Species interactions weakly modify climate‐induced tree co‐occurrence patterns

Aims

Species distributions are hypothesized to be underlain by a complex association of processes that span multiple spatial scales including biotic interactions, dispersal limitation, fine‐scale resource gradients and climate. Species disequilibrium with climate may reflect the effects of non‐climatic processes on species distributions, yet distribution models have rarely directly considered non‐climatic processes. Here, we use a Joint Species Distribution Model (JSDM) to investigate the influence of non‐climatic factors on species co‐occurrence patterns and to directly quantify the relative influences of climate and alternative processes that may generate correlated responses in species distributions, such as species interactions, on tree co‐occurrence patterns.

Location

US Rocky Mountains.

Methods

We apply a Bayesian JSDM to simultaneously model the co‐occurrence patterns of ten dominant tree species across the Rocky Mountains, and evaluate climatic and residual correlations from the fitted model to determine the relative contribution of each component to observed co‐occurrence patterns. We also evaluate predictions generated from the fitted model relative to a single‐species modelling approach.

Results

For most species, correlation due to climate covariates exceeded residual correlation, indicating an overriding influence of broad‐scale climate on co‐occurrence patterns. Accounting for covariance among species did not significantly improve predictions relative to a single‐species approach, providing limited evidence for a strong independent influence of species interactions on distribution patterns.

Conclusions

Overall, our findings indicate that climate is an important driver of regional biodiversity patterns and that interactions between dominant tree species contribute little to explain species co‐occurrence patterns among Rocky Mountain trees.     

Species‐time‐area and phylogenetic‐time‐area relationships in tropical tree communities

The species‐area relationship (SAR) has proven to be one of the few strong generalities in ecology. The temporal analog of the SAR, the species‐time relationship (STR), has received considerably less attention. Recent work primarily from the temperate zone has aimed to merge the SAR and the STR into a synthetic and unified species‐time‐area relationship (STAR) as originally envisioned by Preston (1960). Here we test this framework using two tropical tree communities and extend it by deriving a phylogenetic‐time‐area relationship (PTAR). The work finds some support for Preston's prediction that diversity‐time relationships, both species and phylogenetic, are sensitive to the spatial scale of the sampling. Contrary to the Preston's predictions we find a decoupling of diversity‐area and diversity‐time relationships in both forests as the time period used to quantify the diversity‐area relationship changes. In particular, diversity‐area and diversity‐time relationships are positively correlated using the initial census to quantify the diversity‐area relationship, but weakly or even negatively correlated when using the most recent census. Thus, diversity‐area relationships could forecast the temporal accumulation of biodiversity of the forests, but they failed to “back‐cast” the temporal accumulation of biodiversity suggesting a decoupling of space and time.     

Using space‐for‐time substitution and time sequence approaches in invasion ecology

1. Invasion biologists use two main approaches to evaluate the effects of non‐native species (NNS) on diversity of native species (DNS), namely space‐for‐time and time approaches. These approaches have pitfalls related to lack of controls: the former lacks pre‐invasion data, while the latter often lacks data from non‐invaded sites. 2. We propose a framework that combines space‐for‐time and time approaches and which should result in more focused mechanistic hypotheses and experiments to test the causes of invasibility and the effects of NNS on DNS. We illustrate the usefulness of our framework using two case studies: one with the submersed macrophyte, Hydrilla verticillata, in reservoir and the other with the fish, Geophagus proximus, in a large river–floodplain system. 3. Hydrilla verticillata invaded sites with DNS similar to that found in non‐invaded sites, indicating that biotic and/or abiotic factors did not influence invasion success; however, DNS increased over time in invaded sites compared with non‐invaded sites, suggesting that H. verticillata facilitated natives. In contrast, G. proximus invaded sites with higher DNS than non‐invaded sites, suggesting that biotic and/or abiotic factors favouring natives were important for invasion success, but DNS increased in invaded and non‐invaded sites over time, indicating that an independent factor contributed to DNS increases. 4. Conclusions from both studies would have been inaccurate or incomplete if the space‐for‐time and time approaches had not been used in combination as proposed in our framework.     

The Mediterranean Sea as a ‘cul‐de‐sac’ for endemic fishes facing climate change

The Mediterranean Sea is a hotspot of biodiversity, and climate warming is expected to have a significant influence on its endemic fish species. However, no previous studies have predicted whether fish species will experience geographic range extensions or contractions as a consequence of warming. Here, we projected the potential future climatic niches of 75 Mediterranean Sea endemic fish species based on a global warming scenario implemented with the Mediterranean model OPAMED8 and a multimodel inference, which included uncertainty. By 2070–2099, the average surface temperature of the Mediterranean Sea was projected to warm by 3.1 °C. Projections for 2041–2060 are that 25 species would qualify for the International Union for the Conservation of Nature and Natural Resources (IUCN) Red List, and six species would become extinct. By 2070–2099, 45 species were expected to qualify for the IUCN Red List whereas 14 were expected to become extinct. By the middle of the 21st century, the coldest areas of the Mediterranean Sea (Adriatic Sea and Gulf of Lion) would act as a refuge for cold‐water species, but by the end of the century, those areas were projected to become a ‘cul‐de‐sac’ that would drive those species towards extinction. In addition, the range size of endemic species was projected to undergo extensive fragmentation, which is a potentially aggravating factor. Since a majority of endemic fishes are specialists, regarding substratum and diet, we may expect a reduced ability to track projected climatic niches. As a whole, 25% of the Mediterranean Sea continental shelf was predicted to experience a total modification of endemic species assemblages by the end of the 21st century. This expected turnover rate could be mitigated by marine protected areas or accelerated by fishing pressure or competition from exotic fishes. It remains a challenge to predict how these assemblage modifications might affect ecosystem function.     

Reactive oxygen species‐induced parthanatos of immunocytes by human cytomegalovirus‐associated substance

Previous studies have examined various immune evasion strategies of human cytomegalovirus (HCMV) to gain understanding of its pathogenesis. Although the mechanism that underlies immunocyte destruction near HCMV‐infected lesions has yet to be established, it is here shown that substances produced by HCMV‐infected cells induce death in several types of immunocytes, but not in fibroblasts or astrocytomas. These substances contain HCMV proteins and were termed HCMV‐associated insoluble substance (HCMVAIS). The mechanism by which HCMVAIS induces cell death was characterized to improve understanding the death of immunocytes near HCMV‐infected lesions. HCMVAIS were found to trigger production of intracellular nicotinamide adenine dinucleotide phosphate oxidase‐derived reactive oxygen species (ROS), resulting in cell death, this effect being reversed following treatment with ROS inhibitors. Cell death was not induced in splenocytes from NOX‐2 knockout mice. It was hypothesized that DNA damage induced by oxidative stress initiates poly ADP‐ribose polymerase‐1 (PARP‐1)‐mediated cell death, or parthanatos. HCMVAIS‐induced cell death is accompanied by PARP‐1 activation in a caspase‐independent manner, nuclear translocation of apoptosis‐inducing factor (AIF), and DNA fragmentation, which are typical features of parthanatos. Treatment with an AIF inhibitor decreased the rate of HCMVAIS‐induced cell death, this being confirmed by hematoxylin and eosin staining; cell death in most HCMV‐positive foci in serial section samples of a large intestine with HCMV infection was TUNEL‐positive, cleaved caspase 3‐negative and CD45‐positive. Taken together, these data suggest that HCMV inhibits local immune responses via direct killing of immunocytes near HCMV‐infected cells through ROS‐induced parthanatos by HCMVAIS.     

Biodegradation of 1080: Testing soils in south‐eastern Australia for sodium fluoroacetate‐degrading micro‐organisms

Sodium fluoroacetate (1080) is a vertebrate poison commonly used for the control of vertebrate pests in Australia. Long‐term environmental persistence of 1080 from baiting operations has likely nontarget species and environmental impacts and is a matter of public concern. Defluorinating micro‐organisms have been detected in soils of Western and central Australia, and Queensland, but not in south‐eastern Australia. The presence or absence of defluorinating micro‐organisms in soils from south‐eastern Australia will assist in determining whether long‐term environmental persistence of 1080 is or is not occurring. Soils from the Central West Slopes and Plains and Central Tablelands of New South Wales were sampled to investigate the presence and capability of 1080 defluorinating soil micro‐organisms. Thirty‐one species of micro‐organisms were isolated from soils from each site after 10 days incubation in a 20 mM 1080 solution. Of these, 13 isolates showed measurable defluorinating ability when grown in a 1080 and sterile soil suspension. Two species, the bacteria Micromonospora, and the actinomycete Streptosporangium, have not been previously reported for their defluorinating ability. These results indicate that defluorinating micro‐organisms are present in soils in south‐eastern Australia, which adds weight to other studies that found that 1080 is subject to microbiological degradative processes following removal from the bait substrate. Soil micro‐organism defluorination, in combination with physical breakdown and uptake by plants, indicates that fluoroacetate in soils and natural water ways is unlikely to persist. This has implications for the better informed use of 1080 in pest animal management programmes in south‐eastern Australia.     

Protein lysine‐Nζ alkylation and O‐phosphorylation mediated by DTT‐generated reactive oxygen species

Reactive oxygen species (ROS) play crucial roles in physiology and pathology. In this report, we use NMR spectroscopy and mass spectrometry (MS) to demonstrate that proteins (galectin-1, ubiquitin, RNase, cytochrome c, myoglobin, and lysozyme) under reducing conditions with dithiothreitol (DTT) become alkylated at lysine-N_ζ groups and O-phosphorylated at serine and threonine residues. These adduction reactions only occur in the presence of monophosphate, potassium, trace metals Fe/Cu, and oxygen, and are promoted by reactive oxygen species (ROS) generated via DTT oxidation. Superoxide mediates the chemistry, because superoxide dismutase inhibits the reaction, and hydroxyl and phosphoryl radicals are also likely involved. While lysine alkylation accounts for most of the adduction, low levels of phosphorylation are also observed at some serine and threonine residues, as determined by western blotting and MS fingerprinting. The adducted alkyl group is found to be a fragment of DTT that forms a Schiff base at lysine N_ζ groups. Although its exact chemical structure remains unknown, the DTT fragment includes a SH group and a –CHOH–CH₂– group. Chemical adduction appears to be promoted in the context of a well-folded protein, because some adducted sites in the proteins studied are considerably more reactive than others and the reaction occurs to a lesser extent with shorter, unfolded peptides and not at all with small organic molecules. A structural signature involving clusters of positively charged and other polar groups appears to facilitate the reaction. Overall, our findings demonstrate a novel reaction for DTT-mediated ROS chemistry with proteins.     

Novel N‐Acyl‐1H‐imidazole‐1‐carbothioamides: Design,Synthesis, Biological and Computational Studies

The present study reports the convenient synthesis, spectroscopic characterization, bio‐assays and computational evaluation of a novel series of N‐acyl‐1H‐imidazole‐1‐carbothioamides. The screened derivatives displayed excellent antioxidant activity, moderate antibacterial and antifungal potential. The screened derivatives were found to be highly biocompatible against hRBCs. Molecular docking ascertained the mechanism and mode of action towards the molecular target delineating that ligands and complexes were stabilized at the active site by electrostatic and hydrophobic forces in accordance to the corresponding experimental results. Docking simulation provided additional information about the possibilities of inhibitory potential of the compounds against RNA. Computational evaluation predicted that N‐acyl‐1H‐imidazole‐1‐carbothioamides 5c and 5g can serve as potential surrogates for hit to lead generation and design of novel antioxidant and antibacterial agents.     

Projected effects of Climate‐change‐induced flow alterations on stream macroinvertebrate abundances

Global change has the potential to affect river flow conditions which are fundamental determinants of physical habitats. Predictions of the effects of flow alterations on aquatic biota have mostly been assessed based on species ecological traits (e.g., current preferences), which are difficult to link to quantitative discharge data. Alternatively, we used empirically derived predictive relationships for species’ response to flow to assess the effect of flow alterations due to climate change in two contrasting central European river catchments. Predictive relationships were set up for 294 individual species based on (1) abundance data from 223 sampling sites in the Kinzig lower‐mountainous catchment and 67 sites in the Treene lowland catchment, and (2) flow conditions at these sites described by five flow metrics quantifying the duration, frequency, magnitude, timing and rate of flow events using present‐day gauging data. Species’ abundances were predicted for three periods: (1) baseline (1998–2017), (2) horizon 2050 (2046–2065) and (3) horizon 2090 (2080–2099) based on these empirical relationships and using high‐resolution modeled discharge data for the present and future climate conditions. We compared the differences in predicted abundances among periods for individual species at each site, where the percent change served as a proxy to assess the potential species responses to flow alterations. Climate change was predicted to most strongly affect the low‐flow conditions, leading to decreased abundances of species up to ?42%. Finally combining the response of all species over all metrics indicated increasing overall species assemblage responses in 98% of the studied river reaches in both projected horizons and were significantly larger in the lower‐mountainous Kinzig compared to the lowland Treene catchment. Such quantitative analyses of freshwater taxa responses to flow alterations provide valuable tools for predicting potential climate‐change impacts on species abundances and can be applied to any stressor, species, or region.     

Top‐down and bottom‐up control of litter decomposers in streams

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SP‐Designer: a user‐friendly program for designing species‐specific primer pairs from DNA sequence alignments

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Landscape‐scale determinants of non‐native fish communities

Aim Predicting and preventing invasions depends on knowledge of the factors that make ecosystems susceptible to invasion. Current studies generally rely on non‐native species richness (NNSR) as the sole measure of ecosystem invasibility; however, species identity is a critical consideration, given that different ecosystems may have environmental characteristics suitable to different species. Our aim was to examine whether non‐native freshwater fish community composition was related to ecosystem characteristics at the landscape scale. Location United States. Methods We described spatial patterns in non‐native freshwater fish communities among watersheds in the Mid‐Atlantic region of the United States based on records of establishment in the U.S. Geological Survey’s Nonindigenous Aquatic Species Database. We described general relationships between non‐native species and ecosystem characteristics using canonical correspondence analysis. We clustered watersheds by non‐native fish community and described differences among clusters using indicator species analysis. We then assessed whether non‐native communities could be predicted from ecosystem characteristics using random forest analysis and predicted non‐native communities for uninvaded watersheds. We estimated which ecosystem characteristics were most important for predicting non‐native communities using conditional inference trees. Results We identified four non‐native fish communities, each with distinct indicator species. Non‐native communities were predicted based on ecosystem characteristics with an accuracy of 80.6%, with temperature as the most important variable. Relatively uninvaded watersheds were predicted to be invasible by the most diverse non‐native community. Main conclusions Non‐native species identity is an important consideration when assessing ecosystem invasibility. NNSR alone is an insufficient measure of invasibility because ecosystems with equal NNSR may not be equally invasible by the same species. Our findings can help improve predictions of future invasions and focus management and policy decisions on particular species in highly invasible ecosystems.     

Large‐Scale Restoration of Dry Grasslands on Ex‐Arable Land Using a Regional Seed Mixture: Establishment of Target Species

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