Ecological drift and competitive interactions predict unique patterns in temporal fluctuations of population size

Recent studies have highlighted the importance of higher-order competitive interactions in stabilizing population dynamics in multi-species communities. But how does the structure of competitive hierarchies affect population dynamics and extinction processes? We tackled this important question by using spatially explicit simulations of ecological drift (10 species in a homogeneous landscape of 64 patches) in which birth rates were influenced by interspecific competition. Specifically, we examined how transitive (linear pecking orders) and intransitive (pecking orders with loops) competitive hierarchies affected extinction rates and population dynamics in simulated communities through time. In comparison to a pure neutral model, an ecological drift model including transitive competition increased extinction rates, caused synchronous density-dependent population fluctuations, and generated a white-noise distribution of population sizes. In contrast, the drift model with intransitive competitive interactions decreased extinctions rates, caused asynchronous (compensatory) density-dependent population fluctuations, and generated a brown noise distribution of population sizes. We also explored the effect on community stability of more complex patterns of competitive interactions in which pairwise competitive relationships were assigned probabilistically. These probabilistic competition models also generated density-dependent trajectories and a brown noise distribution of population sizes. However, extinction rates and the degree of population synchrony were comparable to those observed in purely neutral communities. Collectively, our results confirm that intransitive competition has a strong and stabilizing effect on local populations in species-poor communities. This effect wanes with increasing species richness. Empirical assemblages characterized by brown spectral noise, density-dependent regulation, and asynchronous (compensatory) population fluctuations may indicate a signature of intransitive competitive interactions

An updated distribution of Solidago ×niederederi (Asteraceae) in Poland

In this paper, an updated map of the distribution of Solidago ×niederederi, a natural hybrid between S. canadensis and S. virgaurea, in Poland is presented using the ATPOL cartogram method. A compiled list of 55 localities of the hybrid within 40 cartogram units (10-km squares) is provided and its negative impact on S. virgaurea is highlighted

A comprehensive framework for the study of species co-occurrences, nestedness and turnover

Binary presence–absence matrices (rows = species, columns = sites) are often used to quantify patterns of species co-occurrence, and to infer possible biotic interactions from these patterns. Previous classifications of co-occurrence patterns as nested, segregated, or modular have led to contradictory results and conclusions. These analyses usually do not incorporate the functional traits of the species or the environmental characteristics of the sites, even though the outcomes of species interactions often depend on trait expression and site quality. Here we address this shortcoming by developing a method that incorporates realized functional and environmental niches, and relates them to species co-occurrence patterns. These niches are defined from n-dimensional ellipsoids, and calculated from the n eigenvectors and eigenvalues of the variance–covariance matrix of measured environmental or trait variables. Average niche overlap among species and the spatial distribution of niches define a triangle plot with vertices of species segregation (low niche overlap), nestedness (high niche overlap), and modular co-occurrence (clusters of overlapping niches). Applying this framework to temperate understorey plant communities in southwest Poland, we found a consistent modular structure of species occurrences, a pattern not detected by conventional presence–absence analysis. These results suggest that, in our case study, habitat filtering is the most important process structuring understorey plant communities. Furthermore, they demonstrate how incorporating trait and environmental data into co-occurrence analysis improves pattern detection and provides a stronger theoretical framework for understanding community structure

Reconciliation of Genome-Scale Metabolic Reconstructions for Comparative Systems Analysis

In the past decade, over 50 genome-scale metabolic reconstructions have been built for a variety of single- and multi- cellular organisms. These reconstructions have enabled a host of computational methods to be leveraged for systems-analysis of metabolism, leading to greater understanding of observed phenotypes. These methods have been sparsely applied to comparisons between multiple organisms, however, due mainly to the existence of differences between reconstructions that are inherited from the respective reconstruction processes of the organisms to be compared. To circumvent this obstacle, we developed a novel process, termed metabolic network reconciliation, whereby non-biological differences are removed from genome-scale reconstructions while keeping the reconstructions as true as possible to the underlying biological data on which they are based. This process was applied to two organisms of great importance to disease and biotechnological applications, Pseudomonas aeruginosa and Pseudomonas putida, respectively. The result is a pair of revised genome-scale reconstructions for these organisms that can be analyzed at a systems level with confidence that differences are indicative of true biological differences (to the degree that is currently known), rather than artifacts of the reconstruction process. The reconstructions were re-validated with various experimental data after reconciliation. With the reconciled and validated reconstructions, we performed a genome-wide comparison of metabolic flexibility between P. aeruginosa and P. putida that generated significant new insight into the underlying biology of these important organisms. Through this work, we provide a novel methodology for reconciling models, present new genome-scale reconstructions of P. aeruginosa and P. putida that can be directly compared at a network level, and perform a network-wide comparison of the two species. These reconstructions provide fresh insights into the metabolic similarities and differences between these important Pseudomonads, and pave the way towards full comparative analysis of genome-scale metabolic reconstructions of multiple species

Droughts in the area of Poland in recent centuries in the light of multi-proxy data

The history of drought occurrence in Poland criteria used were those proposed by McKee et al. (1993) and in the last millennium is poorly known. To improve this modified for the climate conditions of Poland by Lab˛edzki knowledge we have conducted a comprehensive analysis us (2007). ing both proxy data (documentary and dendrochronological) More than 100 droughts were found in documen and instrumental measurements of precipitation. The paper tary sources in the period 1451–1800, including 17 presents the main features of droughts in Poland in recent megadroughts. A greater than average number of droughts centuries, including their frequency of occurrence, cover were observed in the second halves of the 17th century and age, duration, and intensity. The reconstructions of droughts the 18th century in particular. Dendrochronological data con based on all the mentioned sources of data covered the pe firmed this general tendency in the mentioned period. riod 996–2015. Examples of megadroughts were also cho Analysis of SPI (including its lowest values, i.e. droughts) sen using documentary evidence, and some of them were de showed that the long-term frequency of droughts in Poland scribed. has been stable in the last two or three centuries. Extreme Various documentary sources have been used to identify and severe droughts were most frequent in the coastal part droughts in the area of Poland in the period 1451–1800 and of Poland and in Silesia. Most droughts had a duration of 2 to estimate their intensity, spatial coverage, and duration. months (about 60 %–70 %) or 3–4 months (10 %–20 %). Fre Twenty-two local chronologies of trees (pine, oak, and fir quencies of droughts with a duration of 5-or-more months from Poland were taken into account for detecting nega were lower than 10 %. The frequency of droughts of all cat tive pointer years (exceptionally narrow rings). The delimita egories in Poland in the instrumental period 1722–2015 was tion of droughts based on instrumental data (eight long-term greatest in winter, while in the documentary evidence (1451– precipitation series) was conducted using two independent 1800) droughts in this season are rarely mentioned. approaches (Standard Precipitation Index, SPI, calculated for The occurrence of negative pointer years (a good proxy for 1-, 3-, and 24-month timescales, and a new method proposed droughts) was compared with droughts delimited based on by authors). For delimitation of droughts (dry months), the documentary and instrumental data. A good correspondence was found between the timing of occurrence of droughts identified using all three kinds of data (sources)

Differences in the Climate-Growth Relationship of Scots Pine: A Case Study from Poland and Hungary

Scots pine is an adaptable and prevalent European tree species that grows naturally throughout Europe and has been planted in a wide range of environments. Previous studies have indicated that climatic variables affect tree-ring growth patterns in this species, but it is also possible that certain aspects of the growth environment moderate this response. In order to understand the potential impact a shifting climate has on this important species, this study compared the growth response of two populations of Scots pine. Trees from similar bioclimatic regions in Hungary and Poland were compared using the hypothesis that differences in the association between climate and growth would be reflected by the degree of tree-ring width variation. We also wanted to know how changing climatic conditions influenced the temporal stability of the climate–growth signal in the most important periods for tree growth. Clear similarities in the effect of temperature and precipitation on tree-ring width variation were found between the two sites, but there were also some interesting differences. In the late winter to early spring period both populations reacted to warming with a decreasing association with temperature. Summer precipitation was shown to be the dominant factor in controlling ring-width. A decreasing trend in summer precipitation values at both Hungarian and Polish sites resulted in a weakening in correspondence for the Hungarian trees, while the Polish trees showed a significant increase in correlation with summer precipitation. The results indicated that changes in climate influenced the studied trees in different ways which has implications for the future balance of Scots pine growth in Europe

River Regulation Causes Rapid Changes in Relationships Between Floodplain Oak Growth and Environmental Variables

The radial growth of pedunculate oak (Quercus robur), a species often ecologically dominating European deciduous forests, is closely tied up with local environmental variables. The oak tree-ring series usually contain a climatic and hydrologic signal that allows assessing the main drivers of tree growth in various ecosystems. Understanding the climate-growth relationship patterns in floodplains is important for providing insights into the species persistence and longevity in vulnerable riverine ecosystems experiencing human-induced hydrology alteration. Here, we use 139 years long instrumental records of local temperature, precipitation, and water levels in the Dnipro River in Kyiv to demonstrate that the implementation of river regulation has decoupled the established relationship between the radial growth of floodplain oak and local hydro-climatic conditions. Before the river flow has been altered by engineering modifications of 1965–1977, the water level in the Dnipro River was the key driver of oak radial growth, as reflected in the tree-ring width and earlywood width. The construction of two dams has altered the seasonal distribution of water level diminishing the positive effect of high water on oak growth and subsequently reversing this trend to negative, resulting from a seasonal ground water surplus. The decrease in the correlation between oak growth indices and the river’s water level in April–June was unprecedentedly rapid and clearly distinguishable among other changes in the growth-to-climate relationship. Our findings further demonstrate that trees growing in areas exposed to urban development are the most susceptible to downside effects of river regulation

mir-181A/B-1 controls thymic selection of treg cells and tunes their suppressive capacity

The interdependence of selective cues during development of regulatory T cells (Treg cells) in the thymus and their suppressive function remains incompletely understood. Here, we analyzed this interdependence by taking advantage of highly dynamic changes in expression of microRNA 181 family members miR-181a-1 and miR-181b-1 (miR-181a/b-1) during late T-cell development with very high levels of expression during thymocyte selection, followed by massive down-regulation in the periphery. Loss of miR-181a/b-1 resulted in inefficient de novo generation of Treg cells in the thymus but simultaneously permitted homeostatic expansion in the periphery in the absence of competition. Modulation of T-cell receptor (TCR) signal strength in vivo indicated that miR-181a/b-1 controlled Treg-cell formation via establishing adequate signaling thresholds. Unexpectedly, miR-181a/b-1–deficient Treg cells displayed elevated suppressive capacity in vivo, in line with elevated levels of cytotoxic T-lymphocyte–associated 4 (CTLA-4) protein, but not mRNA, in thymic and peripheral Treg cells. Therefore, we propose that intrathymic miR-181a/b-1 controls development of Treg cells and imposes a developmental legacy on their peripheral function