Evaluating the ecological realism of plant species distribution models with ecological indicator values

Species distribution models (SDMs) are routinely applied to assess current as well as future species distributions, for example to assess impacts of future environmental change on biodiversity or to underpin conservation planning. It has been repeatedly emphasized that SDMs should be evaluated based not only on their goodness of fit to the data, but also on the realism of the modelled ecological responses. However, possibilities for the latter are hampered by limited knowledge on the true responses as well as a lack of quantitative evaluation methods. Here we compared modelled niche optima obtained from European-scale SDMs of 1,476 terrestrial vascular plant species with empirical ecological indicator values indicating the preferences of plant species for key environmental conditions. For each plant species we first fitted an ensemble SDM including three modeling techniques (GLM, GAM and BRT) and extracted niche optima for climate, soil, land use and nitrogen deposition variables with a large explanatory power for the occurrence of that species. We then compared these SDM-derived niche optima with the ecological indicator values by means of bivariate correlation analysis. We found weak to moderate correlations in the expected direction between the SDM-derived niche optima and ecological indicator values. The strongest correlation occurred between the modelled optima for growing degree days and the ecological indicator values for temperature. Correlations were weaker for SDM-derived niche optima with a more distal relationship to ecological indicator values (notably precipitation and soil moisture). Further, correlations were consistently highest for BRT, followed by GLM and GAM. Our method gives insight into the ecological realism of modelled niche optima and projected core habitats and can be used to improve SDMs by making a more informed selection of environmental variables and modeling techniques

Using species attributes to characterize late-glacial and early-Holocene environments at Kråkenes, western Norway

Aim: We aim to use species attributes such as distributions and indicator values to reconstruct past biomes, environment, and temperatures from detailed plant‐macrofossil data covering the late glacial to the early Holocene (ca. 14–9 ka). Location: Kråkenes, western Norway. Methods: We applied attributes for present‐day geographical distribution, optimal July and January temperatures, and Ellenberg indicator values for plants in the macrofossil data‐set. We used assemblage weighted means (AWM) to reconstruct past biomes, changes in light (L), nitrogen (N), moisture (F), and soil reaction (R), and temperatures. We compared the temperature reconstructions with previous chironomid‐inferred temperatures. Results: After the start of the Holocene around 11.5 ka, the Arctic‐montane biome, which was stable during the late‐glacial period, shifted successively into the Boreo‐arctic montane, Wide‐boreal, Boreo‐montane, Boreo‐temperate, and Wide‐temperate biomes by ca. 9.0 ka. Circumpolar and Eurasian floristic elements characteristic of the late‐glacial decreased and the Eurosiberian element became prominent. Light demand (L), soil moisture (F), nitrogen (N), and soil reaction (R) show different, but complementary responses. Light‐demanding plants decreased with time. Soil moisture was relatively stable until it increased during organic soil development during the early Holocene. Soil nitrogen increased during the early Holocene. Soil reaction (pH) decreased during the Allerød, but increased during the Younger Dryas. It decreased markedly after the start of the Holocene, reaching low but stable levels in the early Holocene. Mean July and January temperatures show similar patterns to the chironomid‐inferred mean July temperature trends at Kråkenes, but chironomids show larger fluctuations and interesting differences in timing. Conclusion: Assigning attributes to macrofossil species is a useful new approach in palaeoecology. It can demonstrate changes in biomes, ecological conditions, and temperatures. The late‐glacial to early‐Holocene transition may form an analogue for changes observed in the modern arctic and in mountains, with melting glaciers, permafrost thaw, and shrub encroachment into tundra.publishedVersio

The cellular microscopy phenotype ontology

BACKGROUND: Phenotypic data derived from high content screening is currently annotated using free-text, thus preventing the integration of independent datasets, including those generated in different biological domains, such as cell lines, mouse and human tissues. DESCRIPTION: We present the Cellular Microscopy Phenotype Ontology (CMPO), a species neutral ontology for describing phenotypic observations relating to the whole cell, cellular components, cellular processes and cell populations. CMPO is compatible with related ontology efforts, allowing for future cross-species integration of phenotypic data. CMPO was developed following a curator-driven approach where phenotype data were annotated by expert biologists following the Entity-Quality (EQ) pattern. These EQs were subsequently transformed into new CMPO terms following an established post composition process. CONCLUSION: CMPO is currently being utilized to annotate phenotypes associated with high content screening datasets stored in several image repositories including the Image Data Repository (IDR), MitoSys project database and the Cellular Phenotype Database to facilitate data browsing and discoverability

Testing Hardy nonlocality proof with genuine energy-time entanglement

We show two experimental realizations of Hardy ladder test of quantum nonlocality using energy-time correlated photons, following the scheme proposed by A. Cabello \emph{et al.} [Phys. Rev. Lett. \textbf{102}, 040401 (2009)]. Unlike, previous energy-time Bell experiments, these tests require precise tailored nonmaximally entangled states. One of them is equivalent to the two-setting two-outcome Bell test requiring a minimum detection efficiency. The reported experiments are still affected by the locality and detection loopholes, but are free of the post-selection loophole of previous energy-time and time-bin Bell tests.Comment: 5 pages, revtex4, 6 figure

Averages of Fourier coefficients of Siegel modular forms and representation of binary quadratic forms by quadratic forms in four variables

Let $-d$ be a a negative discriminant and let $T$ vary over a set of representatives of the integral equivalence classes of integral binary quadratic forms of discriminant $-d$. We prove an asymptotic formula for $d \to \infty$ for the average over $T$ of the number of representations of $T$ by an integral positive definite quaternary quadratic form and obtain results on averages of Fourier coefficients of linear combinations of Siegel theta series. We also find an asymptotic bound from below on the number of binary forms of fixed discriminant $-d$ which are represented by a given quaternary form. In particular, we can show that for growing $d$ a positive proportion of the binary quadratic forms of discriminant $-d$ is represented by the given quaternary quadratic form.Comment: v5: Some typos correcte

Protecting Clinical Trial Participants and Protecting Data Integrity: Are We Meeting the Challenges?

Susan Ellenberg discusses alternative approaches towards evaluating data as it accumulates in clinical trials, and to protecting the integrity and preventing undue risks to participants, as the trial continues

Contrasting stomatal sensitivity to temperature and soil drought in mature alpine conifers

Conifers growing at high elevations need to optimize their stomatal conductance (g(s)) for maximizing photosynthetic yield while minimizing water loss under less favourable thermal conditions. Yet the ability of high-elevation conifers to adjust their g(s) sensitivity to environmental drivers remains largely unexplored. We used 4 years of sap flow measurements to elucidate intraspecific and interspecific variability of g(s) in Larix decidua Mill. and Picea abies (L.) Karst along an elevational gradient and contrasting soil moisture conditions. Site- and species-specific g(s) response to main environmental drivers were examined, including vapour pressure deficit, air temperature, solar irradiance, and soil water potential. Our results indicate that maximum g(s) of L. decidua is >2 times higher, shows a more plastic response to temperature, and down-regulates g(s) stronger during atmospheric drought compared to P. abies. These differences allow L. decidua to exert more efficient water use, adjust to site-specific thermal conditions, and reduce water loss during drought episodes. The stronger plasticity of g(s) sensitivity to temperature and higher conductance of L. decidua compared to P. abies provide new insights into species-specific water use strategies, which affect species' performance and should be considered when predicting terrestrial water dynamics under future climatic change

Hypophosphorylated SR splicing factors transiently localize around active nucleolar organizing regions in telophase daughter nuclei

Upon completion of mitosis, daughter nuclei assemble all of the organelles necessary for the implementation of nuclear functions. We found that upon entry into daughter nuclei, snRNPs and SR proteins do not immediately colocalize in nuclear speckles. SR proteins accumulated in patches around active nucleolar organizing regions (NORs) that we refer to as NOR-associated patches (NAPs), whereas snRNPs were enriched at other nuclear regions. NAPs formed transiently, persisting for 15–20 min before dissipating as nuclear speckles began to form in G1. In the absence of RNA polymerase II transcription, NAPs increased in size and persisted for at least 2 h, with delayed localization of SR proteins to nuclear speckles. In addition, SR proteins in NAPs are hypophosphorylated, and the SR protein kinase Clk/STY colocalizes with SR proteins in NAPs, suggesting that phosphorylation releases SR proteins from NAPs and their initial target is transcription sites. This work demonstrates a previously unrecognized role of NAPs in splicing factor trafficking and nuclear speckle biogenesis