Testing structural models of psychopathology at the genomic level

Genome‐wide association studies (GWAS) have revealed hundreds of genetic loci associated with the vulnerability to major psychiatric disorders, and post‐GWAS analyses have shown substantial genetic correlations among these disorders. This evidence supports the existence of a higher‐order structure of psychopathology at both the genetic and phenotypic levels. Despite recent efforts by collaborative consortia such as the Hierarchical Taxonomy of Psychopathology (HiTOP), this structure remains unclear. In this study, we tested multiple alternative structural models of psychopathology at the genomic level, using the genetic correlations among fourteen psychiatric disorders and related psychological traits estimated from GWAS summary statistics. The best‐fitting model included four correlated higher‐order factors – externalizing, internalizing, thought problems, and neurodevelopmental disorders – which showed distinct patterns of genetic correlations with external validity variables and accounted for substantial genetic variance in their constituent disorders. A bifactor model including a general factor of psychopathology as well as the four specific factors fit worse than the above model. Several model modifications were tested to explore the placement of some disorders – such as bipolar disorder, obsessive‐compulsive disorder, and eating disorders – within the broader psychopathology structure. The best‐fitting model indicated that eating disorders and obsessive‐compulsive disorder, on the one hand, and bipolar disorder and schizophrenia, on the other, load together on the same thought problems factor. These findings provide support for several of the HiTOP higher‐order dimensions and suggest a similar structure of psychopathology at the genomic and phenotypic levels.     

An empirical assessment of tree branching networks and implications for plant allometric scaling models

Several theories predict whole‐tree function on the basis of allometric scaling relationships assumed to emerge from traits of branching networks. To test this key assumption, and more generally, to explore patterns of external architecture within and across trees, we measure branch traits (radii/lengths) and calculate scaling exponents from five functionally divergent species. Consistent with leading theories, including metabolic scaling theory, branching is area preserving and statistically self‐similar within trees. However, differences among scaling exponents calculated at node‐ and whole‐tree levels challenge the assumption of an optimised, symmetrically branching tree. Furthermore, scaling exponents estimated for branch length change across branching orders, and exponents for scaling metabolic rate with plant size (or number of terminal tips) significantly differ from theoretical predictions. These findings, along with variability in the scaling of branch radii being less than for branch lengths, suggest extending current scaling theories to include asymmetrical branching and differential selective pressures in plant architectures.     

Comparing the performance of different stomatal conductance models using modelled and measured plant carbon isotope ratios (δ13C): implications for assessing physiological forcing

Accurate modelling of long‐term changes in plant stomatal functioning is vital to global climate change studies because changes in evapotranspiration influence temperature via physiological forcing of the climate. Various stomatal models are included in land surface schemes, but their robustness over longer timescales is difficult to validate. We compare the performance of three stomatal models, varying in their degree of complexity, and coupled to a land surface model. This is carried out by simulating the carbon isotope ratio of tree leaves (δ¹³C_leaf) over a period of 53 years, and comparing the results with carbon isotope ratios obtained from tree rings (δ¹³C_stem) measured at six sites in northern Europe. All three stomatal models fail to capture the observed interannual variability in the measured δ¹³C_stem time series. However, the Soil‐Plant‐Atmosphere (SPA) model performs significantly better than the Ball‐Berry (BB) or COX models when tested for goodness‐of‐fit against measured δ¹³C_stem. The δ¹³C_leaf time series simulated using the SPA model are significantly positively correlated (P < 0.05) with measured results over the full time period tested, at all six sites. The SPA model underestimates interannual variability measured in δ¹³C_stem, but is no worse than the BB model and significantly better than the COX model. The inability of current models to adequately replicate changes in stomatal response to rising levels of CO₂ concentrations, and thus to quantify the associated physiological forcing, warrants further investigation.     

Collagen models as a probe in the decay of works of art: synthesis, conformation and immunological studies.

Proteinaceous substances such as collagen, casein and albumin have been widely used as binding media in a variety of works of art. Damages of these 'sensitive' materials, mainly caused of the influence of the environment, are responsible for the overall decay of works of art, and their identification is essential to understand ancient technologies, determine the extent of deterioration and help in future restoration and preservation processes. The most commonly used techniques for the identification of proteinaceous binding media are staining techniques, chromatography, spectrometry and immunological methods, although for the latter no systematic studies have been carried out until now. Aiming at contributing to the development of a reliable and reproducible immunoassay for the evaluation of the collagen-based decay of works of art, sequential polypeptides (Pro-X-Gly)n where X represents amino acid residues Val, Lys, Glu and (Hyp-Val-Gly)n were prepared as models of collagen fragments derived from artificially and naturally aged animal collagens. Conformational studies of the polypeptides by CD revealed the occurrence of polyproline II-like structures comparable with those of collagen. Polypeptides and collagen I were administered to animals, and the induced antibodies were used for the immunochemical detection and differentiation of collagen and collagen fragments. The combined application of (i) anti-collagen antibodies, which strongly interact with native collagen, but poorly recognized by artificially aged collagen and (ii) anti-polypeptide antibodies, which do not associate with native collagen, but are strongly recognized by collagen fragments in naturally or artificially aged collagen, is a valuable tool in determining the extent of decay in works of art.     

Zones of influence for soil organic matter dynamics: A conceptual framework for data and models

Soil organic matter (SOM) is an indicator of sustainable land management as stated in the global indicator framework of the United Nations Sustainable Development Goals (SDG Indicator 15.3.1). Improved forecasting of future changes in SOM is needed to support the development of more sustainable land management under a changing climate. Current models fail to reproduce historical trends in SOM both within and during transition between ecosystems. More realistic spatio‐temporal SOM dynamics require inclusion of the recent paradigm shift from SOM recalcitrance as an ‘intrinsic property’ to SOM persistence as an ‘ecosystem interaction’. We present a soil profile, or pedon‐explicit, ecosystem‐scale framework for data and models of SOM distribution and dynamics which can better represent land use transitions. Ecosystem‐scale drivers are integrated with pedon‐scale processes in two zones of influence. In the upper vegetation zone, SOM is affected primarily by plant inputs (above‐ and belowground), climate, microbial activity and physical aggregation and is prone to destabilization. In the lower mineral matrix zone, SOM inputs from the vegetation zone are controlled primarily by mineral phase and chemical interactions, resulting in more favourable conditions for SOM persistence. Vegetation zone boundary conditions vary spatially at landscape scales (vegetation cover) and temporally at decadal scales (climate). Mineral matrix zone boundary conditions vary spatially at landscape scales (geology, topography) but change only slowly. The thicknesses of the two zones and their transport connectivity are dynamic and affected by plant cover, land use practices, climate and feedbacks from current SOM stock in each layer. Using this framework, we identify several areas where greater knowledge is needed to advance the emerging paradigm of SOM dynamics—improved representation of plant‐derived carbon inputs, contributions of soil biota to SOM storage and effect of dynamic soil structure on SOM storage—and how this can be combined with robust and efficient soil monitoring.     

The evolution of phenotypic plasticity in spatially structured environments: implications of intraspecific competition, plasticity costs and environmental characteristics

We model the evolution of reaction norms focusing on three aspects: frequency-dependent selection arising from resource competition, maintenance and production costs of phenotypic plasticity, and three characteristics of environmental heterogeneity (frequency of environments, their intrinsic carrying capacity and the sensitivity to phenotypic maladaptation in these environments). We show that (i) reaction norms evolve so as to trade adaptation for acquiring resources against cost avoidance; (ii) maintenance costs cause reaction norms to better adapt to frequent rather than to infrequent environments, whereas production costs do not; and (iii) evolved reaction norms confer better adaptation to environments with low rather than with high intrinsic carrying capacity. The two previous findings contradict earlier theoretical results and originate from two previously unexplored features that are included in our model. First, production costs of phenotypic plasticity are only incurred when a given phenotype is actually produced. Therefore, they are proportional to the frequency of environments, and these frequencies thus affect the selection pressure to avoid costs just as much as the selection pressure to improve adaptation. This prevents the frequency of environments from affecting the evolving reaction norm. Secondly, our model describes the evolution of plasticity for a phenotype determining an individual's capability to acquire resources, and thus its realized carrying capacity. When individuals are distributed randomly across environments, they cannot avoid experiencing environments with intrinsically low carrying capacity. As selection pressures arising from the need to improve adaptation are stronger under such extreme conditions than under mild ones, better adaptation to environments with low rather than with high intrinsic carrying capacity results.     

Ambient temperature effects on the extrinsic incubation period of Wuchereria bancrofti in Aedes polynesiensis: implications for filariasis transmission dynamics and distribution in French Polynesia.

Temperature effects on development of the human filarial parasite Wuchereria bancrofti (Cobbold) (Filaridea: Onchocercidae) in the main Pacific vector Aedes polynesiensis Marks (Diptera: Culicidae) are analysed in relation to ambient climatic conditions. A statistical model of the extrinsic cycle duration as a function of temperature is described and used to distinguish three patterns of W. bancrofti transmission dynamics: continuous, fluctuating and discontinuous, occurring from north to south geographically among French Polynesian archipelagos. In the northerly Marquesas Islands (8-11 degrees S) filariasis transmission is continuous and very active, facilitated by perennially high temperatures combined with constantly high rates of man-vector contact. In the southerly Australes Islands (21-28 degrees S) filariasis transmission is seasonally discontinuous and, during the cooler months (May-September), the model predicts virtually no transmission because the cycle duration exceeds the life expectancy of the vector. In the Society Islands (16-18 degrees S), between the Marquesas and Australes, transmission is predicted to be intermediate as expected from their latitude, with seasonally fluctuating transmission potential. In the Tuamotu Islands (also geographically intermediate: 14-23 degrees S), with theoretically perennial transmission potential, transmission occurs only intermittently, being limited by other human and environmental factors whereby man-vector contact is confined to seasonal agricultural situations. Generally, among French Polynesian archipelagos where Aedes polynesiensis is the vector, the transmission potential for W. bancrofti and resulting disease manifestations of lymphatic filariasis in humans are correlated with ambient temperature due to the degree of southern latitude.     

Complete mitochondrial genomes from four subspecies of common chaffinch (Fringilla coelebs): New inferences about mitochondrial rate heterogeneity,neutral theory,and phylogenetic relationships within the order Passeriformes

We describe whole mitochondrial genome sequences from four subspecies of the common chaffinch (Fringilla coelebs), and compare them to 31 publicly available mitochondrial genome sequences from other Passeriformes. Rates and patterns of mitochondrial gene evolution are analyzed at different taxonomic levels within this avian order, and evidence is adduced for and against the nearly neutral theory of molecular evolution and the role of positive selection in shaping genetic variation of this small but critical genome. We find evidence of mitochondrial rate heterogeneity in birds as in other vertebrates, likely due to differences in mutational pressure across the genome. Unlike in gadine fish and some of the human mitochondrial work we do not observe strong support for the nearly neutral theory of molecular evolution; instead evidence from molecular clocks, distribution of dN/dS ratios at different levels of the taxonomic hierarchy and in different lineages, McDonald–Kreitman tests within Fringillidae, and site-specific tests of selection within Passeriformes, all point to a role for positive selection, especially for the complex I NADH dehydrogenase genes. The protein-coding mitogenome phylogeny of the order Passeriformes is broadly consistent with previously-reported molecular findings, but provides support for a sister relationship between the superfamilies Muscicapoidea and Passeroidea on a short basal internode of the Passerida where relationships have been difficult to resolve. An unexpected placement of the Paridae (represented by Hume's groundpecker) within the Muscicapoidea was observed. Consistent with other molecular studies the mtDNA phylogeny reveals paraphyly within the Muscicapoidea and a sister relationship of Fringilla with Carduelis rather than Emberiza.