Phylogenetic scale in ecology and evolution

Aim

Many important patterns and processes vary across the phylogeny and depend on phylogenetic scale. Nonetheless, phylogenetic scale has never been formally conceptualized, and its potential remains largely unexplored. Here, we formalize the concept of phylogenetic scale, review how phylogenetic scale has been considered across multiple fields and provide practical guidelines for the use of phylogenetic scale to address a range of biological questions.

Innovation

We summarize how phylogenetic scale has been treated in macroevolution, community ecology, biogeography and macroecology, illustrating how it can inform, and possibly resolve, some of the longstanding controversies in these fields. To promote the concept empirically, we define phylogenetic grain and extent, scale dependence, scaling and the domains of phylogenetic scale. We illustrate how existing phylogenetic data and statistical tools can be used to investigate the effects of scale on a variety of well‐known patterns and processes, including diversification rates, community structure, niche conservatism or species‐abundance distributions.

Main conclusions

Explicit consideration of phylogenetic scale can provide new and more complete insight into many longstanding questions across multiple fields (macroevolution, community ecology, biogeography and macroecology). Building on the existing resources and isolated efforts across fields, future research centred on phylogenetic scale might enrich our understanding of the processes that together, but over different scales, shape the diversity of life.     

Mixed and non-cognate SNARE complexes. Characterization of assembly and biophysical properties.

Assembly of soluble N-ethylmaleimide-sensitive fusion attachment protein receptor (SNARE) proteins between two opposing membranes is thought to be the key event that initiates membrane fusion. Many new SNARE proteins have recently been localized to distinct intracellular compartments, supporting the view that sets of specific SNAREs are specialized for distinct trafficking steps. We have now investigated whether other SNAREs can form complexes with components of the synaptic SNARE complex including synaptobrevin/VAMP 2, SNAP-25, and syntaxin 1. When the Q-SNAREs syntaxin 2, 3, and 4, and the R-SNARE endobrevin/VAMP 8 were used in various combinations, heat-resistant complexes were formed. Limited proteolysis revealed that these complexes contained a protease-resistant core similar to that of the synaptic complex. All complexes were disassembled by the ATPase N-ethylmaleimide-sensitive fusion protein and its cofactor alpha-SNAP. Circular dichroism spectroscopy showed that major conformational changes occur during assembly, which are associated with induction of structure from unstructured monomers. Furthermore, no preference for synaptobrevin was observed during the assembly of the synaptic complex when endobrevin/VAMP 8 was present in equal concentrations. We conclude that cognate and non-cognate SNARE complexes are very similar with respect to biophysical properties, assembly, and disassembly, suggesting that specificity of membrane fusion in intracellular membrane traffic is not due to intrinsic specificity of SNARE pairing.     

Ecological controls of mammalian diversification vary with phylogenetic scale

Aim

Diversity dynamics remain controversial. Here, we examine these dynamics, together with the ecological factors governing them, across mammalian clades of different ages and sizes, representing different phylogenetic scales. Specifically, we investigate whether the dynamics are bounded or unbounded, biotically or abiotically regulated, stochastic or ecologically deterministic.

Location

Worldwide.

Time period

150 Myr.

Major taxa studied

Mammals.

Methods

Integrating the newest phylogenetic and distributional data by means of several distinct methods, we study the ecology of mammalian diversification within a predictive framework, inspired by classic theory. Specifically, we evaluate the effects of several classes of factors, including climate, topography, geographical area, rates of climatic‐niche evolution, and regional coexistence between related and unrelated species. Next, we determine whether the relative effects of these factors change systematically across clades representing different phylogenetic scales.

Results

We find that young clades diversify at approximately constant rates, medium‐sized clades show diversification slowdowns, and large clades are mostly saturated, suggesting that diversification dynamics change as clades grow and accumulate species. We further find that diversification slowdowns intensify with the degree of regional coexistence between related species, presumably because increased competition for regional resources suppresses the diversification process. The richness at which clades eventually saturate depends on climate; clades residing in tropical climates saturate at low richness, implying that niches become progressively densely packed towards the tropics.

Main conclusions

The diversification process is influenced by a variety of ecological factors, whose relative effects change across phylogenetic scales, producing scale‐dependent dynamics. Different segments of the same phylogeny might therefore support seemingly conflicting results (bounded or unbounded, biotically or abiotically regulated, stochastic or ecologically deterministic diversification), which might have contributed to several outstanding controversies in the field. These conflicts can be reconciled, however, when accounting for phylogenetic scale, which might, in turn, produce a more integrated understanding of global diversity dynamics.     

Steady state peripheral blood provides cells with functional and metabolic characteristics of real hematopoietic stem cells

Hematopoietic stem cells (HSCs), which are located in the bone marrow, also circulate in cord and peripheral blood. Despite high availability, HSCs from steady state peripheral blood (SSPB) are little known and not used for research or cell therapy. We thus aimed to characterize and select HSCs from SSPB by a direct approach with a view to delineating their main functional and metabolic properties and the mechanisms responsible for their maintenance. We chose to work on Side Population (SP) cells which are highly enriched in HSCs in mouse, human bone marrow, and cord blood. However, no SP cells from SSBP have as yet been characterized. Here we showed that SP cells from SSPB exhibited a higher proliferative capacity and generated more clonogenic progenitors than non‐SP cells in vitro. Furthermore, xenotransplantation studies on immunodeficient mice demonstrated that SP cells are up to 45 times more enriched in cells with engraftment capacity than non‐SP cells. From a cell regulation point of view, we showed that SP activity depended on O₂ concentrations close to those found in HSC niches, an effect which is dependent on both hypoxia‐induced factors HIF‐1α and HIF‐2α. Moreover SP cells displayed a reduced mitochondrial mass and, in particular, a lower mitochondrial activity compared to non‐SP cells, while they exhibited a similar level of glucose incorporation. These results provided evidence that SP cells from SSPB displayed properties of very primitive cells and HSC, thus rendering them an interesting model for research and cell therapy.     

Phenomics allows identification of genomic regions affecting maize stomatal conductance with conditional effects of water deficit and evaporative demand

Stomatal conductance is central for the trades‐off between hydraulics and photosynthesis. We aimed at deciphering its genetic control and that of its responses to evaporative demand and water deficit, a nearly impossible task with gas exchanges measurements. Whole‐plant stomatal conductance was estimated via inversion of the Penman–Monteith equation from data of transpiration and plant architecture collected in a phenotyping platform. We have analysed jointly 4 experiments with contrasting environmental conditions imposed to a panel of 254 maize hybrids. Estimated whole‐plant stomatal conductance closely correlated with gas‐exchange measurements and biomass accumulation rate. Sixteen robust quantitative trait loci (QTLs) were identified by genome wide association studies and co‐located with QTLs of transpiration and biomass. Light, vapour pressure deficit, or soil water potential largely accounted for the differences in allelic effects between experiments, thereby providing strong hypotheses for mechanisms of stomatal control and a way to select relevant candidate genes among the 1–19 genes harboured by QTLs. The combination of allelic effects, as affected by environmental conditions, accounted for the variability of stomatal conductance across a range of hybrids and environmental conditions. This approach may therefore contribute to genetic analysis and prediction of stomatal control in diverse environments.     

Identification of SNAREs involved in regulated exocytosis in the pancreatic acinar cell.

The molecular basis of exocytotic membrane fusion in the pancreatic acinar cell was investigated using an in vitro assay that measures both zymogen granule-plasma membrane fusion and granule-granule fusion. These two fusion events were differentially sensitive to Ca(2+), suggesting that they are controlled by different Ca(2+)-sensing mechanisms. Botulinum neurotoxin C (BoNT/C) treatment of the plasma membranes caused cleavage of syntaxin 2, the apical isoform of this Q-SNARE, but did not affect syntaxin 4, the basolateral isoform. BoNT/C also cleaved syntaxin 3, the zymogen granule isoform. BoNT/C treatment of plasma membranes abolished granule-plasma membrane fusion, whereas toxin treatment of the granules reduced granule-plasma membrane fusion and abolished granule-granule fusion. Tetanus toxin cleaved granule-associated synaptobrevin 2 but caused only a small reduction in both granule-plasma membrane fusion and granule-granule fusion. Our results indicate that syntaxin 2 is the isoform that mediates fusion between zymogen granules and the apical plasma membrane of the acinar cell. Syntaxin 3 mediates granule-granule fusion, which might be involved in compound exocytosis. In contrast, the major R-SNARE on the zymogen granule remains to be identified.     

Advantages of sucrose-dependent extracellular polysaccharide production to lactic acid bacteria in sucrose-rich environments

G.A. DYKES, I. GEORNARAS AND A. VON HOLY. 1995. Some possible advantages of sucrosedependent extracellular polysaccharide production to Lactobacillus L191 from baker's yeast were investigated. A ca log 1 plaque-forming units ml^-1decrease in attachment of bacteriophage AB1 to cells of Lactobacillus L191 grown in the presence of sucrose as compared to cells grown in the absence of sucrose was noted. On the other hand, a ca log 1 colony-forming units cm^-2increase in attachment of Lactobacillus L191 to stainless steel surfaces when grown in the presence of sucrose compared to the absence of sucrose was observed. It was concluded that sucrose-dependent extracellular polysaccharide may provide a series of individually small but jointly synergistic selective advantages to strains producing it.