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opencc-zeroMar 2020View details →

Modelling the impact of antibody-dependent enhancement on disease severity of ZIKV and DENV sequential and co-infection

Human infections with viruses of the genus Flavivirus, including dengue virus (DENV) and Zika virus (ZIKV), are of increasing global importance. Due to antibody dependent enhancement, secondary infection with one Flavivirus following primary infection with another {\it Flavivirus} can result in a significantly larger peak viral load with a much higher risk of severe disease. Although several mathematical models have been developed to quantify the virus dynamics in the primary and secondary infections of DENV, little progress has been made regarding secondary infection of DENV after a primary infection of ZIKV, or DENV-ZIKV co-infection. Here, we address this critical gap by developing compartmental models of virus dynamics. We first fitted the models to published data on dengue viral loads of the primary and secondary infections with the observation that the primary infection reaches its peak much more gradually than the secondary infection. We then quantitatively show that antibody dependent enhancement (ADE) is the key factor determining a sharp increase/decrease of viral load near the peak time in the secondary infection. In comparison, our simulations of DENV and ZIKV co-infection (simultaneous rather than sequential) show that ADE has very limited influence on the peak DENV viral load. This indicates pre-existing immunity to ZIKV is the determinant of a high level of ADE effect. Our numerical simulations show that 1) in the absence of ADE effect, a subsequent co-infection is beneficial to the second virus; 2) if ADE is feasible, then a subsequent co-infection can induce greater damage to the host with a higher peak viral load and a much earlier peak time for the second virus, and for the second peak for the first virus.

opencc-zeroNov 2019View details →

Water availability drives above-ground biomass and bird richness in forest restoration plantings to achieve carbon and biodiversity co-benefits

To combat global warming and biodiversity loss we require effective forest restoration that encourages recovery of species diversity and ecosystem function to deliver essential ecosystem services, such as biomass accumulation. Further, understanding how and where to undertake restoration to achieve carbon sequestration and biodiversity conservation would provide an opportunity to finance ecosystem restoration under carbon markets. We surveyed 30 native mixed-species plantings in subtropical forests and woodlands in Australia, and used structural equation modelling to determine vegetation, soil and climate variables most likely driving above-ground biomass accrual and bird richness, and investigate the relationships between plant diversity, above-ground biomass accrual and bird diversity. We focussed on woodland and forest-dependent birds, and functional groups at risk of decline (insectivorous, understorey-nesting, and small-bodied birds). We found that mean moisture availability strongly limits above-ground biomass accrual and bird richness in restoration plantings, indicating potential synergies in choosing sites for carbon and biodiversity purposes. Counter to theory, woody plant richness was a poor direct predictor of above-ground biomass accrual, but was indirectly related via significant, positive effects of stand density. We also found no direct relationship between above-ground biomass accrual and bird richness, likely because of the strong effects of moisture availability on both variables. Instead, moisture availability and patch size strongly and positively influenced the richness of woodland and forest dependent birds. For understorey-nesting birds, however, shrub cover and patch size predicted richness. Stand age or area of native vegetation surrounding the patch did not influence bird richness. Our results suggest that in subtropical biomes, planting larger patches to higher densities, ideally using a diversity of trees and shrubs (characteristics of ecological plantings) in more mesic locations will enhance the provision of carbon and biodiversity co-benefits. Further, ecological plantings will aid the rapid recovery of woodland and forest bird richness, with comparable above-ground biomass accrual to less diverse forestry plantations.

Data from: Genetic effects of landscape, habitat preference, and demography on three co-occurring turtle species

Expanding the scope of landscape genetics beyond the level of single species can help to reveal how species traits influence responses to environmental change. Multispecies studies are particularly valuable in highly threatened taxa, such as turtles, in which the impacts of anthropogenic change are strongly influenced by interspecific differences in life-history strategies, habitat preferences, and mobility. We sampled approximately 1500 individuals of three co-occurring turtle species across a gradient of habitat change (including varying loss of wetlands and agricultural conversion of upland habitats) in the Midwestern USA. We used genetic clustering and multiple regression methods to identify associations between genetic structure and permanent landscape features, past landscape composition, and landscape change in each species. Two aquatic generalists (the painted turtle, Chrysemys picta, and the snapping turtle Chelydra serpentina) both exhibited population genetic structure consistent with isolation-by-distance, modulated by aquatic landscape features. Genetic divergence for the more terrestrial Blanding's turtle (Emydoidea blandingii), on the other hand, was not strongly associated with geographic distance or aquatic features, and Bayesian clustering analysis indicated that many Emydoidea populations were genetically isolated. Despite long generation times, all three species exhibited associations between genetic structure and post-settlement habitat change, indicating that long generation times may not be sufficient to delay genetic drift resulting from recent habitat fragmentation. The concordances in genetic structure observed between aquatic species, as well as isolation in the endangered, long-lived Emydoidea, reinforce the need to consider both landscape composition and demographic factors in assessing differential responses to habitat change in co-occurring species.

Data from: A genome scan for selection signatures comparing farmed Atlantic salmon with two wild populations: testing co-localization among outlier markers, candidate genes, and QTLs for production traits

Comparative genome scans can be used to identify chromosome regions, but not traits, that are putatively under selection. Identification of targeted traits may be more likely in recently domesticated populations under strong artificial selection for increased production. We used a North American Atlantic salmon 6K SNP dataset to locate genome regions of an aquaculture strain (Saint John River) that were highly diverged from that of its putative wild founder population (Tobique River). First, admixed individuals with partial European ancestry were detected using STRUCTURE and removed from the dataset. Outlier loci were then identified as those showing extreme differentiation between the aquaculture population and the founder population. All Arlequin methods identified an overlapping subset of 17 outlier loci, 3 of which were also identified by BayeScan. Many outlier loci were near candidate genes and some were near published quantitative trait loci (QTLs) for growth, appetite, maturity, or disease-resistance. Parallel comparisons using a wild, non-founder population (Stewiacke River) yielded only one overlapping outlier locus as well as a known maturity QTL. We conclude that genome scans comparing a recently domesticated strain with its wild founder population can facilitate identification of candidate genes for traits known to have been under strong artificial selection.

opencc-zeroDec 2012View details →

Data from: Quantitative genetic divergence and standing genetic (co)variance in thermal reaction norms along latitude

Although the potential to adapt to warmer climate is constrained by genetic trade-offs, our understanding of how selection and mutation shape genetic (co)variances in thermal reaction norms is poor. Using 71 isofemale lines of the fly Sepsis punctum, originating from northern, central and southern European climates, we tested for divergence in juvenile development rate across latitude at five experimental temperatures. To investigate effects of evolutionary history in different climates on standing genetic variation in reaction norms, we further compared genetic (co)variances between regions. Flies were reared on either high or low food resources to explore the role of energy-acquisition in determining genetic trade-offs between different temperatures. Although the latter had only weak effects on the strength and sign of genetic correlations, genetic architecture differed significantly between climatic regions, implying that evolution of reaction norms proceeds via different trajectories at high versus low latitude in this system. Accordingly, regional genetic architecture was correlated to region-specific differentiation. Moreover, hot development temperatures were associated with low genetic variance and stronger genetic correlations compared to cooler temperatures. We discuss the evolutionary potential of thermal reaction norms in light of their underlying genetic architectures, evolutionary histories and the materialization of trade-offs in natural environments.

opencc-zeroMay 2020View details →

Data from: Comparing and co-analysing microsatellite and morphological data for species delimitation in the New Zealand native Myosotis pygmaea species group (Boraginaceae)

Delimiting species boundaries in recent plant radiations can be challenging. The New Zealand native Myosotis pygmaea (Boraginaceae) species group is a case in point. This species complex is of interest as it includes threatened species as well as possibly threatened unnamed putative taxa. Integrative taxonomic approaches using multiple lines of evidence are frequently used to overcome the difficulties of identifying lineages resulting from recent radiations. Here we analyse genotypic data from nearly 500 Myosotis individuals using microsatellite markers, and compare and co-analyse this dataset with previously published morphological data. Within the M. pygmaea group, several genetic clusters can be identified, none of which align exactly with the current taxonomy and morphological variation previously identified. When co-analysing the molecular and morphological data, M. brevis can be distinguished from the remainder of the M. pygmaea species group, but no other species or previously recognised morphological groups are supported. Other groupings within the molecular dataset appear to reflect geographic structure. Within the M. pygmaea species group, the resulting pattern of low within, and high between, population genetic variation is consistent with self-fertilization and low levels of seed dispersal.

opencc-zeroDec 2010View details →

Data from: Occasional males in parthenogenetic populations of Asobara japonica (Hymenoptera: Braconidae): low Wolbachia titer or incomplete co-adaptation?

Wolbachia are endosymbiotic bacteria known to manipulate the reproduction of their hosts. Some populations of the parasitoid wasp Asobara japonica are infected with Wolbachia and reproduce parthenogenetically, while other populations are not infected and reproduce sexually. Wolbachia infected A. japonica females regularly produce small numbers of male offspring. Because all females in the field are infected and infected females are not capable of sexual reproduction, male production seems to be maladaptive. We investigated why these females nevertheless produce males. We tested three hypotheses: high rearing temperatures could result in higher offspring sex ratios (more males), low Wolbachia titer of the mother could lead to higher offspring sex ratios and/or the Wolbachia infection is of relatively recent origin and not enough time has passed to allow complete co-adaptation between Wolbachia and host. Thirty-three percent of the Wolbachia infected females produced males and 56% of these males were also infected with Wolbachia. Neither offspring sex ratio nor male infection frequency were significantly affected by rearing temperature or Wolbachia concentration of the mother. The mitochondrial DNA sequence of one of the uninfected populations was identical to that of two of the infected populations. Therefore, the initial Wolbachia infection of A. japonica must have occurred recently. Mitochondrial sequence variation among infected populations suggests that the spread of Wolbachia through the host populations involved horizontal transmission. We conclude that the occasional male production by Wolbachia infected females is most likely a maladaptive side-effect of incomplete co-evolution between symbiont and host in this relatively young infection.

opencc-zeroMay 2019View details →

Data from: Social group signatures in hummingbird displays provide evidence of co-occurrence of vocal and visual learning

Vocal learning, in which animals modify their vocalizations based on social experience, has evolved in several lineages of mammals and birds, including humans. Despite much attention, the question of how this key cognitive trait has evolved remains unanswered. The motor theory for the origin of vocal learning posits that neural centers specialized for vocal learning arose from adjacent areas in the brain devoted to general motor learning. One prediction of this hypothesis is that visual displays that rely on complex motor patterns may also be learned in taxa with vocal learning. While learning of both spoken and gestural languages is well-documented in humans, the occurrence of learned visual displays has rarely been examined in non-human animals. We tested for geographic variation consistent with learning of visual displays in long-billed hermits (Phaethornis longirostris), a lek-mating hummingbird that, like humans, has both learned vocalizations and elaborate visual displays. We found lek-level signatures in both vocal parameters and visual display features, including element proportions, sequence syntax, and fine-scale parameters of elements. This variation was not associated with genetic differentiation between leks. In the absence of genetic differences, geographic variation in vocal signals at small scales is most parsimoniously attributed to learning, suggesting a significant role of social learning in visual display ontogeny. The co-occurrence of learning in vocal and visual displays would be consistent with a parallel evolution of these two signal modalities in this species.

Data from: Dissecting nutrient-related co-expression networks in phosphate starved poplars

Phosphorus (P) is an essential plant nutrient, but its availability is often limited in soil. Here, we studied changes in the transcriptome and in nutrient element concentrations in leaves and roots of poplars (Populus × canescens) in response to P deficiency. P starvation resulted in decreased concentrations of S and major cations (K, Mg, Ca), in increased concentrations of N, Zn and Al, while C, Fe and Mn were only little affected. In roots and leaves >4,000 and >9,000 genes were differently expressed upon P starvation. These genes clustered in eleven co-expression modules of which seven were correlated with distinct elements in the plant tissues. One module (4.7% of all differentially expressed genes) was strongly correlated with changes in the P concentration in the plant. In this module the GO term "response to P starvation" was enriched with phosphoenolpyruvate carboxylase kinases, phosphatases and pyrophosphatases as well as regulatory domains such as SPX, but no phosphate transporters. The P-related module was also enriched in genes of the functional category "galactolipid synthesis". Galactolipids substitute phospholipids in membranes under P limitation. Two modules, one correlated with C and N and the other with biomass, S and Mg, were connected with the P-related module by co-expression. In these modules GO terms indicating "DNA modification" and "cell division" as well as "defense" and "RNA modification" and "signaling" were enriched; they contained phosphate transporters. Bark storage proteins were among the most strongly upregulated genes in the growth-related module suggesting that N, which could not be used for growth, accumulated in typical storage compounds. In conclusion, weighted gene coexpression network analysis revealed a hierarchical structure of gene clusters, which separated phosphate starvation responses correlated with P tissue concentrations from other gene modules, which most likely represented transcriptional adjustments related to down-stream nutritional changes and stress.

Data from: Biological invasion modifies the co-occurrence patterns of insects along a stress gradient

Biological invasions have become one of the most important drivers of biodiversity loss and ecosystem change world-wide. However, it is still unclear how invasions may interact with local abiotic stressors, which are expected to increase as global change intensifies. Furthermore, we know little about the response to biological invasions of insects, despite their disproportionate contribution to global animal biodiversity. The aim of the present work is to investigate the impact of an invasive aquatic insect on the co-occurrence patterns of native species of insects along a salinity gradient, and determine which assembly rules are driving these patterns. First, we characterised the habitat specialisation and functional niches of each species from physiological and biological traits, respectively, and their degree of overlap. Second, we used field data to compare the co-occurrence patterns of native and invasive species in invaded and non-invaded areas of southern Iberia and northern Morocco. Finally, we tested if habitat filtering or niche differentiation assembly rules mediate their co-occurrence. In non-invaded areas, habitat filtering drives habitat segregation of species along the salinity gradient, with a lower contribution of niche differentiation. The presence of the invasive insect modifies the distribution and co-occurrence patterns of native species. In invaded areas, niche differentiation seems to be the main mechanism to avoid competition among the invasive and native species, enabling coexistence and resource partitioning. The combined study of functional niche similarity and abiotic stressor tolerance of invasive and native species can improve our understanding of the effects of invasive species along abiotic stress gradients. This approach may increase our capacity to predict the outcomes of biological invasion in a global change context.

opencc-zeroDec 2013View details →

Data from: Evolutionary relatedness does not predict competition and co-occurrence in natural or experimental communities of green algae

The competition-relatedness hypothesis (CRH) predicts that the strength of competition is the strongest among closely related species and decreases as species become less related. This hypothesis is based on the assumption that common ancestry causes close relatives to share biological traits that lead to greater ecological similarity. Although intuitively appealing, the extent to which phylogeny can predict competition and co-occurrence among species has only recently been rigorously tested, with mixed results. When studies have failed to support the CRH, critics have pointed out at least three limitations: (i) the use of data poor phylogenies that provide inaccurate estimates of species relatedness, (ii) the use of inappropriate statistical models that fail to detect relationships between relatedness and species interactions amidst nonlinearities and heteroskedastic variances, and (iii) overly simplified laboratory conditions that fail to allow eco-evolutionary relationships to emerge. Here, we address these limitations and find they do not explain why evolutionary relatedness fails to predict the strength of species interactions or probabilities of coexistence among freshwater green algae. First, we construct a new data-rich, transcriptome-based phylogeny of common freshwater green algae that are commonly cultured and used for laboratory experiments. Using this new phylogeny, we re-analyse ecological data from three previously published laboratory experiments. After accounting for the possibility of nonlinearities and heterogeneity of variances across levels of relatedness, we find no relationship between phylogenetic distance and ecological traits. In addition, we show that communities of North American green algae are randomly composed with respect to their evolutionary relationships in 99% of 1077 lakes spanning the continental United States. Together, these analyses result in one of the most comprehensive case studies of how evolutionary history influences species interactions and community assembly in both natural and experimental systems. Our results challenge the generality of the CRH and suggest it may be time to re-evaluate the validity and assumptions of this hypothesis.

opencc-zeroDec 2014View details →

Data from: ENSO and frost co-determine decade-long temporal variation in flower and seed production in a subtropical rain forest

Flower and seed production of plants can be greatly influenced by both natural climatic oscillations and local weather extremes. However, owing to the rarity of long-term monitoring studies conducted at a sufficient temporal scale to capture climatic oscillations and the unpredictability of extreme weather events, evidence that demonstrates how these two external forcings act in concert to drive plant reproduction remains scarce. In addition, considerable variation in species' phenological responses to the external climatic forcings was often observed. Phylogenetic relationships may mediate this inter-specific variation, but previous studies yielded inconsistent results when testing this hypothesis. We monitored the flower and seed production in a subtropical rainforest, Fushan, Taiwan (24°45'N, 121°35'E), for over ten years (since September 2002). In March 2005, a record low temperature (-1.3°C) occurred at Fushan and caused great frost damage to plants. We used weekly phenological records and long-term meteorological data to assess the effects of climatic fluctuations and extreme weather event on plant reproductive output. We show that the El Niño Southern Oscillation (ENSO) indices, which integrated local climatic variables at Fushan over several months, were strongly associated with flower and seed production. The 2005 spring frost also had long-lasting effects on the flower and seed production of several species. In particular, we detected phylogenetic signals in the relationships between phenological responses of flowering production and several climatic variables (maximum temperature, irradiance, and ENSO34 index). By contrast, the relationships between seed production and climatic variables, as well as phenological responses to the frost event, did not exhibit a phylogenetic signal. Synthesis: Our findings add to the growing evidence that together the natural climatic oscillation (ENSO) and the extreme weather event (frost) determined the temporal variation in flower and seed production. In addition, phylogenetically closely related species resembled each other in their flowering responses to abiotic variation in this subtropical rainforest. Improved understanding of these abiotic and biotic interactions may help predicting population- and community-level phenological responses under future climate changes.

Data from: Co-occurrence and hybridization of anther-smut pathogens specialized on Dianthus hosts

Host specialization has important consequences for the diversification and ecological interactions of obligate pathogens. The anther-smut disease of natural plant populations, caused by Microbotryum fungi, has been characterized by specialized host-pathogen interactions, which contribute in part to the isolation among these numerous fungal species. This study investigated the molecular variation of Microbotryum pathogens within the geographic and host-specific distributions on wild Dianthus species in southern European Alps. In contrast to prior studies on this pathogen genus, a range of overlapping host specificities was observed for four delineated Microbotryum lineages on Dianthus hosts, and their frequent co-occurrence within single-host populations was quantified at local and regional scales. In addition to potential consequences for direct pathogen competition, the sympatry of Microbotryum lineages led to hybridization between them in many populations, and these admixed genotypes suffered significant meiotic sterility. Therefore, this investigation of the anther-smut fungi reveals how variation in the degrees of host specificity can have major implications for ecological interactions and genetic integrity of differentiated pathogen lineages.

opencc-zeroDec 2011View details →

Data from: Divergent landscape effects on population connectivity in two co-occurring amphibian species

The physical and environmental attributes of landscapes often shape patterns of population connectivity by influencing dispersal and gene flow. Landscape effects on movement are typically evaluated for single species. However, inferences from multiple species are required for multi-species management strategies increasingly being applied in conservation. In this study, I compared the spatial genetic patterns of two amphibian species across the northeastern U.S. and estimated the influence of specific landscape features on observed genetic patterns. The spotted salamander (Ambystoma maculatum) and wood frog (Rana sylvatica) share many ecological attributes related to habitat use, phenology and site fidelity. However, I hypothesized that important differences in their movement patterns and life history would create distinct genetic patterns for each species. Using 14 microsatellite loci, I tested for differences in the level of genetic differentiation between the two species across 22 breeding ponds. The effects of eight landscape features were also estimated by evaluating 32 landscape resistance models. Spotted salamanders exhibited significantly higher genetic differentiation than wood frogs. Different landscape features were also identified as potential drivers of the genetic patterns in each species, with little overlap in model support between species. Collectively, these results provide strong evidence that these two amphibian species interact with the landscape in measurably different ways. The distinct genetic patterns observed are consistent with key differences in movement ability and life history between A. maculatum and R. sylvatica. These results highlight the importance of considering more than one species when assessing the impacts of the landscape matrix on population connectivity, even for ecologically similar species within the same habitats.

opencc-zeroOct 2019View details →

Fire refugia facilitate forest and savanna co‐existence as alternative stable states

Aim: Does complex topography facilitate the establishment and persistence of fire‐ sensitive (forest) vegetation in a fire‐prone landscape? We test the prediction that fire‐sensitive vegetation will establish and persist in areas where the fire return interval is lower due to a topographic hindrance on fire spread. Location: Hluhluwe–iMfolozi Park, KwaZulu Natal, South Africa. Methods: Using aerial photographs from six time periods between 1937 and 2013, we mapped vegetation changes in Hluhluwe–iMfolozi Park (HiP). Using a general‐ ized additive model (GAM), we built a habitat suitability index (HSI) map for forest vegetation based on topographic variables related to fire behaviour and the vegeta‐ tion distribution maps from each time period. We investigated transitions between vegetation types between time periods based on the HSI map, as well as the effects of neighbourhood vegetation on transition probabilities. Results: Forest cover has increased overall from 1937 to 2013, however, this has not been a linear increase with a peak in extent in the early 1990s. The HSI, using topo‐ graphic predictors associated with fire behaviour, correlates with areas of expansion and contraction of forest vegetation. The patterns of expansion and contraction are, however, more nuanced, with the in situ vegetation neighbourhood playing a large role. Main Conclusions: Forest distributions in HiP have not remained static over time and have expanded into areas that were once savannas. This is a dynamic system where both forest and savanna boundaries can change considerably. Fire refugia are impor‐ tant for the long‐term persistence of forests in fire‐prone landscapes.

Data from: Biogeographic barriers drive co-diversification within associated eukaryotes of the Sarracenia alata pitcher plant system

Understanding if the members of an ecological community have co-diversified is a central concern of evolutionary biology, as co-diversification suggests prolonged association and possible coevolution. By sampling associated species from an ecosystem, researchers can better understand how abiotic and biotic factors influence diversification in a region. In particular, studies of co-distributed species that interact ecologically can allow us to disentangle the effect of how historical processes have helped shape community level structure and interactions. Here we investigate the Sarracenia alata pitcher plant system, an ecological community where many species from disparate taxonomic groups live inside the fluid-filled pitcher leaves. Direct sequencing of the eukaryotes present in the pitcher plant fluid enables us to better understand how a host plant can shape and contribute to the genetic structure of its associated inquilines, and to ask whether genetic variation in the taxa are structured in a similar manner to the host plant. We used 454 amplicon-based metagenomics to demonstrate that the pattern of genetic diversity in many, but not all, of the eukaryotic community is similar to that of S. alata, providing evidence that associated eukaryotes share an evolutionary history with the host pitcher plant. Our work provides further evidence that a host plant can influence the evolution of its associated commensals.

Data from: Disentangling biotic interactions, environmental filters, and dispersal limitation as drivers of species co-occurrence

A key focus in ecology is to search for community assembly rules. Here we compare two community modelling frameworks that integrate a combination of environmental and spatial data to identify positive and negative species associations from presence-absence matrices, and incorporate an additional comparison using joint species distribution models (JSDM). The frameworks use a dichotomous logic tree that distinguishes dispersal limitation, environmental requirements, and interspecific interactions as causes of segregated or aggregated species pairs. The first framework is based on a classical null model analysis complemented by tests of spatial arrangement and environmental characteristics of the sites occupied by the members of each species pair (Classic framework). The second framework, (SDM framework) implemented here for the first time, builds on the application of environmentally-constrained null models (or JSDMs) to partial out the influence of the environment, and includes an analysis of the geographical configuration of species ranges to account for dispersal effects. We applied these approaches to examine plot-level species co-occurrence in plant communities sampled along a wide elevation gradient in the Swiss Alps. According to the frameworks, the majority of species pairs were randomly associated, and most of the non-random positive and negative species associations could be attributed to environmental filtering and/or dispersal limitation. These patterns were partly detected also with JSDM. Biotic interactions were detected more frequently in the SDM framework, and by JSDM, than in the Classic framework. All approaches detected species aggregation more often than segregation, perhaps reflecting the important role of facilitation in stressful high-elevation environments. Differences between the frameworks may reflect the explicit incorporation of elevational segregation in the SDM framework and the sensitivity of JSDM to the environmental data. Nevertheless, all methods have the potential to reveal general patterns of species co-occurrence for different taxa, spatial scales, and environmental conditions.

opencc-zeroMay 2020View details →

Data from: Co-introduction of native mycorrhizal fungi and plant seeds accelerates restoration of post-mining landscapes

1. Grasslands are among the most threatened terrestrial biomes, and habitat conservation alone will be insufficient to meet biodiversity goals. While restoration of indigenous grasslands is a priority, conflict with economic objectives means that incorporation of alternative habitats is necessary to offset grassland loss. With up to 800,000 km² of land affected by mining globally, there is an opportunity to create additional grassland habitat in post-mining landscapes. 2. We aimed to assess whether co-introduction of native arbuscular mycorrhizal (AM) fungi and plants is an efficient means of initializing species rich vegetation recovery in barren post-mining landscapes. We established an experiment in three post-mining areas in Estonia, where we seeded plots with native plant seeds and inoculated them with trap cultured native AM fungi from a similar habitat. We measured the abundance and composition of soil AM fungal and aboveground plant communities in two consecutive years using relevés, high-throughput sequencing and fatty acid profiling. 3. Our results demonstrate that co-introduction of native plants and AM fungi is an effective way to establish species rich vegetation in post-mining areas. Co-introduction of symbiotic partners resulted in higher richness, diversity and abundance of plants and AM fungi than when either partner was introduced individually. However, the plant and AM fungal communities in sown and inoculated plots were not distinct from those in uninoculated treatments; they rather formed a subset of all taxa present on the sites but exhibited higher diversity than uninoculated plots. 4. Synthesis and applications: This study shows that managing the below-ground microbiome is an essential part of vegetation restoration. The availability of symbiotic partners can be considered a key aspect determining the diversity of restored vegetation. Targeted inoculations with native and habitat-specific AM fungi could therefore increase restoration success.28-Apr-2020

opencc-zeroJul 2019View details →

Data from: Co-declining mammal-dung beetle faunas throughout the Atlantic Forest biome of South America

The millennial-scale evolutionary relationships between mammals and dung beetles have been eroded due to several drivers of contemporary biodiversity loss. Although some evidence of co-decline has been shown for mammals and dung beetles at some Neotropical sites, a biome-scale analysis for the entire Atlantic Forest of South America would strengthen our understanding of how relictual sets of mammal species can affect dung beetle co-occurrences and co-declines. We therefore collated hundreds of assemblages of both dung beetles and medium- to large-bodied mammals throughout the world's longest tropical forest latitudinal gradient to examine to what extent mammal assemblages may exert a positive influence on dung beetle species composition and functional assembly, and whether this relationship is scale dependent. We also collated several climatic and other environmental variables to examine the degree to which they shape mammal-dung beetle relationships. The relationships between local mammal and dung beetle faunas were examined using regression models, variation partitioning, dissimilarity indices, and ecological networks. We found a clear positive relationship between mammal and dung beetle species richness across this forest biome, indicating an ongoing process of mammal-dung beetle niche-mediated co-decline. We found a strong relationship between the species composition of both taxa, in which dung beetle species dissimilarity apparently track changes in mammalian dissimilarity, typically in 80% of all cases. Co-variables such as phytomass and climatic variables also influenced mammal-dung beetle patterns of co-decline along the Atlantic Forest. We conclude that dung beetle diversity and community assembly are shaped by the remaining co-occurring mammal assemblages and their functional traits, and both groups were governed by environmental features. We emphasize that ecosystem-wide effects of mammal population declines remain poorly understood both quantitatively and qualitatively, and curbing large vertebrate defaunation will ensure the persistence of co-dependent species.

Data from: Phylogeographic concordance factors quantify phylogeographic congruence among co-distributed species in the Sarracenia alata pitcher plant system

Comparative phylogeographic investigations have identified congruent phylogeographic breaks in co-distributed species in nearly every region of the world. The qualitative assessments of phylogeographic patterns traditionally used to identify such breaks, however, are limited because they rely on identifying monophyletic groups across species and do not account for coalescent stochasticity. Only long-standing phylogeographic breaks are likely to be obvious; many species could have had a concerted response to more recent landscape events, yet possess subtle signs of phylogeographic congruence because ancestral polymorphism has not completely sorted. Here we introduce Phylogeographic Concordance Factors (PCFs), a novel method for quantifying phylogeographic congruence across species. We apply this method to the Sarracenia alata pitcher plant system, a carnivorous plant with a diverse array of commensal organisms. We explore whether a group of ecologically associated arthropods have co-diversified with the host pitcher plant, and identify if there is a positive correlation between ecological interaction and PCFs. Results demonstrate that multiple arthropods share congruent phylogeographic breaks with S. alata, and provide evidence that the level of ecological association can be used to predict the degree of similarity in the phylogeographic pattern. This study outlines an approach for quantifying phylogeographic congruence, a central concept in biogeographic research.