A macro-ecological perspective on crassulacean acid metabolism (CAM) photosynthesis evolution in Afro-Madagascan drylands: Eulophiinae orchids as a case study.

Crassulacean acid metabolism (CAM) photosynthesis is an adaptation to water and atmospheric CO2 deficits that has been linked to diversification in dry-adapted plants. We investigated whether CAM evolution can be associated with the availability of new or alternative niches, using Eulophiinae orchids as a case study. Carbon isotope ratios, geographical and climate data, fossil records and DNA sequences were used to: assess the prevalence of CAM in Eulophiinae orchids; characterize the ecological niche of extant taxa; infer divergence times; and estimate whether CAM is associated with niche shifts. CAM evolved in four terrestrial lineages during the late Miocene/Pliocene, which have uneven diversification patterns. These lineages originated in humid habitats and colonized dry/seasonally dry environments in Africa and Madagascar. Additional key features (variegation, heterophylly) evolved in the most species-rich CAM lineages. Dry habitats were also colonized by a lineage that includes putative mycoheterotrophic taxa. These findings indicate that the switch to CAM is associated with environmental change. With its suite of adaptive traits, this group of orchids represents a unique opportunity to study the adaptations to dry environments, especially in the face of projected global aridification.

Repeated Whole-Genome Duplication, Karyotype Reshuffling, and Biased Retention of Stress-Responding Genes in Buckler Mustard.

Whole-genome duplication (WGD) is usually followed by gene loss and karyotype repatterning. Despite evidence of new adaptive traits associated with WGD, the underpinnings and evolutionary significance of such genome fractionation remain elusive. Here, we use Buckler mustard (Biscutella laevigata) to infer processes that have driven the retention of duplicated genes after recurrent WGDs. In addition to the β- and α-WGD events shared by all Brassicaceae, cytogenetic and transcriptome analyses revealed two younger WGD events that occurred at times of environmental changes in the clade of Buckler mustard (Biscutelleae): a mesopolyploidy event from the late Miocene that was followed by considerable karyotype reshuffling and chromosome number reduction and a neopolyploidy event during the Pleistocene. Although a considerable number of the older duplicates presented signatures of retention under positive selection, the majority of retained duplicates arising from the younger mesopolyploidy WGD event matched predictions of the gene balance hypothesis and showed evidence of strong purifying selection as well as enrichment in gene categories responding to abiotic stressors. Retention of large stretches of chromosomes for both genomic copies supported the hypothesis that cycles of WGD and biased fractionation shaped the genome of this stress-tolerant polypolyloid, promoting the adaptive recruitment of stress-responding genes in the face of environmental challenges.

Competitiveness of ALS inhibitors resistant and susceptible biotypes of Greater Beggarticks (Bidens subalternans)

The continuous use of ALS-inhibiting herbicides has led to the evolution of herbicide-resistant weeds worldwide. Greater beggarticks is one of the most troublesome weeds found in the soybean production system in Brazil. Recently, a greater beggarticks biotype that is resistant (R) to ALS inhibitors due to Trp574Leu mutation in the ALS gene was identified. Also, the adaptive traits between susceptible (S) and R to ALS inhibitors biotypes of greater beggarticks were compared. Specifically, we aimed to: (1) evaluate and compare the relative growth rates (RGR) between the biotypes; (2) analyze the seed germination characteristics of R and S biotypes under different temperature conditions; and (3) evaluate their competitive ability in a replacement series study. The experiments were conducted at the University of Arkansas, USA, in 2007 and at Universidade Federal do Rio Grande do Sul (Federal University of Rio Grande do Sul), Brazil, in 2008. Plant proportions for replacement series studies were respectively 100:0, 75:25, 50:50, 25:75 and 0:100, with a total population of 150 plants m-2. There was no difference in RGR between R and S biotypes. The R-biotype germination rate was lower than that of the S biotype. However, at low temperature conditions (15 ºC), the reverse was observed. In general, there is no difference in the competitive ability between R and S greater beggarticks biotypes.

Hair coat characteristics and sweating rate of Braford cows in Brazil

This paper deals with the effects of hair coat characteristics on the sweating rate of Brazilian Braford cows and estimation of heritabilities and genetic correlations of these traits. Data (n=1607) on hair length, coat thickness, hair diameter, number of hairs per unit area, coat reflectance and sweating rate were recorded from heifers and cows of a commercial herd managed on range under extensive system. The data were analyzed considering the following effects on the model for hair coat traits: classes of sires and contemporary groups; linear effects of month and genotype; linear and quadratic effects of age. The effect of sire was important (P<0.05) for all hair coat traits, except for number of hairs; contemporary groups affected (P<0.05) all hair coat traits; the effect of sampling month was important (P<0.05) for hair length and reflectance; genotype affected (P<0.05) hair length, diameter and coat reflectance; the quadratic effect of age was important (P<0.05) only for coat reflectance. Two models were used to analyze the sweating rate. The first model considered the following fixed effects: classes of contemporary groups and sires; linear effect of genotype, coat thickness, hair length, hair diameter, number of hairs, coat reflectance; linear and quadratic effects of time of day, age, air temperature, partial vapour pressure and radiant heat load. The second model used for the sweating rate considered the same fixed effects for the first model, except that the hair coat characteristics were adjusted for important effects used in the models to analyze hair coat traits. All meteorological factors and contemporary groups were important (P<0.05) on variation of sweating rate in both models. The Restricted Maximum. Likelihood (REML) method was used to estimate variance and covariance components under the sire model. Results included heritability estimates in narrow (h(2)) and broad (H) sense for single-trait analyzes: hair thickness (h(2)=0.16; H-2=0.26); hair length (h(2)=0.18; H-2=0.39); number of hairs (h(2)=0.08 +/- 0.07; H-2=0.08 +/- 0.07); hair diameter (h(2)=0.12 +/- 0.07; H-2=0.12 +/- 0.07); coat reflectance (h(2)=0.30; H-2=0.42); and sweating rate (h(2)=0.10 +/- 0.07; H-2=0.10 +/- 0.07). In general, the genetic correlations between the adaptive traits were favorable as for the direction to select for adaptation in tropical environment; however, they presented high standard errors. The results of this study imply that hair coat characteristics and sweating ability are important for the adaptability to heat stress and they must be better studied and further considered for selection for genetic progress of adaptation in tropical environment. (C) 2007 Elsevier B.V All rights reserved.

Vitamina C intra-ovo e estresse por calor na incubação de frangos de corte

Pós-graduação em Zootecnia - FCAV

Life-history strategies associated to reproduction of three Hyphessobrycon species (Characidae) in lentic environments of upper Paraná River basin

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Ecological genetics and conservation genomics of wolf (Canis lupus)

In the present work, we apply both traditional and Next Generation Sequencing (NGS) tools to investigate some of the most important adaptive traits of wolves (Canis lupus). In the first part, we analyze the variability of three Major Histocompatibility Complex (MHC) class II genes in the Italian wolf population, also studying their possible role in mating choice and their influence on fitness traits. In the second section, as part of a larger canid genome project, we will exploit NGS data to investigate the transcript-level differences between the wolf and the dog genome that can be correlated to domestication.

Conserving indigenous animal genetic resources as a coping strategy to adapt to climate change: the Azikheli Buffalo in Northern Mountains of Pakistan

There are clear signs that the agro-pastoralists in the Himalayan and Hindu-Kush mountain ranges will have less cropping opportunities due to reduced possibilities for irrigated agriculture as a result of climate change. The importance of extensive livestock production based on well adapted livestock species may once again increase. This calls for a better documentation and understanding of the adaptation capabilities of indigenous breeds considering a changing environment. The current study investigates the adaptive traits of the Azikheli buffalo to mountain environments through calculating mean, standard error and percentages for different variables. Results from this study suggest that the brown coat color, the small body size and the high fertility are adaptive traits of the Azikheli buffalo that may well suit harsh mountainous environment conditions with greater climate variability. Local farmers find it hard to sustain the Azikheli buffalo’s key adaptive traits because of a low bull to buffalo ratio, possibility of insemination with semen from imported breeds and a lack of institutional support to conserve the Azikheli breed. The breed is crucial for sustaining custodian communities in these mountains and thus needs to be conserved.

Genomic signatures of relaxed disruptive selection associated with speciation reversal in whitefish

Background: Speciation reversal: the erosion of species differentiation via an increase in introgressive hybridization due to the weakening of previously divergent selection regimes, is thought to be an important, yet poorly understood, driver of biodiversity loss. Our study system, the Alpine whitefish (Coregonus spp.) species complex is a classic example of a recent postglacial adaptive radiation: forming an array of endemic lake flocks, with the independent origination of similar ecotypes among flocks. However, many of the lakes of the Alpine radiation have been seriously impacted by anthropogenic nutrient enrichment, resulting in a collapse in neutral genetic and phenotypic differentiation within the most polluted lakes. Here we investigate the effects of eutrophication on the selective forces that have shaped this radiation, using population genomics. We studied eight sympatric species assemblages belonging to five independent parallel adaptive radiations, and one species pair in secondary contact. We used AFLP markers, and applied FST outlier (BAYESCAN, DFDIST) and logistic regression analyses (MATSAM), to identify candidate regions for disruptive selection in the genome and their associations with adaptive traits within each lake flock. The number of outlier and adaptive trait associated loci identified per lake were then regressed against two variables (historical phosphorus concentration and contemporary oxygen concentration) representing the strength of eutrophication. Results: Whilst we identify disruptive selection candidate regions in all lake flocks, we find similar trends, across analysis methods, towards fewer disruptive selection candidate regions and fewer adaptive trait/candidate loci associations in the more polluted lakes. Conclusions: Weakened disruptive selection and a concomitant breakdown in reproductive isolating mechanisms in more polluted lakes has lead to increased gene flow between coexisting Alpine whitefish species. We hypothesize that the resulting higher rates of interspecific recombination reduce either the number or extent of genomic islands of divergence surrounding loci evolving under disruptive natural selection. This produces the negative trend seen in the number of selection candidate loci recovered during genome scans of whitefish species flocks, with increasing levels of anthropogenic eutrophication: as the likelihood decreases that AFLP restriction sites will fall within regions of heightened genomic divergence and therefore be classified as FST outlier loci. This study explores for the first time the potential effects of human-mediated relaxation of disruptive selection on heterogeneous genomic divergence between coexisting species.

Trait physiology and crop modelling as a framework to link phenotypic complexity to underlying genetic systems

New tools derived from advances in molecular biology have not been widely adopted in plant breeding for complex traits because of the inability to connect information at gene level to the phenotype in a manner that is useful for selection. In this study, we explored whether physiological dissection and integrative modelling of complex traits could link phenotype complexity to underlying genetic systems in a way that enhanced the power of molecular breeding strategies. A crop and breeding system simulation study on sorghum, which involved variation in 4 key adaptive traits-phenology, osmotic adjustment, transpiration efficiency, stay-green-and a broad range of production environments in north-eastern Australia, was used. The full matrix of simulated phenotypes, which consisted of 547 location-season combinations and 4235 genotypic expression states, was analysed for genetic and environmental effects. The analysis was conducted in stages assuming gradually increased understanding of gene-to-phenotype relationships, which would arise from physiological dissection and modelling. It was found that environmental characterisation and physiological knowledge helped to explain and unravel gene and environment context dependencies in the data. Based on the analyses of gene effects, a range of marker-assisted selection breeding strategies was simulated. It was shown that the inclusion of knowledge resulting from trait physiology and modelling generated an enhanced rate of yield advance over cycles of selection. This occurred because the knowledge associated with component trait physiology and extrapolation to the target population of environments by modelling removed confounding effects associated with environment and gene context dependencies for the markers used. Developing and implementing this gene-to-phenotype capability in crop improvement requires enhanced attention to phenotyping, ecophysiological modelling, and validation studies to test the stability of candidate genetic regions.

Trait physiology and crop modelling to link phenotypic complexity to underlying genetic systems

New tools derived from advances in molecular biology have not been widely adopted in plant breeding because of the inability to connect information at gene level to the phenotype in a manner that is useful for selection. We explore whether a crop growth and development modelling framework can link phenotype complexity to underlying genetic systems in a way that strengthens molecular breeding strategies. We use gene-to-phenotype simulation studies on sorghum to consider the value to marker-assisted selection of intrinsically stable QTLs that might be generated by physiological dissection of complex traits. The consequences on grain yield of genetic variation in four key adaptive traits – phenology, osmotic adjustment, transpiration efficiency, and staygreen – were simulated for a diverse set of environments by placing the known extent of genetic variation in the context of the physiological determinants framework of a crop growth and development model. It was assumed that the three to five genes associated with each trait, had two alleles per locus acting in an additive manner. The effects on average simulated yield, generated by differing combinations of positive alleles for the traits incorporated, varied with environment type. The full matrix of simulated phenotypes, which consisted of 547 location-season combinations and 4235 genotypic expression states, was analysed for genetic and environmental effects. The analysis was conducted in stages with gradually increased understanding of gene-to-phenotype relationships, which would arise from physiological dissection and modelling. It was found that environmental characterisation and physiological knowledge helped to explain and unravel gene and environment context dependencies. We simulated a marker-assisted selection (MAS) breeding strategy based on the analyses of gene effects. When marker scores were allocated based on the contribution of gene effects to yield in a single environment, there was a wide divergence in rate of yield gain over all environments with breeding cycle depending on the environment chosen for the QTL analysis. It was suggested that knowledge resulting from trait physiology and modelling would overcome this dependency by identifying stable QTLs. The improved predictive power would increase the utility of the QTLs in MAS. Developing and implementing this gene-to-phenotype capability in crop improvement requires enhanced attention to phenotyping, ecophysiological modelling, and validation studies to test the stability of candidate QTLs.

Ecophysiology of Adonis distorta, a high-mountain species endemic of the Central Apennines

Morphological, anatomical and physiological plant and leaf traits of A. distorta, an endemic species of the Central Apennines on the Majella Massif, growing at 2,675 m a.s.l, were analyzed. The length of the phenological cycle starts immediately after the snowmelt at the end of May, lasting 128 ± 10 days. The low A. distorta height  (Hmax= 64 ± 4 mm) and total leaf area (TLA= 38 ± 9 cm2) associated to a high leaf mass area (LMA =11.8±0.6 mg cm−2) and a relatively high leaf tissue density (LTD = 124.6±14.3 mg cm−3) seem to be adaptive traits to the stress factors of the environment where it grows. From a physiological point of view, the high A. distorta photosynthetic rates (PN =19.6 ± 2.3 µmol m−2 s−1) and total chlorophyll content (Chla+b = 0.88 ± 0.13 mg g−1) in July are justified by the favorable temperature. PN decreases by 87% in September at the beginning of plant senescence. Photosynthesis and leaf respiration (RD) variations allow A. distorta to maintain a positive carbon balance during the growing season becoming indicative of the efficiency of plant carbon use. The results could be an important tool for conservation programmes of the A. distorta wild populations.

Influence of frequent nightmares on REM sleep-dependent emotional memory processing

La littérature suggère que le sommeil paradoxal joue un rôle dans l'intégration associative de la mémoire émotionnelle. De plus, les rêves en sommeil paradoxal, en particulier leur nature bizarre et émotionnelle, semblent refléter cette fonction associative et émotionnelle du sommeil paradoxal. La conséquence des cauchemars fréquents sur ce processus est inconnue, bien que le réveil provoqué par un cauchemar semble interférer avec les fonctions du sommeil paradoxal. Le premier objectif de cette thèse était de reproduire conceptuellement des recherches antérieures démontrant que le sommeil paradoxal permet un accès hyper-associatif à la mémoire. L'utilisation d'une sieste diurne nous a permis d'évaluer les effets du sommeil paradoxal, comparativement au sommeil lent et à l’éveil, sur la performance des participants à une tâche sémantique mesurant « associational breadth » (AB). Les résultats ont montré que seuls les sujets réveillés en sommeil paradoxal ont répondu avec des associations atypiques, ce qui suggère que le sommeil paradoxal est spécifique dans sa capacité à intégrer les traces de la mémoire émotionnelle (article 1). En outre, les rapports de rêve en sommeil paradoxal étaient plus bizarres que ceux en sommeil lent, et plus intenses émotionnellement ; ces attributs semblent refléter la nature associative et émotionnelle du sommeil paradoxal (article 2). Le deuxième objectif de la thèse était de préciser si et comment le traitement de la mémoire émotionnelle en sommeil paradoxal est altéré dans le Trouble de cauchemars fréquents (NM). En utilisant le même protocole, nos résultats ont montré que les participants NM avaient des résultats plus élevés avant une sieste, ce qui correspond aux observations antérieures voulant que les personnes souffrant de cauchemars soient plus créatives. Après le sommeil paradoxal, les deux groupes, NM et CTL, ont montré des changements similaires dans leur accès associatif, avec des résultats AB-négatif plus bas et AB-positif plus grands. Une semaine plus tard, seul les participants NM a maintenu ce changement dans leur réseau sémantique (article 3). Ces résultats suggèrent qu’au fil du temps, les cauchemars peuvent interférer avec l'intégration de la mémoire émotionnelle pendant le sommeil paradoxal. En ce qui concerne l'imagerie, les participants NM avaient plus de bizarrerie et plus d’émotion positive, mais pas négative, dans leurs rêveries (article 4). Ces attributs intensifiés suggèrent à nouveau que les participants NM sont plus imaginatifs et créatifs à l’éveil. Dans l'ensemble, les résultats confirment le rôle du sommeil paradoxal dans l'intégration associative de la mémoire émotionnelle. Cependant, nos résultats concernant le Trouble de cauchemars ne sont pas entièrement en accord avec les théories suggérant que les cauchemars sont dysfonctionnels. Le groupe NM a montré plus d’associativité émotionnelle, de même que plus d'imagerie positive et bizarre à l’éveil. Nous proposons donc une nouvelle théorie de sensibilité environnementale associée au Trouble de cauchemar, suggérant qu'une sensibilité accrue à une gamme de contextes environnementaux sous-tendrait les symptômes uniques et la richesse imaginative observés chez les personnes souffrant de cauchemars fréquents. Bien que davantage de recherches doivent être faites, il est possible que ces personnes puissent bénéficier e milieux favorables, et qu’elles puissent avoir un avantage adaptatif à l'égard de l'expression créative, ce qui est particulièrement pertinent lorsque l'on considère leur pronostic et les différents types de traitements.

Resilience of small-scale societies: a view from drylands

To gain insights on long-term social-ecological resilience, we examined adaptive responses of small-scale societies to dryland-related hazards in different regions and chronological periods, spanning from the mid-Holocene to the present. Based on evidence from Africa (Sahara and Sahel), Asia (south margin of the Thar desert), and Europe (South Spain), we discuss key traits and coping practices of small-scale societies that are potentially relevant for building resilience. The selected case studies illustrate four main coping mechanisms: mobility and migration, storage, commoning, and collective action driven by religious beliefs. Ultimately, the study of resilience in the context of drylands emphasizes the importance of adaptive traits and practices that are distinctive of small-scale societies: a strong social-ecological coupling, a solid body of traditional ecological knowledge, and a high degree of internal cohesion and self-organization.

Heterosis in locally adapted sorghum genotypes and potential of hybrids for increased productivity in contrasting environments in Ethiopia

Increased productivity in sorghum has been achieved in the developed world using hybrids. Despite their yield advantage, introduced hybrids have not been adopted in Ethiopia due to the lack of adaptive traits, their short plant stature and small grain size. This study was conducted to investigate hybrid performance and the magnitude of heterosis of locally adapted genotypes in addition to introduced hybrids in three contrasting environments in Ethiopia. In total, 139 hybrids, derived from introduced seed parents crossed with locally adapted genotypes and introduced R lines, were evaluated. Overall, the hybrids matured earlier than the adapted parents, but had higher grain yield, plant height, grain number and grain weight in all environments. The lowland adapted hybrids displayed a mean better parent heterosis (BPH) of 19%, equating to 1160 kg ha− 1 and a 29% mean increase in grain yield, in addition to increased plant height and grain weight, in comparison to the hybrids derived from the introduced R lines. The mean BPH for grain yield for the highland adapted hybrids was 16% in the highland and 52% in the intermediate environment equating to 698 kg ha− 1 and 2031 kg ha− 1, respectively, in addition to increased grain weight. The magnitude of heterosis observed for each hybrid group was related to the genetic distance between the parental lines. The majority of hybrids also showed superiority over the standard check varieties. In general, hybrids from locally adapted genotypes were superior in grain yield, plant height and grain weight compared to the high parents and introduced hybrids indicating the potential for hybrids to increase productivity while addressing farmers' required traits.