Inferring Species Trees Directly from Biallelic Genetic Markers: Bypassing Gene Trees in a Full Coalescent Analysis

The multi-species coalescent provides an elegant theoretical framework for estimating species trees and species demographics from genetic markers. Practical applications of the multi-species coalescent model are, however, limited by the need to integrate or sample over all gene trees possible for each genetic marker. Here we describe a polynomial-time algorithm that computes the likelihood of a species tree directly from the markers under a finite-sites model of mutation, effectively integrating over all possible gene trees. The method applies to independent (unlinked) biallelic markers such as well-spaced single nucleotide polymorphisms (SNPs), and we have implemented it in SNAPP, a Markov chain Monte-Carlo sampler for inferring species trees, divergence dates, and population sizes. We report results from simulation experiments and from an analysis of 1997 amplified fragment length polymorphism (AFLP) loci in 69 individuals sampled from six species of {\em Ourisia} (New Zealand native foxglove)

Speciation in Western Scrub-Jays, Haldane’s rule, and genetic clines in secondary contact

Background Haldane’s Rule, the tendency for the heterogametic sex to show reduced fertility in hybrid crosses, can obscure the signal of gene flow in mtDNA between species where females are heterogametic. Therefore, it is important when studying speciation and species limits in female-heterogametic species like birds to assess the signature of gene flow in the nuclear genome as well. We studied introgression of microsatellites and mtDNA across a secondary contact zone between coastal and interior lineages of Western Scrub-Jays (Aphelocoma californica) to test for a signature of Haldane’s Rule: a narrower cline of introgression in mtDNA compared to nuclear markers. Results Our initial phylogeographic analysis revealed that there is only one major area of contact between coastal and interior lineages and identified five genetic clusters with strong spatial structuring: Pacific Slope, Interior US, Edwards Plateau (Texas), Northern Mexico, and Southern Mexico. Consistent with predictions from Haldane’s Rule, mtDNA showed a narrower cline than nuclear markers across a transect through the hybrid zone. This result is not being driven by female-biased dispersal because neutral diffusion analysis, which included estimates of sex-specific dispersal rates, also showed less diffusion of mtDNA. Lineage-specific plumage traits were associated with nuclear genetic profiles for individuals in the hybrid zone, indicating that these differences are under genetic control. Conclusions This study adds to a growing list of studies that support predictions of Haldane’s Rule using cline analysis of multiple loci of differing inheritance modes, although alternate hypotheses like selection on different mtDNA types cannot be ruled out. That Haldane’s Rule appears to be operating in this system suggests a measure of reproductive isolation between the Pacific Slope and interior lineages. Based on a variety of evidence from the phenotype, ecology, and genetics, we recommend elevating three lineages to species level: A. californica (Pacific Slope); A. woodhouseii (Interior US plus Edwards Plateau plus Northern Mexico); A. sumichrasti (Southern Mexico). The distinctive Edwards Plateau population in Texas, which was monophyletic in mtDNA except for one individual, should be studied in greater detail given habitat threat

Characterisation of the morphology of surface-assembled Au nanoclusters on amorphous carbon

In this study, aberration-corrected scanning transmission electron microscopy is employed to investigate the morphology of Au clusters formed from the aggregation of single atoms sputtered onto an amorphous carbon surface. The morphologies of surface-assembled clusters of N > 100 atoms are referenced against the morphologies of size-selected clusters determined from previously published results. We observe that surface-assembled clusters (at the conditions employed here) are approximately spherical in shape. The structural isomers of the imaged clusters have also been identified, and the distribution of structural types is broadly in agreement with those from size-selected cluster deposition sources. For clusters of approximately 147 atoms, we find a preference for icosahedra over decahedra and truncated octahedra, but at this size there is a high proportion of unidentified/amorphous structures. At around 309 atoms, we find a preference for decahedra over icosahedra and truncated octahedra, but over half the structures remain unidentifiable/amorphous. For sizes above approximately 561 atoms we are able to identify most of the structures, and find decahedra are still the most favoured, although in competition with single-crystal fcc morphologies. The similarity in structure between surface-assembled and size-selected clusters from a cluster source provides evidence of the relevance of size-selected cluster studies to clusters synthesised by other, industrially relevant, methodologies

Enhancement of Multiwalled Carbon Nanotubes’ Electrical Conductivity Using Metal Nanoscale Copper Contacts and Its Implications for Carbon Nanotube-Enhanced Copper Conductivity

Herein, we present an experimental/computational approach for probing the interaction between metal contacts and carbon nanotubes (CNTs) with regard to creating the most efficient, low resistance junction. Tungsten probes have been coated with copper or chromium and the efficiency of nanocontact transport into multiwalled carbon nanotubes (MWCNTs) has been investigated experimentally, using scanning tunneling spectroscopy and nanoscale two-point probe I-V measurements, and in silico, employing DFT calculations. Experimental I-V measurements suggest the relative conductivity of the metal-CNT interaction to be Cu > W > Cr. It has been found that copper when in contact with MWCNTs results in a high density of states at the Fermi level, which contributes states to the conduction band. It was observed that the density of states also increased when chromium and tungsten probes were in contact with CNTs; however, in these cases the density of states increase would only occur under high voltage/high temperature situations. This is demonstrated by an increase in the experimental electrical resistance when compared to the copper probe. These results suggest that in future copper tips should be used when carrying out all intrinsic conduction measurements on CNTs, and they also provide a rationale for the ultraconductivity of Cu-CNT and Cu-graphene composites

11. Some aspects of enhancing natural pest control

Expert assessors Barbara Smith, Game and Wildlife Conservation Trust, UK Tony Harding, Rothamsted Research, UK Anthony Goggin, Linking Environment and Farming (LEAF), UK Felix Wackers, BioBest/University of Lancaster, Belgium/UK Melvyn Fidgett, Syngenta, UK Michael Garratt, University of Reading, UK Michelle Fountain, East Malling Research, UK Phillip Effingham, Greentech Consultants, UK Stephanie Williamson, Pesticides Action Network, UK Toby Bruce, Rothamsted Research, UK Andrew Wilby, Univ..

Exploring young people’s experiences and perceptions of mental health and well-being using photography

© 2019 Association for Child and Adolescent Mental Health Introduction: The mental health of young people is a major global public health concern. A shift in focus towards children and young people’s mental health in the UK has emphasized young people’s voices, as of paramount importance in shaping the path for future quality care provision. The paper examines a study that aimed to explore young people’s perceptions of mental health and well-being using photographs. Method: The methodology employed for this study placed young people at the centre of the research process by using photographs to capture their experiences. Ten young people who attended a youth group used disposable cameras to take photographs of their experiences and perceptions of mental health and well-being. Semi-structured interviews with the young people elicited their narratives behind the images. Data were analysed using photo-elicitation and thematic analysis. Findings: Young people’s experiences of mental health and well-being were internalized and located predominantly in the private and hidden regions of their everyday lives. Stigma, social isolation and marginalization were prevalent whilst spirituality and connection with the environment expressed hope. Conclusion: Mental health appears to be firmly located in the private ‘back regions’ of young individuals’ lives, demonstrating that young people conceptualize these experiences as a vulnerable and hidden part of their being. Understanding the needs of this new generation of youth including the prevalence of stigma, risk of isolation and social exclusion are paramount. Future service provision needs to recognize the extent stigma impacts upon young people’s experiences of mental health and well-being

Combining ultraconserved elements and mtDNA data to uncover lineage diversity in a Mexican highland frog (Sarcohyla; Hylidae)

Molecular studies have uncovered significant diversity in the Mexican Highlands, leading to the description of many new endemic species. DNA approaches to this kind of species discovery have included both mitochondrial DNA (mtDNA) sequencing and multilocus genomic methods. While these marker types have often been pitted against one another, there are benefits to deploying them together, as linked mtDNA data can provide the bridge between uncovering lineages through rigorous multilocus genomic analysis and identifying lineages through comparison to existing mtDNA databases. Here, we apply one class of multilocus genomic marker, ultraconserved elements (UCEs), and linked mtDNA data to a species complex of frogs (Sarcohyla bistincta, Hylidae) found in the Mexican Highlands. We generated data from 1,891 UCEs, which contained 1,742 informative SNPs for S. bistincta and closely related species and captured mitochondrial genomes for most samples. Genetic analyses based on both whole loci and SNPs agree there are six to seven distinct lineages within what is currently described as S. bistincta. Phylogenies from UCEs and mtDNA mostly agreed in their topologies, and the few differences suggested a more complex evolutionary history of the mtDNA marker. Our study demonstrates that the Mexican Highlands still hold substantial undescribed diversity, making their conservation a particularly urgent goal. The Trans-Mexican Volcanic Range stands out as a significant geographic feature in Sarcohyla and may have acted as a dispersal corridor for S. bistincta to spread to the north. Combining multilocus genomic data with linked mtDNA data is a useful approach for identifying potential new species and associating them with already described taxa, which will be especially important in groups with undescribed subadult phenotypes and cryptic species

Delayed self-recognition in children with autism spectrum disorder.

This study aimed to investigate temporally extended self-awareness (awareness of one’s place in and continued existence through time) in autism spectrum disorder (ASD), using the delayed self-recognition (DSR) paradigm (Povinelli et al., Child Development 67:1540–1554, 1996). Relative to age and verbal ability matched comparison children, children with ASD showed unattenuated performance on the DSR task, despite showing significant impairments in theory-of-mind task performance, and a reduced propensity to use personal pronouns to refer to themselves. The results may indicate intact temporally extended self-awareness in ASD. However, it may be that the DSR task is not an unambiguous measure of temporally extended self-awareness and it can be passed through strategies which do not require the possession of a temporally extended self-concept