The 10kTrees Website: A New Online Resource for Primate Phylogeny

The comparative method plays a central role in efforts to uncover the adaptive basis for primate behaviors, morphological traits, and cognitive abilities.[1-4] The comparative method has been used, for example, to infer that living in a larger group selects for a larger neocortex,[5][6] that primate territoriality favors a longer day range relative to home range size,[7] and that sperm competition can account for the evolution of primate testes size.[8][9] Comparison is fundamental for reconstructing behavioral traits in the fossil record, for example, in studies of locomotion and diet.[10-13] Recent advances in comparative methods require phylogenetic information,[2][14-16] but our knowledge of phylogenetic information is imperfect. In the face of uncertainty about evolutionary relationships, which phylogeny should one use? Here we provide a new resource for comparative studies of primates that enables users to run comparative analyses on multiple primate phylogenies Importantly, the 10,000 trees that we provide are not random, but instead use recent systematic methods to create a plausible set of topologies that reflect our certainty about some nodes on the tree and uncertainty about other nodes, given the dataset. The trees also reflect uncertainty about branch lengths.Human Evolutionary Biolog

Magic, Religion, and Science: Secularization Trends and Continued Coexistence

While multiple studies have applied cultural evolutionary perspectives to the study of religion, few studies have examined the cultural evolutionary dynamics of a more secretive but equally ubiquitous form of supernatural belief: magic. We conducted two studies, an American nationally representative survey and a comparative phylogenetic analysis of religious traditions, to test three hypothesized cultural evolutionary drivers for beliefs in magic. We find the greatest support for the hypothesis that magic is employed when it provides its users benefits that are distinct from those provided by either science or religion, some support for secularization (broadly conceived) trends applying to magic, and no evidence that innate and unavoidable features of human cognition are primary drivers of the cultural evolution of magical beliefs. We conclude by suggesting specific hypothesized benefits for magic that may account for the evolution of humanity's facultative (i.e., context‐dependent) use of magical beliefs

Primate Extinction Risk and Historical Patterns of Speciation and Extinction in Relation to Body Mass

Body mass is thought to influence diversification rates, but previous studies have produced ambiguous results. We investigated patterns of diversification across 100 trees obtained from a new Bayesian inference of primate phylogeny that sampled trees in proportion to their posterior probabilities. First, we used simulations to assess the validity of previous studies that used linear models to investigate the links between IUCN Red List status and body mass. These analyses support the use of linear models for ordinal ranked data on threat status, and phylogenetic generalized linear models revealed a significant positive correlation between current extinction risk and body mass across our tree block. We then investigated historical patterns of speciation and extinction rates using a recently developed maximum-likelihood method. Specifically, we predicted that body mass correlates positively with extinction rate because larger bodied organisms reproduce more slowly, and body mass correlates negatively with speciation rate because smaller bodied organisms are better able to partition niche space. We failed to find evidence that extinction rates covary with body mass across primate phylogeny. Similarly, the speciation rate was generally unrelated to body mass, except in some tests that indicated an increase in the speciation rate with increasing body mass. Importantly, we discovered that our data violated a key assumption of sample randomness with respect to body mass. After correcting for this bias, we found no association between diversification rates and mass.Human Evolutionary Biolog

CONCEPTS FOR POWER AND ENERGY ANALYSIS IN NASTIC STRUCTURES

ABSTRACT Nastic structures are potentially high-energy density smart materials that will be capable of achieving controllable deformation and shape change due to internal microactuation that functions on principles found in the biological process of nastic motion. In plants, nastic motion is accomplished through osmotic pressure changes causing a respective increase or decrease in cell volume, thereby causing net movement. In nastic structures, osmotic pressure is increased by moving fluid from low concentration to high concentration areas by means of active transport, powered by adenosine triphosphate (ATP) hydrolysis. Power analysis involves calculating possible ranges of actuation as a result of interior pressure exchanges and hydraulic flux rates which will determine the speed of actuation. Because pressure inside the actuating cylinder is uniform, the cylinder undergoes deformation in all the three dimensions. Predicting the work-energy balance involves considering the factors that determine the total volumetric change, including cylinder wall expansion, surface bulging and stretching, and outside forces that oppose the actuation. The hydraulic flux rates determine both the force magnitude and the actuation speed. Energy analysis considers the pressure variation range needed to accomplish the desired actuation deflection, and the energy required for active transport mechanisms to move the volume of fluid into the nastic actuator. Nonlinear effects are present, as the pressure inside the actuation cylinder increases, it takes more energy for active transport to continue moving fluid into it. The chemical reaction of ATP hydrolysis supplies the energy for active transport, which is related to the ratio of the reactants, to the products, as well as to the pH level. As the pH lowers, more energy is released through ATP hydrolysis. Therefore, as pH decreases, ATP Hydrolysis releases more energy, enabling active transport to move more fluid into the actuation cylinder, thereby increasing the internal osmotic pressure and causing material deformation work and actuation

Shared cultural history as a predictor of political and economic changes among nation states

Political and economic risks arise from social phenomena that spread within and across countries. Regime changes, protest movements, and stock market and default shocks can have ramifications across the globe. Quantitative models have made great strides at predicting these events in recent decades but incorporate few explicitly measured cultural variables. However, in recent years cultural evolutionary theory has emerged as a major paradigm to understand the inheritance and diffusion of human cultural variation. Here, we combine these two strands of research by proposing that measures of socio-linguistic affiliation derived from language phylogenies track variation in cultural norms that influence how political and economic changes diffuse across the globe. First, we show that changes over time in a country's democratic or autocratic character correlate with simultaneous changes among their socio-linguistic affiliations more than with changes of spatially proximate countries. Second, we find that models of changes in sovereign default status favor including socio-linguistic affiliations in addition to spatial data. These findings suggest that better measurement of cultural networks could be profoundly useful to policy makers who wish to diversify commercial, social, and other forms of investment across political and economic risks on an international scale

Metallothionein-I/II expression associates with the astrocyte DNA damage response and not Alzheimer-type pathology in the ageing brain

Oxidative stress and oxidative DNA damage are early features of mild cognitive impairment and Alzheimer’s disease (AD), occurring before the formation of classical AD neuropathology, and resulting from an imbalance between pro- and anti-oxidants. Astrocytes play a major neuroprotective role, producing high levels of anti-oxidants including metallothionein-I and –II (MT-I/II). In the present study we characterized the immunoreactive profile of MT-I/II in the temporal cortex of the Cognitive Function and Ageing Study (CFAS) aging population-representative neuropathology cohort, and examined H2O2-modulation of MT transcription by human astrocytes. MT-I/II is primarily expressed by astrocytes in the aging brain, but is also associated with pyramidal neurons in a small proportion of cases. Astrocyte expression of MT-I/II does not correlate with Alzheimer-type pathology (Aβ plaques and neurofibrillary tangles) but does relate to astrocyte oxidative DNA damage (rs= 0.312, p= 0.006) and the astrocyte response to oxidative DNA damage in vivo (rs= 0.238, p= 0.04), and MT gene expression is significantly induced in human astrocytes response to oxidative stress in vitro (p=0.01). In contrast, neuronal MT-I/II does not relate to oxidative DNA damage or the neuronal DNA damage response, but is significantly higher in cases with high levels of local tangle pathology (p=0.007). As MT-I/II is neuroprotective against oxidative stress, modulation of MT-I/II expression is a potential therapeutic target to treat the onset and progression of cognitive impairment

The effectiveness of the Inspiring Futures parenting programme in improving behavioural and emotional outcomes in primary school children with behavioural or emotional difficulties: study protocol for a randomised controlled trial.

textabstractBackground: There is a need to build the evidence base of early interventions promoting children's health and development in the UK. Malachi Specialist Family Support Services ('Malachi') is a voluntary sector organisation based in the UK that delivers a therapeutic parenting group programme called Inspiring Futures to parents of children identified as having behavioural and emotional difficulties. The programme comprises two parts, delivered sequentially: (1) a group-based programme for all parents for 10-12 weeks, and (2) one-to-one sessions with selected parents from the group-based element for up to 12 weeks. Methods/design: A randomised controlled trial will be conducted to evaluate Malachi's Inspiring Futures parenting programme. Participants will be allocated to one of two possible arms, with follow-up measures at 16 weeks (post-parent group programme) and at 32 weeks (post-one-to-one sessions with selected parents). The sample size is 248 participants with a randomisation allocation ratio of 1:1. The intervention arm will be offered the Inspiring Futures programme. The control group will receive services as usual. The aim is to determine the effectiveness of the Inspiring Futures programme on the primary outcome of behavioural and emotional difficulties of primary school children identified as having behavioural or emotional difficulties. Discussion: This study will further enhance the evidence for early intervention parenting programmes for child behavioural and emotional problems in the UK

Cosmopolitanism, Self-Interest and World Government

Cosmopolitans, if they are interested in seeing their principles realised, must hope that persons worldwide can become motivated to act in accordance with what those principles demand. But although it is important that genuinely moral motives are developed, we should not ignore the potential pragmatic value of self-interested motives to the realisation of cosmopolitan ends. This article considers three such motives: economic self-interest, prudent self-interest and democratic self-interest. I argue that in each case, usefully harnessing these motivations implies or requires global political integration that amounts to ‘world government’. This argument has the effect of reinforcing the already popular view that realising cosmopolitan principles entails global political integration. For those who already endorse that view, my argument will act as supporting evidence; by contrast it represents a challenge to those cosmopolitans who have remained ambivalent about, or indeed have explicitly rejected, the need for global political integration

Development and implementation of high-throughput SNP genotyping in barley

<p>Abstract</p> <p>Background</p> <p>High density genetic maps of plants have, nearly without exception, made use of marker datasets containing missing or questionable genotype calls derived from a variety of genic and non-genic or anonymous markers, and been presented as a single linear order of genetic loci for each linkage group. The consequences of missing or erroneous data include falsely separated markers, expansion of cM distances and incorrect marker order. These imperfections are amplified in consensus maps and problematic when fine resolution is critical including comparative genome analyses and map-based cloning. Here we provide a new paradigm, a high-density consensus genetic map of barley based only on complete and error-free datasets and genic markers, represented accurately by graphs and approximately by a best-fit linear order, and supported by a readily available SNP genotyping resource.</p> <p>Results</p> <p>Approximately 22,000 SNPs were identified from barley ESTs and sequenced amplicons; 4,596 of them were tested for performance in three pilot phase Illumina GoldenGate assays. Data from three barley doubled haploid mapping populations supported the production of an initial consensus map. Over 200 germplasm selections, principally European and US breeding material, were used to estimate minor allele frequency (MAF) for each SNP. We selected 3,072 of these tested SNPs based on technical performance, map location, MAF and biological interest to fill two 1536-SNP "production" assays (BOPA1 and BOPA2), which were made available to the barley genetics community. Data were added using BOPA1 from a fourth mapping population to yield a consensus map containing 2,943 SNP loci in 975 marker bins covering a genetic distance of 1099 cM.</p> <p>Conclusion</p> <p>The unprecedented density of genic markers and marker bins enabled a high resolution comparison of the genomes of barley and rice. Low recombination in pericentric regions is evident from bins containing many more than the average number of markers, meaning that a large number of genes are recombinationally locked into the genetic centromeric regions of several barley chromosomes. Examination of US breeding germplasm illustrated the usefulness of BOPA1 and BOPA2 in that they provide excellent marker density and sensitivity for detection of minor alleles in this genetically narrow material.</p

Overriding water table control on managed peatland greenhouse gas emissions

Global peatlands store more carbon than is naturally present in the atmosphere1,2. However, many peatlands are under pressure from drainage-based agriculture, plantation development and fire, with the equivalent of around 3% of all anthropogenic greenhouse gases emitted from drained peatland3–5. Efforts to curb such emissions are intensifying through the conservation of undrained peatlands and rewetting of drained systems6. Here we report CO2 eddy covariance data from 16 locations and CH4 data from 41 locations in the British Isles, and combine them with published data from sites across all major peatland biomes. We find that the mean annual effective water-table depth (WTDe; that is, the average depth of the aerated peat layer) overrides all other ecosystem- and management-related controls on greenhouse gas fluxes. We estimate that every 10 cm of reduction in WTDe could reduce the net warming impact of CO2 and CH4 emissions (100-year Global Warming Potentials) by at least 3 t CO2e ha-1 yr-1, until WTDe is < 30 cm. Raising water levels further would continue to have a net cooling effect until WTDe is < 10 cm. Our results suggest that greenhouse gas emissions from peatlands drained for agriculture could be greatly reduced without necessarily halting their productive use. Halving WTDe in all drained agricultural peatlands, for example, could reduce emissions by the equivalent of over 1% of global anthropogenic emissions