseyfriedi von Meyer, 1843 in New discoveries in the frog Latonia seyfriedi (Anura: Alytidae) and their impact on taxonomy of the genus Latonia

Fig. 5 Latoniaseyfriedi von Meyer, 1843 (TMH 8438). a, b CT scans of skull roof in dorsal (a) and ventral (b) aspects; c, d frontoparietal in dorsal (c) and ventral (d) aspects (see Roček 1994: fig. 7f); e, f left maxilla in lateral (e) and medial (f) views (see Roček 1994: figs. 9–11); g right maxilla in lateral view; h, i left nasal in dorsal (h) and ventral (i) views; j left squamosal in lateral view (see Roček 1994: pl. 1, fig. 1)

opencc-by-nc-nd-4.0Oct 2015View details →

Supplemental information, code, and data for the MS: Defaunation impacts carbon storage in tropical forests.

# MS_Carbon Supplemental information, code, and data for the MS:  Carolina Bello, Mauro Galetti, Marco A. Pizo, Luiz Fernando S. Magnago, Mariana Ferreira Rocha, Renato A. F. Lima, Carlos A. Peres, Otso Ovaskainen, and Pedro Jordano (2015). Defaunation impacts carbon storage in tropical forests.   *Summary*: Carbon storage is widely acknowledged as one of the most valuable forest ecosystem services. Deforestation, logging, fragmentation and climate change have significant impacts on tropical carbon stocks, however an elusive and yet undetected decrease in carbon storage may be due to defaunation of large seed dispersers. Many large tropical trees with sizeable contributions to carbon stock rely on large vertebrates for seed dispersal and regeneration, yet many of these frugivores are threatened by hunting, illegal trade and habitat loss. We used a large dataset on tree species composition and abundance, seed, fruit and carbon related traits, and plant-animal interactions to estimate the loss of carbon storage capacity of tropical forests in defaunated scenarios. By simulating the local extinction of trees that depend on large frugivores at 31 Atlantic Forest communities, we found that defaunation has the potential to significantly erode carbon storage even when only a small proportion (10%) of large-seeded trees are extirpated.