Causal relationships vs. emergent patterns in the global controls of fire frequency

Global controls on month-by-month fractional burnt area (2000–2005) were investigated by fitting a generalised linear model (GLM) to Global Fire Emissions Database (GFED) data, with 11 predictor variables representing vegetation, climate, land use and potential ignition sources. Burnt area is shown to increase with annual net primary production (NPP), number of dry days, maximum temperature, grazing-land area, grass/shrub cover and diurnal temperature range, and to decrease with soil moisture, cropland area and population density. Lightning showed an apparent (weak) negative influence, but this disappeared when pure seasonal-cycle effects were taken into account. The model predicts observed geographic and seasonal patterns, as well as the emergent relationships seen when burnt area is plotted against each variable separately. Unimodal relationships with mean annual temperature and precipitation, population density and gross domestic product (GDP) are reproduced too, and are thus shown to be secondary consequences of correlations between different controls (e.g. high NPP with high precipitation; low NPP with low population density and GDP). These findings have major implications for the design of global fire models, as several assumptions in current models – most notably, the widely assumed dependence of fire frequency on ignition rates – are evidently incorrect.

A SNP-based consensus genetic map for synteny-based trait targeting in faba bean (Vicia faba L.)

Faba bean (Vicia faba L.) is a globally important nitrogen-fixing legume, which is widely grown in a diverse range of environments. In this work, we mine and validate a set of 845 SNPs from the aligned transcriptomes of two contrasting inbred lines. Each V. faba SNP is assigned by BLAST analysis to a single Medicago orthologue. This set of syntenically anchored polymorphisms were then validated as individual KASP assays, classified according to their informativeness and performance on a panel of 37 inbred lines, and the best performing 757 markers used to genotype six mapping populations. The six resulting linkage maps were merged into a single consensus map on which 687 SNPs were placed on six linkage groups, each presumed to correspond to one of the six V. faba chromosomes. This sequence-based consensus map was used to explore synteny with the most closely-related crop species, lentil, and the most closely related fully sequenced genome, Medicago. Large tracts of uninterrupted colinearity were found between faba bean and Medicago, making it relatively straightforward to predict gene content and order in mapped genetic interval. As a demonstration of this, we mapped a flower colour gene to a 2 cM interval of Vf chromosome 2 which was highly collinear with Mt3. The obvious candidate gene from 77 gene models in the collinear Medicago chromosome segment was the previously characterized MtWD40-1 gene (Mt3g092830, Mt3g092840) controlling anthocyanin production in Medicago and re-sequencing of the Vf orthologue showed a putative causative deletion of the entire 5’ end of the gene.

Investigating subtypes of reward processing deficits as trait markers for depression

Background: Anhedonia, the loss of pleasure in usually enjoyable activities, is a central feature of major depressive disorder (MDD). The aim of the present study was to examine whether young people at a familial risk of depression display signs of anticipatory, motivational or consummatory anhedonia, which would indicate that these deficits may be trait markers for MDD. Methods: The study was completed by 22 participants with a family history of depression (FH+) and 21 controls (HC). Anticipatory anhedonia was assessed by asking participants to rate their anticipated liking of pleasant and unpleasant foods which they imagined tasting when cued with images of the foods. Motivational anhedonia was measured by requiring participants to perform key presses to obtain pleasant chocolate taste rewards or to avoid unpleasant apple tastes. Additionally, physical consummatory anhedonia was examined by instructing participants to rate the pleasantness of the acquired tastes. Moreover, social consummatory anhedonia was investigated by asking participants to make preference-based choices between neutral facial expressions, genuine smiles, and polite smiles. Results: It was found that the FH+ group’s anticipated liking of unpleasant foods was significantly lower than that of the control group. By contrast, no group differences in the pleasantness ratings of the actually experienced tastes or in the amount of performed key presses were observed. However, controls preferred genuine smiles over neutral expressions more often than they preferred polite smiles over neutral expressions, while this pattern was not seen in the FH+ group. Conclusion: These findings suggest that FH+ individuals demonstrate an altered anticipatory response to negative stimuli and show signs of social consummatory anhedonia, which may be trait markers for depression.

EDITOR'S CHOICE: REVIEW: Trait matching of flower visitors and crops predicts fruit set better than trait diversity

Understanding the relationships between trait diversity, species diversity and ecosystem functioning is essential for sustainable management. For functions comprising two trophic levels, trait matching between interacting partners should also drive functioning. However, the predictive ability of trait diversity and matching is unclear for most functions, particularly for crop pollination, where interacting partners did not necessarily co-evolve. World-wide, we collected data on traits of flower visitors and crops, visitation rates to crop flowers per insect species and fruit set in 469 fields of 33 crop systems. Through hierarchical mixed-effects models, we tested whether flower visitor trait diversity and/or trait matching between flower visitors and crops improve the prediction of crop fruit set (functioning) beyond flower visitor species diversity and abundance. Flower visitor trait diversity was positively related to fruit set, but surprisingly did not explain more variation than flower visitor species diversity. The best prediction of fruit set was obtained by matching traits of flower visitors (body size and mouthpart length) and crops (nectar accessibility of flowers) in addition to flower visitor abundance, species richness and species evenness. Fruit set increased with species richness, and more so in assemblages with high evenness, indicating that additional species of flower visitors contribute more to crop pollination when species abundances are similar. Synthesis and applications. Despite contrasting floral traits for crops world-wide, only the abundance of a few pollinator species is commonly managed for greater yield. Our results suggest that the identification and enhancement of pollinator species with traits matching those of the focal crop, as well as the enhancement of pollinator richness and evenness, will increase crop yield beyond current practices. Furthermore, we show that field practitioners can predict and manage agroecosystems for pollination services based on knowledge of just a few traits that are known for a wide range of flower visitor species.

Intraspecific trait variation is correlated with establishment success of alien mammals

Many studies have aimed to identify common predictors of successful introductions of alien species, but the search has had limited success, particularly for animals. Past research focused primarily on mean trait values, even though genetic and phenotypic variation has been shown to play a role in establishment success in plants and some animals (mostly invertebrates). Using a global database describing 511 introduction events representing 97 mammalian species, we show that intraspecific variation in morphological traits is associated with establishment success, even when controlling for the positive effect of propagule pressure. In particular, greater establishment success is associated with more variation in adult body size but, surprisingly, less variation in neonate body size, potentially reflecting distinct trade-offs and constraints that influence population dynamics differently. We find no mean trait descriptors associated with establishment success, although species occupying wider native distribution ranges (which likely have larger niches) are more successful. Our results emphasize the importance of explicitly considering intraspecific variation to predict establishment success in animal species and generally to understand population dynamics. This understanding might improve management of alien species and increase the success of intentional releases, for example, for biocontrol or reintroductions.

Neural signals of “Intensity” but not “Wanting” or “Liking” of rewards may be trait markers for depression

We have shown previously that particpants “at risk” of depression have decreased neural processing of reward suggesting this might be a neural biomarker for depression. However, how the neural signal related to subjective experiences of reward (wanting, liking, intensity) might differ as trait markers for depression, is as yet unknown. Using SPM8 parametric modulation analysis the neural signal related to the subjective report of wanting, liking and intensity was compared between 25 young people with a biological parent with depression (FH) and 25 age/gender matched controls. In a second study the neural signal related to the subjective report of wanting, liking and intensity was compared between 13 unmedicated recovered depressed (RD) patients and 14 healthy age/gender matched controls. The analysis revealed differences in the neural signal for wanting, liking and intensity ratings in the ventral striatum, dmPFC and caudate respectively in the RD group compared to controls . Despite no differences in the FH groups neural signal for wanting and liking there was a difference in the neural signal for intensity ratings in the dACC and anterior insula compared to controls. These results suggest that the neural substrates tracking the intensity but not the wanting or liking for rewards and punishers might be a trait marker for depression.

Dental anxiety and trait anxiety: an investigation of their relationship

Background Anxiety related to dental treatment is a fairly common phenomenon. Some studies have shown that there is an association between dental anxiety and general fears and anxiety, neuroticism and general psychological distress. Aim This study was designed to examine the relationship between dental anxiety and trait anxiety. Subjects and methods The sample consisted of 1,030 individuals (688 women; 342 men), aged 30.8 +/- 11.7 years. The Portuguese version of Corah`s Dental Anxiety Scale (DAS) and State-Trait Anxiety Inventory (STAI-T) were used. Results A statistically significant association between high DAS and high STAI-T, but not between high STAI-T and high DAS, was found. The data indicated that subjects with high dental anxiety tend to present with high trait anxiety, but high trait anxiety seems not to predispose to high dental anxiety. Conclusions Our results indicate that dental anxiety is specific, with its own features, and its development is not necessarily associated with trait anxiety.

Novel Statistical Methods in Quantitative Genetics : Modeling Genetic Variance for Quantitative Trait Loci Mapping and Genomic Evaluation

This thesis develops and evaluates statistical methods for different types of genetic analyses, including quantitative trait loci (QTL) analysis, genome-wide association study (GWAS), and genomic evaluation. The main contribution of the thesis is to provide novel insights in modeling genetic variance, especially via random effects models. In variance component QTL analysis, a full likelihood model accounting for uncertainty in the identity-by-descent (IBD) matrix was developed. It was found to be able to correctly adjust the bias in genetic variance component estimation and gain power in QTL mapping in terms of precision.  Double hierarchical generalized linear models, and a non-iterative simplified version, were implemented and applied to fit data of an entire genome. These whole genome models were shown to have good performance in both QTL mapping and genomic prediction. A re-analysis of a publicly available GWAS data set identified significant loci in Arabidopsis that control phenotypic variance instead of mean, which validated the idea of variance-controlling genes.  The works in the thesis are accompanied by R packages available online, including a general statistical tool for fitting random effects models (hglm), an efficient generalized ridge regression for high-dimensional data (bigRR), a double-layer mixed model for genomic data analysis (iQTL), a stochastic IBD matrix calculator (MCIBD), a computational interface for QTL mapping (qtl.outbred), and a GWAS analysis tool for mapping variance-controlling loci (vGWAS).

MAPfastR : quantitative trait loci mapping in outbred line crosses

MAPfastR is a software package developed to analyze QTL data from inbred and outbred line-crosses. The package includes a number of modules for fast and accurate QTL analyses. It has been developed in the R language for fast and comprehensive analyses of large datasets. MAPfastR is freely available at: http://www.computationalgenetics.se/?page_id=7.

Genome-wide association mapping in a wild avian population identifies a link between genetic and phenotypic variation in a life-history trait

Understanding the genetic basis of traits involved in adaptation is a major challenge in evolutionary biology but remains poorly understood. Here, we use genome-wide association mapping using a custom 50 k single nucleotide polymorphism (SNP) array in a natural population of collared flycatchers to examine the genetic basis of clutch size, an important life-history trait in many animal species. We found evidence for an association on chromosome 18 where one SNP significant at the genome-wide level explained 3.9% of the phenotypic variance. We also detected two suggestive quantitative trait loci (QTLs) on chromosomes 9 and 26. Fitness differences among genotypes were generally weak and not significant, although there was some indication of a sex-by-genotype interaction for lifetime reproductive success at the suggestive QTL on chromosome 26. This implies that sexual antagonism may play a role in maintaining genetic variation at this QTL. Our findings provide candidate regions for a classic avian life-history trait that will be useful for future studies examining the molecular and cellular function of, as well as evolutionary mechanisms operating at, these loci.

Aspects de la syntaxe, de la semantique et de la morphologie des verbes a trait de /complexite/

Cette dissertation porte sur l’analyse syntactico-sémantique des verbes à trait de complexité. Le trait de complexité (Blanche-Benveniste et al. 1984) réunit une classe de verbes connue comme verbes ‘symétriques’, ‘réciproques’ ou ‘collectifs’ sans toutefois se limiter à ces ensembles (cf. grouiller, collectionner, amonceler, scinder, etc.). Ce trait induit une lecture ‘plurielle’ à l’entité formée du lexème verbal et de ses arguments et qui se traduit, sur le plan morphosyntaxique, par deux propriétés: sélection obligatoire d’une position syntaxique (sujet ou objet) au pluriel; en absence de ce pluriel morphologique, le trait de complexité se réalise par la sélection d’un complément prépositionnel correlié à une position syntaxique (sujet ou objet) et l’interprétation de ‘pluriel’ des deux éléments correliés. L’hypothèse générale, et point de départ de cette dissertation, consiste à préciser l’interprétation de ‘pluralité inhérente’ des verbes à trait de complexité comme étant de type ‘collectif’, défini comme désignant du ‘plus d’un en un’ (Jespersen, 1971). La notion de ‘collectif’ est à distinguer de la notion de ‘pluriel’ (Gillon, 1992) et permet d’expliquer le lien entre les deux propriétés morphosyntaxiques présentées. Cette hypothèse générale s’appuie sur la sélection d’un ensemble d’outils d’analyse. Un premier outil vise à rendre compte, du point de vue formel, des réseaux syntactico-sémantiques, par une représentation abstraite de la syntaxe verbale, conçue comme une ‘syntaxe de position’ et où sont délimitées, autour du noyau verbal, deux zones syntaxiques (zone SUJET et zone OBJET) constituées de points d’ancrage du trait de complexité. En tenant compte de la spécificité du ‘collectif’ par rapport à la ‘pluralité’, le recours au concept d’opérateurs de complexité, entendus comme des opérateurs du trait [+discret] (Doetjes, 1999), permet de mieux définir la notion du ‘collectif’ appliquée au domaine verbal. Les différents opérateurs – affixes dérivationnels, constructions prépositionnelles, constructions en SE - se situent à différents niveaux de structuration. L’analyse par ‘opérateurs de complexité’ ([+discret]) présuppose également la prise en compte de la fonction quantitative. Dans cette perspective, ces opérateurs induisent différents degrés de l‘individuation’ des constituants du ‘collectif’ dénoté par la sémantique des verbes à trait de complexité. Les échelles de gradation de [+discret] rendent compte de cette propriété. Les valeurs de ‘plus d’un’ et ‘en un’ dénotées par les expressions verbales à trait de complexité sont interprétées comme faisant partie d’une structure conceptuelle de type ‘tout-intégré’ d’après l’approche lexicale et multidimensionnelle de la sémantique conceptuelle des relations parties/tout de Moltmann (1997).

Breeding value accuracy estimates for growth traits using random regression and multi-trait models in Nelore cattle

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Mapping of quantitative trait loci controlling tick [Riphicephalus (Boophilus) microplus] resistance on bovine chromosomes 5, 7 and 14

Differences in domestication and selection processes have contributed to considerable phenotypic and genotypic differences between Bos taurus and Bos indicus cattle breeds. of particular interest in tropical and subtropical production environments are those genetic differences between subspecies that underlie the phenotypic extremes in tolerance and susceptibility to parasite infection. In general, B. taurus cattle are more susceptible to ectoparasites than B. indicus cattle in tropical environments, and much of this difference is under genetic control. To identify genomic regions involved in tick resistance, we developed a B. taurus x B. indicus F-2 experimental population to map quantitative trait loci (QTL) for resistance to the Riphicephalus (Boophilus) microplus tick. About 300 individuals were measured for parasite load in two seasons (rainy and dry) and genotyped for 23 microsatellite markers covering chromosomes 5, 7 and 14. We mapped a suggestive chromosome-wide QTL for tick load in the rainy season (P < 0.05) on chromosome 5. For the dry season, suggestive (P < 0.10) chromosome-wide QTL were mapped on chromosomes 7 and 14. The additive effect of the QTL on chromosome 14 corresponds to 3.18% of the total observed phenotypic variance. Our QTL-mapping study has identified different genomic regions controlling tick resistance; these QTL were dependent upon the season in which the ticks were counted, suggesting that the QTL in question may depend on environmental factors.