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opencc-zeroJan 2021View details →

Data from: Changes in soil microbial communities in post mine ecological restoration: implications for monitoring using high throughput DNA sequencing

The ecological restoration of ecosystem services and biodiversity is a key intervention used to reverse the impacts of anthropogenic activities such as mining. Assessment of the performance of restoration against completion criteria relies on biodiversity monitoring. However, monitoring usually overlooks soil microbial communities (SMC), despite increased awareness of their pivotal role in many ecological functions. Recent advances in cost, scalability and technology has led to DNA sequencing being considered as a cost-effective biological monitoring tool, particularly for otherwise difficult to survey groups such as microbes. However, such approaches for monitoring complex restoration sites such as post-mined landscapes have not yet been tested. Here we examine bacterial and fungal communities across chronosequences of mine site restoration at three locations in Western Australia to determine if there are consistent changes in SMC diversity, community composition and functional capacity. Although we detected directional changes in community composition indicative of microbial recovery, these were inconsistent between locations and microbial taxa (bacteria or fungi). Assessing functional diversity provided greater understanding of changes in site conditions and microbial recovery than could be determined through assessment of community composition alone. These results demonstrate that high-throughput amplicon sequencing of environmental DNA (eDNA) is an effective approach for monitoring the complex changes in SMC following restoration. Future monitoring of mine site restoration using eDNA should consider archiving samples to provide improved understanding of changes in communities over time. Expansion to include other biological groups (e.g. soil fauna) and substrates would also provide a more holistic understanding of biodiversity recovery.

Data from: Reconstructing long-term human impacts on plant communities: an ecological approach based on lake sediment DNA

Paleoenvironmental studies are essential to understand biodiversity changes over long timescales and to assess the relative importance of anthropogenic and environmental factors. Sedimentary ancient DNA (sedaDNA) is an emerging tool in the field of paleoecology and has proven to be a complementary approach to the use of pollen and macroremains for investigating past community changes. SedaDNA-based reconstructions of ancient environments often rely on indicator taxa or expert knowledge, but quantitative ecological analyses might provide more objective information. Here, we analysed sedaDNA to investigate plant community trajectories in the catchment of a high-elevation lake in the Alps over the last 6400 years. We combined data on past and present plant species assemblages along with sedimentological and geochemical records to assess the relative impact of human activities through pastoralism, and abiotic factors (temperature and soil evolution). Over the last 6400 years, we identified significant variation in plant communities, mostly related to soil evolution and pastoral activities. An abrupt vegetational change corresponding to the establishment of an agropastoral landscape was detected during the Late Holocene, approximately 4500 years ago, with the replacement of mountain forests and tall-herb communities by heathlands and grazed lands. Our results highlight the importance of anthropogenic activities in mountain areas for the long-term evolution of local plant assemblages. SedaDNA data, associated with other paleoenvironmental proxies and present plant assemblages, appear to be a relevant tool for reconstruction of plant cover history. Their integration, in conjunction with classical tools, offers interesting perspectives for a better understanding of long-term ecosystem dynamics under the influence of human-induced and environmental drivers.

opencc-zeroDec 2015View details →

Data from: Ecological and evolutionary diversification within the genus Carex (Cyperaceae): consequences for community assembly in subarctic fens

The concept of limiting similarity predicts that closely related taxa are less likely to co-occur than expected by chance. The degree to which the phylogenetic relatedness in plant communities is in accord with limiting similarity has been little tested at the scale where the consequences of adaptive differentiation during speciation should be most evident: the scale of neighboring, congeneric plants within a community. To quantify species co-occurrence patterns in relation to environment, we sampled sedge species, their rooting level relative to the water table, and the water pH in 2,124 0.25 m² quadrats distributed across 29 subarctic fens in the central Labrador Peninsula. We estimated phylogenetic relationships using four DNA regions (ETS, ITS, matK, trnL-trnF) for all species of Carex (42), Eriophorum (6), and Trichophorum (2) in the region, of which 21, four, and two, respectively, occurred in the sampled fens. We demonstrate that closely related species of Carex are less likely to co-occur than expected by chance using 1) a probabilistic method to test the significance of pairwise co-occurrence patterns of species, and 2) linear mixed modeling to relate these patterns to phylogenetic relationships and ecological tolerances along gradients of substrate pH and rooting level in relation to the water table. The results also indicate that suites of species with significant mutual pairwise co-occurrence belong to distant lineages within the Cariceae-Dulichieae-Scirpeae clade of Cyperaceae and have stabilizing niche differences. We suggest that niche differentiation during the evolution and diversification of a clade of wetland Carex species over the past few million years, especially during the dynamic glacial cycles of the Pleistocene, has resulted in diverse sedge communities that share space and resources in harsh northern peatland habitats.

opencc-zeroDec 2010View details →

Data from: Ecological incumbency impedes stochastic community assembly in Holocene foraminifera from the Huon Peninsula, Papua New Guinea

Persistence in the structure of ecological communities can be predicted both by deterministic and by stochastic theory. Evaluating ecological patterns against the neutral theory of biodiversity provides an appropriate methodology for differentiating between these alternatives. We traced the history of benthic foraminiferal communities from the Huon Peninsula, Papua New Guinea. From the well-preserved uplifted reef terrace at Bonah River we reconstructed the benthic foraminiferal communities during a 2200-year period (9000–6800 yr B.P.) of reef building during the Holocene transgressive sea-level rise. We found that the similarity of foraminiferal communities was consistently above 60%, even when comparing communities on either side of a massive volcanic eruption that smothered the existing reef system with ash. Similarly, species diversity and rank dominance were unchanged through time. However, similarity dropped dramatically in the final stages of reef growth, when accommodation space was reduced as sea-level rise slowed. We compared the community inertia index (CII) computed from the observed species abundances with that predicted from neutral theory. Despite the differences in foraminiferal community composition in the younger part of the reef sequence, we found an overall greater degree of community inertia with less variance in observed communities than was predicted from neutral theory, regardless of foraminiferal community size or species migration rate. Thus, persistent species assemblages could not be ascribed to neutral predictions. Ecological incumbency of established foraminiferal species likely prevented stochastic increases in both migrant and rare taxa at the Bonah River site. Regardless of the structuring mechanisms, our reconstruction of Holocene foraminiferal assemblages provides historical context for the management and potential restoration of degraded species assemblages.

Data from: Abundance inequality in freshwater communities has an ecological origin

The hollow-shaped species abundance distribution (SAD) and its allied rank abundance distribution (RAD)—showing that abundance is unevenly distributed among species—are some of the most studied patterns in ecology. To explain the nature of abundance inequality, I developed a novel framework identifying environmental favorability, which controls the balance between reproduction and immigration, as the ultimate source and species stress tolerance as a proximate factor. Thus, under harsh conditions, only a few tolerant species can reproduce, while some sensitive species can be present in low numbers due to chance immigration. This would lead to high abundance inequality between the two groups of species. Under benign conditions, both groups can reproduce and give rise to higher abundance equality. To test these ideas, I examined the variability in the parameters of a Poisson lognormal fit of the SAD and a square root fit of the RAD in diatom and fish communities across US streams. Indeed, as environmental favorability increased, more sensitive forms were able to establish large populations, diminishing the abundance disparity between locally common and rare species. Finally, it was demonstrated that in diatoms, the RAD belonged to the same family of relationships as those of population density with body size and regional distribution.

opencc-zeroFeb 2020View details →

Community science validates climate suitability projections from ecological niche modeling

Climate change poses an intensifying threat to many bird species, and projections of future climate suitability provide insight into how species may shift their distributions in response. Climate suitability is characterized using ecological niche models (ENMs), which correlate species occurrence data with current environmental covariates and project future distributions using the modeled relationships together with climate predictions. Despite their widespread adoption, ENMs rely on several assumptions that are rarely validated in situ and can be highly sensitive to modeling decisions, precluding their reliability in conservation decision-making. Using data from a novel, large-scale community science program, we developed dynamic occupancy models to validate near-term climate suitability projections for bluebirds and nuthatches in summer and winter. We estimated occupancy, colonization, and extinction dynamics across species' ranges in the United States in relation to projected climate suitability in the 2020s, and used a Gibbs variable selection approach to quantify evidence of species-climate relationships. We also included a Bird Conservation Region strata-level random effect to examine among-strata variation in occupancy that may be attributable to land-use and ecoregional differences. Across species and seasons, we found strong evidence that initial occupancy and colonization were positively related to 2020 climate suitability, illustrating an independent validation of projections from ENMs across a large geographic area. Random strata effects revealed that occupancy probabilities were generally higher than average in core areas and lower than average in peripheral areas of species' ranges, and served as a first step in identifying spatial patterns of occupancy from these community science data. Our findings lend much-needed support to the use of ENM projections for addressing questions about potential climate-induced changes in species' occupancy dynamics. More broadly, our work highlights the value of community scientist observations for ground-truthing projections from statistical models and for refining our understanding of the processes shaping species' distributions under a changing climate.

opencc-zeroDec 2010View details →

Data from: Adaptive radiation and ecological opportunity in Sulawesi and Philippine fanged frog (Limnonectes) communities.

Because island communities are derived from the mainland, they are often less diverse by comparison. However, reduced complexity of island communities can also present ecological opportunities. For example, amphibian diversity on the Indonesian island of Sulawesi is generally lower than in the Philippines, but this island supports a surprisingly diverse endemic assemblage of Sulawesi fanged frogs (genus Limnonectes). To explore evolutionary dynamics of this system, we examined molecular, morphological, and geographical variation of fanged frogs from these two regions. Using genealogical concordance – a conservative standard – we identified 12 species on Sulawesi, only four of which are described. One more species can be distinguished with morphology, and a Bayesian approach to species delimitation suggests our total species estimate on Sulawesi (n = 13) is still an underestimate. After accounting for evolutionary history, a model with multiple body size optima in sympatric Limnonectes species is significantly preferred over a "random walk" model where body size evolves by Brownian motion. Additionally, morphological variation is higher among sympatric than non-sympatric species on Sulawesi, but not in the Philippines. Taken together, these findings suggest that adaptive radiation of fanged frogs on Sulawesi was driven by natural selection to infiltrate ecological niches occupied by other lineages in the Philippines. Our study supports the concept of ecological opportunity in community assembly: diversification in mature communities, such as the Philippines, is limited by a dearth of unoccupied ecological niches. On Sulawesi however, evolutionary novelties originated in a predictable and replicated fashion in response to opportunities presented by a depauperate ancestral community.

opencc-zeroDec 2012View details →

Data from: How to characterize chemical exposure to predict ecologic effects on aquatic communities?

Reliable characterization of exposure is indispensable for ecological risk assessment of chemicals. To deal with mixtures, several approaches have been developed, but their relevance for predicting ecological effects on communities in the field has not been elucidated. In the present study, we compared nine metrics designed for estimating the total toxicity of mixtures regarding their relationship with an effect metric for stream macroinvertebrates. This was done using monitoring data of biota and organic chemicals, mainly pesticides, from five studies comprising 102 streams in several regions of Europe and South-East Australia. Mixtures of less than 10 pesticides per water sample were most common for concurrent exposure. Exposure metrics based on the 5% fraction of a species sensitivity distribution performed best, closely followed by metrics based on the most sensitive species and Daphnia magna as benchmark. Considering only the compound with the highest toxicity and ignoring mixture toxicity was sufficient to estimate toxicity in predominantly agricultural regions with pesticide exposure. The multisubstance Potentially Affected Fraction (msPAF) that combines concentration and response addition was advantageous in the study where further organic toxicants occurred. We give recommendations on exposure metric selection depending on data availability and the involved compounds.

opencc-zeroDec 2015View details →

Data from: Using camera trapping and hierarchical occupancy modelling to evaluate the spatial ecology of an African mammal community

Emerging conservation paradigms have shifted from single to multi-species approaches focused on sustaining biodiversity. Multi-species hierarchical occupancy modelling provides a method for assessing biodiversity while accounting for multiple sources of uncertainty. We analysed camera trapping data with multi-species models using a Bayesian approach to estimate the distributions of a terrestrial mammal community in northern Botswana and evaluate community, group, and species-specific responses to human disturbance and environmental variables. Groupings were based on two life-history traits: body size (small, medium, large and extra-large) and diet (carnivore, omnivore and herbivore). We photographed 44 species of mammals over 6607 trap nights. Camera station-specific estimates of species richness ranged from 8 to 27 unique species, and species had a mean occurrence probability of 0·32 (95% credible interval = 0·21–0·45). At the community level, our model revealed species richness was generally greatest in floodplains and grasslands and with increasing distances into protected wildlife areas. Variation among species' responses was explained in part by our species groupings. The positive influence of protected areas was strongest for extra-large species and herbivores, while medium-sized species actually increased in the non-protected areas. The positive effect of grassland/floodplain cover, alternatively, was strongest for large species and carnivores and weakest for small species and herbivores, suggesting herbivore diversity is promoted by habitat heterogeneity. Synthesis and applications. Our results highlight the importance of protected areas and grasslands in maintaining biodiversity in southern Africa. We demonstrate the utility of hierarchical Bayesian models for assessing community, group and individual species' responses to anthropogenic and environmental variables. This framework can be used to map areas of high conservation value and predict impacts of land-use change. Our approach is particularly applicable to the growing number of camera trap studies world-wide, and we suggest broader application globally will likely result in reduced costs, improved efficiency and increased knowledge of wildlife communities.

opencc-zeroJul 2019View details →

Data from: Cross-scale dynamics in community and disease ecology: relative timescales shape the community ecology of pathogens

Communities of free-living organisms are shaped by processes operating within and among patches of habitat, while pathogen communities are shaped by analogous processes operating within and among hosts. Resource competition (R) theory can describe dynamics within patches or hosts, while metacommunity dynamics describe competition-colonization tradeoffs, extinction debts, and superinfection. However, models at this broader scale often assume instantaneous competitive exclusion in co-inhabited patches or coinfected hosts. Impacts of more gradual competitive exclusion on the abundance, distribution, and diversity of species are less clear. Here, we nest a general resource competition model within a metacommunity framework and manipulate the relative timescales for processes operating within and among patches/hosts. We focus on superinfection in pathogen communities. We compare cases where transmission depends on infection prevalence versus the abundance of pathogens within hosts. Surprisingly, slowing the relative pace of competitive exclusion within hosts can decrease infection prevalence of the inferior competitor and increase prevalence of the superior competitor, depending on transmission and virulence. Slower dynamics reduce the abundance of both pathogens within hosts and promote diversity at multiple scales: coinfections within individual hosts and co-occurrence in the host population. These results highlight surprising feedbacks that can emerge across scales and reinforce the rich cross-scale connections between community and disease ecology.

Data from: Extreme ecological response of a seabird community to unprecedented sea ice cover

Climate change has been predicted to reduce Antarctic sea ice but, instead, sea ice surrounding Antarctica has expanded over the past 30 years, albeit with contrasted regional changes. Here we report a recent extreme event in sea ice conditions in East Antarctica and investigate its consequences on a seabird community. In early 2014, the Dumont d'Urville Sea experienced the highest magnitude sea ice cover (76.8%) event on record (1982–2013: range 11.3–65.3%; mean±95% confidence interval: 27.7% (23.1–32.2%)). Catastrophic effects were detected in the breeding output of all sympatric seabird species, with a total failure for two species. These results provide a new view crucial to predictive models of species abundance and distribution as to how extreme sea ice events might impact an entire community of top predators in polar marine ecosystems in a context of expanding sea ice in eastern Antarctica.

opencc-zeroDec 2017View details →

Data from: Population density and size influence pollen dispersal pattern and mating system of the predominantly outcrossed Banksia nivea (Proteaceae) in a threatened ecological community

Gene flow is a critical component of plant mating systems and influences population fitness, yet pollen dispersal can be highly variable and influenced by natural and anthropogenic fragmentation. Gene flow through pollen dispersal was investigated in two populations of contrasting size and habitat context in Banksia nivea ssp. uliginosa, a rare species in the Busselton ironstone threatened ecological community with a naturally fragmented distribution. Paternity analysis was conducted with seven microsatellite loci to determine mating system parameters and patterns of pollen dispersal. Outcrossing was high in both populations with a similar level of selfing for both populations despite differences in population size, density and vegetation matrix. Most mating occurred within 10 m of a mother plant in the small, clumped population, while more dispersed mating, up to 50 m from a mother plant, was recorded in the large, less dense population. Our results show that population density and size are important influences on mating system parameters and level of pollen dispersal.

Data from: Validating the power of mitochondrial metagenomics for community ecology and phylogenetics of complex assemblages

1. The biodiversity of mixed-species samples of arthropods can be characterized by shotgun sequencing of bulk genomic DNA and subsequent bioinformatics assembly of mitochondrial genomes. Here, we tested the power of mitochondrial metagenomics by conducting Illumina sequencing on mixtures of >2600 individuals of leaf beetles (Chrysomelidae) from 10 communities. 2. Patterns of species richness, community dissimilarity and biomass were assessed from matches of reads against three reference databases, including (i) a custom set of mitogenomes generated for 156 species (89% of species in the study); (ii) mitogenomes obtained by the de novo assembly of sequence reads from the real-world communities; and (iii) a custom set of DNA barcode (cox1-5′) sequences. 3. Species detection against the custom-built reference genomes was very high (>90%). False presences were rare against mitogenomes but slightly higher against the barcode references. False absences were mainly due to the incompleteness of the reference databases and, thus, more prevalent in the de novo data set. Biomass (abundance × body length) and read numbers were strongly correlated, demonstrating the potential of mitochondrial metagenomics for studies of species abundance. 4. A phylogenetic tree from the mitogenomes showed high congruence with known relationships in Chrysomelidae. Patterns of taxonomic and phylogenetic dissimilarity between sites were highly consistent with data from morphological identifications. 5. The power of mitochondrial metagenomics results from the possibility of rapid assembly of mitogenomes from mixtures of specimens and the use of read counts for accurate estimates of key parameters of biodiversity directly from community samples.

opencc-zeroDec 2016View details →

Data from: Ants as ecological indicators of rainforest restoration: community convergence and the development of an Ant Forest Indicator Index in the Australian wet tropics

Ecosystem restoration can help reverse biodiversity loss, but whether faunal communities of forests undergoing restoration converge with those of primary forest over time remains contentious. There is a need to develop faunal indicators of restoration success that more comprehensively reflect changes in biodiversity and ecosystem function. Ants are an ecologically dominant faunal group and are widely advocated as ecological indicators. We examine ant species and functional group responses on a chronosequence of rainforest restoration in northern Australia, and develop a novel method for selecting and using indicator species. Four sampling techniques were used to survey ants at 48 sites, from grassland, through various ages (1–24 years) of restoration plantings, to mature forest. From principal components analysis of seven vegetation metrics, we derived a Forest Development Index (FDI) of vegetation change along the chronosequence. A novel Ant Forest Indicator Index (AFII), based on the occurrences of ten key indicator species associated with either grassland or mature forest, was used to assess ant community change with forest restoration. Grasslands and mature forests supported compositionally distinct ant communities at both species and functional levels. The AFII was strongly correlated with forest development (FDI). At forest restoration sites older than 5–10 years that had a relatively closed canopy, ant communities converged on those of mature rainforest, indicating a promising restoration trajectory for fauna as well as plants. Our findings reinforce the utility of ants as ecological indicators and emphasize the importance of restoration methods that achieve rapid closed-canopy conditions. The novel AFII assessed restoration status from diverse and patchily distributed species, closely tracking ant community succession using comprehensive species-level data. It has wide applicability for assessing forest restoration in a way that is relatively independent of sampling methodology and intensity, and without a need for new comparative data from reference sites.

openOct 2023View details →

Data, Metadata, R-codes and R data files for publication "Comparative ungulate diversity and biomass change with human use and drought: implications for community stability and protected area prioritization in African savannas" by Bartzke et al. in Ecology and Evolution

These files contain data and metadata for modeling ungulate diversity and biomass in the Maasai Mara ecosystem in Kenya in the drought year of 1999 and a year with normal rainfall, 2002. The files also contain R codes and R data files. Metadata.pdf: Metadata for files "mc_333m.csv" and "mc_1km.csv" mc_333m.csv: A data file for 333-meter-by-333-meter sub-blocks. prepare_data.r: R code to impute missing vegetation records in 333-meter-by-333-meter subblocks and summarize the data over 1-kilometer-by-1-kilometer blocks for analysis. krige_vegetation.RData: An R data file containing the imputed vegetation records. mc_1km.csv: A data file for 1-kilometer-by-1-kilometer blocks for analysis. mc_1km.r: R code for modeling ungulate diversity and biomass; mc_1km_mod.RData: An R data file for loading the ungulate diversity and biomass models. mc_1km.RData: An R data file containing model predictions of ungulate diversity and biomass. mc_1km_plots.r: R code for plotting model predictions of ungulate diversity and biomass. MMNR_boundary.shp: A shapefile of the Maasai Mara National Reserve boundary in Kenya and associated files. These files are used for plotting the predictions of ungulate diversity and biomass. MMNR_border.zip: A shapefile and associated files for the Maasai Mara National Reserve border with Tanzania. These files are also used for plotting predictions of ungulate diversity and biomass.

Figure 8 in Variation in a Darwin Wasp (Hymenoptera: Ichneumonidae) Community along an Elevation Gradient in a Tropical Biodiversity Hotspot: Implications for Ecology and Conservation

Figure 8. Vegetation predictors of the pimpline community across traps (n = 30). (a) Epiphyte density against log richness; (b) herb ground cover against the log of inverse Simpson's Index of Diversity;

Figure 7 in Variation in a Darwin Wasp (Hymenoptera: Ichneumonidae) Community along an Elevation Gradient in a Tropical Biodiversity Hotspot: Implications for Ecology and Conservation

Figure 7. Pimplinae community composition, as measured by the first axis of a Non-Metric Multidimensional Scaling analysis (NMDS1, see Figure 6) across sampling sites (n = 15), against the first Principal Component (PC1) of the habitat variables at those sites (see Table 4). The line is the linear regression (±95% CI in gray). The figure demonstrates that pimpline community composition is very strongly associated with differences in habitat characteristics across sites.

Figure 6 in Variation in a Darwin Wasp (Hymenoptera: Ichneumonidae) Community along an Elevation Gradient in a Tropical Biodiversity Hotspot: Implications for Ecology and Conservation

Figure 6. An ordination using Non-metric Multidimensional Scaling (NMDS) of the pimpline community at the site level. Black numbers and points indicate the 15 sampling sites, going from the bottom of the mountain (1) to the top (15). Species are in gray, small lettering.

Figure 4 in Variation in a Darwin Wasp (Hymenoptera: Ichneumonidae) Community along an Elevation Gradient in a Tropical Biodiversity Hotspot: Implications for Ecology and Conservation

Figure 4. Pimplinae wasp community metrics against elevation (altitude) across 30 traps. (a) Abundance; (b) Log10 Species Richness; (c) Log10 Simpson's Index (1/D); and (d) Shannon Index. Lines are the equations of the polynomial linear model in Table 2 with the lowest AICc, ±95%CI; (a,b): cubic models (c,d): quadratic models.

Figure 2 in Variation in a Darwin Wasp (Hymenoptera: Ichneumonidae) Community along an Elevation Gradient in a Tropical Biodiversity Hotspot: Implications for Ecology and Conservation

Figure 2. Some of the Pimplinae wasp species sampled (all are females). (a) Dolichomitus megalourus (scale bar 4 mm), 10 individuals sampled; (b) Neotheronia charli (scale bar 1 mm), 24 individuals sampled; (c) Neotheronia sp. 6 (scale bar 1 mm), 26 individuals sampled; (d) Pimpla caerulea (scale bar 1 mm), 447 individuals sampled; (e) Polysphincta organensis (scale bar 2 mm), 19 individuals sampled; and (f) Polysphincta teresa (scale bar 2 mm), 8 individuals sampled.