Dating placentalia: Morphological clocks fail to close the molecular fossil gap

Dating the origin of Placentalia has been a contentious issue for biologists and paleontologists. Although it is likely that crown‐group placentals originated in the Late Cretaceous, nearly all molecular clock estimates point to a deeper Cretaceous origin. An approach with the potential to reconcile this discrepancy could be the application of a morphological clock. This would permit the direct incorporation of fossil data in node dating, and would break long internal branches of the tree, so leading to improved estimates of node ages. Here, we use a large morphological dataset and the tip‐calibration approach of MrBayes. We find that the estimated date for the origin of crown mammals is much older, ～130–145 million years ago (Ma), than fossil and molecular clock data (～80–90 Ma). Our results suggest that tip calibration may result in estimated dates that are more ancient than those obtained from other sources of data. This can be partially overcome by constraining the ages of internal nodes on the tree; however, when this was applied to our dataset, the estimated dates were still substantially more ancient than expected. We recommend that results obtained using tip calibration, and possibly morphological dating more generally, should be treated with caution.     

Evolutionary dynamics of methicillin-resistant Staphylococcus aureus within a healthcare system

BackgroundIn the past decade, several countries have seen gradual replacement of endemic multi-resistant healthcare-associated methicillin-resistant Staphylococcus aureus (MRSA) with clones that are more susceptible to antibiotic treatment. One example is Singapore, where MRSA ST239, the dominant clone since molecular profiling of MRSA began in the mid-1980s, has been replaced by ST22 isolates belonging to EMRSA-15, a recently emerged pandemic lineage originating from Europe.ResultsWe investigated the population structure of MRSA in Singaporean hospitals spanning three decades, using whole genome sequencing. Applying Bayesian phylogenetic methods we report that prior to the introduction of ST22, the ST239 MRSA population in Singapore originated from multiple introductions from the surrounding region; it was frequently transferred within the healthcare system resulting in a heterogeneous hospital population. Following the introduction of ST22 around the beginning of the millennium, this clone spread rapidly through Singaporean hospitals, supplanting the endemic ST239 population. Coalescent analysis revealed that although the genetic diversity of ST239 initially decreased as ST22 became more dominant, from 2007 onwards the genetic diversity of ST239 began to increase once more, which was not associated with the emergence of a sub-clone of ST239. Comparative genomic analysis of the accessory genome of the extant ST239 population identified that the Arginine Catabolic Mobile Element arose multiple times, thereby introducing genes associated with enhanced skin colonization into this population.ConclusionsOur results clearly demonstrate that, alongside clinical practice and antibiotic usage, competition between clones also has an important role in driving the evolution of nosocomial pathogen populations.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-015-0643-z) contains supplementary material, which is available to authorized users.     

Rocks and clocks: calibrating the Tree of Life using fossils and molecules

A great tradition in macroevolution and systematics has been the ritual squabbling between palaeontologists and molecular biologists. But, because both sides were talking past each other, they could never agree. Practitioners in both fields should play to their strengths and work together: palaeontologists can provide minimum constraints on branching points in the Tree of Life with considerable precision, and estimate the extent of unrecorded prehistory. Molecular tree analysts have remarkable modelling tools in their armoury to convert multiple minimum age constraints into meaningful dated trees. As we discuss here, work should now focus on establishing reasonable, dated trees that satisfy rigorous assessment of the available fossils and careful consideration of molecular tree methods: rocks and clocks together are an unbeatable combination. Reliably dated trees provide, for the first time, the opportunity to explore wider questions in macroevolution.     

Paleontological evidence to date the tree of life

The role of fossils in dating the tree of life has been misunderstood. Fossils can provide good "minimum" age estimates for branches in the tree, but "maximum" constraints on those ages are poorer. Current debates about which are the "best" fossil dates for calibration move to consideration of the most appropriate constraints on the ages of tree nodes. Because fossil-based dates are constraints, and because molecular evolution is not perfectly clock-like, analysts should use more rather than fewer dates, but there has to be a balance between many genes and few dates versus many dates and few genes. We provide "hard" minimum and "soft" maximum age constraints for 30 divergences among key genome model organisms; these should contribute to better understanding of the dating of the animal tree of life.     

Direction repulsion goes global

When viewing two superimposed, translating sets of dots moving in different directions, one overestimates direction difference. This phenomenon of direction repulsion is thought to be driven by inhibitory interactions between directionally tuned motion detectors. However, there is disagreement on where this occurs-at early stages of motion processing, when local motions are extracted; or at the later, global motion-processing stage following "pooling" of these local measures. These two stages of motion processing have been identified as occurring in area V1 and the human homolog of macaque MT/V5, respectively. We designed experiments in which local and global predictions of repulsion are pitted against one another. Our stimuli contained a target set of dots, moving at a uniform speed, superimposed on a "mixed-speed" distractor set. Because the perceived speed of a mixed-speed stimulus is equal to the dots' average speed, a global-processing account of direction repulsion predicts that repulsion magnitude induced by a mixed-speed distractor will be indistinguishable from that induced by a single-speed distractor moving at the same mean speed. This is exactly what we found. These results provide compelling evidence that global-motion interactions play a major role in driving direction repulsion.     

Biochemical Evidence of Selective Nerve Cell Changes in the Normal Ageing Human and Rat Brain

Abstract: Atrophy with ageing of human whole brain, entire temporal lobe, and caudate nucleus was assessed in autopsy specimens, by biochemical techniques. Only the caudate nucleus showed changes. Markers for several neurotransmitter systems were also examined for changes with age. In neocortex and temporal lobe of human brain, small decreases were detected in markers of cholinergic nerve terminals, whereas a large decrease (79%) occurred in the caudate nucleus. Findings were similar in striatum from 3–33-month-old rats. No change occurred in binding of [³H]quinuclidinyl benzilate by human samples. Markers of serotonergic terminals were also unchanged in human and rat brain. By contrast, binding of [³H]lysergic acid diethylamide and [³H]serotonin was decreased (32–81%) in human neocortex and temporal lobe, but not in caudate nucleus. A 43% loss of a marker of γ-aminobutyrate terminals occurred in human neocortex, while [³H]muscimol binding increased (179%). No changes were detected in markers of catecholamine synapses in temporal lobe or rat striatum. Hence, with human ageing there appears to be a loss of markers of γ-aminobutyrate neurones intrinsic to neocortex and acetylcholine cells intrinsic to the caudate nucleus, as well as a change in postsynaptic serotonin receptors in neocortex. These losses are accompanied by relative preservation of markers of ascending projections from basal forebrain and brain stem.     

How to put all your eggs in one basket: empirical patterns of offspring provisioning throughout a mother's lifetime

Maternal effects arise when a mother's phenotype or the environment she experiences influences the phenotype of her progeny. Most studies of adaptive maternal effects are a "snapshot" of a mother's lifetime offspring provisioning and do not generally consider the effects of earlier siblings on those produced later. Here we show that in soil mites, offspring provisioning strategies are dynamic, changing from an emphasis on egg number in young females to egg size in older females. This pattern may be adaptive if it increases the survival of younger offspring that must compete with older, larger siblings. The dynamic shift in egg provisioning was greater in high-food environments in which females lived longer, creating increasing asymmetry in offspring competitive abilities. Females reared in isolation and in the presence of a high-density colony had identical provisioning strategies, suggesting that, unlike males in this species, females do not use pheromones to assess colony size. Our findings suggest that the adaptive significance of maternal effects may be misinterpreted when studies consider only a snapshot of a female's offspring provisioning strategy or when components of the offspring provisioning strategy are studied in isolation.     

Expression of dominant-negative Fas-associated death domain blocks human keratinocyte apoptosis and vesication induced by sulfur mustard

DNA damaging agents up-regulate levels of the Fas receptor or its ligand, resulting in recruitment of Fas-associated death domain (FADD) and autocatalytic activation of caspase-8, consequently activating the executioner caspases-3, -6, and -7. We found that human epidermal keratinocytes exposed to a vesicating dose (300 microm) of sulfur mustard (SM) exhibit a dose-dependent increase in the levels of Fas receptor and Fas ligand. Immunoblot analysis revealed that the upstream caspases-8 and -9 are both activated in a time-dependent fashion, and caspase-8 is cleaved prior to caspase-9. These results are consistent with the activation of both death receptor (caspase-8) and mitochondrial (caspase-9) pathways by SM. Pretreatment of keratinocytes with a peptide inhibitor of caspase-3 (Ac-DEVD-CHO) suppressed SM-induced downstream markers of apoptosis. To further analyze the importance of the death receptor pathway in SM toxicity, we utilized Fas- or tumor necrosis factor receptor-neutralizing antibodies or constructs expressing a dominant-negative FADD (FADD-DN) to inhibit the recruitment of FADD to the death receptor complex and block the Fas/tumor necrosis factor receptor pathway following SM exposure. Keratinocytes pretreated with Fas-blocking antibody or stably expressing FADD-DN and exhibiting reduced levels of FADD signaling demonstrated markedly decreased caspase-3 activity when treated with SM. In addition, the processing of procaspases-3, -7, and -8 into their active forms was observed in SM-treated control keratinocytes, but not in FADD-DN cells. Blocking the death receptor complex by expression of FADD-DN additionally inhibited SM-induced internucleosomal DNA cleavage and caspase-6-mediated nuclear lamin cleavage. Significantly, we further found that altering the death receptor pathway by expressing FADD-DN in human skin grafted onto nude mice reduces vesication and tissue injury in response to SM. These results indicate that the death receptor pathway plays a pivotal role in SM-induced apoptosis and is therefore a target for therapeutic intervention to reduce SM injury.