The Evolution of Modularity in the Mammalian Skull I: Morphological Integration Patterns and Magnitudes

Morphological integration refers to the modular structuring of inter-trait relationships in an organism, which could bias the direction and rate of morphological change, either constraining or facilitating evolution along certain dimensions of the morphospace. Therefore, the description of patterns and magnitudes of morphological integration and the analysis of their evolutionary consequences are central to understand the evolution of complex traits. Here we analyze morphological integration in the skull of several mammalian orders, addressing the following questions: are there common patterns of inter-trait relationships? Are these patterns compatible with hypotheses based on shared development and function? Do morphological integration patterns and magnitudes vary in the same way across groups? We digitized more than 3,500 specimens spanning 15 mammalian orders, estimated the correspondent pooled within-group correlation and variance/covariance matrices for 35 skull traits and compared those matrices among the orders. We also compared observed patterns of integration to theoretical expectations based on common development and function. Our results point to a largely shared pattern of inter-trait correlations, implying that mammalian skull diversity has been produced upon a common covariance structure that remained similar for at least 65 million years. Comparisons with a rodent genetic variance/covariance matrix suggest that this broad similarity extends also to the genetic factors underlying phenotypic variation. In contrast to the relative constancy of inter-trait correlation/covariance patterns, magnitudes varied markedly across groups. Several morphological modules hypothesized from shared development and function were detected in the mammalian taxa studied. Our data provide evidence that mammalian skull evolution can be viewed as a history of inter-module parcellation, with the modules themselves being more clearly marked in those lineages with lower overall magnitude of integration. The implication of these findings is that the main evolutionary trend in the mammalian skull was one of decreasing the constraints to evolution by promoting a more modular architecture.

Genomic Analysis of Wild Tomato Introgressions Determining Metabolism- and Yield-Associated Traits

With the aim of determining the genetic basis of metabolic regulation in tomato fruit, we constructed a detailed physical map of genomic regions spanning previously described metabolic quantitative trait loci of a Solanum pennellii introgression line population. Two genomic libraries from S. pennellii were screened with 104 colocated markers from five selected genomic regions, and a total of 614 bacterial artificial chromosome (BAC)/cosmids were identified as seed clones. Integration of sequence data with the genetic and physical maps of Solanum lycopersicum facilitated the anchoring of 374 of these BAC/cosmid clones. The analysis of this information resulted in a genome-wide map of a nondomesticated plant species and covers 10% of the physical distance of the selected regions corresponding to approximately 1% of the wild tomato genome. Comparative analyses revealed that S. pennellii and domesticated tomato genomes can be considered as largely colinear. A total of 1,238,705 bp from both BAC/cosmid ends and nine large insert clones were sequenced, annotated, and functionally categorized. The sequence data allowed the evaluation of the level of polymorphism between the wild and cultivated tomato species. An exhaustive microsynteny analysis allowed us to estimate the divergence date of S. pennellii and S. lycopersicum at 2.7 million years ago. The combined results serve as a reference for comparative studies both at the macrosyntenic and microsyntenic levels. They also provide a valuable tool for fine-mapping of quantitative trait loci in tomato. Furthermore, they will contribute to a deeper understanding of the regulatory factors underpinning metabolism and hence defining crop chemical composition.

Morphometric analysis and taxonomic revision of the Vriesea paraibica complex (Bromeliaceae)

The species related to Vriesea paraibica (Bromeliaceae, Tillandsioideae) have controversial taxonomic limits. For several decades, this group has been identified in herbarium collections as V. x morreniana, an artificial hybrid that does not grow in natural habitats. The aim of this study was to assess the morphological variation in the V. paraibica complex through morphometric analyses of natural populations. Two sets of analyses were performed: the first involved six natural populations (G1) and the second was carried out on taxa that emerged from the first analysis, but using material from herbarium collections (G2). Univariate ANOVA was used, as well as discriminant analysis of 16 morphometric variables in G1 and 18 in G2. The results of the analyses of the two groups were similar and led to the selection of diagnostic traits of four species. Lengths of the lower and median floral bracts were significant for the separation of red and yellow floral bracts. Vriesea paraibica and V. interrogatoria have red bracts; these two species are differentiated by the widths of the lower and median portions of the inflorescence and by scape length. These structures are larger in the former and smaller in the latter. Of the species with yellow floral bracts, V. eltoniana is distinguished by longer leaf blades and scapes and V. flava is characterized by its shorter sepal lengths. (C) 2009 The Linnean Society of London, Botanical Journal of the Linnean Society, 2009, 159, 163-181.

Three-Dimensional Quantitative Structure-Activity Relationship Study of Antitumor 2-Formylpyridine Thiosemicarbazones Derivatives as Inhibitors of Ribonucleotide Reductase

In order to extend previous SAR and QSAR studies, 3D-QSAR analysis has been performed using CoMFA and CoMSIA approaches applied to a set of 39 alpha-(N)-heterocyclic carboxaldehydes thiosemicarbazones with their inhibitory activity values (IC(50)) evaluated against ribonucleotide reductase (RNR) of H.Ep.-2 cells (human epidermoid carcinoma), taken from selected literature. Both rigid and field alignment methods, taking the unsubstituted 2-formylpyridine thiosemicarbazone in its syn conformation as template, have been used to generate multiple predictive CoMFA and CoMSIA models derived from training sets and validated with the corresponding test sets. Acceptable predictive correlation coefficients (Q(cv)(2) from 0.360 to 0.609 for CoMFA and Q(cv)(2) from 0.394 to 0.580 for CoMSIA models) with high fitted correlation coefficients (r` from 0.881 to 0.981 for CoMFA and r(2) from 0.938 to 0.993 for CoMSIA models) and low standard errors (s from 0.135 to 0.383 for CoMFA and s from 0.098 to 0.240 for CoMSIA models) were obtained. More precise CoMFA and CoMSIA models have been derived considering the subset of thiosemicarbazones (TSC) substituted only at 5-position of the pyridine ring (n=22). Reasonable predictive correlation coefficients (Q(cv)(2) from 0.486 to 0.683 for CoMFA and Q(cv)(2) from 0.565 to 0.791 for CoMSIA models) with high fitted correlation coefficients (r(2) from 0.896 to 0.997 for CoMFA and r(2) from 0.991 to 0.998 for CoMSIA models) and very low standard errors (s from 0.040 to 0.179 for CoMFA and s from 0.029 to 0.068 for CoMSIA models) were obtained. The stability of each CoMFA and CoMSIA models was further assessed by performing bootstrapping analysis. For the two sets the generated CoMSIA models showed, in general, better statistics than the corresponding CoMFA models. The analysis of CoMFA and CoMSIA contour maps suggest that a hydrogen bond acceptor near the nitrogen of the pyridine ring can enhance inhibitory activity values. This observation agrees with literature data, which suggests that the nitrogen pyridine lone pairs can complex with the iron ion leading to species that inhibits RNR. The derived CoMFA and CoMSIA models contribute to understand the structural features of this class of TSC as antitumor agents in terms of steric, electrostatic, hydrophobic and hydrogen bond donor and hydrogen bond acceptor fields as well as to the rational design of this key enzyme inhibitors.

FT-Raman, FTIR and density functional theory studies of a hydrogen-bonded formamide: pyridine complex

Raman and IR experiments have been carried out on formamide (FA) and pyridine (Py) mixtures at different compositions. The appearance of a new Raman band at 996 cm(-1) (nu(1) region of Py), whose intensity depends on the FA concentration, is assigned to an FA: Py adduct and this result is in excellent agreement with those of other authors who employed noisy light-based coherent Raman scattering spectroscopy (I((2)) CARS). Another band at 1587 cm(-1) (nu(8) region of Py) has been observed for the first time by using Raman and IR spectroscopies. Its intensity shows the same dependence on the FA concentration and this fact allows us to also attribute it to an FA: Py adduct. The good relationship between the Raman and IR data demonstrates the potential of the vibrational spectroscopy for this kind of study. Owing to higher absolute Raman scattering cross section, the nu(1) region of Py has been chosen for the quantitative analysis and a stoichiometry of 1 : 1 FA: Py is reported. The experimental data are very well supported by the density functional theory (OFT) calculation, which was employed for the first time to the present system. Furthermore, the actual investigation shows an excellent agreement with those reported from computational calculations for similar systems. A comparison with our previous studies confirms that: the solvent dielectric constant determines the stoichiometry of a given Lewis acid-base adduct in the infinite dilution limit. Copyright (C) 2009 John Wiley & Sons, Ltd.

Genetic Heteroscedasticity for Domestic Animal Traits

Animal traits differ not only in mean, but also in variation around the mean. For instance, one sire’s daughter group may be very homogeneous, while another sire’s daughters are much more heterogeneous in performance. The difference in residual variance can partially be explained by genetic differences. Models for such genetic heterogeneity of environmental variance include genetic effects for the mean and residual variance, and a correlation between the genetic effects for the mean and residual variance to measure how the residual variance might vary with the mean. The aim of this thesis was to develop a method based on double hierarchical generalized linear models for estimating genetic heteroscedasticity, and to apply it on four traits in two domestic animal species; teat count and litter size in pigs, and milk production and somatic cell count in dairy cows. The method developed is fast and has been implemented in software that is widely used in animal breeding, which makes it convenient to use. It is based on an approximation of double hierarchical generalized linear models by normal distributions. When having repeated observations on individuals or genetic groups, the estimates were found to be unbiased. For the traits studied, the estimated heritability values for the mean and the residual variance, and the genetic coefficients of variation, were found in the usual ranges reported. The genetic correlation between mean and residual variance was estimated for the pig traits only, and was found to be favorable for litter size, but unfavorable for teat count.

Fine mapping and replication of QTL in outbred chicken advanced intercross lines

Background: Linkage mapping is used to identify genomic regions affecting the expression of complex traits. However, when experimental crosses such as F2 populations or backcrosses are used to map regions containing a Quantitative Trait Locus (QTL), the size of the regions identified remains quite large, i.e. 10 or more Mb. Thus, other experimental strategies are needed to refine the QTL locations. Advanced Intercross Lines (AIL) are produced by repeated intercrossing of F2 animals and successive generations, which decrease linkage disequilibrium in a controlled manner. Although this approach is seen as promising, both to replicate QTL analyses and fine-map QTL, only a few AIL datasets, all originating from inbred founders, have been reported in the literature. Methods: We have produced a nine-generation AIL pedigree (n = 1529) from two outbred chicken lines divergently selected for body weight at eight weeks of age. All animals were weighed at eight weeks of age and genotyped for SNP located in nine genomic regions where significant or suggestive QTL had previously been detected in the F2 population. In parallel, we have developed a novel strategy to analyse the data that uses both genotype and pedigree information of all AIL individuals to replicate the detection of and fine-map QTL affecting juvenile body weight. Results: Five of the nine QTL detected with the original F2 population were confirmed and fine-mapped with the AIL, while for the remaining four, only suggestive evidence of their existence was obtained. All original QTL were confirmed as a single locus, except for one, which split into two linked QTL. Conclusions: Our results indicate that many of the QTL, which are genome-wide significant or suggestive in the analyses of large intercross populations, are true effects that can be replicated and fine-mapped using AIL. Key factors for success are the use of large populations and powerful statistical tools. Moreover, we believe that the statistical methods we have developed to efficiently study outbred AIL populations will increase the number of organisms for which in-depth complex traits can be analyzed.

Habitat use, reproductive traits and social interactions in a stream-dweller treefrog endemic to the Brazilian Cerrado

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Carcass and cut yields and meat qualitative traits of broilers fed diets containing probiotics and prebiotics

This study evaluated the use of different probiotics, prebiotics and symbiotics on the quality of carcasses and meat of broiler chickens. One hundred and eight day-old Cobb male broilers were used (n=108) in a completely randomized design according to a 3x3 factorial, with 3 probiotics in the diet (no probiotics, probiotics 1, probiotics 2) and 3 prebiotics in the diet (no prebiotics, prebiotics 1, prebiotics 2). There were nine treatments with 4 replicates and 3 birds per replicate. The results showed that the carcass and cut yields, color (L* - lightness, a* - redness, and b* - yellowness), pH, cooking losses, shearing force and sensory analysis were not affected by the use of different growth promoters at 42 days of age. It was concluded that growth promoters supplemented to the diet did not affect the studied quantitative and qualitative parameters of the carcass and breast meat of broiler chickens.

Assessment of DGAT1 and LEP gene polymorphisms in three Nelore (Bos indicus) lines selected for growth and their relationship with growth and carcass traits

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

Quantitative variation in the tropical maize population, ESALQ-PB1

A boa produtividade e os valores intermediários para altura da planta e altura da espiga caracterizam a população de milho ESALQ-PB1 como agronomicamente promissora. São relatadas estimativas de parâmetros para 13 caracteres: altura da planta (PH), altura da espiga (EH), posição relativa da espiga (EP), comprimento do pendão (TL), peso do pendão (TW), número de ramificações do pendão (TB), peso de espigas (EW), peso de grãos (GW), comprimento da espiga (EL), diâmetro da espiga (ED), número de fileiras de grãos (RN), número de grãos por fileira (KR) e prolificidade (PR). Os resultados se referem a um único ambiente (um local e um ano). Foi detectada variação genética para todos os caracteres, e são apresentadas estimativas da variância genética aditiva. Os coeficientes de herdabilidade (indivíduos) variaram de 0,14 a 0,72 e foram considerados altos para PH, EH e TB; intermediários para EP, TL, TW, EL e ED, e baixos para EW, GW, KR e PR. O coeficiente de herdabilidade para médias de progênies mostrou aproximadamente a mesma tendência, variando de 0,40 a 0,75. O maior ganho esperado por seleção foi para TB (27% por ciclo) sob seleção massal e para TW (16,4%) por seleção entre progênies; o menor ganho esperado foi para ED, tanto por seleção massal (1,9%) como por seleção entre progênies (2,9%). Coeficientes de correlação aditiva (rA) 0.5

Contributions and perspectives of chicken genomics in Brazil: from biological model to export commodity

Chicken is one of the most important sources of animal protein for human consumption, and breeding programmes have been responsible for constant improvements in production efficiency and product quality. Furthermore, chicken has largely contributed to fundamental discoveries in biology for the last 100 years. In this article we review recent developments in poultry genomics and their contribution to adding functional information to the already existing structural genomics, including the availability of the complete genome sequence, a comprehensive collection of mRNA sequences ( ESTs), microarray platforms, and their use to complement QTL mapping strategies in the identification of genes that underlie complex traits. Efforts of the Brazilian Poultry Genomics Programme in this area resulted in generation of a resource population, which was used for identification of Quantitative Trait Loci ( QTL) regions, generation of ESTs and candidate gene studies that contributed to furthering our understanding of the complex biological processes involved in growth and muscular development in chicken.

Quantitative trait loci associated with chemical composition of the chicken carcass

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

Mapping quantitative trait loci in Gallus gallus using principal components

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

Mast cells and MMP-9 in the lamina propria during eruption of rat molars: quantitative and immunohistochemical evaluation

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)