Linking recruitment to trophic factors: revisiting the Beverton--Holt recruitment model from a life history and multispecies perspective

The Beverton--Holt recruitment model can be derived from arguments about evolution of life history traits related to foraging and predation risk, along with spatially localized and temporarily competitive relationships in the habitats where juvenile fish forage and face predation risk while foraging. This derivation explicitly represents two key biotic factors, food supply (I) and predator abundance (R), which appear as a risk ratio (R/I) that facilitates modelling of changes in trophic circumstances and analysis of historical data. The same general recruitment relationship is expected whether the juvenile life history is simple or involves a complex sequence of stanzas; in the complex case, the Beverton--Holt parameters represent weighted averages or integrals of risk ratios over the stanzas. The relationship should also apply in settings where there is complex, mesoscale variation in habitat and predation risk, provided that animals sense this variation and move about so as to achieve similar survival at all mesoscale rearing sites. The model predicts that changes in food and predation risk can be amplified violently in settings where juvenile survival rate is low, producing large changes in recruitment rates over time.     

Corals shed bacteria as a potential mechanism of resilience to organic matter enrichment

Understanding the mechanisms of resilience of coral reefs to anthropogenic stressors is a critical step toward mitigating their current global decline. Coral–bacteria associations are fundamental to reef health and disease, but direct observations of these interactions remain largely unexplored. Here, we use novel technology, high-speed laser scanning confocal microscopy on live coral (Pocillopora damicornis), to test the hypothesis that corals exert control over the abundance of their associated bacterial communities by releasing (‘shedding'') bacteria from their surface, and that this mechanism can counteract bacterial growth stimulated by organic inputs. We also test the hypothesis that the coral pathogen Vibrio coralliilyticus can evade such a defense mechanism. This first report of direct observation with high-speed confocal microscopy of living coral and its associated bacterial community revealed a layer (3.3–146.8 μm thick) on the coral surface where bacteria were concentrated. The results of two independent experiments showed that the bacterial abundance in this layer was not sensitive to enrichment (5 mg l⁻¹ peptone), and that coral fragments exposed to enrichment released significantly more bacteria from their surfaces than control corals (P<0.01; 35.9±1.4 × 10⁵ cells cm⁻² coral versus 1.3±0.5 × 10⁵ cells cm⁻² coral). Our results provide direct support to the hypothesis that shedding bacteria may be an important mechanism by which coral-associated bacterial abundances are regulated under organic matter stress. Additionally, the novel ability to watch this ecological behavior in real-time at the microscale opens an unexplored avenue for mechanistic studies of coral–microbe interactions.     

Disrupted phylogeographical microsatellite and chloroplast DNA patterns indicate a vicariance rather than long‐distance dispersal origin for the disjunct distribution of the Chilean endemic Dioscorea biloba (Dioscoreaceae) around the Atacama Desert

Aim The Chilean endemic Dioscorea biloba (Dioscoreaceae) is a dioecious geophyte that shows a remarkable 600 km north–south disjunction in the peripheral arid area of the Atacama Desert. Its restricted present‐day distribution and probable Neogene origin indicate that its populations have a history linked to that of the Atacama Desert, making this an ideal model species with which to investigate the biogeography of the region. Location Chile, Atacama Desert and peripheral arid area. Methods Two hundred and seventy‐five individuals from nine populations were genotyped for seven nuclear microsatellite loci, and plastid trnL–F and trnT–L sequences were obtained for a representative subset of these. Analyses included the estimation of genetic diversity and population structure through clustering, Bayesian and analysis of molecular variance analyses, and statistical parsimony networks of chloroplast haplotypes. Isolation by distance was tested against alternative dispersal hypotheses. Results Microsatellite markers revealed moderate to high levels of genetic diversity within populations, with those from the southern Limarí Valley showing the highest values and northern populations showing less exclusive alleles. Bayesian analysis of microsatellite data identified three genetic groups that corresponded to geographical ranges. Chloroplast phylogeography revealed no haplotypes shared between northern and southern ranges, and little haplotype sharing between the two neighbouring southern valleys. Dispersal models suggested the presence of extinct hypothetical populations between the southern and northern ranges. Main conclusions Our results are consistent with prolonged isolation of the northern and southern groups, mediated by the life‐history traits of the species. Significant isolation was revealed at both large and moderate distances as gene flow was not evident even between neighbouring valleys. Bayesian analyses of microsatellite and chloroplast haplotype diversity identified the southern area of Limarí as the probable area of origin of the species. Our data do not support recent dispersal of D. biloba from the southern range into Antofagasta, but indicate the fragmentation of an earlier wider range, concomitant with the Pliocene–Pleistocene climatic oscillations, with subsequent extinctions of the Atacama Desert populations and the divergence of the peripheral ones as a consequence of genetic drift.     

Floral organogenesis of Chloranthus sessilifolius, with special emphasis on the morphological nature of the androecium of Chloranthus (Chloranthaceae)

 Floral organogenesis of Chloranthus sessilifolius K. F. Wu is described. The inflorescence primordium is dome-like in the beginning and then elongates, and bract primordia initiate almost decussately. Each floral primordium, arising from the axil of a bract, soon becomes a scale-like structure, with three primordia of androecial lobes originating from its abaxial part, and the gynoecial primordium in adaxial position. As the androecial lobes become more distinct, four thecae are already in differentiation, and the gynoecial primordium appears as a shallow disc. The androecial lobes do not extend their length until the thecae approach maturity and the stigma is differentiated. The androecial lobes are united at all the stages of development, and the entire androecium falls off as a unit at the end of anthesis. Based on these results, combined with published evidence from neobotany, palaeobotany and phylogenetic studies, the morphological nature of the androecium of Chloranthus is further discussed. Our studies support the viewpoint that the androecial structure of Chloranthus may have arisen by splitting of a single stamen with 2 marginal thecae. Received May 2, 2001 Accepted December 18, 2001     

Phylogeny of the Altingiaceae based on cpDNA matK, PY-IGS and nrDNA ITS sequences

 Phylogenetic relationships of the three genera of the family Altingiaceae, i.e., Altingia, Liquidambar and Semiliquidambar, based on matK sequences and the intergenic spacer between the psaA and ycf3 genes (PY-IGS) of cpDNA, and on the internal transcribed spacer (ITS) of nrDNA were studied. Phylogenetic trees based on the three data sets (matK, PY-IGS and ITS) were generated using Hamamelis japonica and Mytilaria laosensis (Hamamelidaceae), Cercidiphyllum japonicum (Cercidiphyllaceae), and Daphniphyllum calycinum (Daphniphyllaceae) as outgroups. The partition-homogeneity tests indicated that the three data sets and the combined data are homogeneous. A combined analysis also generated a strongly supported phylogeny. The phylogenetic trees show that the North American and western Asian species, L. styraciflua and L. orientalis, respectively, form a monophyletic group which is sister to the clade including all Asian species in the family. The genus Liquidambar is paraphyletic with Altingia and Semiliquidambar nested within. Phylogenetic analyses of the molecular data indicate that taxonomic reexamination of the generic delimitation in the Altingiaceae is needed. Received December 20, 2000 Accepted June 25, 2001     

Survival costs of reproduction vary with age in North American red squirrels

The costs of reproduction are expected to be higher under unfavourable conditions, so that breeding in years of low food supply should have important costs. In addition, the costs of reproduction may be contingent on the age of individuals, and young growing and old senescent individuals should suffer higher costs than the prime-age ones. We tested these predictions by investigating the costs of reproduction as a function of food availability and age in female North American red squirrels using the long-term data on survival and reproduction. We found that the costs of reproduction were independent of food supply, and we did not detect any trade-off between the current and future reproduction. We also did not detect any survival cost of reproduction for the prime-age females, but found evidence for survival costs in yearlings and old (6 years or above) females with successfully breeding individuals having a lower chance of survival compared with unsuccessful or non-breeding ones. These results supported our prediction that the costs of reproduction depended on the age of female red squirrels and were higher in young growing and old senescent individuals. Our study also indicated that, in contrast to large herbivores, heterogeneity in individual quality and viability selection in red squirrels do not affect the study of trade-offs and of the age variation in life-history traits.     

Characterizing and predicting species distributions across environments and scales: Argentine ant occurrences in the eye of the beholder

Aim Species distribution models (SDMs) or, more specifically, ecological niche models (ENMs) are a useful and rapidly proliferating tool in ecology and global change biology. ENMs attempt to capture associations between a species and its environment and are often used to draw biological inferences, to predict potential occurrences in unoccupied regions and to forecast future distributions under environmental change. The accuracy of ENMs, however, hinges critically on the quality of occurrence data. ENMs often use haphazardly collected data rather than data collected across the full spectrum of existing environmental conditions. Moreover, it remains unclear how processes affecting ENM predictions operate at different spatial scales. The scale (i.e. grain size) of analysis may be dictated more by the sampling regime than by biologically meaningful processes. The aim of our study is to jointly quantify how issues relating to region and scale affect ENM predictions using an economically important and ecologically damaging invasive species, the Argentine ant (Linepithema humile). Location California, USA. Methods We analysed the relationship between sampling sufficiency, regional differences in environmental parameter space and cell size of analysis and resampling environmental layers using two independently collected sets of presence/absence data. Differences in variable importance were determined using model averaging and logistic regression. Model accuracy was measured with area under the curve (AUC) and Cohen's kappa. Results We first demonstrate that insufficient sampling of environmental parameter space can cause large errors in predicted distributions and biological interpretation. Models performed best when they were parametrized with data that sufficiently sampled environmental parameter space. Second, we show that altering the spatial grain of analysis changes the relative importance of different environmental variables. These changes apparently result from how environmental constraints and the sampling distributions of environmental variables change with spatial grain. Conclusions These findings have clear relevance for biological inference. Taken together, our results illustrate potentially general limitations for ENMs, especially when such models are used to predict species occurrences in novel environments. We offer basic methodological and conceptual guidelines for appropriate sampling and scale matching.     

Microsecond Dynamics During the Binding-induced Folding of an Intrinsically Disordered Protein

Tau is an intrinsically disordered protein implicated in many neurodegenerative diseases. The repeat domain fragment of tau, tau-K18, is known to undergo a disorder to order transition in the presence of lipid micelles and vesicles, in which helices form in each of the repeat domains. Here, the mechanism of helical structure formation, induced by a phospholipid mimetic, sodium dodecyl sulfate (SDS) at sub-micellar concentrations, has been studied using multiple biophysical probes. A study of the conformational dynamics of the disordered state, using photoinduced electron transfer coupled to fluorescence correlation spectroscopy (PET-FCS) has indicated the presence of an intermediate state, I, in equilibrium with the unfolded state, U. The cooperative binding of the ligand (L), SDS, to I has been shown to induce the formation of a compact, helical intermediate (IL₅) within the dead time (∼37 µs) of a continuous flow mixer. Quantitative analysis of the PET-FCS data and the ensemble microsecond kinetic data, suggests that the mechanism of induction of helical structure can be described by a U ↔ I ↔ IL₅ ↔ FL₅ mechanism, in which the final helical state, FL₅, forms from IL₅ with a time constant of 50–200 µs. Finally, it has been shown that the helical conformation is an aggregation-competent state that can directly form amyloid fibrils.     

Membrane Binding and Homodimerization of Atg16 Via Two Distinct Protein Regions is Essential for Autophagy in Yeast

Macroautophagy is a bulk degradation mechanism in eukaryotic cells. Efficiency of an essential step of this process in yeast, Atg8 lipidation, relies on the presence of Atg16, a subunit of the Atg12–Atg5-Atg16 complex acting as the E3-like enzyme in the ubiquitination-like reaction. A current view on the functional structure of Atg16 in the yeast S. cerevisiae comes from the two crystal structures that reveal the Atg5-interacting α-helix linked via a flexible linker to another α-helix of Atg16, which then assembles into a homodimer. This view does not explain the results of previous in vitro studies revealing Atg16-dependent deformations of membranes and liposome-binding of the Atg12–Atg5 conjugate upon addition of Atg16. Here we show that Atg16 acts as both a homodimerizing and peripheral membrane-binding polypeptide. These two characteristics are imposed by the two distinct regions that are disordered in the nascent protein. Atg16 binds to membranes in vivo via the amphipathic α-helix (amino acid residues 113–131) that has a coiled-coil-like propensity and a strong hydrophobic face for insertion into the membrane. The other protein region (residues 64–99) possesses a coiled-coil propensity, but not amphipathicity, and is dispensable for membrane anchoring of Atg16. This region acts as a Leu-zipper essential for formation of the Atg16 homodimer. Mutagenic disruption in either of these two distinct domains renders Atg16 proteins that, in contrast to wild type, completely fail to rescue the autophagy-defective phenotype of atg16Δ cells. Together, the results of this study yield a model for the molecular mechanism of Atg16 function in macroautophagy.     

Structural Insights into the Mechanism of Base Excision by MBD4

DNA glycosylases remove damaged or modified nucleobases by cleaving the N-glycosyl bond and the correct nucleotide is restored through subsequent base excision repair. In addition to excising threatening lesions, DNA glycosylases contribute to epigenetic regulation by mediating DNA demethylation and perform other important functions. However, the catalytic mechanism remains poorly defined for many glycosylases, including MBD4 (methyl-CpG binding domain IV), a member of the helix-hairpin-helix (HhH) superfamily. MBD4 excises thymine from G·T mispairs, suppressing mutations caused by deamination of 5-methylcytosine, and it removes uracil and modified uracils (e.g., 5-hydroxymethyluracil) mispaired with guanine. To investigate the mechanism of MBD4 we solved high-resolution structures of enzyme-DNA complexes at three stages of catalysis. Using a non-cleavable substrate analog, 2′-deoxy-pseudouridine, we determined the first structure of an enzyme-substrate complex for wild-type MBD4, which confirms interactions that mediate lesion recognition and suggests that a catalytic Asp, highly conserved in HhH enzymes, binds the putative nucleophilic water molecule and stabilizes the transition state. Observation that mutating the Asp (to Gly) reduces activity by 2700-fold indicates an important role in catalysis, but probably not one as the nucleophile in a double-displacement reaction, as previously suggested. Consistent with direct-displacement hydrolysis, a structure of the enzyme-product complex indicates a reaction leading to inversion of configuration. A structure with DNA containing 1-azadeoxyribose models a potential oxacarbenium-ion intermediate and suggests the Asp could facilitate migration of the electrophile towards the nucleophilic water. Finally, the structures provide detailed snapshots of the HhH motif, informing how these ubiquitous metal-binding elements mediate DNA binding.