Tree recruitment is determined by stand structure and shade tolerance with uncertain role of climate and water relations

1. Tree regeneration is a key process for long‐term forest dynamics, determining changes in species composition and shaping successional trajectories. While tree regeneration is a highly stochastic process, tree regeneration studies often cover narrow environmental gradients only, focusing on specific forest types or species in distinct regions. Thus, the larger‐scale effects of temperature, water availability, and stand structure on tree regeneration are poorly understood.
2. We investigated these effects in respect of tree recruitment (in‐growth) along wide environmental gradients using forest inventory data from Flanders (Belgium), northwestern Germany, and Switzerland covering more than 40 tree species. We employed generalized linear mixed models to capture the abundance of tree recruitment in response to basal area, stem density, shade casting ability of a forest stand as well as site‐specific degree‐day sum (temperature), water balance, and plant‐available water holding capacity. We grouped tree species to facilitate comparisons between species with different levels of tolerance to shade and drought.
3. Basal area and shade casting ability of the overstory had generally a negative impact on tree recruitment, but the effects differed between levels of shade tolerance of tree recruitment in all study regions. Recruitment rates of very shade‐tolerant species were positively affected by shade casting ability. Stem density and summer warmth (degree‐day sum) had similar effects on all tree species and successional strategies. Water‐related variables revealed a high degree of uncertainty and did not allow for general conclusions. All variables had similar effects independent of the varying diameter thresholds for tree recruitment in the different data sets.
4. Synthesis: Shade tolerance and stand structure are the main drivers of tree recruitment along wide environmental gradients in temperate forests. Higher temperature generally increases tree recruitment rates, but the role of water relations and drought tolerance remains uncertain for tree recruitment on cross‐regional scales.

     

Coordinated activation of autophosphorylation sites in the RET receptor tyrosine kinase: importance of tyrosine 1062 for GDNF mediated neuronal differentiation and survival.

The catalytic and signaling activities of RET, a tyrosine kinase receptor for glial cell line-derived neurotrophic factor (GDNF), are controlled by the autophosphorylation of several tyrosine residues in the RET cytoplasmic domain. To analyze the phosphorylation state of individual tyrosines, we generated antibodies recognizing specific phosphotyrosine sites involved in the catalytic (Tyr(905)) and downstream signaling (Tyr(1015), Tyr(1062), and Tyr(1096)) activities of this receptor. Stimulation with GDNF induced coordinated phosphorylation of the 4 tyrosine residues in neuronal cell lines and in primary cultures of sympathetic neurons isolated from rat superior cervical ganglia. Neurturin and artemin, two other members of the GDNF ligand family, also induced synchronized phosphorylation of RET tyrosines with kinetics comparable to those observed with GDNF. Tyrosine phosphorylation was maximal 15 min after ligand stimulation, decaying thereafter with similar kinetics in all 4 residues. Co-stimulation with a soluble form of the GFRalpha1 co-receptor potentiated ligand-dependent phosphorylation of different intracellular tyrosines to a similar extent and increased the survival of superior cervical ganglion neurons compared with treatment with GDNF alone. In vivo, high levels of phosphorylated Tyr(905), Tyr(1015), and Tyr(1062) were detected in embryonic mouse dorsal root ganglia, with a sharp decline at early postnatal stages. Protein transduction of anti-Tyr(P)(1062) antibodies into cultured cells reduced activation of MAPKs ERK1 and ERK2 and the AKT kinase in response to GDNF and diminished GDNF-dependent neuronal differentiation and survival of embryonic sensory neurons from the nodose ganglion. These results demonstrate synchronized utilization of individual RET tyrosine residues in neurons in vivo and reveal an important role for RET Tyr(1062) in mediating neuronal survival by GDNF.     

Efficient Boolean implementation of universal sequence maps (bUSM)

Background  

Recently, Almeida and Vinga offered a new approach for the representation of arbitrary discrete sequences, referred to as Universal Sequence Maps (USM), and discussed its applicability to genomic sequence analysis. Their work generalizes and extends Chaos Game Representation (CGR) of DNA for arbitrary discrete sequences.     

NK cell inhibitory receptor Ly-49C residues involved in MHC class I binding.

Mouse NK cells express Ly-49 receptors specific for classical MHC class I molecules. Several of the Ly-49 receptors have been characterized in terms of function and ligand specificity. However, the only Ly-49 receptor-ligand interaction previously described in detail is that between Ly-49A and H-2D(d), as studied by point mutations in the ligand and the crystal structure of the co-complex of these molecules. It is not known whether other Ly-49 receptors bind MHC class I in a similar manner as Ly-49A. Here we have studied the effect of mutations in Ly-49C on binding to the MHC class I molecules H-2K(b), H-2D(b), and H-2D(d). The MHC class I molecules were used as soluble tetramers to stain transiently transfected 293T cells expressing the mutated Ly-49C receptors. Three of nine mutations in Ly-49C led to loss of MHC class I binding. The three Ly-49C mutations that affected MHC binding correspond to Ly-49A residues that are in contact or close to H-2D(d) in the co-crystal, demonstrating that MHC class I binding by Ly-49C is dependent on residues in the same area as that used by Ly-49A for ligand contacts.     

An environmental gradient dominates ecological and genetic differentiation of marine invertebrates between the North and Baltic Sea

Environmental gradients have emerged as important barriers to structuring populations and species distributions. We set out to test whether the strong salinity gradient from the marine North Sea to the brackish Baltic Sea in northern Europe represents an ecological and genetic break, and to identify life history traits that correlate with the strength of this break. We accumulated mitochondrial cytochrome oxidase subunit 1 sequence data, and data on the distribution, salinity tolerance, and life history for 28 species belonging to the Cnidaria, Crustacea, Echinodermata, Mollusca, Polychaeta, and Gastrotricha. We included seven non‐native species covering a broad range of times since introduction, in order to gain insight into the pace of adaptation and differentiation. We calculated measures of genetic diversity and differentiation across the environmental gradient, coalescent times, and migration rates between North and Baltic Sea populations, and analyzed correlations between genetic and life history data. The majority of investigated species is either genetically differentiated and/or adapted to the lower salinity conditions of the Baltic Sea. Species exhibiting population structure have a range of patterns of genetic diversity in comparison with the North Sea, from lower in the Baltic Sea to higher in the Baltic Sea, or equally diverse in North and Baltic Sea. Two of the non‐native species showed signs of genetic differentiation, their times since introduction to the Baltic Sea being about 80 and >700 years, respectively. Our results indicate that the transition from North Sea to Baltic Sea represents a genetic and ecological break: The diversity of genetic patterns points toward independent trajectories in the Baltic compared with the North Sea, and ecological differences with regard to salinity tolerance are common. The North Sea–Baltic Sea region provides a unique setting to study evolutionary adaptation during colonization processes at different stages by jointly considering native and non‐native species.     

Multiple species delimitation approaches with COI barcodes poorly fit each other and morphospecies – An integrative taxonomy case of Sri Lankan Sericini chafers (Coleoptera: Scarabaeidae)

DNA taxonomy including barcoding and metabarcoding is widely used to explore the diversity in biodiversity hotspots. In most of these hotspot areas, chafers are represented by a multitude of species, which are well defined by the complex shape of male genitalia. Here, we explore how well COI barcode data reflect morphological species entities and thus their usability for accelerated species inventorization. We conducted dedicated field surveys in Sri Lanka to collect the species‐rich and highly endemic Sericini chafers (Coleoptera: Scarabaeidae). Congruence among results of a series of protocols for de novo species delimitation and with morphology‐based species identifications was investigated. Different delimitation methods, such as the Poisson tree processes (PTP) model, Statistical Parsimony Analysis (TCS), Automatic Barcode Gap Discovery (ABGD), Assemble Species by Automatic Partitioning (ASAP), and Barcode Index Number (BIN) assignments, resulted in different numbers of molecular operational taxonomic units (MOTUs). All methods showed both over‐splitting and lumping of morphologically identified species. Only 18 of the observed 45 morphospecies perfectly matched MOTUs from all methods. The congruence of delimitation between MOTUs and morphospecies expressed by the match ratio was low, ranging from 0.57 to 0.67. TCS and multirate PTP (mPTP) showed the highest match ratio, while (BIN) assignment resulted in the lowest match ratio and most splitting events. mPTP lumped more species than any other method. Principal coordinate analysis (PCoA) on a match ratio‐based distance matrix revealed incongruent outcomes of multiple DNA delimitation methods, although applied to the same data. Our results confirm that COI barcode data alone are unlikely to correctly delimit all species, in particular, when using only a single delimitation approach. We encourage the integration of various approaches and data, particularly morphology, to validate species boundaries.     

Studies of lysosomal sialic acid metabolism: retention of sialic acid by Salla disease lysosomes

Purified rat liver lysosomes were incubated in 0.2 M sialic acid resulting in an increase in lysosomal free sialic acid of 3.8 +/- 1.5 nmol/unit beta hexosaminidase. Sialic acid loss by these lysosomes was stimulated 2-3 fold by 25 mM sodium phosphate. Loss of sialic acid by lysosomes from cultured human diploid fibroblasts was similar to that observed in rat liver lysosomes while loss of sialic acid by lysosomes from cultured fibroblasts from a patient with infantile Salla disease occurred much more slowly. Salla disease appears to be the consequence of defective lysosomal transport of sialic acid and is analogous to cystinosis, a disorder of lysosomal amino acid transport.     

Microclimate variability in alpine ecosystems as stepping stones for non‐native plant establishment above their current elevational limit

Alpine environments are currently relatively free from non‐native plant species, although their presence and abundance have recently been on the rise. It is however still unclear whether the observed low invasion levels in these areas are due to an inherent resistance of the alpine zone to invasions or whether an exponential increase in invasion is just a matter of time. Using a seed‐addition experiment on north‐ and south‐facing slopes (cf. microclimatic gradient) on two mountains in subarctic Sweden, we tested the establishment of six non‐native species at an elevation above their current distribution limits and under experimentally enhanced anthropogenic pressures (disturbance, added nutrients and increased propagule pressure). We found a large microclimatic variability in cumulative growing degree days (GDD) (range = 500.77°C, SD = 120.70°C) due to both physiographic (e.g. aspect) and biophysical (e.g. vegetation cover) features, the latter being altered by the experimental disturbance. Non‐native species establishment and biomass production were positively correlated with GDD along the studied microclimatic gradient. However, even though establishment on the north‐facing slopes caught up with that on the south‐facing slopes throughout the growing season, biomass production was limited on the north‐facing slopes due to a shorter growing season. On top of this microclimatic effect, all experimentally imposed anthropogenic factors enhanced non‐native species success. The observed microclimatic effect indicates a potential for non‐native species to use warm microsites as stepping stones for their establishment towards the cold end of the gradient. Combined with anthropogenic pressures this result suggests an increasing risk for plant invasion in cold ecosystems, as such stepping stones in alpine ecosystems are likely to be more common in a future that will combine a warming climate with persistent anthropogenic pressures.